Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397271.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_89.0, 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: 4184555
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 83639 characters in sequence are not A, C, G, or T
File 4 of 11
Found at i:1046853 original size:21 final size:22
Alignment explanation
Indices: 1046818--1046861 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1046808 CTCTTAAAGT
1046818 AATTTAAAATAAAATAACCTAA
1 AATTTAAAATAAAATAACCTAA
* *
1046840 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACCTAA
1046861 A
1 A
1046862 TTAATCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTTAAAATAAAATAACCTAA
Found at i:1047470 original size:27 final size:27
Alignment explanation
Indices: 1047440--1047525 Score: 118
Period size: 27 Copynumber: 3.2 Consensus size: 27
1047430 TCTCTACTAC
*
1047440 TTTATGCTCATGGATAGCTTGTTTATG
1 TTTATGCTCGTGGATAGCTTGTTTATG
** *
1047467 TTTACACTCGTGGATGGCTTGTTTATG
1 TTTATGCTCGTGGATAGCTTGTTTATG
* *
1047494 TTAAGGCTCGTGGATAGCTTGTTTATG
1 TTTATGCTCGTGGATAGCTTGTTTATG
1047521 TTTAT
1 TTTAT
1047526 CCTACCTTGT
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.17, C:0.12, G:0.24, T:0.47
Consensus pattern (27 bp):
TTTATGCTCGTGGATAGCTTGTTTATG
Found at i:1048937 original size:38 final size:38
Alignment explanation
Indices: 1048882--1048955 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
1048872 TTGTATTCAC
* *
1048882 TTGAGTGATTATGCCTTAACCAA-TTGAAAAGGTAGAAA
1 TTGAGTGATTATACCTTAACCAAGAT-AAAAGGTAGAAA
*
1048920 TTGAGTGGTTATACCTTAACCAAGATAAAAGGTAGA
1 TTGAGTGATTATACCTTAACCAAGATAAAAGGTAGA
1048956 GTGATTGTGC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 31 0.97
39 1 0.03
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (38 bp):
TTGAGTGATTATACCTTAACCAAGATAAAAGGTAGAAA
Found at i:1050295 original size:20 final size:20
Alignment explanation
Indices: 1050267--1050304 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1050257 CTTACTGCCT
1050267 CAAAAGTATCAATACATTAG
1 CAAAAGTATCAATACATTAG
* *
1050287 CAAATGTATCGATACATT
1 CAAAAGTATCAATACATT
1050305 TTCAACAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.29
Consensus pattern (20 bp):
CAAAAGTATCAATACATTAG
Found at i:1063563 original size:16 final size:16
Alignment explanation
Indices: 1063542--1063576 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1063532 TTGAGCCGTG
1063542 AAGAAAAAAGAA-AAAA
1 AAGAAAAAA-AATAAAA
1063558 AAGAAAAAAAATAAAA
1 AAGAAAAAAAATAAAA
1063574 AAG
1 AAG
1063577 TGAGAATGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 2 0.11
16 16 0.89
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (16 bp):
AAGAAAAAAAATAAAA
Found at i:1063565 original size:10 final size:9
Alignment explanation
Indices: 1063545--1063575 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1063535 AGCCGTGAAG
1063545 AAAAAAGAA
1 AAAAAAGAA
1063554 AAAAAAGAA
1 AAAAAAGAA
*
1063563 AAAAAATAA
1 AAAAAAGAA
1063572 AAAA
1 AAAA
1063576 GTGAGAATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.90, C:0.00, G:0.06, T:0.03
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:1067231 original size:16 final size:14
Alignment explanation
Indices: 1067197--1067225 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1067187 TTGGTAAATT
1067197 TTTTTTATAAGTTA
1 TTTTTTATAAGTTA
1067211 TTTTTTATAAGTTA
1 TTTTTTATAAGTTA
1067225 T
1 T
1067226 AATTTTAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (14 bp):
TTTTTTATAAGTTA
Found at i:1068953 original size:17 final size:17
Alignment explanation
Indices: 1068902--1068953 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 17
1068892 TGATTGCATT
1068902 AATCTAAAACTAATAAAA
1 AATCTAAAACTAAT-AAA
* * * *
1068920 AATTTGAAGC-AAAAAA
1 AATCTAAAACTAATAAA
1068936 AATCTAAAACTAATAAA
1 AATCTAAAACTAATAAA
1068953 A
1 A
1068954 TGTCATTCCT
Statistics
Matches: 25, Mismatches: 8, Indels: 3
0.69 0.22 0.08
Matches are distributed among these distances:
16 10 0.40
17 8 0.32
18 7 0.28
ACGTcount: A:0.65, C:0.10, G:0.04, T:0.21
Consensus pattern (17 bp):
AATCTAAAACTAATAAA
Found at i:1069502 original size:27 final size:27
Alignment explanation
Indices: 1069448--1069499 Score: 90
Period size: 25 Copynumber: 2.0 Consensus size: 27
1069438 ACACATGTAG
1069448 TTTTCATATTAATAAATGTATATATCT
1 TTTTCATATTAATAAATGTATATATCT
1069475 TTTTCA-A-TAATAAATGTATATATCT
1 TTTTCATATTAATAAATGTATATATCT
1069500 CTTAATTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 18 0.72
26 1 0.04
27 6 0.24
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (27 bp):
TTTTCATATTAATAAATGTATATATCT
Found at i:1071655 original size:15 final size:15
Alignment explanation
Indices: 1071635--1071663 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1071625 AAACCAAAAT
1071635 TAGATTTTGATTTTA
1 TAGATTTTGATTTTA
1071650 TAGATTTTGATTTT
1 TAGATTTTGATTTT
1071664 TTTTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.14, T:0.62
Consensus pattern (15 bp):
TAGATTTTGATTTTA
Found at i:1083728 original size:25 final size:24
Alignment explanation
Indices: 1083700--1083746 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
1083690 AATATTCTAG
*
1083700 TCTAATTAGAATTCAAGTATTATAA
1 TCTAACTAGAATTCAAG-ATTATAA
1083725 TCTAACTAGAATTCAAGATTAT
1 TCTAACTAGAATTCAAGATTAT
1083747 TTCAACAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.38
Consensus pattern (24 bp):
TCTAACTAGAATTCAAGATTATAA
Found at i:1087281 original size:5 final size:5
Alignment explanation
Indices: 1087271--1087299 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1087261 GATGATTTCT
1087271 TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
1087300 TGTTAGGTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (5 bp):
TTTTG
Found at i:1087842 original size:16 final size:17
Alignment explanation
Indices: 1087821--1087854 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1087811 AGATGTATGG
1087821 ATTTGAAATGTGA-ATT
1 ATTTGAAATGTGATATT
*
1087837 ATTTGAAGTGTGATATT
1 ATTTGAAATGTGATATT
1087854 A
1 A
1087855 ATAGGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (17 bp):
ATTTGAAATGTGATATT
Found at i:1090976 original size:74 final size:74
Alignment explanation
Indices: 1090783--1090980 Score: 200
Period size: 74 Copynumber: 2.7 Consensus size: 74
1090773 GCCAATTTAG
* * ** * * * *
1090783 AGACAGAAAAGACTTAGTCGACTAAGAAACATAGTTAGTCGACTAAAAGCTCACTGCTAGATACT
1 AGACAGAGAAGACTTAATCGACTAAGAAGTATAGTTAGTCGACTAAGAGCTCACTACTAGAGAAT
* *
1090848 TTAATTATA
66 TCAATTACA
* * * ** * **
1090857 AGATATAGAAAACTTAATTTATTAAGAAGTATAGTTAGTTAACTAAGAGCTCACTACTAGAGAAT
1 AGACAGAGAAGACTTAATCGACTAAGAAGTATAGTTAGTCGACTAAGAGCTCACTACTAGAGAAT
1090922 TCAATTACA
66 TCAATTACA
* *
1090931 AGGCAGAGAAGACTTAATCGACTAAGAAGTAT-GATCAGTCGACTAAGAGC
1 AGACAGAGAAGACTTAATCGACTAAGAAGTATAG-TTAGTCGACTAAGAGC
1090981 ACTCTATTAG
Statistics
Matches: 95, Mismatches: 28, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
73 1 0.01
74 94 0.99
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (74 bp):
AGACAGAGAAGACTTAATCGACTAAGAAGTATAGTTAGTCGACTAAGAGCTCACTACTAGAGAAT
TCAATTACA
Found at i:1098494 original size:21 final size:19
Alignment explanation
Indices: 1098470--1098510 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
1098460 AACTTAAAAC
1098470 AAAATAACATAAAATTTAACT
1 AAAATAAC-TAAAA-TTAACT
*
1098491 AAAATAACTTAAATTAACT
1 AAAATAACTAAAATTAACT
1098510 A
1 A
1098511 CTCAACATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATAACTAAAATTAACT
Found at i:1102576 original size:21 final size:21
Alignment explanation
Indices: 1102550--1102593 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1102540 AATGGACCCA
1102550 ATTTATCGATAGATGTTCTTC
1 ATTTATCGATAGATGTTCTTC
1102571 ATTTATCGATAGATGTTCTTC
1 ATTTATCGATAGATGTTCTTC
1102592 AT
1 AT
1102594 CTATTAATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.48
Consensus pattern (21 bp):
ATTTATCGATAGATGTTCTTC
Found at i:1102603 original size:21 final size:21
Alignment explanation
Indices: 1102553--1102605 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1102543 GGACCCAATT
* *
1102553 TATCGATAGATGTTCTTCATT
1 TATCAATAGATGTTCTTCATC
*
1102574 TATCGATAGATGTTCTTCATC
1 TATCAATAGATGTTCTTCATC
*
1102595 TATTAATAGAT
1 TATCAATAGAT
1102606 ACAATCCAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.45
Consensus pattern (21 bp):
TATCAATAGATGTTCTTCATC
Found at i:1108016 original size:14 final size:13
Alignment explanation
Indices: 1107992--1108044 Score: 56
Period size: 12 Copynumber: 4.1 Consensus size: 13
1107982 ATCGGTTTTG
1107992 AAAGCAAAAAGAAA
1 AAAG-AAAAAGAAA
*
1108006 GAAGGAAAAAGAAA
1 -AAAGAAAAAGAAA
1108020 AAAG-AAAAGAAA
1 AAAGAAAAAGAAA
*
1108032 AAA-AAGAAGAAA
1 AAAGAAAAAGAAA
1108044 A
1 A
1108045 GTTTAGAGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
12 19 0.56
13 3 0.09
14 9 0.26
15 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:1108021 original size:7 final size:7
Alignment explanation
Indices: 1107992--1108045 Score: 56
Period size: 7 Copynumber: 7.6 Consensus size: 7
1107982 ATCGGTTTTG
*
1107992 AAAGCAA
1 AAAGAAA
1107999 AAAGAAA
1 AAAGAAA
* *
1108006 GAAGGAA
1 AAAGAAA
1108013 AAAGAAA
1 AAAGAAA
1108020 AAAGAAA
1 AAAGAAA
1108027 AGAA-AAA
1 A-AAGAAA
1108034 AAAGAAGA
1 AAAGAA-A
1108042 AAAG
1 AAAG
1108046 TTTAGAGGAG
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
6 2 0.05
7 30 0.77
8 7 0.18
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:1108021 original size:21 final size:21
Alignment explanation
Indices: 1107992--1108045 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
1107982 ATCGGTTTTG
* *
1107992 AAAGCAAAAAG-AAAGAAGGAA
1 AAAGAAAAAAGAAAAGAA-AAA
1108013 AAAGAAAAAAGAAAAGAAAAA
1 AAAGAAAAAAGAAAAGAAAAA
1108034 AAAGAAGAAAAG
1 AAAGAA-AAAAG
1108046 TTTAGAGGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (21 bp):
AAAGAAAAAAGAAAAGAAAAA
Found at i:1108045 original size:17 final size:17
Alignment explanation
Indices: 1107997--1108045 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
1107987 TTTTGAAAGC
*
1107997 AAAAAGAA-AGAAGGAAA
1 AAAAAGAAGA-AAAGAAA
*
1108014 AAGAAAAAAGAAAAGAAA
1 AA-AAAGAAGAAAAGAAA
