Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007918.1 Hibiscus syriacus cultivar Beakdansim tig00110321_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2302251
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 9
Found at i:925736 original size:64 final size:65
Alignment explanation
Indices: 925559--925721 Score: 222
Period size: 65 Copynumber: 2.5 Consensus size: 65
925549 GAATTAATTG
* * * *
925559 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
* ** **
925624 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATA-TTTTCA
925687 A
65 A
925688 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
925722 TGGTGCACCG
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 36 0.42
65 49 0.58
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:935983 original size:31 final size:31
Alignment explanation
Indices: 935945--936099 Score: 215
Period size: 31 Copynumber: 5.0 Consensus size: 31
935935 CCCGAAGGAC
* * *
935945 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
935976 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* * *
936007 CAGTCCGTATGTTCCGAAGAACATAGGTAAT
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
936038 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
936069 CAGTCCATATGTCCAGAA-AACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
936099 C
1 C
936100 CCTCGACCCT
Statistics
Matches: 111, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
30 13 0.12
31 97 0.87
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:936042 original size:62 final size:62
Alignment explanation
Indices: 935945--936097 Score: 240
Period size: 62 Copynumber: 2.5 Consensus size: 62
935935 CCCGAAGGAC
* *
935945 CAGTCCATA-GATTCCGAAGAACCTAGGTAATCAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATG-TTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
*
936007 CAGTCCGTATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
936069 CAGTCCATATG-TCCAGAA-AACATAGGTAA
1 CAGTCCATATGTTCC-GAAGAACATAGGTAA
936098 ACCCTCGACC
Statistics
Matches: 85, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
61 14 0.16
62 70 0.82
63 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (62 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:936321 original size:24 final size:22
Alignment explanation
Indices: 936276--936321 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
936266 ATATACTTGT
*
936276 TTTCACATATATATTCATATCA
1 TTTCACATATACATTCATATCA
936298 TTTCACATATACACTTTCATATCA
1 TTTCACATATACA--TTCATATCA
936322 CATGCCATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 12 0.57
24 9 0.43
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTCACATATACATTCATATCA
Found at i:936950 original size:21 final size:21
Alignment explanation
Indices: 936920--936964 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
936910 ATTCTGTCGT
* *
936920 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
936941 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
936962 TTG
1 TTG
936965 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:951191 original size:35 final size:35
Alignment explanation
Indices: 951159--951224 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
951149 TACAAATTGT
*
951159 AAAAT-ATTATATATTTTCTTTA-AAAATTAAATTC
1 AAAATAATTATATAATTT-TTTACAAAATTAAATTC
*
951193 ATAATAATTATATAATTTTTTACAAAATTAAA
1 AAAATAATTATATAATTTTTTACAAAATTAAA
951225 AATATAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 8 0.29
35 20 0.71
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (35 bp):
AAAATAATTATATAATTTTTTACAAAATTAAATTC
Found at i:967883 original size:16 final size:16
Alignment explanation
Indices: 967862--967895 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
967852 TTACTATTCA
*
967862 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
967878 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
967894 CG
1 CG
967896 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:976469 original size:29 final size:24
Alignment explanation
Indices: 976442--976488 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
976432 CAATTTTTAT
976442 TTTATCTCAATTAACAAGTTAATG
1 TTTATCTCAATTAACAAGTTAATG
976466 TTTATCTCAATTAACAAGTTAAT
1 TTTATCTCAATTAACAAGTTAAT
976489 AATTAGCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (24 bp):
TTTATCTCAATTAACAAGTTAATG
Found at i:977811 original size:2 final size:2
Alignment explanation
Indices: 977799--977830 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
977789 ATTTTTCTAA
*
977799 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
977831 TTTTTATAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:978970 original size:27 final size:26
Alignment explanation
Indices: 978931--978984 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
978921 TTTTAAAAGA
* *
978931 TAAAAATAGATTATTAATGAAAAATAT
1 TAAAAAGAGATTATAAAT-AAAAATAT
* *
978958 TAAAAAGATATTATAAATTAAAATAT
1 TAAAAAGAGATTATAAATAAAAATAT
978984 T
1 T
978985 TAGAGAGACT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (26 bp):
TAAAAAGAGATTATAAATAAAAATAT
Found at i:988856 original size:13 final size:13
Alignment explanation
Indices: 988838--988862 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
988828 AAAACAGGTC
988838 GAATTTAAATTTA
1 GAATTTAAATTTA
988851 GAATTTAAATTT
1 GAATTTAAATTT
988863 TTATATTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
GAATTTAAATTTA
Found at i:989853 original size:60 final size:60
Alignment explanation
Indices: 989732--989863 Score: 151
Period size: 60 Copynumber: 2.2 Consensus size: 60
989722 TAGAAAGAGG
* * * * * *
989732 ATCATATTTTAAGGATGAAATTAGAATGTTCAAAAGATTAAGGATAACTTTAGAATAAAA
1 ATCATAATTTAGGGATGAAATTAAAATATTCAAAAGATTAAAGATAACTTTAAAATAAAA
* * *
989792 ATCATAGTTTAGGGATGAAATTAAAATATTTAAAA-ATCTAAAGATCAA-TTTAAAATTAAA
1 ATCATAATTTAGGGATGAAATTAAAATATTCAAAAGAT-TAAAGAT-AACTTTAAAATAAAA
989852 ATCATAATTTAG
1 ATCATAATTTAG
989864 AGACATAATG
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
59 2 0.03
60 57 0.93
61 2 0.03
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.33
Consensus pattern (60 bp):
ATCATAATTTAGGGATGAAATTAAAATATTCAAAAGATTAAAGATAACTTTAAAATAAAA
Found at i:994401 original size:45 final size:45
Alignment explanation
Indices: 994337--994434 Score: 160
Period size: 45 Copynumber: 2.2 Consensus size: 45
994327 TGAACATGAA
* *
994337 CAGCAGTTGCATGAGCTGCACTTACATCGACATTTTGGGATTGTG
1 CAGCAGCTGCATGAGCTGCACTTACATCGACATTTCGGGATTGTG
* *
994382 CAGCAGCTGCATGAGCTGCACTTACGTCGACATTTCGGGATTTTG
1 CAGCAGCTGCATGAGCTGCACTTACATCGACATTTCGGGATTGTG
994427 CAGCAGCT
1 CAGCAGCT
994435 TGAACATGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.29
Consensus pattern (45 bp):
CAGCAGCTGCATGAGCTGCACTTACATCGACATTTCGGGATTGTG
Found at i:997941 original size:2 final size:2
Alignment explanation
Indices: 997936--998051 Score: 95
Period size: 2 Copynumber: 60.5 Consensus size: 2
997926 AAAATGATAA
* *
997936 AT AT AT AT AT AT AT AT AT AT AT AT CAT AA AT A- AT AT GT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT
**
997977 A- AT AT AT A- AT GC AT AT AT AT AT A- AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
998015 AT AT AT AT ACT AT A- AT AT AA AT AT GCT AT AT A- AT AT A
1 AT AT AT AT A-T AT AT AT AT AT AT AT -AT AT AT AT AT AT A
998052 CGGGAATGTA
Statistics
Matches: 91, Mismatches: 12, Indels: 22
0.73 0.10 0.18
Matches are distributed among these distances:
1 8 0.09
2 78 0.86
3 5 0.05
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (2 bp):
AT
Found at i:998000 original size:22 final size:21
Alignment explanation
Indices: 997936--998038 Score: 108
Period size: 20 Copynumber: 4.9 Consensus size: 21
997926 AAAATGATAA
997936 ATATATAT-ATATATATATAT
1 ATATATATAATATATATATAT
*
997956 ATATCATA-AATA-ATATGTA-
1 ATAT-ATATAATATATATATAT
997975 ATAATATATAATGCATATATATAT
1 AT-ATATATAAT--ATATATATAT
997999 A-ATATATAATATATATATAT
1 ATATATATAATATATATATAT
*
998019 ATATACTATAATATAAATAT
1 ATATA-TATAATATATATAT
998039 GCTATATAAT
Statistics
Matches: 70, Mismatches: 3, Indels: 18
0.77 0.03 0.20
Matches are distributed among these distances:
19 5 0.07
20 26 0.37
21 9 0.13
22 23 0.33
23 6 0.09
24 1 0.01
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (21 bp):
ATATATATAATATATATATAT
Found at i:998207 original size:18 final size:18
Alignment explanation
Indices: 998189--998239 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
998179 CGTTTATACT
998189 ATATAATATAAATAGACTA
1 ATAT-ATATAAATAGACTA
* *
998208 ATATATATAAATATAATA
1 ATATATATAAATAGACTA
998226 ATACTATATAAATA
1 ATA-TATATAAATA
998240 AGATCCAACG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 15 0.52
19 14 0.48
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (18 bp):
ATATATATAAATAGACTA
Found at i:998234 original size:23 final size:23
Alignment explanation
Indices: 998173--998240 Score: 57
Period size: 24 Copynumber: 2.8 Consensus size: 23
998163 GTATAGTCAT
*
998173 ATAATACGTTTATACTATATAATATA
1 ATAATAC-TATATA-TATA-AATATA
*
998199 A-ATAGACTAATATATATAAATATA
1 ATA-ATACT-ATATATATAAATATA
*
998223 ATAATACTATATAAATAA
1 ATAATACTATATATATAA
998241 GATCCAACGA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
23 9 0.26
24 11 0.31
25 7 0.20
26 8 0.23
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (23 bp):
ATAATACTATATATATAAATATA
Found at i:1016695 original size:16 final size:18
Alignment explanation
Indices: 1016653--1016689 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1016643 ACGATGGTTG
1016653 CCAAATATTGTTGAAAAA
1 CCAAATATTGTTGAAAAA
1016671 CCAAATATTGTTGAAAAA
1 CCAAATATTGTTGAAAAA
1016689 C
1 C
1016690 AATATTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.27
Consensus pattern (18 bp):
CCAAATATTGTTGAAAAA
Found at i:1017314 original size:16 final size:16
Alignment explanation
Indices: 1017293--1017350 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 16
1017283 ACAGAGTCTC
*
1017293 TGAATCATTTAATATT
1 TGAATCATTTAACATT
* **
1017309 TGAATCATTTAGCGCT
1 TGAATCATTTAACATT
1017325 T-AATCATTTAACATT
1 TGAATCATTTAACATT
*
1017340 TGAATTATTTA
1 TGAATCATTTA
1017351 GCGCTTAATC
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
15 12 0.36
16 21 0.64
ACGTcount: A:0.34, C:0.10, G:0.09, T:0.47
Consensus pattern (16 bp):
TGAATCATTTAACATT
Found at i:1017330 original size:31 final size:31
Alignment explanation
Indices: 1017295--1017364 Score: 122
Period size: 31 Copynumber: 2.3 Consensus size: 31
1017285 AGAGTCTCTG
*
1017295 AATCATTTAATATTTGAATCATTTAGCGCTT
1 AATCATTTAACATTTGAATCATTTAGCGCTT
*
1017326 AATCATTTAACATTTGAATTATTTAGCGCTT
1 AATCATTTAACATTTGAATCATTTAGCGCTT
1017357 AATCATTT
1 AATCATTT
1017365 TGAAGTAAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.46
Consensus pattern (31 bp):
AATCATTTAACATTTGAATCATTTAGCGCTT
Found at i:1017331 original size:15 final size:15
Alignment explanation
Indices: 1017311--1017364 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
1017301 TTAATATTTG
1017311 AATCATTTAGCGCTT
1 AATCATTTAGCGCTT
* **
1017326 AATCATTTAACATTT
1 AATCATTTAGCGCTT
*
1017341 GAATTATTTAGCGCTT
1 -AATCATTTAGCGCTT
1017357 AATCATTT
1 AATCATTT
1017365 TGAAGTAAAC
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
15 19 0.63
16 11 0.37
ACGTcount: A:0.31, C:0.15, G:0.09, T:0.44
Consensus pattern (15 bp):
AATCATTTAGCGCTT
Found at i:1021709 original size:20 final size:23
Alignment explanation
Indices: 1021670--1021721 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 23
1021660 AGAAATCAAT
*
1021670 ACATAAATATAATATGCAC-AC-
1 ACATATATATAATATGCACAACA
*
1021691 ACATATATAT-ATATTCACAACA
1 ACATATATATAATATGCACAACA
1021713 ACATATATA
1 ACATATATA
1021722 CTACGACACA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 7 0.26
21 11 0.41
22 9 0.33
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.29
Consensus pattern (23 bp):
ACATATATATAATATGCACAACA
Found at i:1023277 original size:3 final size:3
Alignment explanation
Indices: 1023269--1023312 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
1023259 CTGCAAAAGC
* *
1023269 AAT AAT AAT ATT AAT AAT CAT AAT AAT AAT AATT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT A
1023313 TTTAAGCCCG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:1024311 original size:47 final size:47
Alignment explanation
Indices: 1024257--1024355 Score: 117
Period size: 47 Copynumber: 2.1 Consensus size: 47
1024247 ACTAAGACTC
* * *
1024257 TTAAATTGATAAGATTACTTTTTAACGCATACAAATTTACGATTTTT
1 TTAAATTGATAAGATTACATTTTAACGCATACAAACTCACGATTTTT
** * * * *
1024304 TTAAATTGATTCGGTTACATTTTAGCGCATACGAACTCACTATTTTT
1 TTAAATTGATAAGATTACATTTTAACGCATACAAACTCACGATTTTT
1024351 TTAAA
1 TTAAA
1024356 AGAACTCAAC
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.43
Consensus pattern (47 bp):
TTAAATTGATAAGATTACATTTTAACGCATACAAACTCACGATTTTT
Found at i:1032901 original size:41 final size:41
Alignment explanation
Indices: 1032839--1032919 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
1032829 GATTTTGGTG
*
1032839 ATAGTGATTGATGATTAGGTGAAATAGAAAGGCGAAAACGA
1 ATAGTGATTGATGATTAGGTGAAAGAGAAAGGCGAAAACGA
