Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008387.1 Hibiscus syriacus cultivar Beakdansim tig00111151_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: 2491990
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 12
Found at i:1781604 original size:24 final size:24
Alignment explanation
Indices: 1781532--1781606 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
1781522 ATTACGATGC
1781532 AATTCTACGTGGCACTTCGGTGC-
1 AATTCTACGTGGCACTTCGGTGCA
* *
1781555 AATTCTACGCGGTC-CTTTGG-GACA
1 AATTCTACGTGG-CACTTCGGTG-CA
*
1781579 AATTCTATGTGGCACTTCGGTGCA
1 AATTCTACGTGGCACTTCGGTGCA
1781603 AATT
1 AATT
1781607 TATATGAGCT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
22 1 0.02
23 18 0.43
24 22 0.52
25 1 0.02
ACGTcount: A:0.21, C:0.23, G:0.24, T:0.32
Consensus pattern (24 bp):
AATTCTACGTGGCACTTCGGTGCA
Found at i:1782204 original size:21 final size:22
Alignment explanation
Indices: 1782162--1782204 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1782152 CTGTAGCAGT
*
1782162 ACTGTAGCAGGGGAATCGATTC
1 ACTGTAGCAGGGGAACCGATTC
*
1782184 ACTGTAGCA-GGGTACCGATTC
1 ACTGTAGCAGGGGAACCGATTC
1782205 TCTATTTACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (22 bp):
ACTGTAGCAGGGGAACCGATTC
Found at i:1782284 original size:25 final size:25
Alignment explanation
Indices: 1782237--1782285 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1782227 ATTGTGTAAT
* *
1782237 CGGTACTGTAGTAGGTTGCTGTTCA
1 CGGTACTGTAGCAGATTGCTGTTCA
*
1782262 CGGTACTGTAGCAGATTGTTGTTC
1 CGGTACTGTAGCAGATTGCTGTTC
1782286 TTACGTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.16, C:0.16, G:0.31, T:0.37
Consensus pattern (25 bp):
CGGTACTGTAGCAGATTGCTGTTCA
Found at i:1787597 original size:30 final size:30
Alignment explanation
Indices: 1787563--1787632 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 30
1787553 GTTATATGAG
* *
1787563 CTATGTGATAAAGGTATGTAAATGATATGT
1 CTATGTGATAAAGGTATGGAAATAATATGT
*
1787593 CTATGTGATAAAGGTATGGAATTAATATGT
1 CTATGTGATAAAGGTATGGAAATAATATGT
1787623 CTATGTGATA
1 CTATGTGATA
1787633 TGAACTACGT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.37
Consensus pattern (30 bp):
CTATGTGATAAAGGTATGGAAATAATATGT
Found at i:1787954 original size:24 final size:23
Alignment explanation
Indices: 1787866--1787951 Score: 97
Period size: 23 Copynumber: 3.7 Consensus size: 23
1787856 ACGTATTATA
1787866 TGGCA-TTACGGTGCAATTCTACG
1 TGGCACTT-CGGTGCAATTCTACG
1787889 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
1787912 CGGTC-CTTTGG-GACAAATTCTACG
1 TGG-CACTTCGGTG-C-AATTCTACG
1787936 TGGCACTTCGGTGCAA
1 TGGCACTTCGGTGCAA
1787952 ATTTATATGA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
22 1 0.02
23 31 0.58
24 20 0.38
25 1 0.02
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:1790239 original size:34 final size:30
Alignment explanation
Indices: 1790201--1790269 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
1790191 TTGATATAAC
1790201 AATTTAAGGCAAAATAGTTTTTGGACTTGAATTA
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTA
*
1790235 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTA
1790264 AATTTA
1 AATTTA
1790270 TTCAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 9 0.27
30 12 0.36
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTA
Found at i:1790251 original size:30 final size:30
Alignment explanation
Indices: 1790210--1790269 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
1790200 CAATTTAAGG
1790210 CAAAATAGTTTTTGGACTTGAATTAAATTTA
1 CAAAATAGTTTTTGGACTT-AATTAAATTTA
*
1790241 CAAAAT-GTTTTTGGACTTAATTGAATTTA
1 CAAAATAGTTTTTGGACTTAATTAAATTTA
1790270 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 10 0.36
30 12 0.43
31 6 0.21
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (30 bp):
CAAAATAGTTTTTGGACTTAATTAAATTTA
Found at i:1790425 original size:44 final size:44
Alignment explanation
Indices: 1790362--1790465 Score: 208
Period size: 44 Copynumber: 2.4 Consensus size: 44
1790352 CCCCCTGCAG
1790362 GGGTATCCATACCCCCTGAAGGCTTAAATTCTAGATTGCTCGGA
1 GGGTATCCATACCCCCTGAAGGCTTAAATTCTAGATTGCTCGGA
1790406 GGGTATCCATACCCCCTGAAGGCTTAAATTCTAGATTGCTCGGA
1 GGGTATCCATACCCCCTGAAGGCTTAAATTCTAGATTGCTCGGA
1790450 GGGTATCCATACCCCC
1 GGGTATCCATACCCCC
1790466 CAGGGGTATC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 60 1.00
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (44 bp):
GGGTATCCATACCCCCTGAAGGCTTAAATTCTAGATTGCTCGGA
Found at i:1790540 original size:21 final size:21
Alignment explanation
Indices: 1790514--1790554 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1790504 ATTTGAATTT
1790514 TATGAAGGGGTACCGATACCA
1 TATGAAGGGGTACCGATACCA
* *
1790535 TATGAATGGGTATCGATACC
1 TATGAAGGGGTACCGATACC
1790555 CCCTGTACGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (21 bp):
TATGAAGGGGTACCGATACCA
Found at i:1790877 original size:34 final size:32
Alignment explanation
Indices: 1790838--1790907 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1790828 TTTTGTAAAG
*
1790838 GGGAAAGGTACTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTACTAGCTTAGCCCG-G-AAAAACTA
* *
1790872 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTACTAGCTTAGCCCGGAAAAACTA
1790904 GGGA
1 GGGA
1790908 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.33, C:0.16, G:0.31, T:0.20
Consensus pattern (32 bp):
GGGAAAGGTACTAGCTTAGCCCGGAAAAACTA
Found at i:1791839 original size:12 final size:12
Alignment explanation
Indices: 1791817--1791877 Score: 56
Period size: 11 Copynumber: 5.2 Consensus size: 12
1791807 ATATTTAAAT
1791817 ATAAAAGATAATA
1 ATAAAA-ATAATA
1791830 ATAAAAATAA-A
1 ATAAAAATAATA
*
1791841 AT-AAAATAACA
1 ATAAAAATAATA
*
1791852 AT-TAAATAATA
1 ATAAAAATAATA
**
1791863 ACGAAAATAATA
1 ATAAAAATAATA
1791875 ATA
1 ATA
1791878 TAAGATTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
10 7 0.17
11 14 0.35
12 13 0.32
13 6 0.15
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.23
Consensus pattern (12 bp):
ATAAAAATAATA
Found at i:1791848 original size:19 final size:19
Alignment explanation
Indices: 1791812--1791875 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
1791802 TTAAAATATT
* *
1791812 TAAATATAAAAGATAATAA
1 TAAAAATAAAAGAAAATAA
*
1791831 TAAAAATAAAATAAAATAA
1 TAAAAATAAAAGAAAATAA
*
1791850 CAATTAAATAATAACGAAAATAA
1 TAA--AAATAA-AA-GAAAATAA
1791873 TAA
1 TAA
1791876 TATAAGATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 18 0.51
21 6 0.17
22 2 0.06
23 9 0.26
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.23
Consensus pattern (19 bp):
TAAAAATAAAAGAAAATAA
Found at i:1791858 original size:16 final size:17
Alignment explanation