1108032 AAAAAGAAGAAAAG
1 AAAAAGAAGAAAAG
1108046 TTTAGAGGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 13 0.48
18 13 0.48
19 1 0.04
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (17 bp):
AAAAAGAAGAAAAGAAA
Found at i:1109508 original size:25 final size:25
Alignment explanation
Indices: 1109459--1109513 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
1109449 TCTGTGATTT
* **
1109459 ATATATGTGGCAAGGTCACGGGTTG
1 ATATATGTGGCAAGGCCACAAGTTG
* *
1109484 GTATATGTGGCTAGGCCACAAGTTG
1 ATATATGTGGCAAGGCCACAAGTTG
1109509 ATATA
1 ATATA
1109514 CATAATTGCA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.27, C:0.13, G:0.31, T:0.29
Consensus pattern (25 bp):
ATATATGTGGCAAGGCCACAAGTTG
Found at i:1112417 original size:13 final size:13
Alignment explanation
Indices: 1112399--1112423 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1112389 CACTTAGTTA
1112399 ACACATAATATTT
1 ACACATAATATTT
1112412 ACACATAATATT
1 ACACATAATATT
1112424 CACAAGCCAT
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:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
ACACATAATATTT
Found at i:1113264 original size:37 final size:37
Alignment explanation
Indices: 1113222--1113314 Score: 98
Period size: 37 Copynumber: 2.5 Consensus size: 37
1113212 AACCAATGAT
**
1113222 AAGTCAAATCATGCATGGTATTAAAATAACTGA-CAA
1 AAGTCAAATCATGCATGGTACCAAAATAACTGATCAA
* * * * * *
1113258 AGAGTCAAATCATACATAGTACCGAAGTAACTTATGAA
1 A-AGTCAAATCATGCATGGTACCAAAATAACTGATCAA
1113296 AAGTCAAATCATGCATGGT
1 AAGTCAAATCATGCATGGT
1113315 GCCTAGTAAT
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
36 1 0.02
37 41 0.91
38 3 0.07
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.25
Consensus pattern (37 bp):
AAGTCAAATCATGCATGGTACCAAAATAACTGATCAA
Found at i:1114772 original size:28 final size:28
Alignment explanation
Indices: 1114741--1114876 Score: 127
Period size: 28 Copynumber: 5.0 Consensus size: 28
1114731 AAATATTTTA
* * *
1114741 TCTTGTCTAAATTGAGAGAAATATGTTT
1 TCTTGTCTAAATTAAGACAAACATGTTT
* * *
1114769 TCTTGTCTAGA-CAA-A-AAATAT-TTT
1 TCTTGTCTAAATTAAGACAAACATGTTT
* * *
1114793 TCTTATCTTAAATTAATACAAACATATTT
1 TCTTGTC-TAAATTAAGACAAACATGTTT
*
1114822 TCTTGTGTAAATTAAGACAAACATGTTT
1 TCTTGTCTAAATTAAGACAAACATGTTT
* *
1114850 TCTTATCTAAATTAAGATAAACATGTT
1 TCTTGTCTAAATTAAGACAAACATGTT
1114877 AAAGCTGTCA
Statistics
Matches: 89, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
24 9 0.10
25 9 0.10
26 3 0.03
27 2 0.02
28 58 0.65
29 8 0.09
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.42
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAACATGTTT
Found at i:1116031 original size:10 final size:10
Alignment explanation
Indices: 1116016--1116040 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1116006 TGCACATTAT
1116016 CATATATACA
1 CATATATACA
1116026 CATATATACA
1 CATATATACA
1116036 CATAT
1 CATAT
1116041 GTCATATAGC
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:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (10 bp):
CATATATACA
Found at i:1117689 original size:20 final size:21
Alignment explanation
Indices: 1117650--1117691 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1117640 TCTTACATTT
**
1117650 TAAACTCCATCTATGGATAGA
1 TAAACTCCATCTATCAATAGA
1117671 TAAAC-CCATCTATCAATAGA
1 TAAACTCCATCTATCAATAGA
1117691 T
1 T
1117692 GGCACATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (21 bp):
TAAACTCCATCTATCAATAGA
Found at i:1121175 original size:21 final size:21
Alignment explanation
Indices: 1121149--1121190 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1121139 CTTTGTCTGA
1121149 TGCTAGAAACTTGGACTAAAG
1 TGCTAGAAACTTGGACTAAAG
1121170 TGCTAGAAACTTGGACTAAAG
1 TGCTAGAAACTTGGACTAAAG
1121191 GGCATTCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (21 bp):
TGCTAGAAACTTGGACTAAAG
Found at i:1128571 original size:15 final size:16
Alignment explanation
Indices: 1128553--1128585 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
1128543 ACCTCTCTAA
1128553 ATTAAAAGCAAA-TGC
1 ATTAAAAGCAAACTGC
1128568 ATTAAAAGCAAACTGC
1 ATTAAAAGCAAACTGC
1128584 AT
1 AT
1128586 CATCCATAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.52, C:0.15, G:0.12, T:0.21
Consensus pattern (16 bp):
ATTAAAAGCAAACTGC
Found at i:1135694 original size:73 final size:73
Alignment explanation
Indices: 1135607--1135746 Score: 174
Period size: 73 Copynumber: 1.9 Consensus size: 73
1135597 AACATTATCA
* * ** * *
1135607 CTTAGTCGACTAAGTCGTCTCTGTCCCTGAACCTAATTT-TAGACAGTAGGCTCTTAGTTGACTA
1 CTTAGTCGACTAAGTCATCTCTGTCCCTGAACCCAATTTCTAG-CAAAAAGCTCTTAATTGACTA
1135671 ACAAAACTT
65 ACAAAACTT
* * * *
1135680 CTTAGTCGATTAAGTCATTTTTGTCTCTGAACCCAATTTCTAGCAAAAAGCTCTTAATTGACTAA
1 CTTAGTCGACTAAGTCATCTCTGTCCCTGAACCCAATTTCTAGCAAAAAGCTCTTAATTGACTAA
1135745 CA
66 CA
1135747 CTGTCTCTTA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
73 53 0.95
74 3 0.05
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.34
Consensus pattern (73 bp):
CTTAGTCGACTAAGTCATCTCTGTCCCTGAACCCAATTTCTAGCAAAAAGCTCTTAATTGACTAA
CAAAACTT
Found at i:1138660 original size:24 final size:24
Alignment explanation
Indices: 1138614--1138661 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1138604 TGATTAAAAA
* *
1138614 TAAAAATATAAAAATGTATTTAAT
1 TAAAAATATAAAAATATACTTAAT
1138638 TAAAAATA-AAAACATATACTTAAT
1 TAAAAATATAAAA-ATATACTTAAT
1138662 CGAATGTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (24 bp):
TAAAAATATAAAAATATACTTAAT
Found at i:1139413 original size:2 final size:2
Alignment explanation
Indices: 1139397--1139446 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
1139387 ATACAAATAC
* * * * *
1139397 AT AT AT GT AT GT AT AT AT AT AT AG AT AT AT AT GT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1139439 AT AT AT AT
1 AT AT AT AT
1139447 GTTTGTGTGT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1140754 original size:21 final size:21
Alignment explanation
Indices: 1140708--1140754 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
1140698 TCCATGGGGA
* *
1140708 TGCAGGTGAAATTCTCTCTGG
1 TGCAGGTGAAAATCTCTCAGG
*
1140729 AGCAGGTGAATAATCT-TCAGG
1 TGCAGGTGAA-AATCTCTCAGG
1140750 TGCAG
1 TGCAG
1140755 CTGCACCTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (21 bp):
TGCAGGTGAAAATCTCTCAGG
Found at i:1140831 original size:3 final size:3
Alignment explanation
Indices: 1140811--1140851 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
1140801 AACATCACTA
* * *
1140811 TGG TGA TGG TGA TGG TGG TGG TGG TGA TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
1140852 ATGACTGTGG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.07, C:0.00, G:0.59, T:0.34
Consensus pattern (3 bp):
TGG
Found at i:1140835 original size:15 final size:15
Alignment explanation
Indices: 1140811--1140854 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
1140801 AACATCACTA
*
1140811 TGGTGATGGTGATGG
1 TGGTGGTGGTGATGG
1140826 TGGTGGTGGTGATGG
1 TGGTGGTGGTGATGG
1140841 TGGTGGTGGTGATG
1 TGGTGGTGGTGATG
1140855 ACTGTGGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.09, C:0.00, G:0.57, T:0.34
Consensus pattern (15 bp):
TGGTGGTGGTGATGG
Found at i:1140861 original size:15 final size:15
Alignment explanation
Indices: 1140811--1140863 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
1140801 AACATCACTA
* *
1140811 TGGTGATGGTGATGG
1 TGGTGGTGGTGATGC
*
1140826 TGGTGGTGGTGATGG
1 TGGTGGTGGTGATGC
1140841 TGGTGGTGGTGATGAC
1 TGGTGGTGGTGATG-C
1140857 T-GTGGTG
1 TGGTGGTG
1140864 AGGATGAGGC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
15 34 0.97
16 1 0.03
ACGTcount: A:0.09, C:0.02, G:0.55, T:0.34
Consensus pattern (15 bp):
TGGTGGTGGTGATGC
Found at i:1145610 original size:6 final size:6
Alignment explanation
Indices: 1145599--1145628 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1145589 CCGCAGCCAC
1145599 AGGCAG AGGCAG AGGCAG AGGCAG AGGCAG
1 AGGCAG AGGCAG AGGCAG AGGCAG AGGCAG
1145629 CAAATAGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.50, T:0.00
Consensus pattern (6 bp):
AGGCAG
Found at i:1146458 original size:26 final size:23
Alignment explanation
Indices: 1146429--1146483 Score: 56
Period size: 26 Copynumber: 2.3 Consensus size: 23
1146419 ATAAAATTTT
*
1146429 ATTTTGTTAAAAATAAAAATAAAAAA
1 ATTTTATTAAAAAT--AAAT-AAAAA
* *
1146455 ATTTAATTAAACATAAATAAAAA
1 ATTTTATTAAAAATAAATAAAAA
1146478 ATTTTA
1 ATTTTA
1146484 AATCTTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
23 10 0.40
24 4 0.16
26 11 0.44
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (23 bp):
ATTTTATTAAAAATAAATAAAAA
Found at i:1174693 original size:20 final size:21
Alignment explanation
Indices: 1174668--1174707 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1174658 TCCCTAAGTT
1174668 TTAATTAAATTTT-AAGTAAG
1 TTAATTAAATTTTAAAGTAAG
*
1174688 TTAATTAATTTTTAAAGTAA
1 TTAATTAAATTTTAAAGTAA
1174708 ATACTTTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (21 bp):
TTAATTAAATTTTAAAGTAAG
Found at i:1174978 original size:23 final size:23
Alignment explanation
Indices: 1174948--1175001 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
1174938 ACATTATCAA
1174948 ATTAATGAAAATACTAATGATTG
1 ATTAATGAAAATACTAATGATTG
*
1174971 ATTAATGAAAATACTAGTGATTG
1 ATTAATGAAAATACTAATGATTG
1174994 ATTAATGA
1 ATTAATGA
1175002 CTAAACTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.46, C:0.04, G:0.15, T:0.35
Consensus pattern (23 bp):
ATTAATGAAAATACTAATGATTG
Found at i:1183432 original size:20 final size:20
Alignment explanation
Indices: 1183407--1183482 Score: 55
Period size: 20 Copynumber: 3.9 Consensus size: 20
1183397 AATCATTGAA
*
1183407 AAAAATATTAAAAAATCCTT
1 AAAAATATTAAAAAATCATT
** * *
1183427 AAAAATCGTAATAAATAATT
1 AAAAATATTAAAAAATCATT
* ** *
1183447 AAAAAAATTAAAATTTCTTT
1 AAAAATATTAAAAAATCATT
*
1183467 AAAAACA-TAAAAAATC
1 AAAAATATTAAAAAATC
1183483 TTTCAAATTC
Statistics
Matches: 40, Mismatches: 16, Indels: 1
0.70 0.28 0.02
Matches are distributed among these distances:
19 7 0.17
20 33 0.82
ACGTcount: A:0.62, C:0.08, G:0.01, T:0.29
Consensus pattern (20 bp):
AAAAATATTAAAAAATCATT
Found at i:1183597 original size:22 final size:22
Alignment explanation