* *
1032880 ATAGTGATTGATGATTGGGTGAAAGAGAAAGGTGAAAACG
1 ATAGTGATTGATGATTAGGTGAAAGAGAAAGGCGAAAACG
1032920 GAATGTGTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.42, C:0.04, G:0.32, T:0.22
Consensus pattern (41 bp):
ATAGTGATTGATGATTAGGTGAAAGAGAAAGGCGAAAACGA
Found at i:1037622 original size:15 final size:15
Alignment explanation
Indices: 1037602--1037643 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
1037592 TGTAAATAAA
*
1037602 AAAATAAATAAAATT
1 AAAATAAATAAAATG
1037617 AAAATAAATAAAATG
1 AAAATAAATAAAATG
*
1037632 AATA-AAATAAAA
1 AAAATAAATAAAA
1037644 AATAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 8 0.32
15 17 0.68
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (15 bp):
AAAATAAATAAAATG
Found at i:1037628 original size:9 final size:9
Alignment explanation
Indices: 1037595--1037652 Score: 61
Period size: 9 Copynumber: 6.8 Consensus size: 9
1037585 TTGGGTCTGT
1037595 AAATAAA-A
1 AAATAAATA
1037603 AAATAAATA
1 AAATAAATA
1037612 AAAT---TA
1 AAATAAATA
1037618 AAATAAATA
1 AAATAAATA
*
1037627 AAATGAATA
1 AAATAAATA
*
1037636 AAATAAAAA
1 AAATAAATA
1037645 ATAATAAA
1 A-AATAAA
1037653 AAATAATAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
6 6 0.14
8 7 0.17
9 23 0.55
10 6 0.14
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.21
Consensus pattern (9 bp):
AAATAAATA
Found at i:1037635 original size:24 final size:23
Alignment explanation
Indices: 1037595--1037653 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 23
1037585 TTGGGTCTGT
1037595 AAATAAA-AAAATAAATAAAATTA
1 AAATAAATAAAATAAATAAAA-TA
*
1037618 AAATAAATAAAATGAATAAAATA
1 AAATAAATAAAATAAATAAAATA
*
1037641 AAAAATAATAAAA
1 AAATA-AATAAAA
1037654 AATAATAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
23 13 0.41
24 19 0.59
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (23 bp):
AAATAAATAAAATAAATAAAATA
Found at i:1037644 original size:15 final size:14
Alignment explanation
Indices: 1037595--1037663 Score: 56
Period size: 15 Copynumber: 5.0 Consensus size: 14
1037585 TTGGGTCTGT
1037595 AAATAAAAA-AAT-
1 AAATAAAAATAATA
* *
1037607 AAATAAAATTAAAA
1 AAATAAAAATAATA
1037621 TAAAT-AAAATGAATA
1 -AAATAAAAAT-AATA
1037636 AAATAAAAAATAATA
1 AAAT-AAAAATAATA
*
1037651 AAA-AATAATAATA
1 AAATAAAAATAATA
1037664 TACTAAATGT
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
12 8 0.17
13 11 0.24
14 8 0.17
15 14 0.30
16 5 0.11
ACGTcount: A:0.77, C:0.00, G:0.01, T:0.22
Consensus pattern (14 bp):
AAATAAAAATAATA
Found at i:1037652 original size:10 final size:10
Alignment explanation
Indices: 1037637--1037661 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1037627 AAATGAATAA
1037637 AATAAAAAAT
1 AATAAAAAAT
1037647 AATAAAAAAT
1 AATAAAAAAT
1037657 AATAA
1 AATAA
1037662 TATACTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (10 bp):
AATAAAAAAT
Found at i:1037755 original size:30 final size:31
Alignment explanation
Indices: 1037684--1037860 Score: 121
Period size: 36 Copynumber: 5.4 Consensus size: 31
1037674 AATTTATATA
* *
1037684 ATATATATATTTCAAAATATTTTTTAAAATTA-T
1 ATATATATATTTTAAAA-ATGTTTTAAAA--ACT
**
1037717 ATATTATATAATTTTTAAAAAATGTTTTTTAAACT
1 ATA-TATAT-A-TTTT-AAAAATGTTTTAAAAACT
1037752 ATATATTATATTTTAAAAATGTTTTAAAAACTAT
1 ATATA-TATATTTTAAAAATGTTTTAAAAAC--T
*
1037786 ATACTATATAAGTTTTTAAAATGTTTTAAAAACT
1 ATA-TATAT-A-TTTTAAAAATGTTTTAAAAACT
* * *
1037820 ATACA-ATA---TATAAATGTTTTCAAAACT
1 ATATATATATTTTAAAAATGTTTTAAAAACT
1037847 ATATATTATATTTT
1 ATATA-TATATTTT
1037861 GTCAAAAACA
Statistics
Matches: 116, Mismatches: 12, Indels: 33
0.72 0.07 0.20
Matches are distributed among these distances:
27 20 0.17
29 3 0.03
31 1 0.01
32 18 0.16
33 8 0.07
34 20 0.17
35 11 0.09
36 31 0.27
37 4 0.03
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.48
Consensus pattern (31 bp):
ATATATATATTTTAAAAATGTTTTAAAAACT
Found at i:1037762 original size:69 final size:67
Alignment explanation
Indices: 1037684--1037857 Score: 180
Period size: 69 Copynumber: 2.6 Consensus size: 67
1037674 AATTTATATA
* * * **
1037684 ATATATATATTTCAAAATAT-TTTTTAAAATTATATATTATATAA-TTTTTAAAAAATGTTTTTT
1 ATATATATATTTCAAAA-ATGTTTTAAAAACTATATACTATATAAGTTTTT--AAAATGTTTTAA
1037747 AAACT
63 AAACT
*
1037752 ATATATTATATTTTAAAAATGTTTTAAAAACTATATACTATATAAGTTTTTAAAATGTTTTAAAA
1 ATATA-TATATTTCAAAAATGTTTTAAAAACTATATACTATATAAGTTTTTAAAATGTTTTAAAA
1037817 ACT
65 ACT
* * * *
1037820 ATACA-ATA--T-ATAAATGTTTTCAAAACTATATATTATAT
1 ATATATATATTTCAAAAATGTTTTAAAAACTATATACTATAT
1037858 TTTGTCAAAA
Statistics
Matches: 93, Mismatches: 10, Indels: 11
0.82 0.09 0.10
Matches are distributed among these distances:
63 26 0.28
64 1 0.01
66 3 0.03
68 26 0.28
69 32 0.34
70 5 0.05
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (67 bp):
ATATATATATTTCAAAAATGTTTTAAAAACTATATACTATATAAGTTTTTAAAATGTTTTAAAAA
CT
Found at i:1037814 original size:36 final size:34
Alignment explanation
Indices: 1037678--1037832 Score: 136
Period size: 36 Copynumber: 4.4 Consensus size: 34
1037668 AAATGTAATT
* * * *
1037678 TATATA-ATATATATATTTCAAAATATTTTTTAAAAT
1 TATATATATATA-AT-TTTTAAAAT-GTTTTAAAAAC
**
1037714 TATATATTATATAATTTTTAAAAAATGTTTTTTAAAC
1 TATATA-TATATAATTTTT--AAAATGTTTTAAAAAC
*
1037751 TATATAT-TAT-ATTTTAAAAATGTTTTAAAAAC
1 TATATATATATAATTTTTAAAATGTTTTAAAAAC
1037783 TATATACTATATAAGTTTTTAAAATGTTTTAAAAAC
1 TATATA-TATATAA-TTTTTAAAATGTTTTAAAAAC
*
1037819 TATACAATATATAA
1 TATA-TATATATAA
1037833 ATGTTTTCAA
Statistics
Matches: 101, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
32 20 0.20
33 1 0.01
34 8 0.08
35 4 0.04
36 41 0.41
37 17 0.17
38 10 0.10
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (34 bp):
TATATATATATAATTTTTAAAATGTTTTAAAAAC
Found at i:1037902 original size:2 final size:2
Alignment explanation
Indices: 1037890--1037983 Score: 110
Period size: 2 Copynumber: 50.0 Consensus size: 2
1037880 ACTATATTAC
* *
1037890 TA TA TA CA TA TA TA TA TA TA TA -A TA -A AA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1037929 TA TA TA TA TA -A CA -A AA TA -A TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1037968 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
1037984 ACAAAATAAC
Statistics
Matches: 82, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
1 6 0.07
2 76 0.93
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:1038684 original size:86 final size:87
Alignment explanation
Indices: 1038517--1039122 Score: 333
Period size: 84 Copynumber: 7.3 Consensus size: 87
1038507 ATTTTATTGA
* * * * *
1038517 CAGATAGCACTTCTTGTCTTGA-CTATTCTGTAAATTTGGGTTTGCCTCTGAGCTGAATGTAATC
1 CAGATAGCCCTTCTCGACTTAAGCTATTATGTAAATTTGGGTTTGCCTCTGAGCTGAATGTAATC
1038581 TAACTCGAAGGTCTTCGGTTGG
66 TAACTCGAAGGTCTTCGGTTGG
1038603 CAGATAGCCCTTCTCGACTTAAGCTATTATGTAAATTTGGGTTTGCCTCTGAGCTGAATGTAA-C
1 CAGATAGCCCTTCTCGACTTAAGCTATTATGTAAATTTGGGTTTGCCTCTGAGCTGAATGTAATC
1038667 TAACTCGAAGGTCTTCGGTTGG
66 TAACTCGAAGGTCTTCGGTTGG
* ** * * * ** *
1038689 CAGATAGCCATTCTCGACTTAAGCTATGCTGCAAA--T-GATGTGCCT-TGGAGCTGAGCGTAGT
1 CAGATAGCCCTTCTCGACTTAAGCTATTATGTAAATTTGGGTTTGCCTCT-GAGCTGAATGTAAT
* * **
1038750 CGACCTCGAAGGTCTTTTGTTGG
65 CTAACTCGAAGGTCTTCGGTTGG
* * * * * ** * * * * ** *
1038773 CAGACAACCATTCTAGACTTAAGTTATGCTGCAAA--T-GATATACCT-TGGAGCTGAGCGTAGT
1 CAGATAGCCCTTCTCGACTTAAGCTATTATGTAAATTTGGGTTTGCCTCT-GAGCTGAATGTAAT
* * *
1038834 CGAACTCGAATGTCTTTGGTTGG
65 CTAACTCGAAGGTCTTCGGTTGG
** * * * * *
1038857 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAA--T-GATGTGCCT-TGGAGCTGAACGTAGT
1 CAGATAGCCCTTCTCGACTTAAGCTATTATGTAAATTTGGGTTTGCCTCT-GAGCTGAATGTAAT
* **
1038918 CGAACTCGAAGGTCTTTTGTTGG
65 CTAACTCGAAGGTCTTCGGTTGG
* * * * ** * * * *
1038941 CAGACAACCCTACTAGACTTAAG-T-TGCTGCAAA--T-GATGTGCC-CTCGAAGCTGAGTGTAA
1 CAGATAGCCCTTCTCGACTTAAGCTATTATGTAAATTTGGGTTTGCCTCT-G-AGCTGAATGTAA
*
1039000 TCGAACTCG-AGGATC-T---TTGG
64 TCTAACTCGAAGG-TCTTCGGTTGG
* * ** * *
1039020 CAGATAACCCTTCTCGACTTAAGCTA-TATGCAAA--TGATTTTCCCT-TGAAGCTGAGTGTAAT
1 CAGATAGCCCTTCTCGACTTAAGCTATTATGTAAATTTGGGTTTGCCTCTG-AGCTGAATGTAAT
* * *
1039081 CGAACTTGAGGGTC-T---TTGG
65 CTAACTCGAAGGTCTTCGGTTGG
1039100 CAGATAGCCCTTCTCGACTTAAG
1 CAGATAGCCCTTCTCGACTTAAG
1039123 TTATACTGCA
Statistics
Matches: 452, Mismatches: 57, Indels: 28
0.84 0.11 0.05
Matches are distributed among these distances:
79 24 0.05
80 59 0.13
81 7 0.02
82 25 0.06
83 38 0.08
84 188 0.42
86 72 0.16
87 39 0.09
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (87 bp):
CAGATAGCCCTTCTCGACTTAAGCTATTATGTAAATTTGGGTTTGCCTCTGAGCTGAATGTAATC
TAACTCGAAGGTCTTCGGTTGG
Found at i:1038784 original size:84 final size:84
Alignment explanation
Indices: 1038582--1040207 Score: 1485
Period size: 84 Copynumber: 19.7 Consensus size: 84
1038572 AATGTAATCT
** * ** * * *
1038582 AACTCGAAGGTCTTCGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATTATGTAAATTTGGGTTT
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAA--T-GATGT
** * *
1038647 GCCTCT-GAGCTGAATGTA-ACT
63 GCCT-TGGAGCTGAGCGTAGTCG
** * *
1038668 AACTCGAAGGTCTTCGGTTGGCAGATAGCCATTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
1038733 TTGGAGCTGAGCGTAGTCG
66 TTGGAGCTGAGCGTAGTCG
* * * * * * *
1038752 ACCTCGAAGGTCTTTTGTTGGCAGACAACCATTCTAGACTTAAGTTATGCTGCAAATGATATACC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
1038817 TTGGAGCTGAGCGTAGTCG
66 TTGGAGCTGAGCGTAGTCG
* * *
1038836 AACTCGAATGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
*
1038901 TTGGAGCTGAACGTAGTCG
66 TTGGAGCTGAGCGTAGTCG
* * *
1038920 AACTCGAAGGTCTTTTGTTGGCAGACAACCCTACTAGACTTAAG-T-TGCTGCAAATGATGTGCC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-C
* * * *
1038983 CTCGAAGCTGAGTGTAATCG
65 CTTGGAGCTGAGCGTAGTCG
* * *
1039003 AACTCG-AGGATC---T-TTGGCAGATAACCCTTCTCGACTTAAGCTAT-ATGCAAATGATTTTC
1 AACTCGAAGG-TCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGA-TGTG
* * *
1039062 CCTTGAAGCTGAGTGTAATCG
64 CCTTGGAGCTGAGCGTAGTCG
* * * * *
1039083 AACTTGAGGGTC---T-TTGGCAGATAGCCCTTCTCGACTTAAGTTATACTGCAAATGATGTGCC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
1039144 TTGGAGCTGAGCGTAGTCG
66 TTGGAGCTGAGCGTAGTCG
* * * * *
1039163 AACTCAAAGGTCTTTGGTTGGCATATAACTCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG--
* * * * *
1039228 CCTCGAAGCTGAGTGTAATCA
64 CCTTGGAGCTGAGCGTAGTCG
* * * * * * *
1039249 AACTTGAGGGTC---T-TTGGCATATAGCCCTTCTCAACTTAAGTTATGCTGCAAATGATGTGTC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
*
1039310 TTGGAGCTGACCGTAGTCG
66 TTGGAGCTGAGCGTAGTCG
* *
1039329 AACTCAAAGGTC---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
*
1039390 TTGGAGCTGAGCGTAGTCA
66 TTGGAGCTGAGCGTAGTCG
* * * * * *
1039409 AACTCGAAGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAGTTATGTTGTAAATGATATGCC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
* **
1039474 TTAGAGCTGAGCGTAGTAA
66 TTGGAGCTGAGCGTAGTCG
* * ** * * *
1039493 AACTCGAAGCTCTTTTGGTCACAGATAACCCTTCTAG-CGTT--G--A-G-T---TATGATGTAC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGAC-TTAAGCTATGCTGCAAATGATGT-G
* * * *
1039548 CCTCGAAGCTGAGTGTAATCG
64 CCTTGGAGCTGAGCGTAGTCG
* * * *
1039569 AACTCGAGGGTC---T-TTGGCATG-TAGCCCTTCTCGACTTAAGCTATGCTGCAAATAATGTGT
1 AACTCGAAGGTCTTTTGTTGGCA-GATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGC
* * *
1039629 CTTGGAACTGAGCATAGTCA
65 CTTGGAGCTGAGCGTAGTCG
* * * *
1039649 AACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGTTGCAAATGATATGCC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
*
1039714 TTGGAGTTGAGCGTAGTCG
66 TTGGAGCTGAGCGTAGTCG
* * * ** * **
1039733 AACTAGAAGGTCTTTTGGTT-ACAGATAACCCTTCTAG-CTTTGTGTTATGCTATAAATGATGTG
1 AACTCGAAGGTCTTTT-GTTGGCAGATAACCCTTCTCGAC-TTAAGCTATGCTGCAAATGATGTG
* * * *
1039796 CCCTCGAAGCTGAGTGTAATCG
64 -CCTTGGAGCTGAGCGTAGTCG
* * *
1039818 AACTC-AAGGGTC---T-TTGGCAGATAACCCTTCTCGACTTTAGCTATGTTGCAAATGATGTAC
1 AACTCGAA-GGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGC
1039878 CTTGGAGCTGAGCGTAGTCG
65 CTTGGAGCTGAGCGTAGTCG
* * * * * * * *
1039898 AACTCGAATGTATTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATTATGTGCC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
*
1039963 TTGGAGCTGAGCGCAGTCG
66 TTGGAGCTGAGCGTAGTCG
* *
1039982 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGACTTAAG-TCATGCTGCAAATGATATGC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGCT-ATGCTGCAAATGATGTGC
* * *
1040046 CTTCGAAGCTGAGTGTAATCG
65 CTT-GGAGCTGAGCGTAGTCG
* * * * * *
1040067 AAC-CTGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAACTATGTTGAAAATGATATGC
1 AACTC-GAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGC
*
1040131 CTTTGAGCTGAGCGTAGTCG
65 CTTGGAGCTGAGCGTAGTCG
* * * * *
1040151 AACTCGAAAGTC-TTTGTTGGTAGATAACCCTTCT-AACCTTGAGTTATGCTGCAAATG
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGA-CTTAAGCTATGCTGCAAATG
1040208 TTGTCTTTAA
Statistics
Matches: 1265, Mismatches: 221, Indels: 111
0.79 0.14 0.07
Matches are distributed among these distances:
72 15 0.01
73 3 0.00
74 1 0.00
75 6 0.00
76 25 0.02
77 1 0.00
78 2 0.00
79 25 0.02
80 244 0.19
81 54 0.04
82 67 0.05
83 81 0.06
84 565 0.45
85 98 0.08
86 78 0.06