Indices: 1791824--1791877 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 17
1791814 AATATAAAAG
1791824 ATAATAATAAAAATAAA
1 ATAATAATAAAAATAAA
* *
1791841 ATAA-AATAACAATTAA
1 ATAATAATAAAAATAAA
**
1791857 ATAATAACGAAAATAATA
1 ATAATAATAAAAATAA-A
1791875 ATA
1 ATA
1791878 TAAGATTAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 14 0.48
17 11 0.38
18 4 0.14
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (17 bp):
ATAATAATAAAAATAAA
Found at i:1792356 original size:14 final size:13
Alignment explanation
Indices: 1792311--1792360 Score: 61
Period size: 12 Copynumber: 3.9 Consensus size: 13
1792301 CACCGGCCAG
1792311 TCACTATTCACG-
1 TCACTATTCACGC
1792323 TCACTATTC-CGAC
1 TCACTATTCACG-C
1792336 T-ACTATTCATCGC
1 TCACTATTCA-CGC
1792349 TCACTATTCACG
1 TCACTATTCACG
1792361 GTGGCCGGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
11 2 0.06
12 16 0.48
13 5 0.15
14 10 0.30
ACGTcount: A:0.24, C:0.34, G:0.08, T:0.34
Consensus pattern (13 bp):
TCACTATTCACGC
Found at i:1802287 original size:3 final size:3
Alignment explanation
Indices: 1802270--1802324 Score: 85
Period size: 3 Copynumber: 18.0 Consensus size: 3
1802260 TAAAAATGAA
1802270 AAT AAT GAA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1802315 AAAT AAT AAT
1 -AAT AAT AAT
1802325 TAAAACCTGG
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.04
3 42 0.86
4 5 0.10
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1804045 original size:60 final size:59
Alignment explanation
Indices: 1803871--1804056 Score: 223
Period size: 60 Copynumber: 3.1 Consensus size: 59
1803861 GCATCATATG
* * * *
1803871 TCCCCAAACTATGACACTCATTTTAAATTAGTCCTTAAACTTTTAAATATTCTAATTTCA
1 TCCCCAAACTATGA-ACTCATTCTAAATTAGTCCTTAAACTTTTAGATCTTCCAATTTCA
** * * *
1803931 TCATCAAACTATG-ACTCATTCTAAATTAGTCTTTAAAATTTT-GAACATTCCAATTTCA
1 TCCCCAAACTATGAACTCATTCTAAATTAGTCCTTAAACTTTTAGATC-TTCCAATTTCA
* * *
1803989 TCCCCAAACTATGAATCTCATTCTAAATTGGTCCCTAAACTTTTAGATCTGCCAATTTCA
1 TCCCCAAACTATGAA-CTCATTCTAAATTAGTCCTTAAACTTTTAGATCTTCCAATTTCA
1804049 TCCCCAAA
1 TCCCCAAA
1804057 TTCATCCAAA
Statistics
Matches: 105, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
57 1 0.01
58 47 0.45
59 1 0.01
60 53 0.50
61 3 0.03
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (59 bp):
TCCCCAAACTATGAACTCATTCTAAATTAGTCCTTAAACTTTTAGATCTTCCAATTTCA
Found at i:1804356 original size:60 final size:59
Alignment explanation
Indices: 1804200--1804363 Score: 161
Period size: 60 Copynumber: 2.7 Consensus size: 59
1804190 AGGATGAAAT
* * *
1804200 TGAAATTGAAATATTTAGAAAGTCTGGGGACCAATTTAAAATGAAGATCATAGTTTGGAGA
1 TGAAATTGAAATGTTTA-AAAGT-TTGGGACCAATTTAAAATGAAGATCATAGTTTGAAGA
* * * * ** *
1804261 TGAAAATGAAATGTTTGAAAGGTTGAAGATTAATTTATAATGATAG-TCATAGTTT-AAGTA
1 TGAAATTGAAATGTTTAAAAGTTTG-GGACCAATTTAAAATGA-AGATCATAGTTTGAAG-A
*
1804321 TGAAATTGAAATGTTTAAAAGTTTAGGGACCAATTTGAAATGA
1 TGAAATTGAAATGTTTAAAAGTTT-GGGACCAATTTAAAATGA
1804364 GGGCCAGTGA
Statistics
Matches: 81, Mismatches: 18, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
59 4 0.05
60 60 0.74
61 17 0.21
ACGTcount: A:0.41, C:0.04, G:0.21, T:0.33
Consensus pattern (59 bp):
TGAAATTGAAATGTTTAAAAGTTTGGGACCAATTTAAAATGAAGATCATAGTTTGAAGA
Found at i:1804887 original size:39 final size:40
Alignment explanation
Indices: 1804821--1804902 Score: 139
Period size: 39 Copynumber: 2.1 Consensus size: 40
1804811 TAATAAGCAA
*
1804821 GAAAAATTAAAACCTAAAACTTTATGGTTATCTAAACATG
1 GAAAAATTAAAACCTAAAACTTGATGGTTATCTAAACATG
*
1804861 GAAAAATTAAAA-CTAAAACTTGATGGTTATCTAAACTTG
1 GAAAAATTAAAACCTAAAACTTGATGGTTATCTAAACATG
1804900 GAA
1 GAA
1804903 TAAAGAATGA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 28 0.70
40 12 0.30
ACGTcount: A:0.48, C:0.11, G:0.12, T:0.29
Consensus pattern (40 bp):
GAAAAATTAAAACCTAAAACTTGATGGTTATCTAAACATG
Found at i:1806001 original size:5 final size:5
Alignment explanation
Indices: 1805985--1806030 Score: 60
Period size: 5 Copynumber: 9.2 Consensus size: 5
1805975 CGTAATTTTC
1805985 ATAAA GATAAA ATAAA ATAAA ATAAA AT-AA A-AAA ATAAA AGTAAA A
1 ATAAA -ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A-TAAA A
1806031 AGTGTTGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
4 6 0.16
5 21 0.57
6 10 0.27
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.17
Consensus pattern (5 bp):
ATAAA
Found at i:1806031 original size:14 final size:13
Alignment explanation
Indices: 1805991--1806031 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 13
1805981 TTTCATAAAG
1805991 ATAAAATAAAATAAA
1 ATAAAAT-AAA-AAA
1806006 ATAAAATAAAAAA
1 ATAAAATAAAAAA
1806019 ATAAAAGTAAAAA
1 ATAAAA-TAAAAA
1806032 GTGTTGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.36
14 9 0.36
15 7 0.28
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (13 bp):
ATAAAATAAAAAA
Found at i:1808381 original size:130 final size:130
Alignment explanation
Indices: 1808095--1808579 Score: 483
Period size: 133 Copynumber: 3.7 Consensus size: 130
1808085 TGGTCATTTA
* * * * *
1808095 AGGGTGACACGGCTCTTACATGATGAGGAGATCTGGTCGGTGGATGACACGGCTCATACGTGATG
1 AGGGTGACACGGCTCCTACATGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCCTACGTGATG
* * * * * *
1808160 AAGAGTTA-TAGCCATCTTTAGGAAGGGTTATAACACGGTTCCTACGCGATGAGGATGACTGGTT
66 AGGA-TGACAAGCCATCTTTA-G--GGATGATAACACGGTTCTTACGCGATGAGGATGACTGGTT
1808224 ATCT
127 ATCT
* * * * *
1808228 AGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGATATGTTTCCTACGCGATG
1 AGGGTGACACGGCTCCTACATGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCCTACGTGATG
* ** * *
1808293 AGGATGACAAGCCATCTTTAGGGATGATAACACGATTCTTACATGATAAGGACGACTGGTTATCT
66 AGGATGACAAGCCATCTTTAGGGATGATAACACGGTTCTTACGCGATGAGGATGACTGGTTATCT
* * * * * *** *
1808358 AGGGTGACACAGCTCCTACGTGATGAGAAGGTATGGTC-GGGGATGATATAATTCCTACGTAATG
1 AGGGTGACACGGCTCCTACATGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCCTACGTGATG
* * * * * * *
1808422 GGGACGGCATGCCATCTTTAGGGAGGGTGATAACATGGTTCTTATGCGATGAGGATGGCTGGTTA
66 AGGATGACAAGCCATCTTTAGGGA---TGATAACACGGTTCTTACGCGATGAGGATGACTGGTTA
1808487 TC-
128 TCT
* *
1808489 AGGGGTGACACGACTCCTACATGATGAGGAGGTTTGGGT-GGGGGATGACACGGTTCCTACGTGA
1 A-GGGTGACACGGCTCCTACATGATGAGGAGGTCT-GGTCGGGGGATGACACGGTTCCTACGTGA
** *
1808553 TGAGGATGGTAGGCCATCTTTAGGGAT
64 TGAGGATGACAAGCCATCTTTAGGGAT
1808580 AAAGGTTTCA
Statistics
Matches: 291, Mismatches: 54, Indels: 17
0.80 0.15 0.05
Matches are distributed among these distances:
129 42 0.14
130 72 0.25
131 1 0.00
132 63 0.22
133 113 0.39
ACGTcount: A:0.25, C:0.16, G:0.33, T:0.26
Consensus pattern (130 bp):
AGGGTGACACGGCTCCTACATGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCCTACGTGATG
AGGATGACAAGCCATCTTTAGGGATGATAACACGGTTCTTACGCGATGAGGATGACTGGTTATCT
Found at i:1808998 original size:33 final size:34
Alignment explanation
Indices: 1808960--1809026 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
1808950 TGAATCCTCG
1808960 AAGATG-CCCCAACATTCAATGTTGATTGCTTCA
1 AAGATGCCCCCAACATTCAATGTTGATTGCTTCA
* *
1808993 AAGATGCCCCCAATATTCGATGTTGATTGCTTCA
1 AAGATGCCCCCAACATTCAATGTTGATTGCTTCA
1809027 GCACTGATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 6 0.19
34 25 0.81
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.31
Consensus pattern (34 bp):
AAGATGCCCCCAACATTCAATGTTGATTGCTTCA
Found at i:1810060 original size:25 final size:24
Alignment explanation
Indices: 1810032--1810120 Score: 76
Period size: 25 Copynumber: 3.7 Consensus size: 24
1810022 TCTTGTCTTC
1810032 TTTTTTCTCTTTGCTTTTTCTTTGA
1 TTTTTTCTCTTTG-TTTTTCTTTGA
* * **
1810057 -TTTTGCT-TTT-CTTTTCTTTTCT
1 TTTTTTCTCTTTGTTTTTC-TTTGA
* *
1810079 TTTTTTCTTTTTGTTTTTCTTTGC
1 TTTTTTCTCTTTGTTTTTCTTTGA
1810103 TTCTTTTCTCTTTGTTTT
1 TT-TTTTCTCTTTGTTTT
1810121 GATTAGATCT
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
21 5 0.10
22 3 0.06
23 9 0.18
24 14 0.28
25 19 0.38
ACGTcount: A:0.01, C:0.16, G:0.07, T:0.76
Consensus pattern (24 bp):
TTTTTTCTCTTTGTTTTTCTTTGA
Found at i:1814263 original size:2 final size:2
Alignment explanation
Indices: 1814256--1814280 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1814246 GCTCCTCGTG
1814256 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1814281 TTCAAAGGTC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1815238 original size:3 final size:3
Alignment explanation
Indices: 1815230--1815273 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
1815220 TAATATATGT
* *
1815230 ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA AAA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1815274 CTATTTTGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:1817619 original size:19 final size:19
Alignment explanation
Indices: 1817591--1817648 Score: 53
Period size: 23 Copynumber: 2.8 Consensus size: 19
1817581 TTAATCTTTT
*
1817591 AATAATATATTTTAATTTA
1 AATAAAATATTTTAATTTA
*
1817610 AATAAAATATAATAATTATTTTA
1 AATAAAATAT--T--TTAATTTA
*
1817633 AATCAAATATTTTAAT
1 AATAAAATATTTTAAT
1817649 CGGTATTATC
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
19 13 0.42
21 2 0.06
23 16 0.52
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
AATAAAATATTTTAATTTA
Found at i:1819154 original size:216 final size:216
Alignment explanation
Indices: 1818513--1819205 Score: 1043
Period size: 216 Copynumber: 3.3 Consensus size: 216
1818503 AATTAAGAAT
*
1818513 TAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATAAATTAAACAACACACATTGATGGG
1 TAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATAAATTAAACAACACACATTGATGAG
* * * *
1818578 GGATCAAATTGAAATAATTTTAAAATGTGAGGTTGAAATTAATATAAAAAAGTACTAAATTATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTTAAATTAATAAAAAAAAGTACTAAATTATAC
**
1818643 -CTATTTAAAAAGTTACAGGCCAATTAAAAAATATAAATAAGTAATAAGTATGGGTCAATTTCAG
131 TC-ATTTAAAAAGTTATGGGCCAATTAAAAAATATAAATAAGTAATAAGTATGGGTCAATTTCAG
*
1818707 ATGA-AAATATAATTTTTAGGAC
195 AT-ACAAATATAATTTTAAGGAC
* *
1818729 TAAATTGAACAAATATGAAATTAAAAATAGAAAATTTAAATAAATT-----A-A-ACATTGATGA
1 TAAATTGAACAAATATGAAATTACAAAT-TAAAATTTAAATAAATTAAACAACACACATTGATGA
*
1818787 GGGATCAAATCGAAATAATTTTAAATTGTGAGGTTTAAATTAATAAAAAAAAGTGCTAAATTATA
65 GGGATCAAATCGAAATAATTTTAAATTGTGAGGTTTAAATTAATAAAAAAAAGTACTAAATTATA
* *
1818852 ATCATTTAAAAAGTTATGGGCCAATT-AAAAATATAAATAAGTAATAAATATGGGTCAATTTCAG
130 CTCATTTAAAAAGTTATGGGCCAATTAAAAAATATAAATAAGTAATAAGTATGGGTCAATTTCAG
*
1818916 ATACAAATATAATTTCAAGGAC
195 ATACAAATATAATTTTAAGGAC
*
1818938 TAAATTGAACAAATATGAAATTACAAATTAAATTTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATAAATTAAACAACACACATTGATGAG
* * * *
1819003 AGATCAAATCAAAATAATTTTAAATTGTGAGGTTTAAATTAATACAAAAAAGTACTAAATAATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTTAAATTAATAAAAAAAAGTACTAAATTATAC
* *
1819068 TCATTTAAAAAGTTATGGGTCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGA
131 TCATTTAAAAAGTTATGGGCCAATTAAAAAATATAAATAAGTAATAAGTATGGGTCAATTTCAGA
*
1819133 TTCAAATATAATTTTAAGGAC
196 TACAAATATAATTTTAAGGAC
* * *
1819154 TAAATTAAACAACTAT---ATTACAAATTAAATTTTAAATAAATTAAACAACACA
1 TAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATAAATTAAACAACACA
1819206 AAGGTGTCAA
Statistics
Matches: 436, Mismatches: 30, Indels: 25
0.89 0.06 0.05
Matches are distributed among these distances:
208 16 0.04
209 82 0.19
210 90 0.21
211 2 0.00
212 1 0.00
213 37 0.08
214 1 0.00
215 94 0.22
216 97 0.22
217 16 0.04
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.31
Consensus pattern (216 bp):
TAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATAAATTAAACAACACACATTGATGAG
GGATCAAATCGAAATAATTTTAAATTGTGAGGTTTAAATTAATAAAAAAAAGTACTAAATTATAC
TCATTTAAAAAGTTATGGGCCAATTAAAAAATATAAATAAGTAATAAGTATGGGTCAATTTCAGA
TACAAATATAATTTTAAGGAC
Found at i:1819311 original size:2 final size:2
Alignment explanation
Indices: 1819300--1819484 Score: 175
Period size: 2 Copynumber: 92.0 Consensus size: 2
1819290 TTGAAACAAC
1819300 TA TA -A TA TA TA TA 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 TA TA TA TA TA TA TA
* *
1819341 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA AA CTA TA TA GTT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
* * * *
1819384 TA TA TA AA GTA TA TG T- TA TA TA TA TA AA CTA TA TA T- TT TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* *
1819426 TT TA TA TA TA TA CTA TA TA TA AA CTA TA TA T- TA TA TA TA T- TA
1 TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* *
1819468 TG TA TA AA CTA TA TA TA
1 TA TA TA TA -TA TA TA TA
1819485 CCATGTATAA
Statistics
Matches: 152, Mismatches: 18, Indels: 26
0.78 0.09 0.13
Matches are distributed among these distances:
1 6 0.04
2 138 0.91
3 8 0.05
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1819490 original size:20 final size:20
Alignment explanation
Indices: 1819457--1819504 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1819447 AACTATATAT
**
1819457 TATATATATTATGTATAAAC
1 TATATATACCATGTATAAAC
1819477 TATATATACCATGTATAAAC
1 TATATATACCATGTATAAAC
1819497 TATA-ATAC
1 TATATATAC
1819505 TATATAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (20 bp):
TATATATACCATGTATAAAC
Found at i:1819580 original size:25 final size:24
Alignment explanation
Indices: 1819516--1819592 Score: 64
Period size: 27 Copynumber: 2.9 Consensus size: 24
1819506 ATATAGTTTA
*
1819516 TATAAATTATATGAATTATATATAAAC