Indices: 1183572--1183616 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1183562 AAGACCCTAG
*
1183572 AAAT-GCTTGAAAAATCTTTAAA
1 AAATAGCTT-AAAAAACTTTAAA
1183594 AAATAGCTTAAAAAACTTTAAA
1 AAATAGCTTAAAAAACTTTAAA
1183616 A
1 A
1183617 GTCTATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.29
Consensus pattern (22 bp):
AAATAGCTTAAAAAACTTTAAA
Found at i:1184853 original size:11 final size:10
Alignment explanation
Indices: 1184839--1185602 Score: 106
Period size: 10 Copynumber: 73.5 Consensus size: 10
1184829 AAAAGAGCCC
1184839 AAAAATCCTTT
1 AAAAATCC-TT
*
1184850 AAAAAACCTT
1 AAAAATCCTT
1184860 AACAAATCCTT
1 AA-AAATCCTT
1184871 AAAAAT--TGT
1 AAAAATCCT-T
**
1184880 AATAAATAATT
1 AA-AAATCCTT
*
1184891 AAGAAA-AC-T
1 AA-AAATCCTT
1184900 AAAAATCCCTT
1 AAAAAT-CCTT
*
1184911 AAAAA-CAC-A
1 AAAAATC-CTT
*
1184920 AAAAATCTTT
1 AAAAATCCTT
* *
1184930 CAAATTCCTT
1 AAAAATCCTT
1184940 GAAAAATCTCTT
1 -AAAAATC-CTT
1184952 AAAAA-CCTT
1 AAAAATCCTT
* *
1184961 AAATATCTTT
1 AAAAATCCTT
*
1184971 AAAAGGTCCTT
1 AAAA-ATCCTT
*
1184982 AAAAATGCTT
1 AAAAATCCTT
*
1184992 AAAAATCCATG
1 AAAAATCC-TT
1185003 AAAAGA-CCTT
1 AAAA-ATCCTT
* *
1185013 AAAATTGCTTT
1 AAAAAT-CCTT
*
1185024 AAAATAT-TTT
1 AAAA-ATCCTT
*
1185034 AAAAATAGCTT
1 AAAAAT-CCTT
*
1185045 CAAGAAT--TT
1 -AAAAATCCTT
*
1185054 ATAAAATTTCTT
1 A-AAAA-TCCTT
*
1185066 TAAAATCCTT
1 AAAAATCCTT
1185076 GAAAACA-CCTT
1 -AAAA-ATCCTT
1185087 AAAAATCCTT
1 AAAAATCCTT
**
1185097 TGAAAT-CTAT
1 AAAAATCCT-T
**
1185107 CAAAAAAAGCTT
1 --AAAAATCCTT
*
1185119 AAAAATGCTT
1 AAAAATCCTT
*
1185129 AAAAA--ATT
1 AAAAATCCTT
* *
1185137 -AATATCGTT
1 AAAAATCCTT
*
1185146 AAAAGGA-CATT
1 AAAA--ATCCTT
*
1185157 AAAAATGCTT
1 AAAAATCCTT
***
1185167 AAAAAAAT-AAA
1 --AAAAATCCTT
*
1185178 AAAAAGACCTT
1 AAAAA-TCCTT
**
1185189 AAAAATGTTT
1 AAAAATCCTT
*
1185199 CAAAAATCTTT
1 -AAAAATCCTT
*
1185210 AAAAAATTGCTT
1 -AAAAA-TCCTT
*
1185222 AAAAAAACCTT
1 -AAAAATCCTT
1185233 AAAAAT-CTAT
1 AAAAATCCT-T
*
1185243 AAAATTCCTT
1 AAAAATCCTT
1185253 AAAAATCCTT
1 AAAAATCCTT
1185263 GAAAACA-CCTT
1 -AAAA-ATCCTT
1185274 AAAAATCCTT
1 AAAAATCCTT
** *
1185284 TCAAATCCATGA
1 AAAAATCC-T-T
*
1185296 AAAAAACCTT
1 AAAAATCCTT
*
1185306 AAAAATGCTT
1 AAAAATCCTT
*
1185316 AAAATTACCTT
1 AAAAAT-CCTT
* **
1185327 AAATATGTTT
1 AAAAATCCTT
**
1185337 AAAAAGAGCTT
1 AAAAA-TCCTT
*
1185348 AAAAATCTCTAAA
1 AAAAATC-CT--T
*
1185361 AAAAAGCCTT
1 AAAAATCCTT
1185371 AAAAAATCCTT
1 -AAAAATCCTT
*
1185382 AAAAAT-CAT
1 AAAAATCCTT
**
1185391 AATAAATAATT
1 AA-AAATCCTT
**
1185402 AAAAA-AATT
1 AAAAATCCTT
1185411 AAAAATCTCTT
1 AAAAATC-CTT
* *
1185422 AAAAA-CATA
1 AAAAATCCTT
*
1185431 AAAAATCTTT
1 AAAAATCCTT
* *
1185441 TAAATTCCTT
1 AAAAATCCTT
*
1185451 GAAAAATCTTT
1 -AAAAATCCTT
1185462 GAAAAA-CCTT
1 -AAAAATCCTT
* **
1185472 GAATGT-CTAT
1 AAAAATCCT-T
*
1185482 AAAGGGA-CCTT
1 AAA--AATCCTT
*
1185493 AAAAATGCTT
1 AAAAATCCTT
* *
1185503 AAAAATTCATA
1 AAAAA-TCCTT
***
1185514 AAAAAAGGTT
1 AAAAATCCTT
*
1185524 AAAAATGCTT
1 AAAAATCCTT
*
1185534 CAAAAATCTTT
1 -AAAAATCCTT
*
1185545 ATAAAATGACTT
1 A-AAAAT-CCTT
*
1185557 AAAAACCCTT
1 AAAAATCCTT
1185567 AAAAAT-CTAT
1 AAAAATCCT-T
*
1185577 AAAATTCCTT
1 AAAAATCCTT
* *
1185587 CAAAATTCTT
1 AAAAATCCTT
1185597 GAAAAA
1 -AAAAA
1185603 AAGCTTAAAA
Statistics
Matches: 542, Mismatches: 133, Indels: 156
0.65 0.16 0.19
Matches are distributed among these distances:
7 3 0.01
8 7 0.01
9 66 0.12
10 214 0.39
11 197 0.36
12 47 0.09
13 8 0.01
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.29
Consensus pattern (10 bp):
AAAAATCCTT
Found at i:1184969 original size:41 final size:41
Alignment explanation
Indices: 1184899--1184996 Score: 103
Period size: 41 Copynumber: 2.4 Consensus size: 41
1184889 TTAAGAAAAC
* *
1184899 TAAAAATCCCTTAAAAACACAAAAAATCTTTCAAA-TTCCT
1 TAAAAATCCCTTAAAAACACAAAAAATCTTTAAAAGGTCCT
* * *
1184939 TGAAAAATCTCTTAAAAAC-CTTAAATATCTTTAAAAGGTCCT
1 T-AAAAATCCCTTAAAAACAC-AAAAAATCTTTAAAAGGTCCT
*
1184981 TAAAAAT-GCTTAAAAA
1 TAAAAATCCCTTAAAAA
1184997 TCCATGAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
40 10 0.20
41 34 0.69
42 5 0.10
ACGTcount: A:0.49, C:0.17, G:0.04, T:0.30
Consensus pattern (41 bp):
TAAAAATCCCTTAAAAACACAAAAAATCTTTAAAAGGTCCT
Found at i:1185035 original size:21 final size:20
Alignment explanation
Indices: 1185011--1185071 Score: 59
Period size: 22 Copynumber: 2.9 Consensus size: 20
1185001 TGAAAAGACC
1185011 TTAAAATTGCTTTAAAATATT
1 TTAAAATTGCTTTAAAAT-TT
* *
1185032 TTAAAAATAGCTTCAAGAATTT
1 TT-AAAATTGCTTTAA-AATTT
* *
1185054 ATAAAATTTCTTTAAAAT
1 TTAAAATTGCTTTAAAAT
1185072 CCTTGAAAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
20 3 0.09
21 12 0.38
22 14 0.44
23 3 0.09
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.43
Consensus pattern (20 bp):
TTAAAATTGCTTTAAAATTT
Found at i:1185203 original size:21 final size:20
Alignment explanation
Indices: 1185179--1185288 Score: 69
Period size: 21 Copynumber: 5.2 Consensus size: 20
1185169 AAAAATAAAA
*
1185179 AAAAGACCTTAAAAATGTTTC
1 AAAA-ACCTTAAAAATCTTTC
* **
1185200 AAAAATCTTTAAAAAATTGCTTAA
1 AAAAA-CCTT-AAAAA-T-CTTTC
*
1185224 AAAAACCTTAAAAATCTAT-
1 AAAAACCTTAAAAATCTTTC
* * *
1185243 AAAATTCCTTAAAAATCCTTG
1 AAAA-ACCTTAAAAATCTTTC
1185264 AAAACACCTTAAAAATCCTTTC
1 AAAA-ACCTTAAAAAT-CTTTC
1185286 AAA
1 AAA
1185289 TCCATGAAAA
Statistics
Matches: 68, Mismatches: 14, Indels: 13
0.72 0.15 0.14
Matches are distributed among these distances:
19 4 0.06
20 15 0.22
21 22 0.32
22 16 0.24
23 4 0.06
24 7 0.10
ACGTcount: A:0.51, C:0.16, G:0.04, T:0.29
Consensus pattern (20 bp):
AAAAACCTTAAAAATCTTTC
Found at i:1185319 original size:21 final size:21
Alignment explanation
Indices: 1185295--1185386 Score: 78
Period size: 21 Copynumber: 4.2 Consensus size: 21
1185285 CAAATCCATG
1185295 AAAAAAACCTTAAAAATGCTT
1 AAAAAAACCTTAAAAATGCTT
** * *
1185316 AAAATTACCTTAAATATGTTT
1 AAAAAAACCTTAAAAATGCTT
* *
1185337 AAAAAGAGCTTAAAAAT-CTCT
1 AAAAAAACCTTAAAAATGCT-T
*
1185358 AAAAAAAAGCCTTAAAAAATCCTT
1 -AAAAAAA-CCTT-AAAAATGCTT
1185382 AAAAA
1 AAAAA
1185387 TCATAATAAA
Statistics
Matches: 55, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
20 1 0.02
21 31 0.56
22 6 0.11
23 8 0.15
24 7 0.13
25 2 0.04
ACGTcount: A:0.55, C:0.13, G:0.05, T:0.26
Consensus pattern (21 bp):
AAAAAAACCTTAAAAATGCTT
Found at i:1185385 original size:23 final size:22
Alignment explanation
Indices: 1185295--1185426 Score: 64
Period size: 21 Copynumber: 6.2 Consensus size: 22
1185285 CAAATCCATG
* *
1185295 AAAAAAACCTTAAAAAT-GCTT
1 AAAAAAAGCTTAAAAATCTCTT
** * * *
1185316 AAAATTACCTTAAATATGT-TT
1 AAAAAAAGCTTAAAAATCTCTT
* *
1185337 AAAAAGAGCTTAAAAATCTCTA
1 AAAAAAAGCTTAAAAATCTCTT
1185359 AAAAAAAGCCTTAAAAAATC-CTT
1 AAAAAAAG-CTT-AAAAATCTCTT
* * **
1185382 --AAAAATCATAATAAAT-AATT
1 AAAAAAAGCTTAA-AAATCTCTT
1185402 AAAAAAA--TTAAAAATCTCTT
1 AAAAAAAGCTTAAAAATCTCTT
1185422 AAAAA
1 AAAAA
1185427 CATAAAAAAT
Statistics
Matches: 84, Mismatches: 18, Indels: 19
0.69 0.15 0.16
Matches are distributed among these distances:
19 6 0.07
20 18 0.21
21 35 0.42
22 13 0.15
23 5 0.06
24 7 0.08
ACGTcount: A:0.58, C:0.11, G:0.04, T:0.27
Consensus pattern (22 bp):
AAAAAAAGCTTAAAAATCTCTT
Found at i:1185471 original size:21 final size:21
Alignment explanation
Indices: 1185431--1185474 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1185421 TAAAAACATA
* **
1185431 AAAAATCTTTTAAATTCCTTG
1 AAAAATCTTTGAAAAACCTTG
1185452 AAAAATCTTTGAAAAACCTTG
1 AAAAATCTTTGAAAAACCTTG
1185473 AA
1 AA
1185475 TGTCTATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.34
Consensus pattern (21 bp):
AAAAATCTTTGAAAAACCTTG
Found at i:1185842 original size:301 final size:303
Alignment explanation
Indices: 1185186--1185924 Score: 799
Period size: 301 Copynumber: 2.4 Consensus size: 303
1185176 AAAAAAAGAC
* * * ** *
1185186 CTTAAAAATGTTTCAAAAA-TCTTTAAAAAATTGCTTAAAAAAACCTTAAAAATC--TATAAAAT
1 CTTAAAAATGCTT-AAAAATTC-ATAAAAAA-AGCTTAAAAATGCTTTAAAAATCTTTATAAAAT
** * * *
1185248 TCCTTAAAAATCCTTGAAAACACCT-TAAAAATCCTTTCAAATCCATGAAAAAAACCTTAAAAAT
63 GACTTAAAAAACCTT-AAAA-ATCTATAAAATTCCTTTCAAATCCATGAAAAAAACCTTAAAAAT
* * ** * *
1185312 GCTTAAAATTACCTTAAATATGTTTAAAAAGAGCTTAAAAATCTCTAAAAAAAAGCCTTAAAAAA
126 GCTTAAAATGACCTTAAACATGCCTAAAAAGAGCATAAAAATCTCTAAAAAAAAGCCTCAAAAAA
*
1185377 TCCTTAAAAATCATAATAAATAATTAAAAAAATTAAAAATCTCTTAAAAACATAAAAAATCTTTT
191 TCCTTAAAAATCATAATAAATAATTAAAAAAATTAAAAATCTCTTAAAAACATAAAAAATCTTTC
* * * * *
1185442 AAATTCCTTGAAAAATCTTTGAAAAACCTTGAATGTCTATAAAGGGAC
256 AAATTCCTTGAAAAATCTTTGAAAAAACTTAAATATCTATAAAGGAAA
* *
1185490 CTTAAAAATGCTTAAAAATTCATAAAAAAAGGTTAAAAATGCTTCAAAAATCTTTATAAAATGAC
1 CTTAAAAATGCTTAAAAATTCATAAAAAAAGCTTAAAAATGCTTTAAAAATCTTTATAAAATGAC
* * * *
1185555 TTAAAAACCCTTAAAAATCTATAAAATTCC-TTCAAAATTCTTGAAAAAAAGCTTAAAAATGCTT
66 TTAAAAAACCTTAAAAATCTATAAAATTCCTTTC-AAATCCATGAAAAAAACCTTAAAAATGCTT
* * * * * *
1185619 AGAATGATCTTAAACATGCCTGAAAAGAGCATAAAAATCTCT-GAAAAAA-TCTCCAAAAATCCT
130 AAAATGACCTTAAACATGCCTAAAAAGAGCATAAAAATCTCTAAAAAAAAGCCTCAAAAAATCCT
* *
1185682 TAAAAATTATAATAAATAATTTAAAAAATTAAAAAT-TCCTTAAAAACATAAAAAATCTTTCAAA
195 TAAAAATCATAATAAATAATTAAAAAAATTAAAAATCT-CTTAAAAACATAAAAAATCTTTCAAA
* *
1185746 TTCCTTGAAAAATCTCTT-AAAAAATTTAAATAT-TGTTAAA-GAAA
259 TTCCTTGAAAAATCT-TTGAAAAAACTTAAATATCT-ATAAAGGAAA
* *
1185790 CTTTAAAATGCTTAAAAA-TC-TACAAAAAAGATCTTAAAATTGCTTTAAAAATCTTT-TAAAAG
1 CTTAAAAATGCTTAAAAATTCATA-AAAAAAG--CTTAAAAATGCTTTAAAAATCTTTATAAAA-
* * * * * *
1185852 TGGCTTAAAAAACTTTAAAAATCTATAAAATT-TTGTTAAAATCCTTG-AAAACACCTTAAAAAT
62 TGACTTAAAAAACCTTAAAAATCTATAAAATTCCT-TTCAAATCCATGAAAAAAACCTTAAAAAT
*
1185915 TCTTTAAAAT
126 GC-TTAAAAT
1185925 TCATAAAAGA
Statistics
Matches: 368, Mismatches: 52, Indels: 33
0.81 0.11 0.07
Matches are distributed among these distances:
298 2 0.01
299 9 0.02
300 41 0.11
301 164 0.45
302 33 0.09
303 85 0.23
304 34 0.09
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.31
Consensus pattern (303 bp):
CTTAAAAATGCTTAAAAATTCATAAAAAAAGCTTAAAAATGCTTTAAAAATCTTTATAAAATGAC
TTAAAAAACCTTAAAAATCTATAAAATTCCTTTCAAATCCATGAAAAAAACCTTAAAAATGCTTA
AAATGACCTTAAACATGCCTAAAAAGAGCATAAAAATCTCTAAAAAAAAGCCTCAAAAAATCCTT
AAAAATCATAATAAATAATTAAAAAAATTAAAAATCTCTTAAAAACATAAAAAATCTTTCAAATT