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (84 bp):
AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
TTGGAGCTGAGCGTAGTCG
Found at i:1039833 original size:489 final size:485
Alignment explanation
Indices: 1038567--1040207 Score: 1743
Period size: 489 Copynumber: 3.3 Consensus size: 485
1038557 TTTGCCTCTG
* * * **
1038567 AGCTGAATGTAATCTAACTCGAAGGTCTTCGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATTA
1 AGCTGAGTGTAATCGAACTCGAGGGTC-T---TTGGCAGATAGCCCTTCTCGACTTAAGCTATGC
* * * ** * * *
1038632 TGTAAATTTGGGTTTGCCTCT-GAGCTGAATGTA-ACTAACTCGAAGGTCTTCGGTTGGCAGATA
62 TGCAAA--T-GATGTGCCT-TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATA
* * * * *
1038695 GCCATTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGACCTCGAA
123 ACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTAGAA
* * * *
1038760 GGTCTTTT-GTTGGCAGACAACCATTCTAGACTTAAGTTATGCTGCAAATGATATACCTTGGAGC
188 GGTCTTTTGGTT--CAGATAACCCTTCTAG-CTTAAGTTATGCTGCAAATGATGTGCCTTGGAGC
*
1038824 TGAGCGTAGTCGAACTCGAATGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGC
250 TGAGCGTAGTCGAACTC-AAGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGC
* * * *
1038889 AAATGATGTGCCTTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGACAACCCTAC
310 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGAAGATAACCCTTC
* * * * * *
1038954 TAGACTTAAGT-TGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGATC-TT
375 TAGACTTAAGTATGTTGCAAATGATGTGCCTTAG-AGCTGAGCGTAGTCGAACTCGAAGATCTTT
* * *
1039017 TGG-CAGATAACCCTTCTCGACTTAAGCTATATGCAAATGATTTTCCCTTGA
439 TGGTCAGATAACCCTTCTAGACTTAAG-TATATG--AATGA--TACCCTCGA
* * *
1039068 AGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATACTGCA
1 AGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCA
* * *
1039133 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCATATAACTCTTCT
66 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
* * * * * * *
1039198 CGACTTAAGTTATGCTGCAAATGATGTGCCCCTCGAAGCTGAGTGTAATCAAACTTGAGGGTC-T
131 CGACTTAAGTTATGCTGCAAATGATGTG--CCTTGGAGCTGAGCGTAGTCGAACTAGAAGGTCTT
* * * * *
1039262 TTGG--CATATAGCCCTTCTCAACTTAAGTTATGCTGCAAATGATGTGTCTTGGAGCTGACCGTA
194 TTGGTTCAGATAACCCTTCT-AGCTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTA
1039325 GTCGAACTCAAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
258 GTCGAACTC-AAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
* * *
1039390 TTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAGTT
322 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGAAGATAACCCTTCTAGACTTAAG-T
* * ** *
1039455 ATGTTGTAAATGATATGCCTTAGAGCTGAGCGTAGTAAAACTCGAAGCTCTTTTGGTCACAGATA
386 ATGTTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGATCTTTTGGT--CAGATA
*
1039520 ACCCTTCTAG-CGTTGAGT-TATG-ATG-TACCCTCGA
449 ACCCTTCTAGAC-TTAAGTATATGAATGATACCCTCGA
1039554 AGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCATG-TAGCCCTTCTCGACTTAAGCTATGCTGC
1 AGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCA-GATAGCCCTTCTCGACTTAAGCTATGCTGC
* * * * *
1039618 AAATAATGTGTCTTGGAACTGAGCATAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
65 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
* * *
1039683 TCGACTTAAGTTATGTTGCAAATGATATGCCTTGGAGTTGAGCGTAGTCGAACTAGAAGGTCTTT
130 TCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTAGAAGGTCTTT
** ** * * *
1039748 TGGTTACAGATAACCCTTCTAGCTTTGTGTTATGCTATAAATGATGTGCCCTCGAAGCTGAGTGT
195 TGGTT-CAGATAACCCTTCTAGC-TTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGT
* * * * *
1039813 AATCGAACTCAAGGGTCTTTGGCAGATAACCCTTCTCGACTTTAGCTATGTTGCAAATGATGTAC
257 AGTCGAACTCAA-GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGC
* * * * *
1039878 CTTGGAGCTGAGCGTAGTCGAACTCGAATGTATTTTGTTGGCAA-ATAACCCTTCTTGCCTTGAG
321 CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGG-AAGATAACCCTTCTAGACTTAAG
* * * * *
1039942 CTATGTTGCAAATTATGTGCCTTGGAGCTGAGCGCAGTCGAACTCGAAGGTCTTTTGTTGGCAGA
385 -TATGTTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGATCTTTTG--GTCAGA
* * *
1040007 TAACCCTTCTTGACTTAAGTCATGCTGCAAATGATATGCCTTCGA
447 TAACCCTTCTAGACTTAAGT-AT-ATG--AATGATA--CCCTCGA
* *
1040052 AGCTGAGTGTAATCGAAC-CTGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAACTATG
1 AGCTGAGTGTAATCGAACTC-GAGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATG
* * * * * *
1040116 TTGAAAATGATATGCCTTTGAGCTGAGCGTAGTCGAACTCGAAAGTCTTT-GTTGGTAGATAACC
61 CTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACC
* *
1040180 CTTCT-AACCTTGAGTTATGCTGCAAATG
126 CTTCTCGA-CTTAAGTTATGCTGCAAATG
1040208 TTGTCTTTAA
Statistics
Matches: 962, Mismatches: 137, Indels: 82
0.81 0.12 0.07
Matches are distributed among these distances:
484 25 0.03
485 5 0.01
486 150 0.16
487 3 0.00
488 34 0.04
489 297 0.31
490 25 0.03
491 25 0.03
492 6 0.01
493 65 0.07
494 37 0.04
495 61 0.06
496 5 0.01
497 62 0.06
498 30 0.03
500 3 0.00
501 60 0.06
502 69 0.07
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (485 bp):
AGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCA
AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
CGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTAGAAGGTCTTTT
GGTTCAGATAACCCTTCTAGCTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
GAACTCAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGAAGATAACCCTTCTAGACTTAAGTATGTT
GCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGATCTTTTGGTCAGATAACCCTTC
TAGACTTAAGTATATGAATGATACCCTCGA
Found at i:1039932 original size:573 final size:571
Alignment explanation
Indices: 1038685--1040058 Score: 1750
Period size: 573 Copynumber: 2.4 Consensus size: 571
1038675 AGGTCTTCGG
*
1038685 TTGGCAGATAGCCATTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* * * * * * *
1038750 CGACCTCGAAGGTCTTTTGTTGGCAGACAACCATTCTAGACTTAAGTTATGCTGCAAATGATATA
66 CGAACTCGAAAGT-TTTTGTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTG
* *
1038815 CCTTGGAGCTGAGCGTAGTCGAACTCGAATGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAG
130 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAG
* * * * ** * * **
1038880 CTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGA
195 TTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTAAAACTCGAAGCTCTTTTGGTCACAGA
*
1038945 CAACCCTACTAGACTTAAGTTGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGA
260 CAACCCTACTAGACTTAAGTT-CT---AATGATGTACCCTCGAAGCTGAGTGTAATCGAACTCGA
* *
1039010 GGATCTTTGGCAGATAACCCTTCTCGACTTAAGCTATATGCAAATGATTTTCCCTTGAAGCTGAG
321 GGATCTTTGGCAGATAACCCTTCTCGACTTAAGCTATATGCAAATAATTGT-CCTTGAAGCTGAG
** * * * * *
1039075 TGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATACTGCAAATGATG
385 CATAATCAAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATA
* * * *
1039140 TGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCATATAACTCTTCTCGACTTA
450 TGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGACAGATAACCCTTCTAGACTTA
* **
1039205 AGTTATGCTGCAAATGATGTGCCCCTCGAAGCTGAGTGTAATCAAACTTGAGGGTCT
515 AGTTATGCTACAAATGATGTGCCCCTCGAAGCTGAGTGTAATCAAACTCAAGGGTCT
* * * * *
1039262 TTGGCATATAGCCCTTCTCAACTTAAGTTATGCTGCAAATGATGTGTCTTGGAGCTGACCGTAGT
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* * * *
1039327 CGAACTC-AAAG-GTCT-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGC
66 CGAACTCGAAAGTTTTTGTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGC
* *
1039389 CTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAGT
131 CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGT
* * *
1039454 TATGTTGTAAATGATATGCCTTAGAGCTGAGCGTAGTAAAACTCGAAGCTCTTTTGGTCACAGAT
196 TATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTAAAACTCGAAGCTCTTTTGGTCACAGAC
* * *
1039519 AACCCTTCTAG-CGTTGAG-T-T-ATGATGTACCCTCGAAGCTGAGTGTAATCGAACTCGAGGGT
261 AACCCTACTAGAC-TTAAGTTCTAATGATGTACCCTCGAAGCTGAGTGTAATCGAACTCGAGGAT
* *
1039580 CTTTGGCATG-TAGCCCTTCTCGACTTAAGCTATGCTGCAAATAATGTGT-CTTGGAA-CTGAGC
325 CTTTGGCA-GATAACCCTTCTCGACTTAAGCTAT-ATGCAAATAAT-TGTCCTT-GAAGCTGAGC
* **
1039642 ATAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGTTGCAAATG
386 ATAATCAAACTCGAAGGTC--T--TTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATG
*
1039707 ATATGCCTTGGAGTTGAGCGTAGTCGAACT-AGAAGGTCTTTTGGTT-ACAGATAACCCTTCTAG
447 ATATGCCTTGGAGCTGAGCGTAGTCGAACTCA-AAGGTC-TTTGGTTGACAGATAACCCTTCTAG
** * *
1039770 -CTTTGTGTTATGCTATAAATGATGTG-CCCTCGAAGCTGAGTGTAATCGAACTCAAGGGTCT
510 AC-TTAAGTTATGCTACAAATGATGTGCCCCTCGAAGCTGAGTGTAATCAAACTCAAGGGTCT
* * * *
1039831 TTGGCAGATAACCCTTCTCGACTTTAGCTATGTTGCAAATGATGTACCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* * * * * * *
1039896 CGAACTCGAATGTATTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATTATGTG
66 CGAACTCGAAAGT-TTTTGTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTG
* * *
1039961 CCTTGGAGCTGAGCGCAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGACTTAAG
130 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAG
* *
1040026 TCATGCTGCAAATGATATGCCTTCGAAGCTGAG
195 TTATGCTGCAAATGATATGCCTTAG-AGCTGAG
1040059 TGTAATCGAA
Statistics
Matches: 688, Mismatches: 92, Indels: 37
0.84 0.11 0.05
Matches are distributed among these distances:
566 91 0.13
567 13 0.02
568 3 0.00
569 97 0.14
570 109 0.16
571 7 0.01
572 4 0.01
573 287 0.42
574 9 0.01
576 3 0.00
577 65 0.09
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (571 bp):
TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
CGAACTCGAAAGTTTTTGTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGC
CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGT
TATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTAAAACTCGAAGCTCTTTTGGTCACAGAC
AACCCTACTAGACTTAAGTTCTAATGATGTACCCTCGAAGCTGAGTGTAATCGAACTCGAGGATC
TTTGGCAGATAACCCTTCTCGACTTAAGCTATATGCAAATAATTGTCCTTGAAGCTGAGCATAAT
CAAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATATGCCTT
GGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGACAGATAACCCTTCTAGACTTAAGTTAT
GCTACAAATGATGTGCCCCTCGAAGCTGAGTGTAATCAAACTCAAGGGTCT
Found at i:1044627 original size:13 final size:12
Alignment explanation
Indices: 1044597--1044661 Score: 55
Period size: 13 Copynumber: 5.2 Consensus size: 12
1044587 ATTGGGCCTG
1044597 TAAATAAAATGAAA
1 TAAATAAAAT--AA
1044611 TAAATTAAAATAA
1 TAAA-TAAAATAA
1044624 TAAATGAATAA-AA
1 TAAAT-AA-AATAA
1044637 TAAA-AAAATAA
1 TAAATAAAATAA
1044648 TAAA-AATAATAA
1 TAAATAA-AATAA
1044660 TA
1 TA
1044662 TACTAAATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
10 2 0.04
11 10 0.22
12 8 0.17
13 14 0.30
14 6 0.13
15 6 0.13
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (12 bp):
TAAATAAAATAA
Found at i:1044635 original size:21 final size:22
Alignment explanation
Indices: 1044598--1044647 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
1044588 TTGGGCCTGT
*
1044598 AAATAAAATGAAATAAATTAAAA
1 AAAT-AAATGAAATAAAATAAAA
*
1044621 TAATAAATG-AATAAAATAAAA
1 AAATAAATGAAATAAAATAAAA
1044642 AAATAA
1 AAATAA
1044648 TAAAAATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 16 0.67
22 5 0.21
23 3 0.12
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (22 bp):
AAATAAATGAAATAAAATAAAA
Found at i:1044637 original size:16 final size:15
Alignment explanation
Indices: 1044599--1044674 Score: 57
Period size: 17 Copynumber: 4.7 Consensus size: 15
1044589 TGGGCCTGTA
1044599 AATAAAATGAAATAAAT
1 AATAAAAT--AATAAAT
1044616 --TAAAATAATAAAT
1 AATAAAATAATAAAT
*
1044629 GAATAAAATAAAAAAAT
1 -AATAAAAT-AATAAAT
1044646 AATAAAAATAATAATAT
1 AAT-AAAATAATAA-AT
*
1044663 ACTAAATATAAT
1 AATAAA-ATAAT
1044675 TTATATAATA
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
13 7 0.14
15 6 0.12
16 16 0.33
17 20 0.41
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.26
Consensus pattern (15 bp):
AATAAAATAATAAAT
Found at i:1044652 original size:9 final size:9
Alignment explanation
Indices: 1044619--1044659 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
1044609 AATAAATTAA
1044619 AATAATAAAT
1 AATAA-AAAT
1044629 GAAT-AAAAT
1 -AATAAAAAT
1044638 AA-AAAAAT
1 AATAAAAAT
1044646 AATAAAAAT
1 AATAAAAAT
1044655 AATAA
1 AATAA
1044660 TATACTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 9 0.32
9 15 0.54
10 1 0.04
11 3 0.11
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (9 bp):
AATAAAAAT
Found at i:1044715 original size:34 final size:33
Alignment explanation
Indices: 1044676--1044858 Score: 135
Period size: 35 Copynumber: 5.4 Consensus size: 33
1044666 AAATATAATT
*
1044676 TATATAATATATATTTCAAAATATTTTTTAAAAC
1 TATATAATATATATTTTAAAATA-TTTTTAAAAC
* *
1044710 TATATATTATATTTTTTTAAAA-ATGTTTTAAAAC
1 TATATAATATA-TATTTTAAAATAT-TTTTAAAAC
* * *
1044744 TATATATTATATAGTTTTTAAAATGTTTTAAAAAC
1 TATATAATATATA--TTTTAAAATATTTTTAAAAC
* * *
1044779 TATACATATATAAATGTTTTTAAAATA--TTTCAAAC
1 TAT--ATA-ATATAT-ATTTTAAAATATTTTTAAAAC
*
1044814 T-TAT-AT-TATATTTTAAAAATATTTTCAAAAC
1 TATATAATATATATTTT-AAAATATTTTTAAAAC
1044845 TATATAATTATATA
1 TATATAA-TATATA
1044859 AATTTTCGAA
Statistics
Matches: 117, Mismatches: 16, Indels: 31
0.71 0.10 0.19
Matches are distributed among these distances:
28 4 0.03
29 8 0.07
30 2 0.02
31 7 0.06
32 5 0.04
33 3 0.03
34 33 0.28