1 TATAAA-TATAT-ATTTATATAT-AAC
* *
1819543 TATACAATTTATATTTATATATAAT
1 TATA-AATATATATTTATATATAAC
1819568 TATAAACTATATAGTTTTATATATA
1 TATAAA-TATATA--TTTATATATA
1819593 TAGTATATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
24 2 0.05
25 11 0.26
26 9 0.21
27 18 0.43
28 2 0.05
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (24 bp):
TATAAATATATATTTATATATAAC
Found at i:1819773 original size:9 final size:9
Alignment explanation
Indices: 1819759--1819802 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
1819749 GAACTATATG
1819759 TATAAACTA
1 TATAAACTA
1819768 TATAAAC--
1 TATAAACTA
1819775 TAT--A-TA
1 TATAAACTA
1819781 TATAAACTA
1 TATAAACTA
1819790 TATAAACTA
1 TATAAACTA
1819799 TATA
1 TATA
1819803 GTATATACCT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
5 1 0.03
6 3 0.10
7 3 0.10
8 1 0.03
9 22 0.73
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (9 bp):
TATAAACTA
Found at i:1819776 original size:22 final size:22
Alignment explanation
Indices: 1819750--1819816 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
1819740 TTTACAGATG
1819750 AACTATATGTATAAACTATATA
1 AACTATATGTATAAACTATATA
*
1819772 AACTATATATATAAACTATATA
1 AACTATATGTATAAACTATATA
*
1819794 AACTATATAGTATATACCTATAT
1 AACTATAT-GTATA-AACTATAT
1819817 TATAGTTTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 29 0.73
23 4 0.10
24 7 0.17
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.37
Consensus pattern (22 bp):
AACTATATGTATAAACTATATA
Found at i:1819793 original size:13 final size:13
Alignment explanation
Indices: 1819766--1819793 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1819756 ATGTATAAAC
1819766 TATATAAACTATA
1 TATATAAACTATA
1819779 TATATAAACTATA
1 TATATAAACTATA
1819792 TA
1 TA
1819794 AACTATATAG
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:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (13 bp):
TATATAAACTATA
Found at i:1819942 original size:38 final size:40
Alignment explanation
Indices: 1819892--1820006 Score: 141
Period size: 38 Copynumber: 2.9 Consensus size: 40
1819882 TATTTTATAC
1819892 TATATA-TGAACTATAGTTTACATATAAACTATATAGTT-
1 TATATACTGAACTATAGTTTACATATAAACTATATAGTTA
1819930 TATATACT-AACTATAGTTTACATATAAAC--TATAGTTGA
1 TATATACTGAACTATAGTTTACATATAAACTATATAGTT-A
* *
1819968 TATTTACGTATGAACTATAGTTTACATATGAACTATATA
1 TATATAC---TGAACTATAGTTTACATATAAACTATATA
1820007 TAAAACTATA
Statistics
Matches: 66, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
36 7 0.11
38 33 0.50
39 1 0.02
41 1 0.02
42 20 0.30
44 4 0.06
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.41
Consensus pattern (40 bp):
TATATACTGAACTATAGTTTACATATAAACTATATAGTTA
Found at i:1819997 original size:18 final size:18
Alignment explanation
Indices: 1819895--1820004 Score: 96
Period size: 18 Copynumber: 5.7 Consensus size: 18
1819885 TTTATACTAT
1819895 ATATGAACTATAGTTTAC
1 ATATGAACTATAGTTTAC
* *
1819913 ATATAAACTATATAGTTTAT
1 ATATGAAC--TATAGTTTAC
1819933 ATACT-AACTATAGTTTAC
1 ATA-TGAACTATAGTTTAC
*
1819951 ATATAAACTATAGTTGATATTTAC
1 ATATGAACTATA---G---TTTAC
*
1819975 GTATGAACTATAGTTTAC
1 ATATGAACTATAGTTTAC
1819993 ATATGAACTATA
1 ATATGAACTATA
1820005 TATAAAACTA
Statistics
Matches: 76, Mismatches: 6, Indels: 20
0.75 0.06 0.20
Matches are distributed among these distances:
17 1 0.01
18 42 0.55
20 15 0.20
21 3 0.04
24 15 0.20
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (18 bp):
ATATGAACTATAGTTTAC
Found at i:1820033 original size:2 final size:2
Alignment explanation
Indices: 1820020--1820068 Score: 53
Period size: 2 Copynumber: 23.0 Consensus size: 2
1820010 AACTATAGTT
* *
1820020 TA TA TT TA TA TA TA TA TA TA TA TA TA AA CTA TA TA TA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA
1820064 GTA TA
1 -TA TA
1820069 ATTTACATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 35 0.88
3 5 0.12
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1820039 original size:23 final size:24
Alignment explanation
Indices: 1820013--1820088 Score: 68
Period size: 23 Copynumber: 3.2 Consensus size: 24
1820003 TATATAAAAC
*
1820013 TATAGTTTATATTTATATATA-TA
1 TATAGTATATATTTATATATACTA
**
1820036 TATA-TATATAAACTATATATACTA
1 TATAGTATAT-ATTTATATATACTA
*
1820060 TATAGTATA-ATTTACATATGAACTA
1 TATAGTATATATTTATATAT--ACTA
1820085 TATA
1 TATA
1820089 TAAAAATTCT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
22 4 0.10
23 20 0.48
24 6 0.14
25 12 0.29
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (24 bp):
TATAGTATATATTTATATATACTA
Found at i:1820078 original size:25 final size:25
Alignment explanation
Indices: 1820013--1820088 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
1820003 TATATAAAAC
* *
1820013 TATAGTTTATATTTATATATATA-TA
1 TATAGTATA-ATTTACATATATACTA
1820038 TATA-TATAA---ACTATATATACTA
1 TATAGTATAATTTAC-ATATATACTA
1820060 TATAGTATAATTTACATATGA-ACTA
1 TATAGTATAATTTACATAT-ATACTA
1820085 TATA
1 TATA
1820089 TAAAAATTCT
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
20 1 0.02
21 7 0.17
22 6 0.14
23 6 0.14
24 3 0.07
25 16 0.38
26 3 0.07
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (25 bp):
TATAGTATAATTTACATATATACTA
Found at i:1820143 original size:28 final size:28
Alignment explanation
Indices: 1820092--1820148 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
1820082 CTATATATAA
* *
1820092 AAATTCTAAACCCTAAACTATAAAATAT
1 AAATCCTAAACCCTAAACCATAAAATAT
* *
1820120 AAATCCTAAACCCTAAACCCTAAACTAT
1 AAATCCTAAACCCTAAACCATAAAATAT
1820148 A
1 A
1820149 CATTATATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.25
Consensus pattern (28 bp):
AAATCCTAAACCCTAAACCATAAAATAT
Found at i:1820190 original size:18 final size:18
Alignment explanation
Indices: 1820164--1820285 Score: 89
Period size: 18 Copynumber: 7.1 Consensus size: 18
1820154 TATAGTTTAT
1820164 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
* *
1820182 TAATATATATAGACTATA
1 TAGTATATATAAACTATA
* *
1820200 TGGTATATATAAGCTATA
1 TAGTATATATAAACTATA
* * **
1820218 CATTATATAT-AGTTCAT-
1 TAGTATATATAAACT-ATA
1820235 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
*
1820253 TA-T-TATAGT--TC-AT-
1 TAGTATATA-TAAACTATA
1820266 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
1820284 TA
1 TA
1820286 TTAATTTATT
Statistics
Matches: 78, Mismatches: 16, Indels: 20
0.68 0.14 0.18
Matches are distributed among these distances:
13 2 0.03
14 4 0.05
15 5 0.06
16 5 0.06
17 17 0.22
18 45 0.58
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (18 bp):
TAGTATATATAAACTATA
Found at i:1820288 original size:31 final size:32
Alignment explanation
Indices: 1820140--1820286 Score: 154
Period size: 31 Copynumber: 4.4 Consensus size: 32