CCTTGAAAAATCTTTGAAAAAACTTAAATATCTATAAAGGAAA
Found at i:1185848 original size:22 final size:21
Alignment explanation
Indices: 1185823--1185873 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
1185813 AAAAAAGATC
* *
1185823 TTAAAATTGCTTTAAAAATCTT
1 TTAAAATGGC-TTAAAAAACTT
1185845 TTAAAAGTGGCTTAAAAAACTT
1 TTAAAA-TGGCTTAAAAAACTT
*
1185867 TAAAAAT
1 TTAAAAT
1185874 CTATAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 21 0.84
23 3 0.12
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (21 bp):
TTAAAATGGCTTAAAAAACTT
Found at i:1186022 original size:321 final size:319
Alignment explanation
Indices: 1185576--1187059 Score: 1246
Period size: 321 Copynumber: 4.5 Consensus size: 319
1185566 TAAAAATCTA
* * * * * * * *
1185576 TAAAATTCCTTCAAAATTCTTGAAAAAAAGCTTAAAAATGCTTAGAATGATCTTAAACATGCCTG
1 TAAAAATCCTTTAAAATTCATAAAAAAAAGCTTAAAAATACTTAGAATGACCTTAAACATGCTTA
* * *
1185641 AAAAGAGCATAAAAATCTCTGAAAAAATCTCCAAAAATCCTTAAAAATTATAATAAATAATTTAA
66 AAAAGAGCCTAAAAATCTTTG-----A-----AAAAA-CCTTAAAAACTATAATAAATAA-TTAA
*
1185706 AAAATTAAAAATTCCTTAAAAACATAAAAAATCTTTCAAATTCCTTGAAAAATCTCTTAAAAAAT
119 AAAATTAAAAATTCCTTAAAAACATAAAAAATCTTTCAAATTCCTTGAAAAATCTCTTAAAAAAC
* * * *
1185771 TTAAATAT-TGTTAAAGAAACTTTAAAATGCTTAAAAATCTACAAAAAAGATCTTAAAATTGCTT
184 TTAAATATCT-TTAAAGAGACCTTAAAATGCTTAAAAATCTA-AAAAAAGACCTTAAAAATGCTT
* * *
1185835 TAAAAATCTTTTAAAAGTGGCTTAAAAAACTTTAAAAATCTATAAAATTTTGTTAAAATCCTTGA
247 TAAAAATCTTTTAAAAATGGCTTAAAAAACTTTAAAAATCCATAAAATTTTGTAAAAATCCTTGA
1185900 AAACACCT
312 AAACACCT
* * * * *
1185908 TAAAAATTCTTTAAAATTCATAAAAGAAAGTTTAAAAATACTTATAATGACCTTAAATATGCTTA
1 TAAAAATCCTTTAAAATTCATAAAAAAAAGCTTAAAAATACTTAGAATGACCTTAAACATGCTTA
* *
1185973 AGAAA-AGCCTAAAAATATTTGAAAAAACCTTAAAAACTATAATAAATAATTAAGAAAATTGAAA
66 A-AAAGAGCCTAAAAATCTTTGAAAAAACCTTAAAAACTATAATAAATAATTAA-AAAATTAAAA
* * * * *
1186037 A-TCTCTTAAAAACATCAAAAATCTTTCAAAGTCCATGAAAAATCTCTTCAAAACCTTAAATATC
129 ATTC-CTTAAAAACATAAAAAATCTTTCAAATTCCTTGAAAAATCTCTTAAAAAACTTAAATATC
* * * * * *
1186101 TTTAAAGGGACCTTAAAATCCTTAAAAATCCAAGAAAAAGATCTTAAAAATGC-TTCAAAATTTT
193 TTTAAAGAGACCTTAAAATGCTTAAAAATCTAA-AAAAAGACCTTAAAAATGCTTTAAAAATCTT
*
1186165 TTAAAAAATGGCTTAACAAAA-TTTAAAAATCCACAAAATTCATTG--AAAATCCTTGAAAACAC
257 TT-AAAAATGGCTTAA-AAAACTTTAAAAATCCATAAAATT--TTGTAAAAATCCTTGAAAACAC
1186227 CT
318 CT
* *
1186229 TAAAAATCCTTTGAAATCTTTATAAAAAAAAAAGCTTAAAAATGA-TTAGAATGACCTTAAACAT
1 TAAAAATCCTTT-AAA-ATTCAT--AAAAAAAAGCTTAAAAAT-ACTTAGAATGACCTTAAACAT
* * * *
1186293 TCTTATAAAAGAGCCTAAAAATCCTTAAAAAAAATTAAAAATTCCTTAAAAA-TCATAAAAAATA
61 GCTTA-AAAAGAGCCTAAAAAT-CTT--------TGAAAAA-ACCTTAAAAACT-ATAATAAATA
* * * *
1186357 ATTAAACAAATTAAAAATTGCTTAAAAATATAAAAAATCTTTCAAGTTCCGTGAAAAATCTCTTA
114 ATTAAA-AAATTAAAAATTCCTTAAAAACATAAAAAATCTTTCAAATTCCTTGAAAAATCTCTTA
* * * * * *
1186422 AAAACCTTAAATATCTTTTAAGGGACATTAAAA--ATT--CAA--T--AAAAAGACCTTAAAAAT
178 AAAAACTTAAATATCTTTAAAGAGACCTTAAAATGCTTAAAAATCTAAAAAAAGACCTTAAAAAT
* * * * * *
1186479 G-TTTCCAAAATC-TGTAAAAAGTAGCTTGAAAAACCTTAAAAATCCATAAAATTTCT-AAAAAA
243 GCTTT-AAAAATCTTTTAAAAA-TGGCTTAAAAAACTTTAAAAATCCATAAAATTT-TGTAAAAA
1186541 TCCTTGAAAACACCT
305 TCCTTGAAAACACCT
* * *
1186556 TAAAAATCCTTTAAAA-T-A-AATAAAAAAGCTAAAAAATGCTTAGAATGACCTGAAATC-TGCT
1 TAAAAATCCTTTAAAATTCATAA-AAAAAAGCTTAAAAATACTTAGAATGACCTTAAA-CATGCT
* * * *
1186617 TAAAAAGAG-CTAAAAAATCTTTGAAAAAATCTTTAAAAATTGTAATAAATAATTAAAAAAATAA
64 TAAAAAGAGCCT-AAAAATCTTTGAAAAAA-CCTTAAAAACTATAATAAATAATTAAAAAATTAA
* * * *
1186681 AAA-TCCTTTAAAAACAGAAAAAATCTTTCAAATTCCTAGAAAATTTCTCTTAAAAATCTTAAAT
127 AAATTCC-TTAAAAACATAAAAAATCTTTCAAATTCCTTGAAAA-ATCTCTTAAAAAACTTAAAT
* * * * * * *
1186745 ATCCTTAAA-AGGACCTTAAAATTGCTTAAAGATCCTTGAAAACAG-CCTTAAAATTGCTTCAAC
190 ATCTTTAAAGA-GACCTTAAAA-TGCTTAAAAAT-C-TAAAAAAAGACCTTAAAAATGCTTTAAA
* * * * *** * *
1186808 AATATTTTAAAAATGGCTTTAAAAGCTTTAAAAATTCATAAAATTCCCTAAAAATACTTGAAACC
251 AATCTTTTAAAAATGGCTTAAAAAACTTTAAAAATCCATAAAATTTTGTAAAAATCCTTGAAAAC
1186873 ACCT
316 ACCT
* * * * * *
1186877 TGAAAATCCTTTGAAA-TCTATGAAAAAAAA-TTTAAAAATGCTTATAATGACCTTAAACATCCT
1 TAAAAATCCTTTAAAATTC-AT-AAAAAAAAGCTTAAAAATACTTAGAATGACCTTAAACATGCT
* * * * * *
1186940 TAAAAAGGGCCTAAAAATCCTTAAAAAAAACTTAAAAAATCCAAAAAAATTGTAATCAATAATTA
64 TAAAAAGAGCCTAAAAATCTTTGAAAAAACCTT-AAAAA--C--------TATAATAAATAATTA
*
1187005 AAAAATTTAAAAATTCCTTAGAAACATAAAAAATCTTTCAAATTCCTTGAGAAAA
118 AAAAA-TTAAAAATTCCTTAAAAACATAAAAAATCTTTCAAATTCCTTGA-AAAA
1187060 AAACCTTAAA
Statistics
Matches: 944, Mismatches: 129, Indels: 156
0.77 0.10 0.13
Matches are distributed among these distances:
309 2 0.00
310 40 0.04
311 62 0.07
312 1 0.00
314 2 0.00
316 1 0.00
319 5 0.01
320 34 0.04
321 296 0.31
322 31 0.03
323 63 0.07
324 9 0.01
325 43 0.05
326 26 0.03
327 78 0.08
328 6 0.01
332 68 0.07
333 22 0.02
334 38 0.04
335 14 0.01
336 102 0.11
337 1 0.00
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.29
Consensus pattern (319 bp):
TAAAAATCCTTTAAAATTCATAAAAAAAAGCTTAAAAATACTTAGAATGACCTTAAACATGCTTA
AAAAGAGCCTAAAAATCTTTGAAAAAACCTTAAAAACTATAATAAATAATTAAAAAATTAAAAAT
TCCTTAAAAACATAAAAAATCTTTCAAATTCCTTGAAAAATCTCTTAAAAAACTTAAATATCTTT
AAAGAGACCTTAAAATGCTTAAAAATCTAAAAAAAGACCTTAAAAATGCTTTAAAAATCTTTTAA
AAATGGCTTAAAAAACTTTAAAAATCCATAAAATTTTGTAAAAATCCTTGAAAACACCT
Found at i:1186331 original size:20 final size:21
Alignment explanation
Indices: 1186308--1186384 Score: 70
Period size: 20 Copynumber: 3.8 Consensus size: 21
1186298 TAAAAGAGCC
1186308 TAAAAA-TCCTTAAAAAAAAT
1 TAAAAATTCCTTAAAAAAAAT
**
1186328 TAAAAATTCCTTAAAAATCA-
1 TAAAAATTCCTTAAAAAAAAT
* ** *
1186348 TAAAAAATAATT-AAACAAAT
1 TAAAAATTCCTTAAAAAAAAT
*
1186368 TAAAAATTGCTTAAAAA
1 TAAAAATTCCTTAAAAA
1186385 TATAAAAAAT
Statistics
Matches: 42, Mismatches: 12, Indels: 5
0.71 0.20 0.08
Matches are distributed among these distances:
19 4 0.10
20 24 0.57
21 14 0.33
ACGTcount: A:0.62, C:0.09, G:0.01, T:0.27
Consensus pattern (21 bp):
TAAAAATTCCTTAAAAAAAAT
Found at i:1186392 original size:20 final size:20
Alignment explanation
Indices: 1186329--1186394 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
1186319 AAAAAAAATT
*
1186329 AAAAATTCCTTAAAAATCATA
1 AAAAATTACTTAAAAAT-ATA
* *
1186350 AAAAA-TAATTAAACAA-ATT
1 AAAAATTACTTAAA-AATATA
*
1186369 AAAAATTGCTTAAAAATATA
1 AAAAATTACTTAAAAATATA
1186389 AAAAAT
1 AAAAAT
1186395 CTTTCAAGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
19 9 0.25
20 20 0.56
21 7 0.19
ACGTcount: A:0.64, C:0.08, G:0.02, T:0.27
Consensus pattern (20 bp):
AAAAATTACTTAAAAATATA
Found at i:1186550 original size:11 final size:10
Alignment explanation
Indices: 1186507--1186572 Score: 55
Period size: 10 Copynumber: 6.6 Consensus size: 10
1186497 AAGTAGCTTG
1186507 AAAAA-CCTT
1 AAAAATCCTT
*
1186516 AAAAATCCAT
1 AAAAATCCTT
* * *
1186526 AAAATTTCTA
1 AAAAATCCTT
1186536 AAAAATCCTT
1 AAAAATCCTT
1186546 GAAAACA-CCTT
1 -AAAA-ATCCTT
1186557 AAAAATCCTT
1 AAAAATCCTT
*
1186567 TAAAAT
1 AAAAAT
1186573 AAATAAAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
9 6 0.14
10 29 0.66
11 8 0.18
12 1 0.02
ACGTcount: A:0.53, C:0.18, G:0.02, T:0.27
Consensus pattern (10 bp):
AAAAATCCTT
Found at i:1186560 original size:21 final size:20
Alignment explanation
Indices: 1186503--1186571 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
1186493 TAAAAAGTAG
1186503 CTTGAAAAACCTTAAAAATC
1 CTTGAAAAACCTTAAAAATC
* ** *
1186523 CAT-AAAATTTCTAAAAAATC
1 CTTGAAAA-ACCTTAAAAATC
1186543 CTTGAAAACACCTTAAAAATC
1 CTTGAAAA-ACCTTAAAAATC
*
1186564 CTTTAAAA
1 CTTGAAAA
1186572 TAAATAAAAA
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
19 4 0.11
20 13 0.35
21 20 0.54
ACGTcount: A:0.51, C:0.19, G:0.03, T:0.28
Consensus pattern (20 bp):
CTTGAAAAACCTTAAAAATC
Found at i:1186581 original size:21 final size:21
Alignment explanation
Indices: 1186534--1186582 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
1186524 ATAAAATTTC
**
1186534 TAAAAAATCCTTGAAAACACC
1 TAAAAAATCCTTGAAAACAAA
* * *
1186555 TTAAAAATCCTTTAAAATAAA
1 TAAAAAATCCTTGAAAACAAA
1186576 TAAAAAA
1 TAAAAAA
1186583 GCTAAAAAAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.59, C:0.14, G:0.02, T:0.24
Consensus pattern (21 bp):
TAAAAAATCCTTGAAAACAAA
Found at i:1186581 original size:41 final size:40
Alignment explanation
Indices: 1186503--1186582 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 40
1186493 TAAAAAGTAG
***
1186503 CTTGAAAAACCTTAAAAATCCATAAAATTTCTAAAAAATC
1 CTTGAAAAACCTTAAAAATCCATAAAATAAATAAAAAATC
*
1186543 CTTGAAAACACCTTAAAAATCCTTTAAAATAAATAAAAAA
1 CTTGAAAA-ACCTTAAAAATCC-ATAAAATAAATAAAAAA
1186583 GCTAAAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 8 0.24
41 13 0.38
42 13 0.38
ACGTcount: A:0.55, C:0.16, G:0.03, T:0.26
Consensus pattern (40 bp):
CTTGAAAAACCTTAAAAATCCATAAAATAAATAAAAAATC
Found at i:1186708 original size:19 final size:18
Alignment explanation
Indices: 1186639--1186708 Score: 52
Period size: 20 Copynumber: 3.7 Consensus size: 18
1186629 AAAAATCTTT
*
1186639 GAAAAAATCTTTAAAAATT
1 GAAAAAATCTTTAAAAA-A
* **
1186658 GTAATAAATAATTAAAAAA
1 G-AAAAAATCTTTAAAAAA
1186677 -ATAAAAATCCTTTAAAAACA
1 GA-AAAAAT-CTTTAAAAA-A
1186697 GAAAAAATCTTT
1 GAAAAAATCTTT
1186709 CAAATTCCTA
Statistics
Matches: 39, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
17 1 0.03
18 5 0.13
19 12 0.31
20 20 0.51
21 1 0.03
ACGTcount: A:0.60, C:0.07, G:0.04, T:0.29
Consensus pattern (18 bp):
GAAAAAATCTTTAAAAAA
Found at i:1186780 original size:31 final size:32
Alignment explanation
Indices: 1186729--1186803 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
1186719 GAAAATTTCT
* * *
1186729 CTTAAAAAT-CTTAAATATCCTT-AAAA-GGAC
1 CTTAAAATTGCTTAAAGATCCTTGAAAACAG-C
1186759 CTTAAAATTGCTTAAAGATCCTTGAAAACAGC
1 CTTAAAATTGCTTAAAGATCCTTGAAAACAGC
1186791 CTTAAAATTGCTT
1 CTTAAAATTGCTT
1186804 CAACAATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
30 8 0.21
31 12 0.31
32 18 0.46
33 1 0.03
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.32
Consensus pattern (32 bp):
CTTAAAATTGCTTAAAGATCCTTGAAAACAGC
Found at i:1186975 original size:21 final size:21
Alignment explanation
Indices: 1186899--1186977 Score: 59
Period size: 21 Copynumber: 3.8 Consensus size: 21