35 38 0.32
36 1 0.01
37 12 0.10
38 4 0.03
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (33 bp):
TATATAATATATATTTTAAAATATTTTTAAAAC
Found at i:1044778 original size:35 final size:34
Alignment explanation
Indices: 1044701--1044858 Score: 157
Period size: 34 Copynumber: 4.6 Consensus size: 34
1044691 TCAAAATATT
*
1044701 TTTTAAAACTATATATTATAT-TTTTTTAAAAATG
1 TTTTAAAACTATATATTATATAGTTTTT-AAAATG
1044735 TTTTAAAACTATATATTATATAGTTTTTAAAATG
1 TTTTAAAACTATATATTATATAGTTTTTAAAATG
* *
1044769 TTTTAAAAACTATACATATATAAATGTTTTTAAAAT-
1 TTTT-AAAACTATATAT-TATATA-GTTTTTAAAATG
* * * *
1044805 ATTTCAAACT-TATA-T-TATA-TTTTAAAAATA
1 TTTTAAAACTATATATTATATAGTTTTTAAAATG
1044835 TTTTCAAAACTATATAATTATATA
1 TTTT-AAAACTATAT-ATTATATA
1044859 AATTTTCGAA
Statistics
Matches: 104, Mismatches: 10, Indels: 19
0.78 0.08 0.14
Matches are distributed among these distances:
29 9 0.09
30 3 0.03
31 8 0.08
32 4 0.04
33 1 0.01
34 35 0.34
35 25 0.24
36 8 0.08
37 11 0.11
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (34 bp):
TTTTAAAACTATATATTATATAGTTTTTAAAATG
Found at i:1044836 original size:29 final size:33
Alignment explanation
Indices: 1044676--1044857 Score: 126
Period size: 34 Copynumber: 5.4 Consensus size: 33
1044666 AAATATAATT
* *
1044676 TATATAA-TATATATTTCAAAATATTTTTTAAAAC
1 TATATAATTATAT-TTTAAAAATA-TTTTCAAAAC
*
1044710 TATAT-ATTATATTTTTTTAAAAATGTTTT-AAAAC
1 TATATAATTATA---TTTTAAAAATATTTTCAAAAC
* * * *
1044744 TATATATTATATAGTTTTTAAAATGTTTTAAAAAC
1 TATATAAT-TATA-TTTTAAAAATATTTTCAAAAC
* * *
1044779 TATACATATATAAATGTTTTTAAAATA-TTTC-AAAC
1 TAT--ATA-AT-TATATTTTAAAAATATTTTCAAAAC
1044814 T-TAT-ATTATATTTTAAAAATATTTTCAAAAC
1 TATATAATTATATTTTAAAAATATTTTCAAAAC
1044845 TATATAATTATAT
1 TATATAATTATAT
1044858 AAATTTTCGA
Statistics
Matches: 121, Mismatches: 13, Indels: 29
0.74 0.08 0.18
Matches are distributed among these distances:
29 12 0.10
30 6 0.05
31 5 0.04
32 5 0.04
33 8 0.07
34 34 0.28
35 18 0.15
36 15 0.12
37 14 0.12
38 4 0.03
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (33 bp):
TATATAATTATATTTTAAAAATATTTTCAAAAC
Found at i:1044856 original size:38 final size:41
Alignment explanation
Indices: 1044814--1044897 Score: 97
Period size: 40 Copynumber: 2.1 Consensus size: 41
1044804 TATTTCAAAC
*
1044814 TTATATTATATTTT-AAAAAT-ATT-TTCAAAACTATATA-A
1 TTATATTAAATTTTCAAAAATCATTATTCAAAA-TATATATA
* *
1044852 TTATA-TAAATTTTCGAAAATCATTATTCGAAATATATATA
1 TTATATTAAATTTTCAAAAATCATTATTCAAAATATATATA
1044892 TTATAT
1 TTATAT
1044898 ATTTATAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
37 7 0.18
38 10 0.26
39 9 0.24
40 12 0.32
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.46
Consensus pattern (41 bp):
TTATATTAAATTTTCAAAAATCATTATTCAAAATATATATA
Found at i:1044890 original size:2 final size:2
Alignment explanation
Indices: 1044883--1044927 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
1044873 ATTATTCGAA
*
1044883 AT AT AT AT AT -T AT AT AT TT AT A- AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1044922 AT AT AT
1 AT AT AT
1044928 CAAACGAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
1 3 0.08
2 35 0.92
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1044912 original size:8 final size:10
Alignment explanation
Indices: 1044883--1044927 Score: 60
Period size: 9 Copynumber: 4.8 Consensus size: 10
1044873 ATTATTCGAA
1044883 ATATATATAT
1 ATATATATAT
*
1044893 -TATATATTT
1 ATATATATAT
1044902 ATA-ATA-AT
1 ATATATATAT
1044910 ATATATATAT
1 ATATATATAT
1044920 ATATATAT
1 ATATATAT
1044928 CAAACGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
8 4 0.13
9 14 0.47
10 12 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
ATATATATAT
Found at i:1048308 original size:7 final size:7
Alignment explanation
Indices: 1048298--1048322 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1048288 TTATATCATA
1048298 TATATTT
1 TATATTT
1048305 TATATTT
1 TATATTT
1048312 TATATTT
1 TATATTT
1048319 TATA
1 TATA
1048323 ATTAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
TATATTT
Found at i:1049876 original size:62 final size:62
Alignment explanation
Indices: 1049796--1049926 Score: 140
Period size: 62 Copynumber: 2.1 Consensus size: 62
1049786 TAAAATAGTT
* * *
1049796 ATAATTTTGATAAATTTAAGGATCT-TTTTGTAACAATTTCATAAGTTGAATGTTCA-TTTATA
1 ATAA-TTTAATAAATTTAAGGAT-TATTTTGTAACAATTTCAGAAGTTGAATGATCATTTTATA
* *** * *
1049858 ATAATTTAATAAATTTTAATGATTATTTTGTAATTGTTTGAGAAGTTTAATGATCATTTTATA
1 ATAATTTAATAAA-TTTAAGGATTATTTTGTAACAATTTCAGAAGTTGAATGATCATTTTATA
1049921 ATAATT
1 ATAATT
1049927 AAAATATTCT
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
61 9 0.16
62 36 0.63
63 12 0.21
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.49
Consensus pattern (62 bp):
ATAATTTAATAAATTTAAGGATTATTTTGTAACAATTTCAGAAGTTGAATGATCATTTTATA
Found at i:1056079 original size:22 final size:22
Alignment explanation
Indices: 1056054--1056098 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1056044 AATATATTGT
* *
1056054 AAAGTATCGATCCTTTTTATAA
1 AAAGAATCGATACTTTTTATAA
*
1056076 AAAGAATCGATACTTTTTTTAA
1 AAAGAATCGATACTTTTTATAA
1056098 A
1 A
1056099 GTTATGTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (22 bp):
AAAGAATCGATACTTTTTATAA
Found at i:1056480 original size:23 final size:23
Alignment explanation
Indices: 1056450--1056499 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
1056440 ATACTTTACA
*
1056450 ATATAAGCACTACCTATTACATT
1 ATATAAGCACTACCTATTACATC
*
1056473 ATATAAGCGCTACCTATTACATC
1 ATATAAGCACTACCTATTACATC
1056496 ATAT
1 ATAT
1056500 TTTTACCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (23 bp):
ATATAAGCACTACCTATTACATC
Found at i:1056532 original size:441 final size:447
Alignment explanation
Indices: 1055643--1057882 Score: 2607
Period size: 490 Copynumber: 4.8 Consensus size: 447
1055633 AAAAGGATCG
*
1055643 ATACTTTTTTTAAAGTTATGTAATTTATATTTCAA-TTTTTTAATAGTGTTTCATGTTTTCCACC
1 ATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACC
* * *
1055707 TACAATATTAATTTAATAATTTCATTTGCACAAAAAAAATTTGATTGTTTTGATATTTTATAAAA
66 TACAATATTAATTTAATAATTTCATTTACATAAAAAATATTTGATTGTTTTGATATTTTATAAAA
*
1055772 TAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAATATATATGT
131 TATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAATATATATGT
* * ****
1055837 TTATTGTTTTTAATTTAATGATAATATATACCGTAACATAAAAAATAAATCATTAGATAAATATA
196 TTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATA
*
1055902 ATTACTAAATTGATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGA
261 ATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGA
* * * * * *
1055967 AATAAGTATTGATACTTCTATAAAAAGGATAGATACTTTACAATATAAGCGCTACCTATTACATC
326 AAAAAGTATGGACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACATT
*** * * * * * ** * ** *
1056032 ATAT---TTTTACCTAATATATTGTAAAGTATCGATCCT-TTTTA-T-AAAAAG--A-ATCG
391 ATATAAGCGCTACCTATTACA-T-CATA-TTTTTA-CCTATTATATTGAAAGTGCTACA-CT
*
1056085 ATACTTTTTTTAAAGTTATGTAATTTATGTTTCAAGTTTTTTAATAGTGTTTCATGTTTTCCACC
1 ATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACC
1056150 TACAATATTAATTTAATAATTTCATTTACATAAAAAATTATTTGATTGTTTTGATATTTTATAAA
66 TACAATATTAATTTAATAATTTCATTTACATAAAAAA-TATTTGATTGTTTTGATATTTTATAAA
*
1056215 ATATTATTTAGAATTTAAATTTAACAATATTAACCAAA-ATAAAAATAAATATGT-A-ATATATG
130 ATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAATATATATG
1056277 TTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTAT
195 TTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTAT
*
1056342 AATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTA
260 AATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTG
1056407 AAAAAAGTATGGACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACAT
325 AAAAAAGTATGGACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACAT
1056472 TATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTATA
390 TATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTG--C-TAC-------
*
1056537 AAAAGTCG
445 ---A--CT
* * *
1056545 ATACTTTTTTTAAAGTTATGTAACTTATTTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCAT
1 ATACTTTTTTTAAAGTTATGTAATTTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTCCAC
1056610 CTACAATATTAATTTAATAATTTCATTTACATAAAAAATATTTGATTGTTTTGATATTTTATAAA
65 CTACAATATTAATTTAATAATTTCATTTACATAAAAAATATTTGATTGTTTTGATATTTTATAAA
*
1056675 ATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGAAATATATATG
130 ATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAATATATATG
1056740 TTTATTGTTTTTAATTTAATAAT-ATATAT--CGTAACGTAAAAAATAAATCATTAGACGCCTAT
195 TTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTAT
*
1056802 AATTATTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTG
260 AATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTG
*
1056867 AAAAAA-TATTGACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACAT
325 AAAAAAGTATGGACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACAT
* *
1056931 TATATAAACGCTACCTATTACATTATATAAGTGCTACTATTACATCATATTTTTACTTATTATAT
390 TATAT-AA-G----C----GC------T-A---C--CTATTACATCATATTTTTACCTATTATAT
1056996 TGAAAGTG-T-C-C-
433 TGAAAGTGCTACACT
* * * * *
1057007 ATACTTTTTATAAAAAG-GATCGATACTTT-T-TTTAAAGTTATGTAATTTATGTTTCAATTTTT
1 ATACTTTTT-T-TAAAGTTAT-G-TAATTTATGTTTCAA-TT-T-T--TTTA----A--------
1057069 TTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACATAAAAAAATA
45 ----TAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAT-AAAAAATA
1057134 TTTGATTGTTTT-ATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGA
105 TTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGA
*
1057198 TAATAATAAATATGTAATATATATATTTATTGTTTTTAATTTAATAATAATATATACCGTAACGT
170 TAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGT
*
1057263 AAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTAAAAAGATAA
235 AAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAA
*
1057328 CCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGAACACTTTTATAAAAAGGATAGATACTTT
300 CCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGATACTTT
1057393 ACAATATAAGCACTACCTATAACATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTA
365 ACAATATAAG------------C---------A--CTACCTATTACATTATATAAGCGCTACCTA
*
1057458 TTACATCATATTTTTACCTATTATATTGAAAGTG-T--TC-
407 TTACATCATATTTTTACCTATTATATTGAAAGTGCTACACT
* * * * * *
1057495 ATACTTTTTATAAAAAG-GATCG-ATATTTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTT
1 ATACTTTTT-T-TAAAGTTAT-GTA-ATTTATGTTTCAA-TT-T-T--TTTA---AT--------
* *
1057558 TTAACAGTGTTTCATGTTTTCCACATACAATATTAATTTAATAATTTCATTTACACAAAAAATTA
46 -----AGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACATAAAAAA-TA
*
1057623 TTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATATTAACCAAAGA
105 TTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGA
1057688 TAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGT
170 TAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGT
1057753 AAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAA
235 AAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAA
* * *
1057818 CCTTAAATTAATGTTTTTCACAGTGAAAAAAATATGAACACTTTTATAAAAAGGATAGATACTTT
300 CCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGATACTTT
1057883 TTATAAAAAG
Statistics
Matches: 1606, Mismatches: 70, Indels: 196
0.86 0.04 0.10
Matches are distributed among these distances:
440 3 0.00
441 200 0.12
442 38 0.02
443 84 0.05
444 72 0.04
448 1 0.00
459 63 0.04
460 205 0.13
461 80 0.05
462 16 0.01
463 41 0.03
464 7 0.00
465 6 0.00
467 4 0.00
469 1 0.00
475 1 0.00
476 3 0.00
477 1 0.00
479 1 0.00
481 36 0.02
483 149 0.09
484 26 0.02
486 103 0.06
487 44 0.03
488 69 0.04
489 82 0.05
490 243 0.15
493 1 0.00
494 1 0.00
499 1 0.00
500 1 0.00
504 1 0.00
508 2 0.00
509 2 0.00
510 18 0.01
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (447 bp):
ATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACC
TACAATATTAATTTAATAATTTCATTTACATAAAAAATATTTGATTGTTTTGATATTTTATAAAA
TATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAATATATATGT
TTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATA
ATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGA
AAAAAGTATGGACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACATT
ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGCTACACT
Found at i:1056944 original size:23 final size:23
Alignment explanation
Indices: 1056909--1056980 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
1056899 ATACTTTACA
*
1056909 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
1056932 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
1056955 ATATAAGTGCTA-CTATTACATC
1 ATATAAGCGCTACCTATTACATT
1056977 ATAT
1 ATAT
1056981 TTTTACTTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 13 0.30
23 31 0.70
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.36
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:1057423 original size:23 final size:23
Alignment explanation
Indices: 1057396--1057468 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
1057386 ATACTTTACA
* *
1057396 ATATAAGCACTACCTATAACATT
1 ATATAAGCGCTACCTATTACATT