1820130 CCCTAAACCC
* *
1820140 TAAACTATACATTATATAGTTTATTAGTATATA
1 TAAACTATATA-TATATAGTTCATTAGTATATA
* *
1820173 TAAACTATATAATATATA-TAGACTATATGGTATATA
1 TAAACTATAT-ATATATAGT--TC-AT-TAGTATATA
*
1820209 TAAGCTATACATTATATATAGTTCATTAGTATATA
1 TAAACTAT--A-TATATATAGTTCATTAGTATATA
1820244 TAAACTATATAT-TATAGTTCATTAGTATATA
1 TAAACTATATATATATAGTTCATTAGTATATA
1820275 TAAACTATATAT
1 TAAACTATATAT
1820287 TAATTTATTA
Statistics
Matches: 97, Mismatches: 8, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
31 31 0.32
32 4 0.04
33 16 0.16
34 1 0.01
35 17 0.18
36 17 0.18
37 1 0.01
38 8 0.08
39 2 0.02
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.43
Consensus pattern (32 bp):
TAAACTATATATATATAGTTCATTAGTATATA
Found at i:1820423 original size:60 final size:60
Alignment explanation
Indices: 1820359--1820471 Score: 145
Period size: 60 Copynumber: 1.9 Consensus size: 60
1820349 AACAAATTTT
* * ** * *
1820359 AAATATGAAGCTTAAGTTAAAAAATTGTAACATTAAATTTGGATTAAATTAAAAAAGTTG
1 AAATATGAAGATTAAATTAAAAAATTACAACAATAAATTTGGACTAAATTAAAAAAGTTG
* * *
1820419 AAATATGAAGATTAAATTAATATATTACATCAATAAATTTGGACTAAATTAAA
1 AAATATGAAGATTAAATTAAAAAATTACAACAATAAATTTGGACTAAATTAAA
1820472 CAAATATAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 44 1.00
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.34
Consensus pattern (60 bp):
AAATATGAAGATTAAATTAAAAAATTACAACAATAAATTTGGACTAAATTAAAAAAGTTG
Found at i:1825019 original size:24 final size:24
Alignment explanation
Indices: 1824953--1825051 Score: 100
Period size: 24 Copynumber: 4.3 Consensus size: 24
1824943 AAACATAATT
* *
1824953 CAGGTCAAGTAGCATATCATAATC
1 CAGGTCAAGTATCATATCAAAATC
*
1824977 CATGTCAAG--TC--AT-AAAATC
1 CAGGTCAAGTATCATATCAAAATC
*
1824996 CAGGTCAAGTATCATATAAAAATC
1 CAGGTCAAGTATCATATCAAAATC
* * *
1825020 CAGGTTAAATATCATATCAAGATC
1 CAGGTCAAGTATCATATCAAAATC
1825044 CAGGTCAA
1 CAGGTCAA
1825052 AAACCAGATA
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
19 13 0.21
20 2 0.03
21 2 0.03
22 1 0.02
23 2 0.03
24 41 0.67
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.25
Consensus pattern (24 bp):
CAGGTCAAGTATCATATCAAAATC
Found at i:1825249 original size:21 final size:21
Alignment explanation
Indices: 1825225--1825274 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
1825215 AATCCTAATA
1825225 TAAATAATCTTAATATTTATT
1 TAAATAATCTTAATATTTATT
1825246 TAAATAATCTTAATATTTATT
1 TAAATAATCTTAATATTTATT
1825267 TAAATAAT
1 TAAATAAT
1825275 ATACGAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAATAATCTTAATATTTATT
Found at i:1825787 original size:29 final size:28
Alignment explanation
Indices: 1825739--1825919 Score: 107
Period size: 29 Copynumber: 6.4 Consensus size: 28
1825729 AACAACTATT
* *
1825739 TTACGAAAATAGCATCATTTTAAAAAAAA
1 TTACCAAAATATCA-CATTTTAAAAAAAA
*
1825768 TTACCAAAATATCACAATTTTAAAAATAA
1 TTACCAAAATATCAC-ATTTTAAAAAAAA
* ** *
1825797 TTACTAAAATAT-AGTTTTTTAAAAAAA
1 TTACCAAAATATCACATTTTAAAAAAAA
*** *
1825824 TTA-CAAAATTATCTTTTTTTTAAAAAAA
1 TTACCAAAA-TATCACATTTTAAAAAAAA
* * * *
1825852 TTA-CAAAATTAGCACCTTTTCAAAATAA
1 TTACCAAAA-TATCACATTTTAAAAAAAA
* * ** *
1825880 TTACCAGAATAGCACCATTTTCCAAATAA
1 TTACCAAAATATCA-CATTTTAAAAAAAA
*
1825909 TTACCAGAATA
1 TTACCAAAATA
1825920 GCACCCAGTC
Statistics
Matches: 127, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
26 4 0.03
27 16 0.13
28 45 0.35
29 62 0.49
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.34
Consensus pattern (28 bp):
TTACCAAAATATCACATTTTAAAAAAAA
Found at i:1825816 original size:28 final size:27
Alignment explanation
Indices: 1825756--1825883 Score: 114
Period size: 28 Copynumber: 4.6 Consensus size: 27
1825746 AATAGCATCA
* *
1825756 TTTTAAAAAAAATTACCAAAATATCACA
1 TTTTTAAAAAAATTA-CAAAATATCACT
* *
1825784 ATTTTAAAAATAATTACTAAAATAT-AGT
1 TTTTTAAAAA-AATTAC-AAAATATCACT
**
1825812 TTTTTAAAAAAATTACAAAATTATCTTT
1 TTTTTAAAAAAATTACAAAA-TATCACT
* *
1825840 TTTTTAAAAAAATTACAAAATTAGCACC
1 TTTTTAAAAAAATTACAAAA-TATCACT
* *
1825868 TTTTCAAAATAATTAC
1 TTTTTAAAAAAATTAC
1825884 CAGAATAGCA
Statistics
Matches: 83, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
26 4 0.05
27 9 0.11
28 58 0.70
29 12 0.14
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.38
Consensus pattern (27 bp):
TTTTTAAAAAAATTACAAAATATCACT
Found at i:1825892 original size:28 final size:29
Alignment explanation
Indices: 1825861--1825924 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
1825851 ATTACAAAAT
1825861 TAGCACC-TTTTCAAAATAATTACCAGAA
1 TAGCACCATTTTCAAAATAATTACCAGAA
*
1825889 TAGCACCATTTTCCAAATAATTACCAGAA
1 TAGCACCATTTTCAAAATAATTACCAGAA
1825918 TAGCACC
1 TAGCACC
1825925 CAGTCAACGG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 7 0.21
29 27 0.79
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.27
Consensus pattern (29 bp):
TAGCACCATTTTCAAAATAATTACCAGAA
Found at i:1829616 original size:44 final size:46
Alignment explanation
Indices: 1829496--1829621 Score: 150
Period size: 47 Copynumber: 2.8 Consensus size: 46
1829486 TATAAAATCT
* *
1829496 CTTACCATTT-ATCCCATAAGCTCGTAAGATTATTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
1829541 CTTACCATTTAAATTCCACAAGCTCGTAAGCTTATTTTTCCAATATA
1 CTTACCATTT-AATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
1829588 CTTTCCA-TT-ATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTT
1829622 GCATGGTTAC
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
44 22 0.31
45 10 0.14
46 2 0.03
47 36 0.51
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (46 bp):
CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:1833678 original size:6 final size:6
Alignment explanation
Indices: 1833662--1833758 Score: 54
Period size: 6 Copynumber: 15.3 Consensus size: 6
1833652 TCTCTCATTT
* * * *
1833662 TTTTCTC TTTTTC -TTTTC TTTCTC GTTTTCATT TTTTTC TTCTTC GTTTTC
1 TTTT-TC TTTTTC TTTTTC TTTTTC -TTTT--TC TTTTTC TTTTTC TTTTTC
* * *
1833713 ATTTTC ATTTTC TTTTTC TATATTTTC TTTTTC TATTT- TTTTTC TT
1 TTTTTC TTTTTC TTTTTC --T-TTTTC TTTTTC TTTTTC TTTTTC TT
1833759 CTTATGTTTT
Statistics
Matches: 71, Mismatches: 11, Indels: 17
0.72 0.11 0.17
Matches are distributed among these distances:
5 9 0.13
6 43 0.61
7 8 0.11
8 5 0.07
9 6 0.08
ACGTcount: A:0.06, C:0.18, G:0.02, T:0.74
Consensus pattern (6 bp):
TTTTTC
Found at i:1833683 original size:17 final size:15
Alignment explanation
Indices: 1833659--1833779 Score: 53
Period size: 15 Copynumber: 7.1 Consensus size: 15
1833649 TCATCTCTCA
1833659 TTTTTTTCTCTTTTTC
1 TTTTTTT-TCTTTTTC
*
1833675 TTTTCTTTCTCGTTTTC
1 TTTT-TTT-TCTTTTTC
1833692 ATTTTTTTCTTCTTCGTTTTC
1 --TTTTTT-TTC-T--TTTTC