1186889 GAAATCTATG
* *
1186899 AAAAAAAATTTAAAAATGCTT
1 AAAAAAAACTTAAAAATCCTT
* ** * *
1186920 ATAATGACCTTAAACATCCTT
1 AAAAAAAACTTAAAAATCCTT
*** *
1186941 AAAAAGGGCCTAAAAATCCTT
1 AAAAAAAACTTAAAAATCCTT
1186962 AAAAAAAACTTAAAAA
1 AAAAAAAACTTAAAAA
1186978 ATCCAAAAAA
Statistics
Matches: 41, Mismatches: 17, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.56, C:0.14, G:0.06, T:0.24
Consensus pattern (21 bp):
AAAAAAAACTTAAAAATCCTT
Found at i:1187103 original size:22 final size:21
Alignment explanation
Indices: 1187056--1187113 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 21
1187046 ATTCCTTGAG
1187056 AAAAAAACCTT-AAAAATGCT
1 AAAAAAACCTTAAAAAATGCT
** *
1187076 TCAAAAATCTTAAAAAATGGCT
1 AAAAAAACCTTAAAAAAT-GCT
1187098 AAAAAAACCTTAAAAA
1 AAAAAAACCTTAAAAA
1187114 TCCATAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 8 0.27
21 6 0.20
22 16 0.53
ACGTcount: A:0.60, C:0.14, G:0.05, T:0.21
Consensus pattern (21 bp):
AAAAAAACCTTAAAAAATGCT
Found at i:1187122 original size:21 final size:20
Alignment explanation
Indices: 1187056--1187114 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 20
1187046 ATTCCTTGAG
1187056 AAAAAAACCTTAAAAATGCT
1 AAAAAAACCTTAAAAATGCT
** *
1187076 TCAAAAATCTTAAAAAATGGCT
1 AAAAAAACCTT-AAAAAT-GCT
1187098 AAAAAAACCTTAAAAAT
1 AAAAAAACCTTAAAAAT
1187115 CCATAAAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 8 0.26
21 12 0.39
22 11 0.35
ACGTcount: A:0.59, C:0.14, G:0.05, T:0.22
Consensus pattern (20 bp):
AAAAAAACCTTAAAAATGCT
Found at i:1187342 original size:21 final size:21
Alignment explanation
Indices: 1187282--1187400 Score: 61
Period size: 21 Copynumber: 5.8 Consensus size: 21
1187272 ATTAAAAATT
* * *
1187282 AAAAATATTTTAAAAACATT-
1 AAAAATCTCTTAAAAACCTTG
* * **
1187302 AAAAATTTGTTAAACTCCTTG
1 AAAAATCTCTTAAAAACCTTG
1187323 AAAAATCTCTTAAAAACCTT-
1 AAAAATCTCTTAAAAACCTTG
*
1187343 AAATATC-CTTAAAAGGACC-TG
1 AAAAATCTCTTAAAA--ACCTTG
* * *
1187364 AAAAAT-GCTTAAAAATTCATG
1 AAAAATCTCTTAAAAA-CCTTG
1187385 AAAAAGTC-CTTAAAAA
1 AAAAA-TCTCTTAAAAA
1187401 TGCTTCAAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
19 8 0.10
20 23 0.29
21 38 0.49
22 9 0.12
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.29
Consensus pattern (21 bp):
AAAAATCTCTTAAAAACCTTG
Found at i:1187399 original size:11 final size:10
Alignment explanation
Indices: 1187317--1187496 Score: 80
Period size: 10 Copynumber: 17.2 Consensus size: 10
1187307 TTTGTTAAAC
1187317 TCCTTGAAAAA
1 TCCTT-AAAAA
1187328 TCTCTTAAAAA
1 TC-CTTAAAAA
*
1187339 -CCTTAAATA
1 TCCTTAAAAA
1187348 TCCTTAAAAGGA
1 TCCTTAAAA--A
*
1187360 -CCTGAAAAA
1 TCCTTAAAAA
*
1187369 TGCTTAAAAA
1 TCCTTAAAAA
* *
1187379 TTCATGAAAAA
1 -TCCTTAAAAA
1187390 GTCCTTAAAAA
1 -TCCTTAAAAA
*
1187401 TGCTTCAAAAA
1 TCCTT-AAAAA
** *
1187412 TATTTTAAAAT
1 T-CCTTAAAAA
*
1187423 TAGCTTAAGAAA
1 T-CCTTAA-AAA
*
1187435 T-CTAAAAAA
1 TCCTTAAAAA
* *
1187444 TCCATAAAAT
1 TCCTTAAAAA
*
1187454 TCCTTGAAAA
1 TCCTTAAAAA
1187464 TCCTTGAAAAGA
1 TCCTT-AAAA-A
1187476 -CCTTAAAAA
1 TCCTTAAAAA
* *
1187485 TTCTTTAAAA
1 TCCTTAAAAA
1187495 TC
1 TC
1187497 TATGAAATAA
Statistics
Matches: 127, Mismatches: 29, Indels: 27
0.69 0.16 0.15
Matches are distributed among these distances:
9 13 0.10
10 52 0.41
11 52 0.41
12 10 0.08
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.30
Consensus pattern (10 bp):
TCCTTAAAAA
Found at i:1187479 original size:21 final size:21
Alignment explanation
Indices: 1187455--1187494 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1187445 CCATAAAATT
*
1187455 CCTTGAAAATCCTTGAAAAGA
1 CCTTAAAAATCCTTGAAAAGA
* *
1187476 CCTTAAAAATTCTTTAAAA
1 CCTTAAAAATCCTTGAAAA
1187495 TCTATGAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.30
Consensus pattern (21 bp):
CCTTAAAAATCCTTGAAAAGA
Found at i:1190421 original size:18 final size:19
Alignment explanation
Indices: 1190395--1190442 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
1190385 GTGATGGGTG
*
1190395 AAAAGAATATTTTA-AAAT
1 AAAATAATATTTTATAAAT
*
1190413 AAAATAATATTTTATTAAT
1 AAAATAATATTTTATAAAT
1190432 AAAATAATATT
1 AAAATAATATT
1190443 AAAATATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
AAAATAATATTTTATAAAT
Found at i:1191421 original size:21 final size:21
Alignment explanation
Indices: 1191404--1191446 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1191394 CAAAAGAGGG
1191404 AAGAAAGGAGAAAAAAGAAAA
1 AAGAAAGGAGAAAAAAGAAAA
*
1191425 AAGAAAGGAGAAAGAAGAAAA
1 AAGAAAGGAGAAAAAAGAAAA
1191446 A
1 A
1191447 GACTTGAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (21 bp):
AAGAAAGGAGAAAAAAGAAAA
Found at i:1191910 original size:25 final size:25
Alignment explanation
Indices: 1191882--1191934 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
1191872 AATATATATA
* *
1191882 TGGCAAGGCCATAGGATGATATACG
1 TGGCAAGGCCACAAGATGATATACG
* *
1191907 TGGCTAGGCCACAAGTTGATATACG
1 TGGCAAGGCCACAAGATGATATACG
1191932 TGG
1 TGG
1191935 TTACAACCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.28, C:0.17, G:0.32, T:0.23
Consensus pattern (25 bp):
TGGCAAGGCCACAAGATGATATACG
Found at i:1197966 original size:641 final size:644
Alignment explanation
Indices: 1196701--1197988 Score: 2537
Period size: 641 Copynumber: 2.0 Consensus size: 644
1196691 AAAACAAGGA
1196701 AAGTATAAAAAGAACTAAAGAAGAAAAGAAAACTAAGATTTGTCAAGTCTTCGATTCTTAATCTT
1 AAGTATAAAAAGAACTAAAGAAGAAAAGAAAACTAAGATTTGTCAAGTCTTCGATTCTTAATCTT
1196766 CAAGAGTTTTTCCTTACTTTCTTGCTTGCTTGATGGCTCTTTTTCTTCAGAGAAAATCTATCTTA
66 CAAGAGTTTTTCCTTACTTTCTTGCTTGCTTGATGGCTCTTTTTCTTCAGAGAAAATCTATCTTA
1196831 ATTGTTACTTTCAAGTGCTCTAAAGGGGTCTTTAAACAAGGCTCAAAATCTTACTCAAAATCAAC
131 ATTGTTACTTTCAAGTGCTCTAAAGGGGTCTTTAAACAAGGCTCAAAATCTTACTCAAAATCAAC
1196896 TTTTGGAATTTATGCCTATGAGGTTTATCGTGTTGTGCCATAATTCCATTTTCTCAACACCTTGG
196 TTTTGGAATTTATGCCTATGAGGTTTATCGTGTTGTGCCATAATTCCATTTTCTCAACACCTTGG
1196961 TATCGAGCTCTTTGTTTATTTATTTTTTTTTTTGAGTTCTTCCTCTGGCATTTGTGGCGCCTAGT
261 TATCGAGCTCTTTGTTTA-TTATTTTTTTTTTTGAGTTCTTCCTCTGGCATTTGTGGCGCCTAGT
1197026 CTTTGTTTTGAAGTTTTGCATTACTTTTTTTCATGACATTGCTACACCCATTCAGCGATGGTAGG
325 CTTTGTTTTGAAGTTTTGCATTACTTTTTTTCATGACATTGCTACACCCATTCAGCGATGGTAGG
1197091 GAAGGCCAATGTTCTATTTTTGAGTCCAAATTTTGCTTTCTTTCTTTGATTTAAACTCCTTCAAA
390 GAAGGCCAATGTTCTATTTTTGAGTCCAAATTTTGCTTTCTTTCTTTGATTTAAACTCCTTCAAA
1197156 TGAGCACCTACAAAAGCACAAAACCACATTACTATTTTCATTAAAACAGACCTAAATCAATCTAA
455 TGAGCACCTACAAAAGCACAAAACCACATTACTATTTTCATTAAAACAGACCTAAATCAATCTAA
1197221 AATCAACTCAAATAAAACTACCTAAGTAACTTAAAATGAAACTTAAAATAAACTCCTAAAATGAG
520 AATCAACTCAAATAAAACTACCTAAGTAACTTAAAATGAAACTTAAAATAAACTCCTAAAATGAG
1197286 ACTAATTCATGTCAAAACTTAAAGACTTAGTTGATTTTAATGCTCAAAAAGTGACAACAT
585 ACTAATTCATGTCAAAACTTAAAGACTTAGTTGATTTTAATGCTCAAAAAGTGACAACAT
1197346 AAGTATAAAAAGAACTAAAGAAGAAAAGAAAACTAAGATTTGTCAAGTCTTCGATTCTTAATCTT
1 AAGTATAAAAAGAACTAAAGAAGAAAAGAAAACTAAGATTTGTCAAGTCTTCGATTCTTAATCTT
1197411 CAAGAGTTTTTCCTTACTTTCTTGCTTGCTTGATGGCTCTTTTTCTTCAGAGAAAATCTATCTTA
66 CAAGAGTTTTTCCTTACTTTCTTGCTTGCTTGATGGCTCTTTTTCTTCAGAGAAAATCTATCTTA
1197476 ATTGTTACTTTCAAGTGCTCTAAAGGGGTCTTTAAACAAGGCTCAAAATCTTACTCAAAATCAAC
131 ATTGTTACTTTCAAGTGCTCTAAAGGGGTCTTTAAACAAGGCTCAAAATCTTACTCAAAATCAAC
1197541 TTTTGGAATTTATGCCTATGAGGTTTATCGTGTTGTGCCATAATTCCATTTTCTCAACACCTTGG
196 TTTTGGAATTTATGCCTATGAGGTTTATCGTGTTGTGCCATAATTCCATTTTCTCAACACCTTGG
1197606 TATCGAGCTCTTTGTTTA-T-TTTTTTTTTTTGAGTTCTTCCTCTGGCATTTGTGGCGCCTAGTC
261 TATCGAGCTCTTTGTTTATTATTTTTTTTTTTGAGTTCTTCCTCTGGCATTTGTGGCGCCTAGTC
1197669 TTTGTTTTGAAGTTTTGCATTAC-TTTTTTCATGACATTGCTACACCCATTCAGCGATGGTAGGG
326 TTTGTTTTGAAGTTTTGCATTACTTTTTTTCATGACATTGCTACACCCATTCAGCGATGGTAGGG
1197733 AAGGCCAATGTTCTATTTTTGAGTCCAAATTTTGCTTTCTTTCTTTGATTTAAACTCCTTCAAAT
391 AAGGCCAATGTTCTATTTTTGAGTCCAAATTTTGCTTTCTTTCTTTGATTTAAACTCCTTCAAAT
1197798 GAGCACCTACAAAAGCACAAAACCACATTACTATTTTCATTAAAACAGACCTAAATCAATCTAAA
456 GAGCACCTACAAAAGCACAAAACCACATTACTATTTTCATTAAAACAGACCTAAATCAATCTAAA
*
1197863 TTCAACTCAAATAAAACTACCTAAGTAACTTAAAATGAAACTTAAAATAAACTCCTAAAATGAGA
521 ATCAACTCAAATAAAACTACCTAAGTAACTTAAAATGAAACTTAAAATAAACTCCTAAAATGAGA
1197928 CTAATTCATGTCAAAACTTAAAGACTTAGTTGATTTTAATGCTCAAAAAGTGACAACAT
586 CTAATTCATGTCAAAACTTAAAGACTTAGTTGATTTTAATGCTCAAAAAGTGACAACAT
1197987 AA
1 AA
1197989 CTCTATATTA
Statistics
Matches: 642, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
641 296 0.46
642 67 0.10
643 1 0.00
645 278 0.43
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (644 bp):
AAGTATAAAAAGAACTAAAGAAGAAAAGAAAACTAAGATTTGTCAAGTCTTCGATTCTTAATCTT
CAAGAGTTTTTCCTTACTTTCTTGCTTGCTTGATGGCTCTTTTTCTTCAGAGAAAATCTATCTTA
ATTGTTACTTTCAAGTGCTCTAAAGGGGTCTTTAAACAAGGCTCAAAATCTTACTCAAAATCAAC
TTTTGGAATTTATGCCTATGAGGTTTATCGTGTTGTGCCATAATTCCATTTTCTCAACACCTTGG
TATCGAGCTCTTTGTTTATTATTTTTTTTTTTGAGTTCTTCCTCTGGCATTTGTGGCGCCTAGTC
TTTGTTTTGAAGTTTTGCATTACTTTTTTTCATGACATTGCTACACCCATTCAGCGATGGTAGGG
AAGGCCAATGTTCTATTTTTGAGTCCAAATTTTGCTTTCTTTCTTTGATTTAAACTCCTTCAAAT
GAGCACCTACAAAAGCACAAAACCACATTACTATTTTCATTAAAACAGACCTAAATCAATCTAAA
ATCAACTCAAATAAAACTACCTAAGTAACTTAAAATGAAACTTAAAATAAACTCCTAAAATGAGA
CTAATTCATGTCAAAACTTAAAGACTTAGTTGATTTTAATGCTCAAAAAGTGACAACAT
Found at i:1198106 original size:17 final size:17
Alignment explanation
Indices: 1198084--1198116 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1198074 GAAAGCAATT
1198084 GTAAATGACGAAAACAC
1 GTAAATGACGAAAACAC
*
1198101 GTAAATGATGAAAACA
1 GTAAATGACGAAAACA
1198117 AATAGCTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.12, G:0.18, T:0.15
Consensus pattern (17 bp):
GTAAATGACGAAAACAC
Found at i:1199304 original size:292 final size:293
Alignment explanation
Indices: 1198773--1199361 Score: 1090
Period size: 292 Copynumber: 2.0 Consensus size: 293
1198763 TAACATACTT
1198773 AAGAGTGAAGGATGAAAAATTGAAAACTTATTATAAGCTAAGCTATATAAACTAGGTGTTTGACA
1 AAGAGTGAAGGATGAAAAATTGAAAACTTATTATAAGCTAAGCTATATAAACTAGGTGTTTGACA
*
1198838 AAAAAGAAAGGCAATATTAGGCTCAAAGGGATATATTAAGGATAGAAATATATAAAGCTAAGCTC
66 AAAAAGAAAGGCAATATTAGGCTCAAAGGGATATACTAAGGATAGAAATATATAAAGCTAAGCTC
1198903 AAAAGGCTCAAACAATCCAAAGATGGTCTAATTCATTTCCTTAACTAAGTATTCTTAGTATTTGG
131 AAAAGGCTCAAACAATCCAAAGATGGTCTAATTCATTTCCTTAACTAAGTATTCTTAGTATTTGG