*
1057419 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
1057442 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
1057465 ATAT
1 ATAT
1057469 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.40, C:0.22, G:0.05, T:0.33
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:1057742 original size:490 final size:486
Alignment explanation
Indices: 1056009--1057882 Score: 3161
Period size: 490 Copynumber: 3.9 Consensus size: 486
1055999 ATACTTTACA
* * * *
1056009 ATATAAGCGCTACCTATTACATCATATTTTTACCTAATATATTGTAAAGTATCGATCCTTTTTAT
1 ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTG-AAAGTGTCCATACTTTTTAT
* *
1056074 AAAAAGAATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAAGTTTTTTAATAGTGTTTCA
65 AAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCA
1056139 TGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACATAAAAAATTATTTGATTGTTTTGA
130 TGTTTTCCA-CTACAATATTAATTTAATAATTTCATTTACATAAAAAA-TATTTGATTGTTTTGA
*
1056204 TATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAA-ATAAAAATAAATATG
193 TATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATG
1056268 T-A-ATATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCAT
258 TAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCAT
1056331 TAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGT
323 TAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGT
* *
1056396 TTTCCACAGTAAAAAAAGTATGGACACTTTTATAAAAAGGATAGATACTTTACAATATAAG----
388 TTTCCACAGTGAAAAAA-TATGAACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACT
1056457 --------C---------A--CTACCTATTACATT
452 ACCTATAACATTATATAAACGCTACCTATTACATT
1056473 ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATAC-TTTTATA
1 ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATA
* *
1056537 AAAA-G-TCGATACTTTTTTTAAAGTTATGTAACTTATTTTTCAATTTTTTTTAATAGTGTTTCA
66 AAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAA-TTTTTTTAATAGTGTTTCA
1056600 TGTTTTCCATCTACAATATTAATTTAATAATTTCATTTACATAAAAAATATTTGATTGTTTTGAT
130 TGTTTTCCA-CTACAATATTAATTTAATAATTTCATTTACATAAAAAATATTTGATTGTTTTGAT
*
1056665 ATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGA
194 ATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGT
1056730 AATATATATGTTTATTGTTTTTAATTTAATAAT-ATATAT--CGTAACGTAAAAAATAAATCATT
259 AATATATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATT
*
1056792 AGACGCCTATAATTATTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTT
324 AGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTT
1056857 TTCCACAGTGAAAAAATATTG-ACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTA
389 TTCCACAGTGAAAAAATA-TGAACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTA
*
1056921 CCTATTACATTATATAAACGCTACCTATTACATT
453 CCTATAACATTATATAAACGCTACCTATTACATT
* *
1056955 ATATAAGTGCTA-CTATTACATCATATTTTTACTTATTATATTGAAAGTGTCCATACTTTTTATA
1 ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATA
1057019 AAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCAT
66 AAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCAT
1057084 GTTTTCCACCTACAATATTAATTTAATAATTTCATTTACATAAAAAAATATTTGATTGTTTT-AT
131 GTTTTCCA-CTACAATATTAATTTAATAATTTCATTTACAT-AAAAAATATTTGATTGTTTTGAT
1057148 ATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGT
194 ATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGT
*
1057213 AATATATATATTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATT
259 AATATATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATT
*
1057278 AGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTAAAAAGATAACCTTAAATTAATGTT
324 AGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTT
1057343 TTCCACAGTGAAAAAAGTATGAACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTA
389 TTCCACAGTGAAAAAA-TATGAACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTA
1057408 CCTATAACATTATATAAACGCTACCTATTACATT
453 CCTATAACATTATATAAACGCTACCTATTACATT
*
1057442 ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTTCATACTTTTTATA
1 ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATA
* *
1057507 AAAAGGATCGATATTTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCA
66 AAAAGGATCGATA-CTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCA
*
1057572 TGTTTTCCACATACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGA
130 TGTTTTCCAC-TACAATATTAATTTAATAATTTCATTTACATAAAAAA-TATTTGATTGTTTTGA
*
1057637 TATTTTATAAAATATTATTTAGTATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATG
193 TATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATG
1057702 TAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCAT
258 TAATATATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCAT
1057767 TAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGT
323 TAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGT
*
1057832 TTTTCACAGTGAAAAAAATATGAACACTTTTATAAAAAGGATAGATACTTT
388 TTTCCACAGTG-AAAAAATATGAACACTTTTATAAAAAGGATAGATACTTT
1057883 TTATAAAAAG
Statistics
Matches: 1334, Mismatches: 33, Indels: 60
0.93 0.02 0.04
Matches are distributed among these distances:
459 40 0.03
460 205 0.15
461 79 0.06
462 18 0.01
463 40 0.03
464 43 0.03
471 1 0.00
480 1 0.00
481 43 0.03
482 36 0.03
483 159 0.12
484 62 0.05
486 104 0.08
487 89 0.07
488 70 0.05
489 102 0.08
490 236 0.18
491 6 0.00
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (486 bp):
ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATA
AAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCAT
GTTTTCCACTACAATATTAATTTAATAATTTCATTTACATAAAAAATATTTGATTGTTTTGATAT
TTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAA
TATATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAG
ACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTT
CCACAGTGAAAAAATATGAACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCT
ATAACATTATATAAACGCTACCTATTACATT
Found at i:1057903 original size:22 final size:22
Alignment explanation
Indices: 1057844--1057904 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
1057834 TTCACAGTGA
* *
1057844 AAAAAATATGAACAC-TTTTAT
1 AAAAAGTATGGACACTTTTTAT
* * *
1057865 AAAAAGGATAGATACTTTTTAT
1 AAAAAGTATGGACACTTTTTAT
1057887 AAAAAGTATGGACACTTT
1 AAAAAGTATGGACACTTT
1057905 CAATATAATA
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
21 10 0.32
22 21 0.68
ACGTcount: A:0.48, C:0.08, G:0.11, T:0.33
Consensus pattern (22 bp):
AAAAAGTATGGACACTTTTTAT
Found at i:1057953 original size:23 final size:23
Alignment explanation
Indices: 1057922--1057994 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
1057912 ATAGGTAAAA
*
1057922 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
1057945 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
1057968 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
1057991 ATAT
1 ATAT
1057995 TGTAAAGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1058366 original size:200 final size:200
Alignment explanation
Indices: 1058110--1059307 Score: 2159
Period size: 200 Copynumber: 6.0 Consensus size: 200
1058100 GCATTAATAT
* *
1058110 TTCATTCTGGA-CAAAAATATCGACACAAACTAAAAAATTGTCGATACATGATTTAGACCTATTC
1 TTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGATACATTATTTAGACCTATTC
*
1058174 TCTCATAAAACCGATATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGG
66 TCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGG
1058239 GTTTCGATGTTTATCGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTT
131 GTTTCGATGTTTATCGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTT
1058304 TGCCA
196 TGCCA
* * * *
1058309 TTCATTATAGACCAAAAATATCAACACAAACTACAAAAGTGTCGATACATTATTTAGACCTATTC
1 TTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGATACATTATTTAGACCTATTC
*
1058374 TCTCATAAAATCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGG
66 TCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGG
*
1058439 GTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTT
131 GTTTCGATGTTTATCGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTT
1058504 TGCCA
196 TGCCA
1058509 TTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGATACATTATTTAGACCTATTC
1 TTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGATACATTATTTAGACCTATTC
* *
1058574 TCTCATAAAACAGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATATTTATGG
66 TCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGG
1058639 GTTTCGATGTTTATCGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTT
131 GTTTCGATGTTTATCGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTT
1058704 TGCCA
196 TGCCA
1058709 TTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGATACATTATTTAGACCTATTC
1 TTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGATACATTATTTAGACCTATTC
* *
1058774 TCTCATAAAACCGTTATACTTGTACCGGTTAGATTGAAAAATTACCTATTATATTATACTTATGG
66 TCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGG
*
1058839 GTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTT
131 GTTTCGATGTTTATCGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTT
1058904 TGCCA
196 TGCCA
*
1058909 TTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTTGATACATTATTTAGACCTATTC
1 TTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGATACATTATTTAGACCTATTC
*
1058974 CCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGG
66 TCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGG
*
1059039 GTTTCGATGTTTATCGGATCGATACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTT
131 GTTTCGATGTTTATCGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTT
1059104 TGCCA
196 TGCCA
* * *
1059109 TTCATTCT-GACCAAAAATATCGATACAAAATACAAAAGTGTCGATACATTATTTAGACCTATTC
1 TTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGATACATTATTTAGACCTATTC
* *
1059173 TCTCATAAAACCGGTATACTTGTACCGATTAGATTGAAAAATTACCTATTACATTATACTTTTGG
66 TCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGG
* *
1059238 GTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCA-CCTGTT
131 GTTTCGATGTTTATCGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTT
1059302 TGCCA
196 TGCCA
1059307 T
1 T
1059308 ATTGTAAATT
Statistics
Matches: 960, Mismatches: 38, Indels: 3
0.96 0.04 0.00
Matches are distributed among these distances:
198 12 0.01
199 178 0.19
200 770 0.80
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.36
Consensus pattern (200 bp):
TTCATTCTGGACCAAAAATATCGACACAAACTAAAAAAGTGTCGATACATTATTTAGACCTATTC
TCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGG
GTTTCGATGTTTATCGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTT
TGCCA
Found at i:1059552 original size:18 final size:18
Alignment explanation
Indices: 1059529--1059589 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
1059519 TCTCATTCAT
*
1059529 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
1059547 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
1059566 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
1059585 AATTA
1 AATTA
1059590 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:1059565 original size:19 final size:19
Alignment explanation
Indices: 1059541--1059589 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1059531 TTATATTCAC
1059541 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
1059560 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1059579 ATACAAAATTA
1 ATACAAAATTA
1059590 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1061501 original size:21 final size:21
Alignment explanation
Indices: 1061476--1061540 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
1061466 CCCCTTATGC
* *
1061476 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1061497 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
1061518 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1061539 CT
1 CT
1061541 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:1064088 original size:181 final size:182
Alignment explanation
Indices: 1063739--1064210 Score: 696
Period size: 181 Copynumber: 2.6 Consensus size: 182
1063729 CGTACTTACG
*
1063739 AAAGTATCGACACTTTCAATATATCCGGTATCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
1063804 TAT-ATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
* *
1063868 AAGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
131 AAGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCATTATATT
*
1063919 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCAGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
1063984 TATCATATTTTTACATGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
* ** * *
1064049 AGGATTTAAAACTGTTTCTCTTTTAAATTCACGAAGTGTCGATCATTATATT
131 AAGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCATTATATT
* * * * * ** *
1064101 AAAGTACCGACACTTTAAATGTATCCGGTAGCGTTTTACCGGTTTTATTATTTCAATACCGTTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
1064166 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
1064211 AATTTGGATC
Statistics
Matches: 261, Mismatches: 29, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
180 66 0.25
181 98 0.38
182 97 0.37
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AAGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCATTATATT
Found at i:1064224 original size:182 final size:181
Alignment explanation
Indices: 1063739--1064225 Score: 658
Period size: 182 Copynumber: 2.7 Consensus size: 181
1063729 CGTACTTACG
*
1063739 AAAGTATCGACACTTTCAATATATCCGGTATCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
1063804 TAT-ATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTT--TTAAAGTATCGACACATT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAATT--AGTATCGACACATT
* *
1063866 ATAAGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
129 ATAAGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCATTATAT
*
1063919 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCAGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * * *
1063984 TATCATATTTTTACATGGTATATCGTTTTGGATCGATACATTTTTTAA-AAGTATCGACACTTTA
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACA-TTTTTAATTAGTATCGACACATTA
* ** * *
1064048 TAGGATTTAAAACTGTTTCTCTTTTAAATTCACGAAGTGTCGATCATTATATT
130 TAAGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCATTATA-T
* * * * * ** *
1064101 AAAGTACCGACACTTTAAATGTATCCGGTAGCGTTTTACCGGTTTTATTATTTCAATACCGTTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * * * *
1064166 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTTAATTTGGATCGACAC
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAATTAGTATCGACAC
1064226 GAATCGACAA
Statistics
Matches: 269, Mismatches: 32, Indels: 10
0.86 0.10 0.03
Matches are distributed among these distances:
180 66 0.25
181 97 0.36
182 106 0.39
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (181 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAATTAGTATCGACACATTAT
AAGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCATTATAT
Found at i:1070717 original size:28 final size:30
Alignment explanation
Indices: 1070636--1070718 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 30
1070626 TTATTTTTCT
* *
1070636 AAAAACAACCT-TAAATTCTTTTAAAATATA
1 AAAAACACCCTCTAAATT-TTCTAAAATATA
* * *
1070666 AAAAACACCCTCTAAAATTGCTAAAATATC
1 AAAAACACCCTCTAAATTTTCTAAAATATA
*
1070696 AGAAAC-CCC-CTAAATTTTCTAAA
1 AAAAACACCCTCTAAATTTTCTAAA
1070719 CACCCAATAC
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
28 12 0.27
29 3 0.07
30 24 0.55
31 5 0.11
ACGTcount: A:0.49, C:0.20, G:0.02, T:0.28
Consensus pattern (30 bp):
AAAAACACCCTCTAAATTTTCTAAAATATA
Found at i:1070801 original size:120 final size:120
Alignment explanation
Indices: 1070647--1070891 Score: 400
Period size: 120 Copynumber: 2.0 Consensus size: 120
1070637 AAAACAACCT
*
1070647 TAAATTCTTTTAAAATATAAAAAACACCCTCTAAAATTGCTAAAATATCAGAAACCCCCTAAATT
1 TAAATTCTTTTAAAATATAAAAAACACCCTCTAAAATTGATAAAATATCAGAAACCCCCTAAATT
1070712 TTCTAAACACCCAATACTTGCTGACCATTCCTTGCAGCCCGCAACCATCGCCCCC
66 TTCTAAACACCCAATACTTGCTGACCATTCCTTGCAGCCCGCAACCATCGCCCCC
* * *
1070767 TAAATTCTTTTAAAATATCAAAAACACCCTCTAAAATTTATAAAATATCAGAAACTCCCTAAATT
1 TAAATTCTTTTAAAATATAAAAAACACCCTCTAAAATTGATAAAATATCAGAAACCCCCTAAATT
* * * **
1070832 TTGTAAACACCCAATACTTGCTGACCATTCCTTGCCGTCCGCCCCCATCGCCCCC
66 TTCTAAACACCCAATACTTGCTGACCATTCCTTGCAGCCCGCAACCATCGCCCCC
*
1070887 AAAAT
1 TAAAT
1070892 CTCTACTCAT
Statistics
Matches: 115, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
120 115 1.00
ACGTcount: A:0.36, C:0.30, G:0.07, T:0.27
Consensus pattern (120 bp):
TAAATTCTTTTAAAATATAAAAAACACCCTCTAAAATTGATAAAATATCAGAAACCCCCTAAATT
TTCTAAACACCCAATACTTGCTGACCATTCCTTGCAGCCCGCAACCATCGCCCCC
Found at i:1070838 original size:28 final size:29
Alignment explanation
Indices: 1070763--1070838 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 29
1070753 CAACCATCGC
*
1070763 CCCCTAAATTCTTTTAAAATATCAAAAACA
1 CCCCTAAATT-TTATAAAATATCAAAAACA
* *
1070793 CCCTCTAAAATTTATAAAATATCAGAAAC-
1 CCC-CTAAATTTTATAAAATATCAAAAACA
* *
1070822 TCCCTAAATTTTGTAAA
1 CCCCTAAATTTTATAAA
1070839 CACCCAATAC
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 12 0.31
29 2 0.05
30 19 0.49
31 6 0.15
ACGTcount: A:0.45, C:0.21, G:0.03, T:0.32
Consensus pattern (29 bp):
CCCCTAAATTTTATAAAATATCAAAAACA
Found at i:1075570 original size:30 final size:29
Alignment explanation
Indices: 1075520--1075596 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 29
1075510 TCATTTTTTA
*
1075520 AATATATTCGGTCATTTTTAGCGCCTAAT
1 AATATTTTCGGTCATTTTTAGCGCCTAAT
* *
1075549 AATATTTTCGGTTATTTTTTAGCGCTTAAT
1 AATATTTTCGGTCA-TTTTTAGCGCCTAAT
1075579 AATA-TTTCTGGTCATTTT
1 AATATTTTC-GGTCATTTT
1075597 CGGTCATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 20 0.48
30 22 0.52
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.49
Consensus pattern (29 bp):
AATATTTTCGGTCATTTTTAGCGCCTAAT
Found at i:1082813 original size:60 final size:60
Alignment explanation
Indices: 1082685--1082813 Score: 152
Period size: 60 Copynumber: 2.1 Consensus size: 60
1082675 AATATTCGAG
* * * * *
1082685 TGACCATTTTGTAACTTTTAATAGTCGAGGGACTCAACAGAGCAATGCCCTATAGTCGTA
1 TGACCATTTTGTAACTTTCAATAGTCGAGAGACTCAACAGAACAATACCCTATAGTCGGA
* * * * *
1082745 TGATCATTTTGTAACTTTCAATAGTCGAGAGACTCAATAGAACACTATCTTATAGTCAGGA
1 TGACCATTTTGTAACTTTCAATAGTCGAGAGACTCAACAGAACAATACCCTATAGTC-GGA
1082806 -GACCATTT
1 TGACCATTT
1082814 ATCTACTTTA
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 55 0.96
61 2 0.04
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (60 bp):
TGACCATTTTGTAACTTTCAATAGTCGAGAGACTCAACAGAACAATACCCTATAGTCGGA
Found at i:1083714 original size:2 final size:2
Alignment explanation
Indices: 1083707--1083786 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
1083697 ACTACGATCA
1083707 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1083749 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1083787 TTTTATATTT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1102220 original size:157 final size:157
Alignment explanation
Indices: 1101934--1102253 Score: 622
Period size: 157 Copynumber: 2.0 Consensus size: 157
1101924 GAAGGAAGTT
*
1101934 ATCAACAATGCCCATGTAAACATGGTAAGATGAATATTTCAAATTCTAGTATTGGATGGTTCTTT
1 ATCAACAATGCCCATGTAAACATGGTAAGATGAATATTCCAAATTCTAGTATTGGATGGTTCTTT
1101999 AAGTTAATCTTATTTCGGCATCTCCTCTATTTGTGGAGACCTCTACTACTAGACCAGAAAAACCT
66 AAGTTAATCTTATTTCGGCATCTCCTCTATTTGTGGAGACCTCTACTACTAGACCAGAAAAACCT
1102064 GTAGAATACAAGAAAACATATTTAGAG
131 GTAGAATACAAGAAAACATATTTAGAG
*
1102091 ATCAACAATGCCCATGTAAACATGGTAAGATGAATATTCCAAATTCTAGTATTGGATTGTTCTTT
1 ATCAACAATGCCCATGTAAACATGGTAAGATGAATATTCCAAATTCTAGTATTGGATGGTTCTTT
1102156 AAGTTAATCTTATTTCGGCATCTCCTCTATTTGTGGAGACCTCTACTACTAGACCAGAAAAACCT
66 AAGTTAATCTTATTTCGGCATCTCCTCTATTTGTGGAGACCTCTACTACTAGACCAGAAAAACCT
1102221 GTAGAATACAAGAAAACATATTTAGAG
131 GTAGAATACAAGAAAACATATTTAGAG
1102248 ATCAAC
1 ATCAAC
1102254 TCCAATGATG
Statistics
Matches: 161, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
157 161 1.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (157 bp):
ATCAACAATGCCCATGTAAACATGGTAAGATGAATATTCCAAATTCTAGTATTGGATGGTTCTTT
AAGTTAATCTTATTTCGGCATCTCCTCTATTTGTGGAGACCTCTACTACTAGACCAGAAAAACCT
GTAGAATACAAGAAAACATATTTAGAG
Found at i:1113004 original size:15 final size:16
Alignment explanation
Indices: 1112984--1113016 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1112974 GATCAAAGAA
1112984 AATAAAA-AAAAACAT
1 AATAAAATAAAAACAT
1112999 AATAAAATAAAAACAT
1 AATAAAATAAAAACAT
1113015 AA
1 AA
1113017 ACAAAATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (16 bp):
AATAAAATAAAAACAT
Found at i:1113022 original size:17 final size:16
Alignment explanation
Indices: 1112987--1113029 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
1112977 CAAAGAAAAT
*
1112987 AAAA-AAAAACATAAT
1 AAAATAAAAACATAAC
1113002 AAAATAAAAACATAAAC
1 AAAATAAAAACAT-AAC
1113019 AAAATGAAAAA
1 AAAAT-AAAAA
1113030 TTACCGATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 8 0.33
17 7 0.29
18 5 0.21
ACGTcount: A:0.79, C:0.07, G:0.02, T:0.12
Consensus pattern (16 bp):
AAAATAAAAACATAAC
Found at i:1114943 original size:14 final size:15
Alignment explanation
Indices: 1114914--1114944 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1114904 CGATTCAAAG
1114914 GGCATAAAGTTTCTT
1 GGCATAAAGTTTCTT
1114929 GGCATAAAG-TTCTT
1 GGCATAAAGTTTCTT
1114943 GG
1 GG
1114945 TTTCCAATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (15 bp):
GGCATAAAGTTTCTT
Found at i:1123501 original size:6 final size:6
Alignment explanation
Indices: 1123490--1123516 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1123480 AAATTAAAGT
1123490 ATAAAA ATAAAA ATAAAA ATAAAA ATA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATA
1123517 TAGTAACGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:1125995 original size:20 final size:19
Alignment explanation
Indices: 1125957--1125995 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1125947 TATTTTATTT
*
1125957 TATTTTTTAAATTTCAAAC
1 TATTTTTTAAATTTAAAAC
*
1125976 TATTTTTTAATTATTAAAAC
1 TATTTTTTAAAT-TTAAAAC
1125996 ATTAAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTTTTTAAATTTAAAAC
Found at i:1128952 original size:17 final size:17
Alignment explanation
Indices: 1128932--1128965 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1128922 AGTCTTTCAA
*
1128932 TTAATTTTATATTTTAT
1 TTAATTTCATATTTTAT
*
1128949 TTAATTTCATTTTTTAT
1 TTAATTTCATATTTTAT
1128966 CGTAATTCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (17 bp):
TTAATTTCATATTTTAT
Found at i:1130492 original size:41 final size:41
Alignment explanation
Indices: 1130422--1130502 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 41
1130412 TTAAATTATT
* * * *
1130422 AAATAAATTAAATTCAAGTGTTTTGATTTTAACTCAAAATC
1 AAATAAACTAAATTCAAATATTTTAATTTTAACTCAAAATC
* * *
1130463 AAATAAACTAAATTTAAATATTTTAATTTTGACTTAAAAT
1 AAATAAACTAAATTCAAATATTTTAATTTTAACTCAAAAT
1130503 TGAACATGTT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (41 bp):
AAATAAACTAAATTCAAATATTTTAATTTTAACTCAAAATC
Found at i:1136266 original size:18 final size:18
Alignment explanation
Indices: 1136245--1136288 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
1136235 AACAATATCC
1136245 AATTAATCGATAATATTA
1 AATTAATCGATAATATTA
*
1136263 AATTAATTGATAATATTA
1 AATTAATCGATAATATTA
1136281 AATTAATC
1 AATTAATC
1136289 AACAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (18 bp):
AATTAATCGATAATATTA
Found at i:1142523 original size:30 final size:31
Alignment explanation
Indices: 1142489--1142549 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
1142479 ATCACTGAGT
*
1142489 TTAT-ATTTAAACGGTGGAGTGATCCAAATA
1 TTATAATTTAAACGGTGAAGTGATCCAAATA
1142519 TTATAATTTAAACGGTGAAGTGATCCAAATA
1 TTATAATTTAAACGGTGAAGTGATCCAAATA
1142550 GAGTCAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 4 0.14
31 25 0.86
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (31 bp):
TTATAATTTAAACGGTGAAGTGATCCAAATA
Found at i:1142822 original size:23 final size:24
Alignment explanation
Indices: 1142796--1142848 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
1142786 AATTTATCAA
1142796 TAATTATAATGTT-AATTAAAATT
1 TAATTATAATGTTAAATTAAAATT
* *
1142819 TAATTTTAATTTTAAATTAAAATT
1 TAATTATAATGTTAAATTAAAATT
1142843 T-ATTAT
1 TAATTAT
1142849 TACTATTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
TAATTATAATGTTAAATTAAAATT
Found at i:1145391 original size:21 final size:21
Alignment explanation
Indices: 1145342--1145383 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1145332 TTTAGAACCG
1145342 ATTAAATTATTCTCTAAATCT
1 ATTAAATTATTCTCTAAATCT
1145363 ATTAAATTAATT-TCTAAATCT
1 ATTAAATT-ATTCTCTAAATCT
1145384 TTTTAATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTAAATTATTCTCTAAATCT
Found at i:1145481 original size:23 final size:21
Alignment explanation
Indices: 1145426--1145466 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1145416 AATTACTAAA
1145426 TATAATATAAAAATATATTTT
1 TATAATATAAAAATATATTTT
1145447 TATAATATAAAAATAT-TTTT
1 TATAATATAAAAATATATTTT
1145467 GTTTATGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TATAATATAAAAATATATTTT
Found at i:1149824 original size:216 final size:220
Alignment explanation
Indices: 1149436--1149876 Score: 845
Period size: 216 Copynumber: 2.0 Consensus size: 220
1149426 TACCTTGTGA
1149436 TCATCTCAATTTATTAAAAAAAGTGTTTATCAAACCCCGATTAAGAAACCCTAAAAAGATGTTAT
1 TCATCTCAATTTATTAAAAAAAGTGTTTATCAAACCCCGATTAAGAAACCCTAAAAAGATGTTAT
1149501 TGGAGAGAGTTTTGATGTGTGTGTTTAAAAAGAGAGAATCTGATACCCAACACTATAATTCCAAG
66 TGGAGAGAGTTTTGATGTGTGTGTTTAAAAAGAGAGAATCTGATACCCAACACTATAATTCCAAG
1149566 CTTAAGCCATTTTGGTTGCACATATTTTTTTATTTTTTTTTTACTTTTTTTCATCTCTAATGTCT
131 CTTAAGCCATTTTGGTTGCACATATTTTTTTATTTTTTTTTTACTTTTTTTCATCTCTAATGTCT
1149631 TTCATAAG-TGTTTACAAGTTCGAG
196 TTCATAAGTTGTTTACAAGTTCGAG
1149655 TCATCTCAATTTATT-AAAAAAGTGTTTATC-AACCCCGATTAAGAAACCCT-AAAAGATGTTAT
1 TCATCTCAATTTATTAAAAAAAGTGTTTATCAAACCCCGATTAAGAAACCCTAAAAAGATGTTAT
*
1149717 TGGAGAGAGTTTTGATGTGTGTGTTTTAAAAGAGAGAATCTGATACCCAACACTATAATTCCAAG
66 TGGAGAGAGTTTTGATGTGTGTGTTTAAAAAGAGAGAATCTGATACCCAACACTATAATTCCAAG
1149782 CTTAAGCCATTTTGGTTGCACATATTTTTTTATTTTTTTTTTACTTTTTTTCATCTCTAATGTCT
131 CTTAAGCCATTTTGGTTGCACATATTTTTTTATTTTTTTTTTACTTTTTTTCATCTCTAATGTCT