1833713 ATTTTCATTTTCTTTTTC
1 -TTTT--TTTTCTTTTTC
* *
1833731 TATATTTTCTTTTTC
1 TTTTTTTTCTTTTTC
* *
1833746 TATTTTTTTTCTTCTTA
1 --TTTTTTTTCTTTTTC
* *
1833763 TGTTTTTTCTTCTTC
1 TTTTTTTTCTTTTTC
1833778 TT
1 TT
1833780 ATAATATATG
Statistics
Matches: 82, Mismatches: 12, Indels: 23
0.70 0.10 0.20
Matches are distributed among these distances:
15 25 0.30
16 4 0.05
17 24 0.29
18 9 0.11
19 5 0.06
20 5 0.06
21 8 0.10
22 2 0.02
ACGTcount: A:0.06, C:0.17, G:0.02, T:0.74
Consensus pattern (15 bp):
TTTTTTTTCTTTTTC
Found at i:1833699 original size:27 final size:26
Alignment explanation
Indices: 1833669--1833758 Score: 71
Period size: 27 Copynumber: 3.3 Consensus size: 26
1833659 TTTTTTTCTC
1833669 TTTTTCTTTTCTTTCTCGTTTTCA-TT
1 TTTTTCTTTTCTTTCTC-TTTTCATTT
1833695 TTTTTCTTCTTCGTTT-TCATTTTCATTTT
1 TTTTTCTT-TTC-TTTCTC-TTTTCA-TTT
*
1833724 CTTTTTCTATAT-TTTCT-TTTTCTATTT
1 -TTTTTCT-TTTCTTTCTCTTTTC-ATTT
1833751 TTTTTCTT
1 TTTTTCTT
1833759 CTTATGTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
25 1 0.02
26 15 0.28
27 19 0.35
28 7 0.13
29 3 0.06
30 8 0.15
31 1 0.02
ACGTcount: A:0.07, C:0.17, G:0.02, T:0.74
Consensus pattern (26 bp):
TTTTTCTTTTCTTTCTCTTTTCATTT
Found at i:1833704 original size:20 final size:22
Alignment explanation
Indices: 1833675--1833717 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
1833665 TCTCTTTTTC
1833675 TTTTCTTTC-TCGTTTTCATTT
1 TTTTCTTTCTTCGTTTTCATTT
1833696 TTTTC-TTCTTCGTTTTCATTT
1 TTTTCTTTCTTCGTTTTCATTT
1833717 T
1 T
1833718 CATTTTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.05, C:0.19, G:0.05, T:0.72
Consensus pattern (22 bp):
TTTTCTTTCTTCGTTTTCATTT
Found at i:1833725 original size:21 final size:20
Alignment explanation
Indices: 1833680--1833726 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
1833670 TTTTCTTTTC
*
1833680 TTTC-TCGTTTTCATTTTTT
1 TTTCTTCGTTTTCATTTTAT
1833699 TCTTCTTCGTTTTCATTTTCAT
1 T-TTCTTCGTTTTCATTTT-AT
1833721 TTTCTT
1 TTTCTT
1833727 TTTCTATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 1 0.04
20 3 0.12
21 18 0.75
22 2 0.08
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.70
Consensus pattern (20 bp):
TTTCTTCGTTTTCATTTTAT
Found at i:1833753 original size:15 final size:15
Alignment explanation
Indices: 1833719--1833752 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1833709 TTTCATTTTC
1833719 ATTTTCTTTTTCTAT
1 ATTTTCTTTTTCTAT
1833734 ATTTTCTTTTTCTAT
1 ATTTTCTTTTTCTAT
1833749 -TTTT
1 ATTTT
1833753 TTTCTTCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTTTCTTTTTCTAT
Found at i:1833775 original size:18 final size:17
Alignment explanation
Indices: 1833748--1833781 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
1833738 TCTTTTTCTA
1833748 TTTTTTTTCTTCTTATG
1 TTTTTTTTCTTCTTATG
1833765 TTTTTTCTTCTTCTTAT
1 TTTTTT-TTCTTCTTAT
1833782 AATATATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.06, C:0.15, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTTTTTTCTTCTTATG
Found at i:1836270 original size:44 final size:46
Alignment explanation
Indices: 1836150--1836275 Score: 150
Period size: 47 Copynumber: 2.8 Consensus size: 46
1836140 TATAAAATCT
* *
1836150 CTTACCATTT-ATCCCATAAGCTCGTAAGATTATTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
1836195 CTTACCATTTAAATTCCACAAGCTCGTAAGCTTATTTTTCCAATATA
1 CTTACCATTT-AATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
1836242 CTTTCCA-TT-ATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTT
1836276 GCTGGTTACC
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
44 22 0.31
45 10 0.14
46 2 0.03
47 36 0.51
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (46 bp):
CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:1841903 original size:24 final size:23
Alignment explanation
Indices: 1841848--1841952 Score: 93
Period size: 24 Copynumber: 4.4 Consensus size: 23
1841838 AAAACATAAT
* * * *
1841848 TCAGGTCAAGTAGCAGATTAGAA
1 TCAGGTCAAGTATCATATAAAAA
*
1841871 TCCATGTCAAGTATCATATAAAAA
1 T-CAGGTCAAGTATCATATAAAAA
1841895 TACAGGTCAAGTATCATATAAAAA
1 T-CAGGTCAAGTATCATATAAAAA
* * * *
1841919 TCTAGGTCAAATATTATATCAAGA
1 TC-AGGTCAAGTATCATATAAAAA
1841943 TCTAGGTCAA
1 TC-AGGTCAA
1841953 AAACCAGATA
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
23 2 0.03
24 67 0.97
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (23 bp):
TCAGGTCAAGTATCATATAAAAA
Found at i:1841953 original size:24 final size:24
Alignment explanation
Indices: 1841876--1841953 Score: 95
Period size: 24 Copynumber: 3.2 Consensus size: 24
1841866 TAGAATCCAT
*
1841876 GTCAAGTATCATATAAAAATAC-AG
1 GTCAAATATCATATAAAAAT-CTAG
*
1841900 GTCAAGTATCATATAAAAATCTAG
1 GTCAAATATCATATAAAAATCTAG
* * *
1841924 GTCAAATATTATATCAAGATCTAG
1 GTCAAATATCATATAAAAATCTAG
1841948 GTCAAA
1 GTCAAA
1841954 AACCAGATAA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
23 1 0.02
24 48 0.98
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (24 bp):
GTCAAATATCATATAAAAATCTAG
Found at i:1842737 original size:29 final size:29
Alignment explanation
Indices: 1842658--1842743 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 29
1842648 AACAACCATT
* *
1842658 TTACGAAAATAACATTATTTTCAAAAAAAA
1 TTACCAAAATATCATTATTTTC-AAAAAAA
** *
1842688 TTACCAAAATATCACCATTTTCAAAATAA
1 TTACCAAAATATCATTATTTTCAAAAAAA
* * *
1842717 TTACTAAAATATCATTTTTTTTAAAAA
1 TTACCAAAATATCATTATTTTCAAAAA
1842744 TGACGAAATT
Statistics
Matches: 45, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 27 0.60
30 18 0.40
ACGTcount: A:0.50, C:0.13, G:0.01, T:0.36
Consensus pattern (29 bp):
TTACCAAAATATCATTATTTTCAAAAAAA
Found at i:1842760 original size:23 final size:23
Alignment explanation
Indices: 1842732--1842777 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1842722 AAAATATCAT
*
1842732 TTTTTTTAAAAATGACGAAATTA
1 TTTTTTTAAAAATGACAAAATTA
* *
1842755 TTTTTTTTAAAATTACAAAATTA
1 TTTTTTTAAAAATGACAAAATTA
1842778 GTACCCTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (23 bp):
TTTTTTTAAAAATGACAAAATTA
Found at i:1842820 original size:30 final size:29
Alignment explanation
Indices: 1842784--1842840 Score: 105
Period size: 29 Copynumber: 1.9 Consensus size: 29
1842774 ATTAGTACCC
1842784 TTTTCAAAATAATTACCAGAATAGCACCAT
1 TTTTC-AAATAATTACCAGAATAGCACCAT
1842814 TTTTCAAATAATTACCAGAATAGCACC
1 TTTTCAAATAATTACCAGAATAGCACC
1842841 CGATCAACGG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (29 bp):
TTTTCAAATAATTACCAGAATAGCACCAT
Found at i:1845096 original size:21 final size:22
Alignment explanation
Indices: 1845065--1845108 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1845055 TGAATGAATG
1845065 AATATATTAATTATTTGAAATA
1 AATATATTAATTATTTGAAATA