* *
1198968 TTTCGAGAGAGAATCAAACAAATTCTAAAATTCATGAGATAACCAAAATTCTACATCAACATAAA
196 TTTCGAGAGAGAATCAAACAAATTCTAAAAGTCATGACATAACCAAAATTCTACATCAACATAAA
1199033 CCATATTTAAATATGCACAATAATTCTAAGCAA
261 CCATATTTAAATATGCACAATAATTCTAAGCAA
* * *
1199066 AAGAGTGAGGGATGCAAAATTGAAAACTTATTATAAGCTAGGCTATATAAACTAGGTGTTTGACA
1 AAGAGTGAAGGATGAAAAATTGAAAACTTATTATAAGCTAAGCTATATAAACTAGGTGTTTGACA
1199131 AAAAA-AAAGGCAATATTAGGCTCAAAGGGATATACTAAGGATAGAAATATATAAAGCTAAGCTC
66 AAAAAGAAAGGCAATATTAGGCTCAAAGGGATATACTAAGGATAGAAATATATAAAGCTAAGCTC
1199195 AAAAGGCTCAAACAATCCAAAGATGGTCTAATTCATTTCCTTAACTAAGTATTCTTAGTATTTGG
131 AAAAGGCTCAAACAATCCAAAGATGGTCTAATTCATTTCCTTAACTAAGTATTCTTAGTATTTGG
*
1199260 TTTCGAGAGAGAATCAAACAAATTCTAAAAGTCATGACATAACCAAAATTCTACGTCAACATAAA
196 TTTCGAGAGAGAATCAAACAAATTCTAAAAGTCATGACATAACCAAAATTCTACATCAACATAAA
* *
1199325 CCGTATTTAAATATGTACAATAATTCTAAGCAA
261 CCATATTTAAATATGCACAATAATTCTAAGCAA
1199358 AAGA
1 AAGA
1199362 CAATGTGCTC
Statistics
Matches: 287, Mismatches: 9, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
292 220 0.77
293 67 0.23
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (293 bp):
AAGAGTGAAGGATGAAAAATTGAAAACTTATTATAAGCTAAGCTATATAAACTAGGTGTTTGACA
AAAAAGAAAGGCAATATTAGGCTCAAAGGGATATACTAAGGATAGAAATATATAAAGCTAAGCTC
AAAAGGCTCAAACAATCCAAAGATGGTCTAATTCATTTCCTTAACTAAGTATTCTTAGTATTTGG
TTTCGAGAGAGAATCAAACAAATTCTAAAAGTCATGACATAACCAAAATTCTACATCAACATAAA
CCATATTTAAATATGCACAATAATTCTAAGCAA
Found at i:1201985 original size:3 final size:3
Alignment explanation
Indices: 1201977--1202009 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1201967 TCTTATTTGC
*
1201977 CAT CAT CAT CAT CAT CAT CAT CAC CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1202010 ACATGCATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.30
Consensus pattern (3 bp):
CAT
Found at i:1204854 original size:17 final size:17
Alignment explanation
Indices: 1204832--1204871 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
1204822 TTAGTCTTGA
1204832 ACCTTTAATGTAAATTC
1 ACCTTTAATGTAAATTC
1204849 ACCTTTAATGTAAATTC
1 ACCTTTAATGTAAATTC
1204866 ACCTTT
1 ACCTTT
1204872 TTTAACATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.42
Consensus pattern (17 bp):
ACCTTTAATGTAAATTC
Found at i:1223141 original size:70 final size:70
Alignment explanation
Indices: 1223063--1223195 Score: 169
Period size: 70 Copynumber: 1.9 Consensus size: 70
1223053 CATCTCATGG
* *
1223063 CATACATCTTATATCATAACTAATGAATCATTATCATGCA-TAGCCCATAGTGTACAAGAATATA
1 CATACATCTCATATCATAACTAATGAATCATTATAATG-ATTAGCCCATAGTGTACAAGAATATA
1223127 CCAAAA
65 CCAAAA
* ** * * * *
1223133 CATACATCTCATATCTTAACTCCTGAATCATTCTAATGATTAGCCCTTATTGTACATGAATAT
1 CATACATCTCATATCATAACTAATGAATCATTATAATGATTAGCCCATAGTGTACAAGAATAT
1223196 CTCGTGGCAT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
69 1 0.02
70 52 0.98
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (70 bp):
CATACATCTCATATCATAACTAATGAATCATTATAATGATTAGCCCATAGTGTACAAGAATATAC
CAAAA
Found at i:1223207 original size:70 final size:70
Alignment explanation
Indices: 1223054--1223218 Score: 163
Period size: 70 Copynumber: 2.4 Consensus size: 70
1223044 CAACACATAC
* * *
1223054 ATCTCATGGCATACATCTTATATCATAACTAATGAATCATTATCATGCATAGCCCATAGTGTACA
1 ATCTCATGGCATACATCTCATATCTTAACTAATGAATCATTATAATGCATAGCCCATAGTGTACA
1223119 AGAAT
66 AGAAT
*** ** * * *
1223124 ATAC-CAAAACATACATCTCATATCTTAACTCCTGAATCATTCTAATG-ATTAGCCCTTATTGTA
1 AT-CTCATGGCATACATCTCATATCTTAACTAATGAATCATTATAATGCA-TAGCCCATAGTGTA
*
1223187 CATGAAT
64 CAAGAAT
* * *
1223194 ATCTCGTGGCATACGTTTCATATCT
1 ATCTCATGGCATACATCTCATATCT
1223219 CATAATCATT
Statistics
Matches: 74, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
69 2 0.03
70 71 0.96
71 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (70 bp):
ATCTCATGGCATACATCTCATATCTTAACTAATGAATCATTATAATGCATAGCCCATAGTGTACA
AGAAT
Found at i:1226818 original size:40 final size:40
Alignment explanation
Indices: 1226763--1226840 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
1226753 TTGACTATTT
*
1226763 TTCACCTTAGTGGGGTTTTCAACCTTGCCAAGATTGGTGA
1 TTCACCTTAGTGGGGTTTTCAACCTCGCCAAGATTGGTGA
*
1226803 TTCACCTTAGTGGGGTTTTCAACCTCGCCACGATTGGT
1 TTCACCTTAGTGGGGTTTTCAACCTCGCCAAGATTGGT
1226841 ATCTTTTACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.35
Consensus pattern (40 bp):
TTCACCTTAGTGGGGTTTTCAACCTCGCCAAGATTGGTGA
Found at i:1232603 original size:20 final size:21
Alignment explanation
Indices: 1232580--1232631 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1232570 GGCAAGCGAA
* *
1232580 AGTCAACTTTAAGA-AGCCAT
1 AGTCAACTATAACAGAGCCAT
* *
1232600 AGTCGACTATAACAGAGGCAT
1 AGTCAACTATAACAGAGCCAT
1232621 AGTCAACTATA
1 AGTCAACTATA
1232632 GAAGGCCAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.23
Consensus pattern (21 bp):
AGTCAACTATAACAGAGCCAT
Found at i:1238542 original size:12 final size:12
Alignment explanation
Indices: 1238525--1238549 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1238515 AGGCTTAATA
1238525 TTAATATTATAT
1 TTAATATTATAT
1238537 TTAATATTATAT
1 TTAATATTATAT
1238549 T
1 T
1238550 ACTTGTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTAATATTATAT
Found at i:1239448 original size:21 final size:19
Alignment explanation
Indices: 1239420--1239464 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
1239410 GTTATTATGC
1239420 GTTA-AGCTCAAAAAAATATT
1 GTTACAGCT-AAAAAAA-ATT
*
1239440 GTTACAGCTGAAAAAAATT
1 GTTACAGCTAAAAAAAATT
1239459 GTTACA
1 GTTACA
1239465 TGCTTTAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 9 0.39
20 10 0.43
21 4 0.17
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.29
Consensus pattern (19 bp):
GTTACAGCTAAAAAAAATT
Found at i:1239631 original size:34 final size:34
Alignment explanation
Indices: 1239568--1239742 Score: 165
Period size: 34 Copynumber: 5.0 Consensus size: 34
1239558 AACCAACACC
* * *
1239568 AACTTCAACA-TCAGATATTACACGTCAAGGCCAA
1 AACTTCAACACT-AGATATTACATGCCAAGGTCAA
*
1239602 AACTTCAACACTAGATATTACATACCAAGGTCAA
1 AACTTCAACACTAGATATTACATGCCAAGGTCAA
* *
1239636 AGCTT-AACCACTAGATATTACATGCTAAGGTCAA
1 AACTTCAA-CACTAGATATTACATGCCAAGGTCAA
** * *
1239670 AGTTTCACCACTAGATGTTACATGCCAAGGTCAA
1 AACTTCAACACTAGATATTACATGCCAAGGTCAA
**
1239704 AGCTTAGCTTCAGTACTAGATATTACATGCCAAGGTCAA
1 A----A-CTTCAACACTAGATATTACATGCCAAGGTCAA
1239743 CACCAGATGT
Statistics
Matches: 117, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
33 2 0.02
34 85 0.73
35 2 0.02
39 28 0.24
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (34 bp):
AACTTCAACACTAGATATTACATGCCAAGGTCAA
Found at i:1239691 original size:68 final size:70
Alignment explanation
Indices: 1239580--1239742 Score: 195
Period size: 68 Copynumber: 2.3 Consensus size: 70
1239570 CTTCAACATC
* * * **
1239580 AGATATTACACGTCAAGGCCAAAACTTCAACACTAGATATTACATACCAAGGTCAAAGCTTAAC-
1 AGATATTACATGCCAAGGTCAAAGTTTCAACACTAGATATTACATACCAAGGTCAAAGCTTAACT
1239644 C-ACT
66 CAACT
* * * * *
1239648 AGATATTACATGCTAAGGTCAAAGTTTCACCACTAGATGTTACATGCCAAGGTCAAAGCTTAGCT
1 AGATATTACATGCCAAGGTCAAAGTTTCAACACTAGATATTACATACCAAGGTCAAAGCTTAAC-
1239713 TCAGTACT
65 TCA--ACT
1239721 AGATATTACATGCCAAGGTCAA
1 AGATATTACATGCCAAGGTCAA
1239743 CACCAGATGT
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
68 54 0.68
70 1 0.01
73 24 0.30
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.25
Consensus pattern (70 bp):
AGATATTACATGCCAAGGTCAAAGTTTCAACACTAGATATTACATACCAAGGTCAAAGCTTAACT
CAACT
Found at i:1239747 original size:68 final size:64
Alignment explanation
Indices: 1239609--1239762 Score: 163
Period size: 68 Copynumber: 2.3 Consensus size: 64
1239599 CAAAACTTCA
* * *
1239609 ACACTAGATATTACATACCAAGGTCAAAGCTTAACCACTAGATATTACATGCTAAGGTCAAAGTT
1 ACACTAGATGTTACATGCCAAGGTCAAAGCTTAACCACTAGATATTACATGCCAAGGTCAAA---
1239674 TC
63 TC
*
1239676 ACCACTAGATGTTACATGCCAAGGTCAAAGCTTAGCTTCAGTACTAGATATTACATGCCAAGGTC
1 A-CACTAGATGTTACATGCCAAGGTCAAAGCTTAAC--C---ACTAGATATTACATGCCAAGGTC
1239741 -AA-C
60 AAATC
1239744 AC-C-AGATGTTACATGCCAA
1 ACACTAGATGTTACATGCCAA
1239763 AGTAAAATAA
Statistics
Matches: 77, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
65 16 0.21
66 1 0.01
67 2 0.03
68 33 0.43
70 1 0.01
72 2 0.03
73 22 0.29
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (64 bp):
ACACTAGATGTTACATGCCAAGGTCAAAGCTTAACCACTAGATATTACATGCCAAGGTCAAATC
Found at i:1239789 original size:12 final size:13
Alignment explanation
Indices: 1239761--1239788 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1239751 GTTACATGCC
1239761 AAAGTAAAATAAA
1 AAAGTAAAATAAA
1239774 AAAGTAAAATAAA
1 AAAGTAAAATAAA
1239787 AA
1 AA
1239789 GCGTGAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (13 bp):
AAAGTAAAATAAA
Found at i:1243835 original size:3 final size:3
Alignment explanation
Indices: 1243827--1243894 Score: 93
Period size: 3 Copynumber: 22.3 Consensus size: 3
1243817 ATACTAACTC
**
1243827 AAT AAT AAT AAT AAT CTT CCAA- AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT --AAT AAT AAT AAT AAT AAT AAT AAT AAT
1243873 AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
1243895 TCATTCAATG
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
2 2 0.03
3 56 0.97
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1246827 original size:24 final size:25
Alignment explanation
Indices: 1246780--1246828 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
1246770 GGTCCCTTCA
* *
1246780 AAATTTTTAAATTTTTTTACATATT
1 AAATGTTTAAATTTTGTTACATATT
*
1246805 AAATGTTT-AATTTTGTTATATATT
1 AAATGTTTAAATTTTGTTACATATT
1246829 CTTTTAATGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (25 bp):
AAATGTTTAAATTTTGTTACATATT
Found at i:1254985 original size:31 final size:32
Alignment explanation
Indices: 1254911--1254982 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 32
1254901 ATTCAAATTC
* * *
1254911 AAATTATTTTGAATTTTAATTGTCTTGGTTCT
1 AAATTATTTTAAATTTGAATCGTCTTGGTTCT
* *
1254943 -AATTATTTTAAATTTGAATCGTTTTGGTTTT
1 AAATTATTTTAAATTTGAATCGTCTTGGTTCT
1254974 AAATTATTT
1 AAATTATTT
1254983 AAAGTTCATA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 26 0.76
32 8 0.24
ACGTcount: A:0.28, C:0.04, G:0.11, T:0.57