1149847 TTCATAAGTTGTTTACAAGTTCGAG
196 TTCATAAGTTGTTTACAAGTTCGAG
1149872 TCATC
1 TCATC
1149877 AACCCCTCTT
Statistics
Matches: 220, Mismatches: 1, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
216 149 0.68
217 41 0.19
218 15 0.07
219 15 0.07
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (220 bp):
TCATCTCAATTTATTAAAAAAAGTGTTTATCAAACCCCGATTAAGAAACCCTAAAAAGATGTTAT
TGGAGAGAGTTTTGATGTGTGTGTTTAAAAAGAGAGAATCTGATACCCAACACTATAATTCCAAG
CTTAAGCCATTTTGGTTGCACATATTTTTTTATTTTTTTTTTACTTTTTTTCATCTCTAATGTCT
TTCATAAGTTGTTTACAAGTTCGAG
Found at i:1158031 original size:95 final size:94
Alignment explanation
Indices: 1157919--1158181 Score: 339
Period size: 95 Copynumber: 2.7 Consensus size: 94
1157909 AAATTATAAT
1157919 ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCTGGCTTTA
1 ATTATA-ATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCC-GGCTTTA
1157984 TGAATAAGATTCAGCTAGCATGATAAAGGTG
64 TGAATAAGATTCAGCTAGCATGATAAAGGTG
*
1158015 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTAT
1 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACG-CCCGGCTTTAT
* * * *
1158080 GGATAATATTCAGTTAGCCTGATAAAGGTG
65 GAATAAGATTCAGCTAGCATGATAAAGGTG
* * * * * * *
1158110 ATTATAATAT-CTATACAATGATATTAAGATGTCCCTCTAAAACAATTGGTTAAATGTCCCGGCT
1 ATTATAATATACAATA-AA-G--CTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACG-CCCGGCT
1158174 TTATGAAT
61 TTATGAAT
1158182 TCAGCTAGCC
Statistics
Matches: 147, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
94 4 0.03
95 92 0.63
96 10 0.07
98 41 0.28
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (94 bp):
ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCGGCTTTATG
AATAAGATTCAGCTAGCATGATAAAGGTG
Found at i:1159185 original size:72 final size:73
Alignment explanation
Indices: 1159093--1159236 Score: 204
Period size: 72 Copynumber: 2.0 Consensus size: 73
1159083 AATGCAGATG
*
1159093 ATTTATCTCACTTAAGATTGTTTTTCTTAAAAC-AGACTTTGTCTCACTTGAGACTGATTT-ACT
1 ATTTATCTCACTTAAGATTGTTTTTCTTAAAACAAGA-TTTGTCTCACTTGAGACCGATTTCACT
1159156 CGAAAGAAT
65 CGAAAGAAT
* ** *
1159165 ATTTATTTCACTCT-AGATTGTTTTTCTTAAAACAAGATTTGTCTCGTTTGAGACCGTTTTCACT
1 ATTTATCTCACT-TAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGATTTCACT
1159229 CGAAAGAA
65 CGAAAGAA
1159237 GGCATTTCAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
72 49 0.77
73 15 0.23
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (73 bp):
ATTTATCTCACTTAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGATTTCACTC
GAAAGAAT
Found at i:1159289 original size:73 final size:71
Alignment explanation
Indices: 1159093--1159290 Score: 179
Period size: 72 Copynumber: 2.7 Consensus size: 71
1159083 AATGCAGATG
* * * * *
1159093 ATTTATCTCACTTAAGATTGTTTTTCTTAAAAC-AGACTTTGTCTCACTTGAGACTGATTTACTC
1 ATTTATTTCACTCAAGA-TCTTTTTCTTAAAACAAGA-TTTATCTCACTTGAGACCGATTTACTC
*
1159157 GAAAGAAT
64 GAAAGAAC
* * * ** *
1159165 ATTTATTTCACTCTAGATTGTTTTTCTTAAAACAAGATTTGTCTCGTTTGAGACCGTTTTCACTC
1 ATTTATTTCACTCAAGA-TCTTTTTCTTAAAACAAGATTTATCTCACTTGAGACCGATTT-ACTC
1159230 GAAAGAAGGC
64 GAAAGAA--C
*
1159240 ATTTCATTTCACTCAAGA-CTTTTT-TT-AAAGAAGATTTTATCTCACTTGAGA
1 ATTT-ATTTCACTCAAGATCTTTTTCTTAAAACAAGA-TTTATCTCACTTGAGA
1159291 TAGTTTCCCT
Statistics
Matches: 106, Mismatches: 14, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
72 56 0.53
73 29 0.27
74 5 0.05
75 4 0.04
76 12 0.11
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (71 bp):
ATTTATTTCACTCAAGATCTTTTTCTTAAAACAAGATTTATCTCACTTGAGACCGATTTACTCGA
AAGAAC
Found at i:1159327 original size:39 final size:39
Alignment explanation
Indices: 1159270--1159424 Score: 147
Period size: 39 Copynumber: 4.1 Consensus size: 39
1159260 TTTTTTAAAG
*
1159270 AAGATTTTATCTCA-CTTGAGATAGTTTCCCTCGAAACAA
1 AAGATTTTATCT-ATCTTGAGACAGTTTCCCTCGAAACAA
* * * * * *
1159309 AAGATTTTATCTAGCTTGAGATAGTTTCCTTCAAAATAG
1 AAGATTTTATCTATCTTGAGACAGTTTCCCTCGAAACAA
* * * *
1159348 AAGATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC--
1 AAGATTTTATCTATCTTGAGACAGTTTCCCTCGAAACAA
* * *
1159385 AA-ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
1 AAGATTTTATCTATCTTGAGACAGTTTCCCTCGAAACAA
1159423 AA
1 AA
1159425 TCTTTGGATA
Statistics
Matches: 99, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
36 33 0.33
37 2 0.02
38 3 0.03
39 61 0.62
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (39 bp):
AAGATTTTATCTATCTTGAGACAGTTTCCCTCGAAACAA
Found at i:1159398 original size:36 final size:36
Alignment explanation
Indices: 1159351--1159675 Score: 303
Period size: 36 Copynumber: 9.0 Consensus size: 36
1159341 AAAATAGAAG
1159351 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
1 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
*
1159387 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
1 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
* *
1159423 A------ATCT-TTG-GATATGTTT-TACATT-AAACAA
1 ATTTTGTCTCTCTTGAGACA-GTTTCT-C-TTGAAACAA
* * * * *
1159452 ATTTCGTCTCCCTTGAGACAGATTCTTTTGGAACTAA
1 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AA
* *
1159489 GTTTTCTCTCTCTTGAGACAGTTTCTCTTGAAACAA
1 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
* *
1159525 ATTTTTTCTTTGTCTCTCTTGAAACAATTTCTCTTGAAA-AA
1 A-----T-TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
* *
1159566 ATTTTTGTCTCTCTTGAGACAGTTTCCCTTTAAACAA
1 A-TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
* * *
1159603 ATTTTATCTCTCTTGAGTCAGTTTCCCTTGAAACAA
1 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
* *
1159639 ATTTTGTCTCTCTTTAGACAGTTTCCCTTGAAACAA
1 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
1159675 A
1 A
1159676 ATCTTTGAAT
Statistics
Matches: 237, Mismatches: 31, Indels: 42
0.76 0.10 0.14
Matches are distributed among these distances:
28 3 0.01
29 15 0.06
30 5 0.02
35 4 0.02
36 140 0.59
37 38 0.16
41 4 0.02
42 28 0.12
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (36 bp):
ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
Found at i:1159559 original size:15 final size:15
Alignment explanation
Indices: 1159539--1159569 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1159529 TTTCTTTGTC
*
1159539 TCTCTTGAAACAATT
1 TCTCTTGAAAAAATT
1159554 TCTCTTGAAAAAATT
1 TCTCTTGAAAAAATT
1159569 T
1 T
1159570 TTGTCTCTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.42
Consensus pattern (15 bp):
TCTCTTGAAAAAATT
Found at i:1159711 original size:66 final size:68
Alignment explanation
Indices: 1159538--1159818 Score: 259
Period size: 72 Copynumber: 4.0 Consensus size: 68
1159528 TTTTCTTTGT
* * *
1159538 CTCTCTTGAAACAATTTCTCTTGAAA-AAATTTTTGTCTCTCTTGAGACAGTTTCCCTTTAAACA
1 CTCTCTTGAATCAGTTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
1159602 AATTTTA
65 AA---TA
* * *
1159609 TCTCTCTTGAGTCAGTTTCCCTTGAAACAAATTTTGTCTCTCTTTAGACAGTTTCCCTTGAAACA
1 -CTCTCTTGAATCAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
1159674 AA-A
65 AATA
* * *
1159677 -TCT-TTGAAT-ATGTTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACGGTTTCTCTTGAAAC
1 CTCTCTTGAATCA-G-TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
*
1159739 AAAGTTTTGT
64 AAA----T-A
*
1159749 CTCTCTTGAGA-CAGTTTCTCTTGAAACAAAATTGTCTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 CTCTCTTGA-ATCAGTTTCTCTTGAAAC-AAA---T-TTTGTCTCTCTTGAGACAGTTTCCCTTG
1159813 AAACAA
60 AAACAA
1159819 TTTTTGTCTC
Statistics
Matches: 176, Mismatches: 15, Indels: 30
0.80 0.07 0.14
Matches are distributed among these distances:
64 1 0.01
65 6 0.03
66 50 0.28
68 1 0.01
72 56 0.32
73 19 0.11
74 8 0.05
75 2 0.01
77 1 0.01
78 32 0.18
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.41
Consensus pattern (68 bp):
CTCTCTTGAATCAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
ATA
Found at i:1159729 original size:102 final size:103
Alignment explanation
Indices: 1159588--1159780 Score: 298
Period size: 102 Copynumber: 1.9 Consensus size: 103
1159578 CTTGAGACAG
* * *
1159588 TTTCCCTTTAAACAAATTTTATCTCTCTTGAGTCAGTTTCCCTTGAAACAAA-TTTTGTCTCTCT
1 TTTCCCTTGAAACAAATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCT
*
1159652 TTAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGT
66 TGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGT
* * * *
1159690 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACGGTTTCTCTTGAAACAAAGTTTTGTCTCTCT
1 TTTCCCTTGAAACAAATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCT
*
1159755 TGAGACAGTTTCTCTTGAAACAAAAT
66 TGAGACAGTTTCCCTTGAAACAAAAT
1159781 TGTCTTTGTC
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
102 45 0.56
103 36 0.44
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (103 bp):
TTTCCCTTGAAACAAATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCT
TGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGT
Found at i:1159757 original size:37 final size:37
Alignment explanation
Indices: 1159690--1159834 Score: 204
Period size: 37 Copynumber: 3.9 Consensus size: 37
1159680 TTGAATATGT
* *
1159690 TTTCTCTTGAAACAAA-TTTTGTCTCCCTTGAGACGG
1 TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
1159726 TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
1159763 TTTCTCTTGAAACAAAATTGTCTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAA--GT-TTTGTCTCTCTTGAGACAG
* *
1159804 TTTCTCTTGAAAC-AATTTTTGTCTCTTTTGA
1 TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGA
1159835 AAGAAATTTT
Statistics
Matches: 100, Mismatches: 4, Indels: 10
0.88 0.04 0.09
Matches are distributed among these distances:
36 29 0.29
37 32 0.32
38 3 0.03
39 2 0.02
40 2 0.02
41 32 0.32
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.43
Consensus pattern (37 bp):
TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
Found at i:1159836 original size:21 final size:21
Alignment explanation
Indices: 1159806--1159855 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1159796 TGAGACAGTT
*
1159806 TCTCTTGAAACAATTTTTGTC
1 TCTCTTGAAACAAATTTTGTC
* *
1159827 TCTTTTGAAAGAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
1159848 TCTCTTGA
1 TCTCTTGA
1159856 GATAGTTTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTGTC
Found at i:1159864 original size:98 final size:94
Alignment explanation
Indices: 1159732--1159911 Score: 254
Period size: 93 Copynumber: 1.9 Consensus size: 94
1159722 ACGGTTTCTC
* **
1159732 TTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATTGTCTTTGTCTCTCTT
1 TTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA---T-TTTGTCTCTCCC
*
1159797 GAGACAGTTTCTCTTGAAACAATTTTTGTCTCTT
61 GAGACAGTTTCCCTTGAAACAATTTTTGTCTCTT
* *
1159831 TTGAAAGAAA-TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCTCCCGAGAC
1 TTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCCCGAGAC
1159895 AGTTTCCCTTGAAACAA
66 AGTTTCCCTTGAAACAA
1159912 AATCTTTGAA
Statistics
Matches: 75, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
93 31 0.41
94 1 0.01
97 3 0.04
98 31 0.41
99 9 0.12
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.40
Consensus pattern (94 bp):
TTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCCCGAGAC
AGTTTCCCTTGAAACAATTTTTGTCTCTT
Found at i:1159871 original size:36 final size:36
Alignment explanation
Indices: 1159831--1159912 Score: 128
Period size: 36 Copynumber: 2.3 Consensus size: 36
1159821 TTTGTCTCTT
* *
1159831 TTGAAAGAAATTTTGTCTCTCTTGAGATAGTTTCCC
1 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCC
**
1159867 TTGAAACAAATTTTGTCTCTCCCGAGACAGTTTCCC
1 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCC
1159903 TTGAAACAAA
1 TTGAAACAAA
1159913 ATCTTTGAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (36 bp):
TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCC
Found at i:1160053 original size:73 final size:73
Alignment explanation
Indices: 1159925--1160085 Score: 214
Period size: 73 Copynumber: 2.2 Consensus size: 73
1159915 CTTTGAATAT
* * * * ** * *
1159925 GTTTTCCTTGAAACAAATTTCATCTCCCTTGAGACGGTTTCTTTTGGAACTAAGTTTTGTCTCTC
1 GTTTTTCTTGAAACAAATTTCATCTACCTAGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTC
1159990 TTGAGACA
66 TTGAGACA
** *
1159998 GTTTTTCTTGAAACAAATTTTGTCTATCTAGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTC
1 GTTTTTCTTGAAACAAATTTCATCTACCTAGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTC
1160063 TTGAGACA
66 TTGAGACA
*
1160071 GTTTCTCTTGAAACA
1 GTTTTTCTTGAAACA
1160086 CCAATCTTTG
Statistics
Matches: 76, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
73 76 1.00
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (73 bp):
GTTTTTCTTGAAACAAATTTCATCTACCTAGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTC
TTGAGACA
Found at i:1160069 original size:37 final size:36
Alignment explanation
Indices: 1159927--1160085 Score: 194
Period size: 37 Copynumber: 4.4 Consensus size: 36
1159917 TTGAATATGT
** * *
1159927 TTTC-CTTGAAACAAATTTCATCTCCCTTGAGACGG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * *
1159962 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
* * *
1159999 TTTTTCTTGAAACAAATTTTGTCTATCTAGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