* *
1845087 AATATA-TAATTTTTTTAAATA
1 AATATATTAATTATTTGAAATA
1845108 A
1 A
1845109 TCATATCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
AATATATTAATTATTTGAAATA
Found at i:1845114 original size:21 final size:20
Alignment explanation
Indices: 1845065--1845130 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 20
1845055 TGAATGAATG
* *
1845065 AATATATTAATTATTTGAAAT
1 AATATA-TAATTTTTTTAAAT
1845086 AAATATATAATTTTTTTAAAT
1 -AATATATAATTTTTTTAAAT
*
1845107 AATCATATCTATTATTTTTAAAT
1 AAT-ATAT-AATT-TTTTTAAAT
1845130 A
1 A
1845131 TTATTGAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
20 3 0.08
21 16 0.42
22 9 0.24
23 10 0.26
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (20 bp):
AATATATAATTTTTTTAAAT
Found at i:1847382 original size:216 final size:215
Alignment explanation
Indices: 1847015--1847658 Score: 1041
Period size: 215 Copynumber: 3.0 Consensus size: 215
1847005 TTATTATTTT
*
1847015 ATTAGGAATTAAGATAGAGTTAAAACAATTATCTTTAGTTTATTATTATTAGGAACTAGG--A-T
1 ATTAGGAATTAAGATAGAGTTAAAACAATTATCTTTAGTTTATTATTATTAGGAATTAGGATAGT
1847077 A--G-TATTGTTATTTTTATTATTATTTTCAAGTATTAGTCATACTACAACAAGGACTCCTTCAC
66 ATTGTTATTGTTATTTTTATTATTATTTTCAAGTATTAGTCATACTACAACAAGGACTCCTTCAC
* * *
1847139 CCTACATAAAGGAGGCTCTTCCCACCATTGTAAACACATATTTTCTTGAATACAATACATTGAGA
131 CCTATATAAAGGAGGCTCCTCCCACCATTGTAAACACATCTTTTCTTGAATACAATACATTGAGA
* *
1847204 GCTTATCTTTGCAAGTGTTG
196 GTTTATCTTTGCAAGTATTG
* *
1847224 ATTAGGAACTAAGATAAAGTTAAAAACAATTATCTTTAGTTTATTATTATTAGGAATTAGGATAG
1 ATTAGGAATTAAGATAGAGTT-AAAACAATTATCTTTAGTTTATTATTATTAGGAATTAGGATAG
*
1847289 TATTGTTATTGTTATTTTTATTATTATTTTTAAGTATTAGTCATACTACAACAAGGACTCCTTCA
65 TATTGTTATTGTTATTTTTATTATTATTTTCAAGTATTAGTCATACTACAACAAGGACTCCTTCA
*
1847354 CCCTATATAAAGGAGGCTCCTCCCACCATTATAAACACATCTTTTCTTGAATACAATACATTGAG
130 CCCTATATAAAGGAGGCTCCTCCCACCATTGTAAACACATCTTTTCTTGAATACAATACATTGAG
* * *
1847419 AGTTTATGTTTGCAAGAATTA
195 AGTTTATCTTTGCAAGTATTG
1847440 ATTAGGAATTAAGATAGAGTTAAAACAATTATCTTTAGTTTATTATTATTAGGAATTAGGATAGT
1 ATTAGGAATTAAGATAGAGTTAAAACAATTATCTTTAGTTTATTATTATTAGGAATTAGGATAGT
* * * *
1847505 ATTGTTATTATTATTTTTATTATTATTTTCAAGTGTTAGTCATACTACAACAAAGACTCATTCAC
66 ATTGTTATTGTTATTTTTATTATTATTTTCAAGTATTAGTCATACTACAACAAGGACTCCTTCAC
* * *
1847570 CTTATATAAAGGAGGCTTCTCCCACCATTGTAAA-ATCGTCTTTTCTTGAATACAATACATTGAG
131 CCTATATAAAGGAGGCTCCTCCCACCATTGTAAACA-CATCTTTTCTTGAATACAATACATTGAG
1847634 AGTTTATCTTTGCAAGTATTG
195 AGTTTATCTTTGCAAGTATTG
1847655 ATTA
1 ATTA
1847659 CTTGTTCCTT
Statistics
Matches: 400, Mismatches: 27, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
209 19 0.05
210 38 0.09
212 1 0.00
213 2 0.00
214 1 0.00
215 185 0.46
216 154 0.38
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39
Consensus pattern (215 bp):
ATTAGGAATTAAGATAGAGTTAAAACAATTATCTTTAGTTTATTATTATTAGGAATTAGGATAGT
ATTGTTATTGTTATTTTTATTATTATTTTCAAGTATTAGTCATACTACAACAAGGACTCCTTCAC
CCTATATAAAGGAGGCTCCTCCCACCATTGTAAACACATCTTTTCTTGAATACAATACATTGAGA
GTTTATCTTTGCAAGTATTG
Found at i:1847524 original size:12 final size:12
Alignment explanation
Indices: 1847504--1847533 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1847494 ATTAGGATAG
*
1847504 TATTGTTATTAT
1 TATTTTTATTAT
1847516 TATTTTTATTAT
1 TATTTTTATTAT
1847528 TATTTT
1 TATTTT
1847534 CAAGTGTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (12 bp):
TATTTTTATTAT
Found at i:1847986 original size:15 final size:15
Alignment explanation
Indices: 1847965--1848003 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
1847955 GTCTTTATTT
1847965 ATCTTTATTATCTTA
1 ATCTTTATTATCTTA
* *
1847980 GTCTTTATTGTCTTA
1 ATCTTTATTATCTTA
1847995 ATCTTTATT
1 ATCTTTATT
1848004 CTTGATTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.21, C:0.13, G:0.05, T:0.62
Consensus pattern (15 bp):
ATCTTTATTATCTTA
Found at i:1848506 original size:41 final size:39
Alignment explanation
Indices: 1848461--1848630 Score: 153
Period size: 41 Copynumber: 4.2 Consensus size: 39
1848451 TACATATATT
* *
1848461 GTGGCGTTTTTAGACAAACACCTCTAAAACCTAGTACTTTA
1 GTGGCGTTTTCA-ACAAACACCGCTAAAA-CTAGTACTTTA
* *
1848502 GTGGCGTTGTTCAACAAACACCGCTAAAATTCAATACTTTA
1 GTGGCGTT-TTCAACAAACACCGCTAAAACT-AGTACTTTA
* * * * *
1848543 ATGGAGTTTT-AACCAAAAAACCGCTAAATACTCGTAATTTA
1 GTGGCGTTTTCAA-C-AAACACCGCTAAA-ACTAGTACTTTA
**
1848584 GTGGCGTTTTCCAACAAACGTCGCTAAAACATAGTACTTTA
1 GTGGCGTTTT-CAACAAACACCGCTAAAAC-TAGTACTTTA
1848625 GTGGCG
1 GTGGCG
1848631 CTTTAATAAA
Statistics
Matches: 103, Mismatches: 18, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
39 2 0.02
40 6 0.06
41 87 0.84
42 6 0.06
43 2 0.02
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (39 bp):
GTGGCGTTTTCAACAAACACCGCTAAAACTAGTACTTTA
Found at i:1848737 original size:43 final size:43
Alignment explanation
Indices: 1848661--1848747 Score: 106
Period size: 43 Copynumber: 2.0 Consensus size: 43
1848651 GAAAGACTCA
* * *
1848661 TACATTAGTGGTGTTTTTTTTAATAAACACCGCAA-TTTATCAG
1 TACATTAGTGGCGTTTTATTTAACAAACACCGCAAGTTTA-CAG
*
1848704 TACATTAGTGGCGTTTCTATTT-ACAAACGCCGCAAGTTTACAG
1 TACATTAGTGGCGTTT-TATTTAACAAACACCGCAAGTTTACAG
1848747 T
1 T
1848748 TTCTAAGTCT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
43 30 0.79
44 8 0.21
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (43 bp):
TACATTAGTGGCGTTTTATTTAACAAACACCGCAAGTTTACAG
Found at i:1851932 original size:41 final size:41
Alignment explanation
Indices: 1851875--1852123 Score: 187
Period size: 43 Copynumber: 6.1 Consensus size: 41
1851865 AAGGTAATTA
1851875 GCGGCGTTTGTTCTAAAAACGCCGCTATAGATCTGACCTTT
1 GCGGCGTTTGTTCTAAAAACGCCGCTATAGATCTGACCTTT
* * * *
1851916 GCGGCGTTTGTACTAAAAGCGTCGCTATAGATCTGATCTTTT
1 GCGGCGTTTGTTCTAAAAACGCCGCTATAGATCTGA-CCTTT
* * * * **
1851958 GCAGCGTTTGTTCTAAAAACACCGCTATATAAACAAACCTGTT
1 GCGGCGTTTGTTCTAAAAACGCCGCTATA-GATCTGACCT-TT
* * *
1852001 GCAGCGTTTGTTCTAAAAACGCCGCTATATATATCGACC--T
1 GCGGCGTTTGTTCTAAAAACGCCGCTATAGATCT-GACCTTT
* **
1852041 ------TTTG---GAACAAACGCCGCTATAGATAGAGACCTTTT
1 GCGGCGTTTGTTCTAA-AAACGCCGCTATAGAT-CTGACC-TTT
*
1852076 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTTGACCTATT
1 GCGGCGTTTGTTCTAAAAACGCCGCTATAGATC-TGACCT-TT
1852119 GCGGC
1 GCGGC
1852124 ATTTTTTGGA
Statistics
Matches: 161, Mismatches: 27, Indels: 38
0.71 0.12 0.17
Matches are distributed among these distances:
31 2 0.01
32 19 0.12
34 4 0.02
35 1 0.01
40 1 0.01
41 37 0.23
42 32 0.20
43 63 0.39
44 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.30
Consensus pattern (41 bp):
GCGGCGTTTGTTCTAAAAACGCCGCTATAGATCTGACCTTT
Found at i:1852985 original size:43 final size:43
Alignment explanation
Indices: 1852913--1853155 Score: 362