Consensus pattern (32 bp):
AAATTATTTTAAATTTGAATCGTCTTGGTTCT
Found at i:1257307 original size:6 final size:6
Alignment explanation
Indices: 1257296--1257324 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1257286 AACACTTCGT
1257296 CCACGG CCACGG CCACGG CCACGG CCACG
1 CCACGG CCACGG CCACGG CCACGG CCACG
1257325 CCCAGTGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.52, G:0.31, T:0.00
Consensus pattern (6 bp):
CCACGG
Found at i:1260093 original size:61 final size:60
Alignment explanation
Indices: 1259982--1260100 Score: 150
Period size: 61 Copynumber: 2.0 Consensus size: 60
1259972 TATTTTGTAA
** *
1259982 AATTTCTATTGATACATTCAACAATGTATCAATAGACTTGAGTCAAGAGACATCTTGTTG
1 AATTTCTACCGATACATTCAACAATGTATCAATAGACTTGAGTAAAGAGACATCTTGTTG
* * * *
1260042 AATTTCTACCGATACATTCACCAAATGTATCAATAGATTTGTG-AAAGGAGACATTTTGT
1 AATTTCTACCGATACATTCAAC-AATGTATCAATAGACTTGAGTAAA-GAGACATCTTGT
1260101 AAAAAATGTA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
60 21 0.42
61 29 0.58
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (60 bp):
AATTTCTACCGATACATTCAACAATGTATCAATAGACTTGAGTAAAGAGACATCTTGTTG
Found at i:1264626 original size:12 final size:13
Alignment explanation
Indices: 1264607--1264642 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
1264597 CAGAATAGTT
1264607 TCTTGCTGCCTCC
1 TCTTGCTGCCTCC
1264620 T-TTGCTGCCT-C
1 TCTTGCTGCCTCC
1264631 TCTTGCTGCCTC
1 TCTTGCTGCCTC
1264643 AAAAATCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.10
12 18 0.86
13 1 0.05
ACGTcount: A:0.00, C:0.42, G:0.17, T:0.42
Consensus pattern (13 bp):
TCTTGCTGCCTCC
Found at i:1271555 original size:53 final size:53
Alignment explanation
Indices: 1271466--1271567 Score: 127
Period size: 53 Copynumber: 1.9 Consensus size: 53
1271456 TTTCACATTT
* * *
1271466 AAAAAGCAAGAATCTGATTGTGGATTGTGTATGGGTTATCGCTTGATCTCATC
1 AAAAAGCAAGAATCTGATTGTGGATTCTGTAAGGGTTATCACTTGATCTCATC
* *
1271519 AAAAAGCAAGAATCT-CTTCGTGGATTACT-TAAGGGTTATCATTTGATCT
1 AAAAAGCAAGAATCTGATT-GTGGATT-CTGTAAGGGTTATCACTTGATCT
1271568 TGCGAAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
52 2 0.05
53 39 0.93
54 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (53 bp):
AAAAAGCAAGAATCTGATTGTGGATTCTGTAAGGGTTATCACTTGATCTCATC
Found at i:1271662 original size:50 final size:49
Alignment explanation
Indices: 1271582--1271725 Score: 148
Period size: 50 Copynumber: 2.9 Consensus size: 49
1271572 AAAAAATTAT
* *
1271582 TGTAAGGGTTATCACTTGATCTAGCTAAAAAGCAAGAATCCCTTGTGGATTG
1 TGTAAGGGTTACCACTT-ATC-A-TTAAAAAGCAAGAATCCCTTGTGGATTG
* * **
1271634 TGTAAGGGTTACCATTTATTATTTAAAAA-CAAGAATTCTTTTGTGGATTG
1 TGTAAGGGTTACCACTTATCA-TTAAAAAGCAAGAA-TCCCTTGTGGATTG
* * *
1271684 TGTAAGGGTTATCACTTCTCATTAAAAAGTAAGAAT-CCTTGT
1 TGTAAGGGTTACCACTTATCATTAAAAAGCAAGAATCCCTTGT
1271726 CAGTAGATTG
Statistics
Matches: 76, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
48 4 0.05
49 14 0.18
50 41 0.54
51 2 0.03
52 15 0.20
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.36
Consensus pattern (49 bp):
TGTAAGGGTTACCACTTATCATTAAAAAGCAAGAATCCCTTGTGGATTG
Found at i:1289804 original size:49 final size:50
Alignment explanation
Indices: 1289727--1289841 Score: 137
Period size: 49 Copynumber: 2.3 Consensus size: 50
1289717 NNNNNNNNNN
* *
1289727 ACCTGACATCATATCA-TCATCTGGAATCATCTACGGATGA-AACATTCAT
1 ACCTCACATCATATCATTCATCTGGAATCATCTACGGAT-ATAACATACAT
* ** * *
1289776 ATCTCACATCATATCATTGTTC-GGAATCATTTATGGATATAACATACAT
1 ACCTCACATCATATCATTCATCTGGAATCATCTACGGATATAACATACAT
1289825 ACCTCACATCATATCAT
1 ACCTCACATCATATCAT
1289842 AATTCATCAC
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
48 1 0.02
49 52 0.93
50 3 0.05
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.32
Consensus pattern (50 bp):
ACCTCACATCATATCATTCATCTGGAATCATCTACGGATATAACATACAT
Found at i:1318617 original size:75 final size:73
Alignment explanation
Indices: 1318538--1318700 Score: 175
Period size: 73 Copynumber: 2.2 Consensus size: 73
1318528 TATTGGAGAG
* * * * *** * *
1318538 GCAAAGGTTGATTCTCAAAAAATCAAAAAGCTGTCGACATTAGGGTGTGACGAAAAGAATCAATA
1 GCAAAGATTGATTCTCAAAAAA-CAAAAAGCTCTAGAC-CTAAAATGAGACAAAAAGAATCAATA
1318603 TCTCAAGCAT
64 TCTCAAGCAT
** *
1318613 GCAAAGATT-AGTTCTTGAAAAACAAAAAGCTCTAGACCTAAAATGAGACAAAAAGAATCTATAT
1 GCAAAGATTGA-TTCTCAAAAAACAAAAAGCTCTAGACCTAAAATGAGACAAAAAGAATCAATAT
1318677 CTCAAGCAT
65 CTCAAGCAT
*
1318686 GGAAAGATTGATTCT
1 GCAAAGATTGATTCT
1318701 TAGAAAATAG
Statistics
Matches: 73, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
73 41 0.56
74 15 0.21
75 17 0.23
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.23
Consensus pattern (73 bp):
GCAAAGATTGATTCTCAAAAAACAAAAAGCTCTAGACCTAAAATGAGACAAAAAGAATCAATATC
TCAAGCAT
Found at i:1319112 original size:20 final size:21
Alignment explanation
Indices: 1319087--1319134 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
1319077 AAGGTAGTGC
*
1319087 AAAGTTATATC-TCTATTGC-A
1 AAAGTTATACCGT-TATTGCAA
1319107 AAAGTTATACCGTTATTGCAA
1 AAAGTTATACCGTTATTGCAA
1319128 AAAGTTA
1 AAAGTTA
1319135 ATGAAAGGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (21 bp):
AAAGTTATACCGTTATTGCAA
Found at i:1319161 original size:52 final size:50
Alignment explanation
Indices: 1319070--1319205 Score: 148
Period size: 52 Copynumber: 2.7 Consensus size: 50
1319060 TTATACCTCC
* * * * *
1319070 ATTGCAAAAGGTAGTGCAAA-GTTATATCTCTATTGCAAAAGTTATACCGTT
1 ATTGC-AAAGGTAATG-AAAGGTTATACCTCCATTACAAAAGTTATACCCTT
*
1319121 ATTGCAAAAAGTTAATGAAAGGTTATACCTCCATTACAAAAGTTATACCCTT
1 ATTGC--AAAGGTAATGAAAGGTTATACCTCCATTACAAAAGTTATACCCTT
* * *
1319173 ATTGCAAAGGTAGTGTAAGGTTATGCCTCCATT
1 ATTGCAAAGGTAATGAAAGGTTATACCTCCATT
1319206 GTAAAAGAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
50 24 0.33
51 8 0.11
52 41 0.56
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Consensus pattern (50 bp):
ATTGCAAAGGTAATGAAAGGTTATACCTCCATTACAAAAGTTATACCCTT
Found at i:1322099 original size:37 final size:38
Alignment explanation
Indices: 1322028--1322100 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 38
1322018 CTATAGTGTA
*
1322028 TGATGCCATCTGTTGGGAGATTACTCCTGATGATGATTG
1 TGATGCCATCTGTT-GGAGATTACTCCAGATGATGATTG
*
1322067 TGATGGCATCTGTT-GAGATTACTCCA-AGTGATGA
1 TGATGCCATCTGTTGGAGATTACTCCAGA-TGATGA
1322101 CAACATCAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 1 0.03
37 17 0.55
39 13 0.42
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.34
Consensus pattern (38 bp):
TGATGCCATCTGTTGGAGATTACTCCAGATGATGATTG
Found at i:1326385 original size:23 final size:21
Alignment explanation
Indices: 1326335--1326386 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 21
1326325 AATATTTATT
1326335 ATTTTAAT-AATTTATTTAAA
1 ATTTTAATAAATTTATTTAAA
**
1326355 ATAGTAATAAATTGTTATTTAAA
1 ATTTTAATAAA-T-TTATTTAAA
1326378 ATTTTAATA
1 ATTTTAATA
1326387 TGATTATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 6 0.24
21 2 0.08
22 1 0.04
23 16 0.64
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (21 bp):
ATTTTAATAAATTTATTTAAA
Found at i:1326458 original size:21 final size:21
Alignment explanation
Indices: 1326432--1326486 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
1326422 TATATTTTAT
1326432 TTAAATATTAATAATTTATAA
1 TTAAATATTAATAATTTATAA
1326453 TTAAATATTAATAATTTATAA
1 TTAAATATTAATAATTTATAA
1326474 TTAAATATTAATA
1 TTAAATATTAATA
1326487 TCATTATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTAAATATTAATAATTTATAA
Found at i:1335893 original size:2 final size:2
Alignment explanation
Indices: 1335888--1335915 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1335878 TGTGTGTGCC
1335888 TA TA TA TA 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
1335916 CTTTAATTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1345317 original size:44 final size:44
Alignment explanation
Indices: 1345269--1345354 Score: 172
Period size: 44 Copynumber: 2.0 Consensus size: 44
1345259 CCTCAAAATG
1345269 TGTCAAAATAACTCTATATAATAAAGTTATCAATAAGTCATGAA
1 TGTCAAAATAACTCTATATAATAAAGTTATCAATAAGTCATGAA
1345313 TGTCAAAATAACTCTATATAATAAAGTTATCAATAAGTCATG
1 TGTCAAAATAACTCTATATAATAAAGTTATCAATAAGTCATG
1345355 GATGAAATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.33
Consensus pattern (44 bp):
TGTCAAAATAACTCTATATAATAAAGTTATCAATAAGTCATGAA
Found at i:1354008 original size:30 final size:29
Alignment explanation
Indices: 1353948--1354019 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 29
1353938 CATTTTTTTT
*
1353948 ATTTTCT-TCTTTATCTTTCATTGAACCA
1 ATTTTCTCCCTTTATCTTTCATTGAACCA
*
1353976 ATTTGTCTCCCTTTCATCTTTCA-TGCACCA
1 ATTT-TCTCCCTTT-ATCTTTCATTGAACCA
1354006 ATTTTCT-CCTTTAT
1 ATTTTCTCCCTTTAT
1354020 TCATTAGTCC
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
27 2 0.05
28 9 0.23
29 6 0.15
30 14 0.36
31 8 0.21
ACGTcount: A:0.18, C:0.26, G:0.04, T:0.51
Consensus pattern (29 bp):
ATTTTCTCCCTTTATCTTTCATTGAACCA
Found at i:1354023 original size:31 final size:31
Alignment explanation
Indices: 1353956--1354014 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
1353946 TTATTTTCTT
1353956 CTTT-ATCTTTCATTGAACCAATTTGTCTCC
1 CTTTCATCTTTCATTGAACCAATTTGTCTCC
*
1353986 CTTTCATCTTTCA-TGCACCAATTT-TCTCC
1 CTTTCATCTTTCATTGAACCAATTTGTCTCC
1354015 TTTATTCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 5 0.19
30 14 0.52
31 8 0.30
ACGTcount: A:0.19, C:0.31, G:0.05, T:0.46
Consensus pattern (31 bp):
CTTTCATCTTTCATTGAACCAATTTGTCTCC
Found at i:1354618 original size:14 final size:15
Alignment explanation
Indices: 1354597--1354638 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
1354587 TAGAAATATT
1354597 TAAATATTATTTTAA
1 TAAATATTATTTTAA
1354612 T-AATATT-TTATTAA
1 TAAATATTATT-TTAA
1354626 TAAAATATTATTT
1 T-AAATATTATTT
1354639 ATTTTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 2 0.09
14 11 0.48
15 1 0.04
16 7 0.30
17 2 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAAATATTATTTTAA
Found at i:1360428 original size:17 final size:16
Alignment explanation
Indices: 1360399--1360437 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
1360389 ATACAAAAAC
*
1360399 ATAAAACTTAACTTAA
1 ATAAAACTAAACTTAA
1360415 ATAATAACTAAACTTAAA
1 ATAA-AACTAAACTT-AA