1160035 TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACAG
1160072 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
1160086 CCAATCTTTG
Statistics
Matches: 103, Mismatches: 18, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
35 4 0.04
36 40 0.39
37 59 0.57
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.40
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:1165426 original size:16 final size:17
Alignment explanation
Indices: 1165387--1165429 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1165377 ACAACAGTCT
1165387 AATGATAAAAAATATTA
1 AATGATAAAAAATATTA
* *
1165404 TAT-ATAATAAA-ATTA
1 AATGATAAAAAATATTA
1165419 AATGATAAAAA
1 AATGATAAAAA
1165430 TGTTATGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
15 6 0.29
16 13 0.62
17 2 0.10
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (17 bp):
AATGATAAAAAATATTA
Found at i:1170741 original size:3 final size:3
Alignment explanation
Indices: 1170733--1170766 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1170723 TACATTATTG
1170733 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1170767 TTAAAATGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1174154 original size:37 final size:37
Alignment explanation
Indices: 1174045--1174154 Score: 98
Period size: 36 Copynumber: 2.9 Consensus size: 37
1174035 AGTTAAATGT
* * * * *
1174045 AACTTAAAATGTTATATTTTTTTAATATTTT-TATTA
1 AACTGAAAATATTATATTTTTATAATATTTTAGATGA
* *
1174081 AACTGAAAATATTACATTATTTATAACATTTTTAGATGA
1 AACTGAAAATATTATATT-TTTATAATA-TTTTAGATGA
* *
1174120 CAATTG-AAATATTATATTTTTGTAATATTTTAGAT
1 -AACTGAAAATATTATATTTTTATAATATTTTAGAT
1174155 TCAATGAAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
36 15 0.25
37 15 0.25
38 11 0.19
39 14 0.24
40 4 0.07
ACGTcount: A:0.39, C:0.05, G:0.06, T:0.50
Consensus pattern (37 bp):
AACTGAAAATATTATATTTTTATAATATTTTAGATGA
Found at i:1174464 original size:24 final size:23
Alignment explanation
Indices: 1174424--1174471 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
1174414 TGATCAAATG
1174424 ATATTATTTTAGTATTTATATAT
1 ATATTATTTTAGTATTTATATAT
*
1174447 ATATATATTTT-GTGATTTTTATAT
1 ATAT-TATTTTAGT-ATTTATATAT
1174471 A
1 A
1174472 GAATCTCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.60
Consensus pattern (23 bp):
ATATTATTTTAGTATTTATATAT
Found at i:1174966 original size:22 final size:19
Alignment explanation
Indices: 1174941--1174987 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
1174931 TATCGATTTA
*
1174941 TAACAAATCGATTACTTCTAG
1 TAACAAA-CAATTACTTC-AG
1174962 TTAAC-AACAATTACTTCAG
1 -TAACAAACAATTACTTCAG
1174981 TAACAAA
1 TAACAAA
1174988 ATACTGATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 9 0.39
21 2 0.09
22 4 0.17
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.30
Consensus pattern (19 bp):
TAACAAACAATTACTTCAG
Found at i:1176284 original size:31 final size:31
Alignment explanation
Indices: 1176238--1176314 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
1176228 AGCGGTTGAA
* *
1176238 TGATTGATTTATTATAAATCGATAATATTAG
1 TGATCGATTTGTTATAAATCGATAATATTAG
* *
1176269 TTATCGATTTGTTATAAATTGATAATATTAG
1 TGATCGATTTGTTATAAATCGATAATATTAG
*
1176300 TGATCAATTTGTTAT
1 TGATCGATTTGTTAT
1176315 TTTAAAACTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.48
Consensus pattern (31 bp):
TGATCGATTTGTTATAAATCGATAATATTAG
Found at i:1181014 original size:13 final size:13
Alignment explanation
Indices: 1180996--1181021 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1180986 TGACCCATTC
1180996 GATTAGCAACGGA
1 GATTAGCAACGGA
1181009 GATTAGCAACGGA
1 GATTAGCAACGGA
1181022 TCGGATAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.31, T:0.15
Consensus pattern (13 bp):
GATTAGCAACGGA
Found at i:1187714 original size:29 final size:29
Alignment explanation
Indices: 1187672--1187730 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
1187662 TATAAATGAA
*
1187672 AATCTCTCCTTGCCTCTTTGTTCCAACTG
1 AATCTCTCCTTGCCTCTTAGTTCCAACTG
1187701 AATCTCTCCTTGCCTCTTAGTTCCAACTG
1 AATCTCTCCTTGCCTCTTAGTTCCAACTG
1187730 A
1 A
1187731 TATGTACATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.17, C:0.34, G:0.10, T:0.39
Consensus pattern (29 bp):
AATCTCTCCTTGCCTCTTAGTTCCAACTG
Found at i:1187760 original size:78 final size:79
Alignment explanation
Indices: 1187622--1187781 Score: 277
Period size: 78 Copynumber: 2.0 Consensus size: 79
1187612 GTAATCAAGA
* * * *
1187622 AATCTCTCCTTTCCTCTTTGTTCCAACTGAATATGTACGTTATAAATGAAAATCTCTCCTTGCCT
1 AATCTCTCCTTGCCTCTTAGTTCCAACTGAATATGTACATGATAAATGAAAATCTCTCCTTGCCT
1187687 CTTTGTTCCAACTG
66 CTTTGTTCCAACTG
1187701 AATCTCTCCTTGCCTCTTAGTTCCAACTG-ATATGTACATGATAAATGAAAATCTCTCCTTGCCT
1 AATCTCTCCTTGCCTCTTAGTTCCAACTGAATATGTACATGATAAATGAAAATCTCTCCTTGCCT
1187765 CTTTGTTCCAACTG
66 CTTTGTTCCAACTG
1187779 AAT
1 AAT
1187782 ATGTACGTTA
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
78 50 0.65
79 27 0.35
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (79 bp):
AATCTCTCCTTGCCTCTTAGTTCCAACTGAATATGTACATGATAAATGAAAATCTCTCCTTGCCT
CTTTGTTCCAACTG
Found at i:1187773 original size:49 final size:51
Alignment explanation
Indices: 1187701--1187803 Score: 165
Period size: 49 Copynumber: 2.1 Consensus size: 51
1187691 GTTCCAACTG
1187701 AATCTCTCCTTGCCTCTTAGTTCCAACTG-ATATGTACATGATAAATGA-A
1 AATCTCTCCTTGCCTCTTAGTTCCAACTGAATATGTACATGATAAATGAGA
* * *
1187750 AATCTCTCCTTGCCTCTTTGTTCCAACTGAATATGTACGTTATAAATGAGA
1 AATCTCTCCTTGCCTCTTAGTTCCAACTGAATATGTACATGATAAATGAGA
1187801 AAT
1 AAT
1187804 AACTTCACAT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
49 28 0.57
50 17 0.35
51 4 0.08
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (51 bp):
AATCTCTCCTTGCCTCTTAGTTCCAACTGAATATGTACATGATAAATGAGA
Found at i:1192319 original size:22 final size:22
Alignment explanation
Indices: 1192294--1192336 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1192284 TTACAGTTGT
1192294 CAATTTGGACTTCAACAAGCTC
1 CAATTTGGACTTCAACAAGCTC
*
1192316 CAATTTGGACTTTAACAAGCT
1 CAATTTGGACTTCAACAAGCT
1192337 GTCAATTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (22 bp):
CAATTTGGACTTCAACAAGCTC
Found at i:1199156 original size:28 final size:28
Alignment explanation
Indices: 1199114--1199169 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
1199104 ATGTGGACTG
1199114 GTAAACCAGCCGATTATTCAAACCTCTA
1 GTAAACCAGCCGATTATTCAAACCTCTA
**
1199142 GTAAACCAGTTGATTATTCAAACCTCTA
1 GTAAACCAGCCGATTATTCAAACCTCTA
1199170 TGTATTTGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.29
Consensus pattern (28 bp):
GTAAACCAGCCGATTATTCAAACCTCTA
Found at i:1201955 original size:24 final size:26
Alignment explanation
Indices: 1201906--1201957 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
1201896 TATTTCCATT
*
1201906 ATATTTAAATAGTATATTATTATTTA
1 ATATATAAATAGTATATTATTATTTA
*
1201932 ATATATAAATGGTAT-TTATT-TTTA
1 ATATATAAATAGTATATTATTATTTA
1201956 AT
1 AT
1201958 CCTGAACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 6 0.25
25 5 0.21
26 13 0.54
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (26 bp):
ATATATAAATAGTATATTATTATTTA
Found at i:1203186 original size:22 final size:22
Alignment explanation
Indices: 1203124--1203189 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
1203114 CTTACCACTA
* *
1203124 CAACTAGACAAACACACAACCC
1 CAACTAAACAAACACACAAACC
*
1203146 CAACTAAACAAACAAACAAACC
1 CAACTAAACAAACACACAAACC
1203168 CAACTAAACAAA-ATCACAAACC
1 CAACTAAACAAACA-CACAAACC
1203190 AGTTGAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 1 0.03
22 38 0.97
ACGTcount: A:0.58, C:0.35, G:0.02, T:0.06
Consensus pattern (22 bp):
CAACTAAACAAACACACAAACC
Found at i:1205587 original size:30 final size:30
Alignment explanation
Indices: 1205498--1205590 Score: 105
Period size: 30 Copynumber: 3.1 Consensus size: 30
1205488 AATTTTATAT
* *
1205498 ATTTTATTAATTTAATTCTAATTTAAAATA
1 ATTTTATTAATATAATTCTAATTAAAAATA
* * **
1205528 CTTTTATTAATATAATCCTAATTCGAAATA
1 ATTTTATTAATATAATTCTAATTAAAAATA
* * *
1205558 ATTTTATTAATATAGTTCTGACTAAAAATA
1 ATTTTATTAATATAATTCTAATTAAAAATA
1205588 ATT
1 ATT
1205591 CAATAATTTG
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (30 bp):
ATTTTATTAATATAATTCTAATTAAAAATA
Found at i:1205752 original size:23 final size:23
Alignment explanation
Indices: 1205704--1205745 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
1205694 GTATCATAAA
1205704 AAATATTAAATTGATAAAATTTT
1 AAATATTAAATTGATAAAATTTT
*
1205727 AAATA-TAAA-TGATTAAATT
1 AAATATTAAATTGATAAAATT
1205746 AATTAAAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 4 0.22
23 5 0.28
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (23 bp):
AAATATTAAATTGATAAAATTTT
Found at i:1208800 original size:99 final size:99
Alignment explanation
Indices: 1208626--1208827 Score: 262
Period size: 99 Copynumber: 2.0 Consensus size: 99
1208616 CTTCAAAGAT
* *
1208626 CTCAGCATCATGAGCTGTCTCATTAGCAGCATTTGTACCAATAAAGTTCAGACCAGATTCGGCAG
1 CTCAGCATCATGAGCTGTCTCATTAGCAGCATTTGTACCAATAAAGTTCAAACCAAATTCGGCAG
*
1208691 ATGGCAGACCGATATCCAAGAAGCGACTTTGTTC
66 ATGACAGACCGATATCCAAGAAGCGACTTTGTTC
* * * * *
1208725 CTCAGCATCATGAGCTGTCTCGTTAGCAGCTTTTGTACCATTGAAGTTCAAACGAAACTT-GGCA
1 CTCAGCATCATGAGCTGTCTCATTAGCAGCATTTGTACCAATAAAGTTCAAACCAAA-TTCGGCA
* * ** **
1208789 GATGACGGACCGGTATCTGAGAAGTTACTTTGTTC
65 GATGACAGACCGATATCCAAGAAGCGACTTTGTTC
1208824 CTCA
1 CTCA
1208828 ACTGAAACCT
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
99 86 0.98
100 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (99 bp):
CTCAGCATCATGAGCTGTCTCATTAGCAGCATTTGTACCAATAAAGTTCAAACCAAATTCGGCAG
ATGACAGACCGATATCCAAGAAGCGACTTTGTTC
Found at i:1211314 original size:16 final size:16
Alignment explanation
Indices: 1211278--1211328 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
1211268 CATTTGAAAT
1211278 TTAATTAAACTTA-AATA
1 TTAATT-AA-TTATAATA
*
1211295 -TAATTATTTATAATA
1 TTAATTAATTATAATA
1211310 TTAATTAATTATAAT-
1 TTAATTAATTATAATA
1211325 TTAA
1 TTAA
1211329 ATATGGATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
14 3 0.10
15 9 0.30
16 18 0.60
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
TTAATTAATTATAATA
Found at i:1211987 original size:12 final size:12
Alignment explanation
Indices: 1211967--1212018 Score: 54
Period size: 12 Copynumber: 4.2 Consensus size: 12
1211957 GATAAAAAAT
1211967 GAAAATAATAAA
1 GAAAATAATAAA
*
1211979 GAAAGTAATAAA
1 GAAAATAATAAA
1211991 CG--AATGACATAAA
1 -GAAAAT-A-ATAAA
1212004 GAAAATAATAAA
1 GAAAATAATAAA
1212016 GAA
1 GAA
1212019 TAAAAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
11 2 0.06
12 21 0.64
13 7 0.21
14 3 0.09
ACGTcount: A:0.67, C:0.04, G:0.13, T:0.15
Consensus pattern (12 bp):
GAAAATAATAAA
Found at i:1212046 original size:24 final size:25
Alignment explanation
Indices: 1212007--1212102 Score: 76
Period size: 24 Copynumber: 3.8 Consensus size: 25
1211997 ACATAAAGAA
1212007 AATAATAAAGAATAAAAAAATAAATG
1 AATAA-AAAGAATAAAAAAATAAATG
*
1212033 AATAAAAA-AATAAAGATAA-AAATG
1 AATAAAAAGAATAAA-AAAATAAATG
*
1212057 AATAAAATA-AAT-GAAAAATAAA-G
1 AATAAAA-AGAATAAAAAAATAAATG
* *
1212080 AAGAAAAAATAATGAAAAAAATA
1 AA-TAAAAAGAAT-AAAAAAATA
1212103 TAACAACTAA
Statistics
Matches: 58, Mismatches: 5, Indels: 14
0.75 0.06 0.18
Matches are distributed among these distances:
23 7 0.12
24 29 0.50
25 10 0.17
26 12 0.21
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (25 bp):
AATAAAAAGAATAAAAAAATAAATG
Found at i:1212088 original size:25 final size:26
Alignment explanation
Indices: 1212020--1212098 Score: 89
Period size: 24 Copynumber: 3.2 Consensus size: 26
1212010 AATAAAGAAT
1212020 AAAAA-AATAAATGAATAAAA-AAAT-
1 AAAAATAA-AAATGAATAAAATAAATG
*
1212044 AAAGATAAAAATGAATAAAATAAATG
1 AAAAATAAAAATGAATAAAATAAATG
1212070 AAAAATAAAGAA-GAA-AAAAT-AATG
1 AAAAATAAA-AATGAATAAAATAAATG
1212094 AAAAA
1 AAAAA
1212099 AATATAACAA
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
24 25 0.51
25 11 0.22
26 11 0.22
27 2 0.04
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (26 bp):
AAAAATAAAAATGAATAAAATAAATG
Found at i:1212088 original size:46 final size:45
Alignment explanation
Indices: 1212022--1212217 Score: 127
Period size: 46 Copynumber: 4.2 Consensus size: 45
1212012 TAAAGAATAA
*
1212022 AAAAATAAATGAATAAAAAAATAAAGATAAAAATGAATAAAA-TAAAT
1 AAAAATAAA-GAA-GAAAAAATAAAGA-AAAAATGAATAAAACTAAAT
*
1212069 GAAAAATAAAGAAGAAAAAATAATGAAAAAA--ATATAACAACTAAAT
1 -AAAAATAAAGAAGAAAAAATAAAGAAAAAATGA-ATAA-AACTAAAT
* * * * *
1212115 AAAAAAATAAGAAGATAATATAAATAAAGAAATGAATAAAACATATAT
1 AAAAATA-AAGAAGAAAAAATAAAGAAA-AAATGAATAAAAC-TAAAT
* * *
1212163 AAGGGAGAT-AAGAA-AATAAAAGTAAAGAATAAAT-AAAAAAAC-AAAT
1 AA---AAATAAAGAAGAA-AAAA-TAAAGAAAAAATGAATAAAACTAAAT
1212209 AAAAATAAA
1 AAAAATAAA
1212218 TAAATAAATA
Statistics
Matches: 117, Mismatches: 17, Indels: 32
0.70 0.10 0.19
Matches are distributed among these distances:
43 4 0.03
44 6 0.05
45 13 0.11
46 37 0.32
47 9 0.08
48 27 0.23
49 13 0.11
50 6 0.05
51 2 0.02
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.17
Consensus pattern (45 bp):
AAAAATAAAGAAGAAAAAATAAAGAAAAAATGAATAAAACTAAAT
Done.