1360433 ATAAA
1 ATAAA
1360438 GCATCATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 4 0.20
17 10 0.50
18 6 0.30
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (16 bp):
ATAAAACTAAACTTAA
Found at i:1368251 original size:68 final size:68
Alignment explanation
Indices: 1368093--1368263 Score: 216
Period size: 68 Copynumber: 2.5 Consensus size: 68
1368083 GATGTGTACT
* * * * * * * *
1368093 ATGAGATTGTGTATATGATGTAAACTCCATATACCATATGAGATGATTCAGTATGTATGATAAAT
1 ATGAGATTATGTATATGATATATATTCCATATACCACATGAGATGATTCAGAAAGCATGATAAAT
1368158 GCC
66 GCC
* * * *
1368161 ATGAGATTATGTATATGATATATATTCCATATACTACATGAGATGATTGAGAAAGCATGTTGAAT
1 ATGAGATTATGTATATGATATATATTCCATATACCACATGAGATGATTCAGAAAGCATGATAAAT
1368226 GCC
66 GCC
* *
1368229 ATGAGATTATGTATATGATATATTTTCCATGTACC
1 ATGAGATTATGTATATGATATATATTCCATATACC
1368264 TTGTGAGATG
Statistics
Matches: 88, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
68 88 1.00
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (68 bp):
ATGAGATTATGTATATGATATATATTCCATATACCACATGAGATGATTCAGAAAGCATGATAAAT
GCC
Found at i:1377055 original size:26 final size:26
Alignment explanation
Indices: 1377024--1377074 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1377014 TTTGTTGCTC
**
1377024 GATATTTATTAACTGTTATTTGACTT
1 GATATTTATTAAAGGTTATTTGACTT
*
1377050 GATATTTGTTAAAGGTTATTTGACT
1 GATATTTATTAAAGGTTATTTGACT
1377075 CAGTCTCTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.27, C:0.06, G:0.16, T:0.51
Consensus pattern (26 bp):
GATATTTATTAAAGGTTATTTGACTT
Found at i:1377407 original size:212 final size:213
Alignment explanation
Indices: 1376986--1377428 Score: 595
Period size: 212 Copynumber: 2.1 Consensus size: 213
1376976 ATATTACCTG
** *
1376986 CTCATCTCCTCTAAAGCTTCTCTGTTAATTTGTTGCTCGATATTTATTAACTGTTATTTGACTTG
1 CTCATCTCCTCTAAAGCTTCTCTGTTAAGATGTTGCTCGATATTTATTAACTGTTATTTGACTTA
* * * * * *
1377051 ATATTTGTTAAAGGTTATTTGACTCAGTCTCTTGATTTTCGCTGATTTTATGTTGATTTTTGTCG
66 ATATTTGTTAAAGGTTATTTAACTCAGTATCTTGATTTCCGCTAATTTTATATTGATTTTTAT--
* ** * *
1377116 CTGATTTTATGCTGATATTCTATAATGTTAACTTTCTGCTCCAGCCAATAAATACAACCTATCTA
129 CTGATTTTATGCTGATATTCTACAACATTAACTCTCTACTCCAGCCAATAAATACAACCTATCTA
* *
1377181 CCTCAATTACAAGACATCCA
194 CCTCAATCACAAGACACCCA
* * * *
1377201 CTCATCTCCTCTAAAGCTTCTCTGTTAGGATGTTGCT-GATATTTCTTAATTGTTATTTGATTTA
1 CTCATCTCCTCTAAAGCTTCTCTGTTAAGATGTTGCTCGATATTTATTAACTGTTATTTGACTTA
** *
1377265 ATATTTGTTAAAGGTTATTTAACTTTGTATCTTGATTTCCTCTAATTTT-TCATTGATTTTATAT
66 ATATTTGTTAAAGGTTATTTAACTCAGTATCTTGATTTCCGCTAATTTTAT-ATTGATTTT-TAT
* **
1377329 -TGATTTTATGTTGATATTCTACAACATTAACTCTCTACTCCAGCTTATAAATACAACCTATCTA
129 CTGATTTTATGCTGATATTCTACAACATTAACTCTCTACTCCAGCCAATAAATACAACCTATCTA
1377393 CCTCAATCACAAGACACCCA
194 CCTCAATCACAAGACACCCA
1377413 CTCATCTCCTCTAAAG
1 CTCATCTCCTCTAAAG
1377429 ATAACCACTA
Statistics
Matches: 200, Mismatches: 26, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
212 90 0.45
213 1 0.00
214 73 0.37
215 36 0.18
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.44
Consensus pattern (213 bp):
CTCATCTCCTCTAAAGCTTCTCTGTTAAGATGTTGCTCGATATTTATTAACTGTTATTTGACTTA
ATATTTGTTAAAGGTTATTTAACTCAGTATCTTGATTTCCGCTAATTTTATATTGATTTTTATCT
GATTTTATGCTGATATTCTACAACATTAACTCTCTACTCCAGCCAATAAATACAACCTATCTACC
TCAATCACAAGACACCCA
Found at i:1381574 original size:27 final size:26
Alignment explanation
Indices: 1381539--1381601 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 26
1381529 GGGTTATATT
1381539 TTTAAATATTAATAATTGATAATTTA
1 TTTAAATATTAATAATTGATAATTTA
*
1381565 TTTATAATATTAATAATT--T-A-TCA
1 TTTA-AATATTAATAATTGATAATTTA
1381588 TTTAAATATTAATA
1 TTTAAATATTAATA
1381602 TTTTATTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
22 10 0.29
23 6 0.17
24 1 0.03
25 1 0.03
26 4 0.11
27 13 0.37
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (26 bp):
TTTAAATATTAATAATTGATAATTTA
Found at i:1381651 original size:34 final size:34
Alignment explanation
Indices: 1381590--1381655 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 34
1381580 ATTTATCATT
1381590 TAAATATTAATATTTTATTTATAATTTAAATGTA
1 TAAATATTAATATTTTATTTATAATTTAAATGTA
*
1381624 TAAAGTATTCATATTTTA-TTATAATTTAAATG
1 TAAA-TATTAATATTTTATTTATAATTTAAATG
1381656 ATATTATGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 18 0.60
35 12 0.40
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (34 bp):
TAAATATTAATATTTTATTTATAATTTAAATGTA
Found at i:1381930 original size:108 final size:107
Alignment explanation
Indices: 1381725--1381937 Score: 347
Period size: 108 Copynumber: 2.0 Consensus size: 107
1381715 TTTAAGATTT
1381725 AAAAGATTTTAATTTATTTAAAATATTAATAATTGATTACTTAAATATTAATATTTTATTTATAA
1 AAAAGATTTTAATTTATTTAAAATATTAATAATTGATTACTTAAATATTAATATTTTATTTATAA
* * **
1381790 TTTAATTATTATTACCATTATTTATTTTTATTTTATTTTTTC
66 TTTAATTATTAATACCATTATATATTAATATTTTATTTTTTC
1381832 AAAAGATTTTTAATTTATTTAAAATATTAATAATTGATTACTTAAATATTAATATTTTATTTATA
1 AAAAGA-TTTTAATTTATTTAAAATATTAATAATTGATTACTTAAATATTAATATTTTATTTATA
**
1381897 ATTTAATTATTAATA-TTTTCATATATTAATATTTTATTTTT
65 ATTTAATTATTAATACCATT-ATATATTAATATTTTATTTTT
1381938 AAATATTAAT
Statistics
Matches: 98, Mismatches: 6, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
107 8 0.08
108 90 0.92
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (107 bp):
AAAAGATTTTAATTTATTTAAAATATTAATAATTGATTACTTAAATATTAATATTTTATTTATAA
TTTAATTATTAATACCATTATATATTAATATTTTATTTTTTC
Found at i:1389501 original size:28 final size:28
Alignment explanation
Indices: 1389449--1389518 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
1389439 AAATAATAAA
*
1389449 AAACATATAACAAACAAATAAATTACACC
1 AAACATA-AATAAACAAATAAATTACACC
* * *
1389478 AAACATAAATAAGCAAATACATTACATC
1 AAACATAAATAAACAAATAAATTACACC
1389506 AAACATAAATAAA
1 AAACATAAATAAA
1389519 ATTTCAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 29 0.81
29 7 0.19
ACGTcount: A:0.63, C:0.17, G:0.01, T:0.19
Consensus pattern (28 bp):
AAACATAAATAAACAAATAAATTACACC
Found at i:1391962 original size:14 final size:14
Alignment explanation
Indices: 1391943--1391974 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1391933 ATTTAGACCA
1391943 ACAAACAACAATTC
1 ACAAACAACAATTC
1391957 ACAAACAACAATTC
1 ACAAACAACAATTC
1391971 ACAA
1 ACAA
1391975 CTGATTGATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.59, C:0.28, G:0.00, T:0.12
Consensus pattern (14 bp):
ACAAACAACAATTC
Found at i:1391998 original size:37 final size:37
Alignment explanation
Indices: 1391948--1392037 Score: 144
Period size: 37 Copynumber: 2.4 Consensus size: 37
1391938 GACCAACAAA
*
1391948 CAACAATTCACAAACAACAATTCACAACTGATTGATC
1 CAACAATTCACAAACAACAATTCACAACTAATTGATC
* *
1391985 CAACAATTCACAAATAATAATTCACAACTAATTGATC
1 CAACAATTCACAAACAACAATTCACAACTAATTGATC
*
1392022 CAAGAATTCACAAACA
1 CAACAATTCACAAACA
1392038 CATTTACACA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.49, C:0.24, G:0.04, T:0.22
Consensus pattern (37 bp):
CAACAATTCACAAACAACAATTCACAACTAATTGATC
Found at i:1401395 original size:1 final size:1
Alignment explanation
Indices: 1401389--1401431 Score: 77
Period size: 1 Copynumber: 43.0 Consensus size: 1
1401379 TCCAGCTTAT
*
1401389 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1401432 GTTATCATTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.98, C:0.02, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1402022 original size:11 final size:11
Alignment explanation
Indices: 1402006--1402036 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1401996 GTTAAGGGTT
1402006 TTTCTTTTTTC
1 TTTCTTTTTTC
*
1402017 TTTCTTTTTTT
1 TTTCTTTTTTC
1402028 TTTCTTTTT
1 TTTCTTTTT
1402037 GGGTAATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:1402030 original size:15 final size:16
Alignment explanation
Indices: 1402005--1402034 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1401995 AGTTAAGGGT
1402005 TTTTCTTTTTTCTTTC
1 TTTTCTTTTTTCTTTC
1402021 TTTT-TTTTTTCTTT
1 TTTTCTTTTTTCTTT
1402035 TTGGGTAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTCTTTTTTCTTTC
Found at i:1406972 original size:4 final size:4
Alignment explanation
Indices: 1406956--1407000 Score: 81
Period size: 4 Copynumber: 11.2 Consensus size: 4
1406946 TTGGAGTAGC
*
1406956 ACAT ACAT GCAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1407001 TATATATGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.49, C:0.24, G:0.02, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:1412062 original size:184 final size:184
Alignment explanation
Indices: 1411753--1412123 Score: 697
Period size: 184 Copynumber: 2.0 Consensus size: 184
1411743 CACCTAGTTT
1411753 TTATAAAGTGAGCTATCCCAAGCTGAATACCCTTACTTACAAATCCAACAAGTGTTACCTTTACA
1 TTATAAAGTGAGCTATCCCAAGCTGAATACCCTTACTTACAAATCCAACAAGTGTTACCTTTACA
*
1411818 CTTCTTTTCTCAAGGACAAGAGTGAAACTTACACTCTTACAAGATAAACTTATAGCTTTTACACT
66 CTTATTTTCTCAAGGACAAGAGTGAAACTTACACTCTTACAAGATAAACTTATAGCTTTTACACT
*
1411883 TCTTTGTAGCACTTTTCTAACTTCTTTTTCTTCTTCTCTTTTTATAGATAGGAA
131 TCTTTGTAGCACTTTTCTAACTTCTTTTTCCTCTTCTCTTTTTATAGATAGGAA
1411937 TTATAAAGTGAGCTATCCCAAGCTGAATACCCTTACTTACAAATCCAACAAGTGTTACCTTTACA
1 TTATAAAGTGAGCTATCCCAAGCTGAATACCCTTACTTACAAATCCAACAAGTGTTACCTTTACA
* *
1412002 CTTATTTTCTCAAGGACAAGATTGAAACTTACACTCTTACAAGATAAGCTTATAGCTTTTACACT
66 CTTATTTTCTCAAGGACAAGAGTGAAACTTACACTCTTACAAGATAAACTTATAGCTTTTACACT
*
1412067 TCTTTGTAGCACTTTTCTAACTTCTTTTTCCTCTTCTTTTTTTATAGATAGGAA
131 TCTTTGTAGCACTTTTCTAACTTCTTTTTCCTCTTCTCTTTTTATAGATAGGAA
1412121 TTA
1 TTA
1412124 AGCCTAAAGA
Statistics
Matches: 182, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
184 182 1.00
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (184 bp):
TTATAAAGTGAGCTATCCCAAGCTGAATACCCTTACTTACAAATCCAACAAGTGTTACCTTTACA
CTTATTTTCTCAAGGACAAGAGTGAAACTTACACTCTTACAAGATAAACTTATAGCTTTTACACT
TCTTTGTAGCACTTTTCTAACTTCTTTTTCCTCTTCTCTTTTTATAGATAGGAA
Found at i:1412199 original size:2 final size:2
Alignment explanation
Indices: 1412192--1412216 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1412182 CAATACATTT
1412192 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
1412217 ATAGATGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Done.