Period size: 43 Copynumber: 5.7 Consensus size: 43
1852903 TAACAATATA
* * *
1852913 TAGCGGCGTTTGT-CAACAAACGCCGCAATAGGTGTTGATATT
1 TAGCGGCGTTTTTCCCACAAACGCCGCAATAGGTGTTGAGATT
* * * * *
1852955 TAGCGGCGTTTTTCCAACAAATGCTGCAATAGGTATTGATATT
1 TAGCGGCGTTTTTCCCACAAACGCCGCAATAGGTGTTGAGATT
*
1852998 TAGCGACGTTTTTCCCACAAACGCCGCAATAGGTGTTGAGATT
1 TAGCGGCGTTTTTCCCACAAACGCCGCAATAGGTGTTGAGATT
1853041 TAGCGGCGTTTTTCCCACAAACGCCGCAATAGGTGTTGAGATT
1 TAGCGGCGTTTTTCCCACAAACGCCGCAATAGGTGTTGAGATT
* *
1853084 TAGCGGCGTTTTTTCCACAAACGCCGCAATAGGTCTTGAGATT
1 TAGCGGCGTTTTTCCCACAAACGCCGCAATAGGTGTTGAGATT
* *
1853127 TAACGGCGTTTTTCCCACAAACACCGCAA
1 TAGCGGCGTTTTTCCCACAAACGCCGCAA
1853156 AAGATCTAGT
Statistics
Matches: 184, Mismatches: 16, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
42 12 0.07
43 172 0.93
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (43 bp):
TAGCGGCGTTTTTCCCACAAACGCCGCAATAGGTGTTGAGATT
Found at i:1853182 original size:86 final size:85
Alignment explanation
Indices: 1852888--1853182 Score: 351
Period size: 86 Copynumber: 3.4 Consensus size: 85
1852878 TGGTAACAAA
* * * * * *
1852888 AAACGCCGCAATAGATAACAATATATAGCGGCG-TTTGTCAACAAACGCCGCAATAGGTGTTGAT
1 AAACGCCGCAATAGGT-ATAGTATATAGCGGCGTTTTTTCCACAAACGCCGCAATAGGTGTTGAG
*
1852952 ATTTAGCGGCGTTTTTCCAAC
65 ATTTAGCGGCGTTTTTCCCAC
* * * * * *
1852973 AAATGCTGCAATAGGTATTGATATTTAGCGACGTTTTTCCCACAAACGCCGCAATAGGTGTTGAG
1 AAACGCCGCAATAGGTATAG-TATATAGCGGCGTTTTTTCCACAAACGCCGCAATAGGTGTTGAG
1853038 ATTTAGCGGCGTTTTTCCCAC
65 ATTTAGCGGCGTTTTTCCCAC
* * *
1853059 AAACGCCGCAATAGGTGTTGAG-ATTTAGCGGCGTTTTTTCCACAAACGCCGCAATAGGTCTTGA
1 AAACGCCGCAATAGGT-AT-AGTATATAGCGGCGTTTTTTCCACAAACGCCGCAATAGGTGTTGA
*
1853123 GATTTAACGGCGTTTTTCCCAC
64 GATTTAGCGGCGTTTTTCCCAC
* * * *
1853145 AAACACCGCAAAAGATCTAGTATATAGCGGCGTTTTTT
1 AAACGCCGCAATAGGTATAGTATATAGCGGCGTTTTTT
1853183 AGAACAAACG
Statistics
Matches: 179, Mismatches: 26, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
84 3 0.02
85 40 0.22
86 134 0.75
87 1 0.01
88 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (85 bp):
AAACGCCGCAATAGGTATAGTATATAGCGGCGTTTTTTCCACAAACGCCGCAATAGGTGTTGAGA
TTTAGCGGCGTTTTTCCCAC
Found at i:1853194 original size:129 final size:129
Alignment explanation
Indices: 1852909--1853181 Score: 374
Period size: 129 Copynumber: 2.1 Consensus size: 129
1852899 TAGATAACAA
* *
1852909 TATATAGCGGCGTTTGTCAACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAACA
1 TATATAGCGGCGTTTTTCAACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCAACA
* * * * * * * *
1852974 AATGCTGCAATAGGTATTGATATTTAGCGACGTTTTTCCCACAAACGCCGCAATAGGTGTTGAG
66 AACGCCGCAATAGGTATTGAGATTTAACGACGTTTTTCCCACAAACACCGCAAAAGATGCTGAG
* *
1853038 -ATTTAGCGGCGTTTTTCCCACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTTCC-A
1 TATATAGCGGCGTTTTT-CAACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCG-TTTTTCCAA
* *
1853101 CAAACGCCGCAATAGGTCTTGAGATTTAACGGCGTTTTTCCCACAAACACCGCAAAAGAT-CT-A
64 CAAACGCCGCAATAGGTATTGAGATTTAACGACGTTTTTCCCACAAACACCGCAAAAGATGCTGA
1853164 G
129 G
1853165 TATATAGCGGCGTTTTT
1 TATATAGCGGCGTTTTT
1853182 TAGAACAAAC
Statistics
Matches: 126, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
127 2 0.02
128 30 0.24
129 87 0.69
130 7 0.06
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.30
Consensus pattern (129 bp):
TATATAGCGGCGTTTTTCAACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCAACA
AACGCCGCAATAGGTATTGAGATTTAACGACGTTTTTCCCACAAACACCGCAAAAGATGCTGAG
Found at i:1853377 original size:21 final size:21
Alignment explanation
Indices: 1853351--1853409 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
1853341 ATTTTCCAAT
* *
1853351 AAACTTTACATCCATAACAAC
1 AAACTTAAAATCCATAACAAC
*
1853372 AAACTTAAAATCCATAACAAG
1 AAACTTAAAATCCATAACAAC
** *
1853393 AAAAATGAAATCCATAA
1 AAACTTAAAATCCATAA
1853410 TAATAAATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.56, C:0.20, G:0.03, T:0.20
Consensus pattern (21 bp):
AAACTTAAAATCCATAACAAC
Found at i:1854816 original size:16 final size:16
Alignment explanation
Indices: 1854754--1854821 Score: 63
Period size: 16 Copynumber: 4.4 Consensus size: 16
1854744 CAACCAACAG
1854754 TTCCAAACATCACAAT
1 TTCCAAACATCACAAT
*
1854770 TTCC--ATATCACAAT
1 TTCCAAACATCACAAT
* *
1854784 TTACC--TCATCCAAAAT
1 TT-CCAAACAT-CACAAT
1854800 TTCCAAACATCACAAT
1 TTCCAAACATCACAAT
1854816 TTCCAA
1 TTCCAA
1854822 CAGTTCCAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
14 11 0.26
15 6 0.14
16 22 0.52
17 3 0.07
ACGTcount: A:0.40, C:0.31, G:0.00, T:0.29
Consensus pattern (16 bp):
TTCCAAACATCACAAT
Found at i:1857735 original size:41 final size:41
Alignment explanation
Indices: 1857678--1858019 Score: 326
Period size: 41 Copynumber: 8.3 Consensus size: 41
1857668 TGTTTGTTCA
1857678 AAAAACGCCACTAAAGTACAGTACTTTAGCGGCGTTTGTAT
1 AAAAACGCCACTAAAGTACAGTACTTTAGCGGCGTTTGTAT
* * * **
1857719 AAAAATGCCACGAAAGTACTAGT-CTATAAAGGCGTTTGT-T
1 AAAAACGCCACTAAAGTAC-AGTACTTTAGCGGCGTTTGTAT
1857759 CAAAAACGCCACTAAAGTACAGTACTTTAGCGGCGTTTGTAT
1 -AAAAACGCCACTAAAGTACAGTACTTTAGCGGCGTTTGTAT
* * * *
1857801 AAAAACACAACAAAAGTACTAGT-CTATAGCGGCGTTTGT-T
1 AAAAACGCCACTAAAGTAC-AGTACTTTAGCGGCGTTTGTAT
* * *
1857841 CAAAAAACGCCACTAAAGTACTAATA-TATAGCGGCGTTTGTTTT
1 --AAAAACGCCACTAAAGTAC-AGTACTTTAGCGGCGTTTG-TAT
* ** * * *
1857885 GAAAACGCCACTAAAG-ATTGTATTTTGGCGGCGTTTGTAG
1 AAAAACGCCACTAAAGTACAGTACTTTAGCGGCGTTTGTAT
*
1857925 AAAAATGCCACTAAAGTACAGT-CTTTAGCGGCGTTTGTAT
1 AAAAACGCCACTAAAGTACAGTACTTTAGCGGCGTTTGTAT
* *
1857965 AAAAGCGCCA-TAAAAGTATTAGTA-TTTAGCGGCGTTTGT-T
1 AAAAACGCCACT-AAAGTA-CAGTACTTTAGCGGCGTTTGTAT
1858005 CAAAAAACGCCACTA
1 --AAAAACGCCACTA
1858020 GAAATGCCGC
Statistics
Matches: 246, Mismatches: 37, Indels: 35
0.77 0.12 0.11
Matches are distributed among these distances:
39 1 0.00
40 52 0.21
41 125 0.51
42 65 0.26
43 2 0.01
44 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (41 bp):
AAAAACGCCACTAAAGTACAGTACTTTAGCGGCGTTTGTAT
Found at i:1857792 original size:82 final size:83
Alignment explanation
Indices: 1857654--1858019 Score: 440
Period size: 82 Copynumber: 4.4 Consensus size: 83
1857644 TCTGTCATTC
* *
1857654 CTAGTCTATAGCAGTGTTTGTTCAAAAAACGCCACTAAAGTACAGTACTTTAGCGGCGTTTGTAT
1 CTAGTCTATAGCGGCGTTTGTTCAAAAAACGCCACTAAAGTACAGTACTTTAGCGGCGTTTGTAT
* *
1857719 AAAAATGCCACGAAAGTA
66 AAAAACGCCACAAAAGTA
**
1857737 CTAGTCTATAAAGGCGTTTGTTC-AAAAACGCCACTAAAGTACAGTACTTTAGCGGCGTTTGTAT
1 CTAGTCTATAGCGGCGTTTGTTCAAAAAACGCCACTAAAGTACAGTACTTTAGCGGCGTTTGTAT
* *
1857801 AAAAACACAACAAAAGTA
66 AAAAACGCCACAAAAGTA
* *
1857819 CTAGTCTATAGCGGCGTTTGTTCAAAAAACGCCACTAAAGTACTAATA-TATAGCGGCGTTTGTT
1 CTAGTCTATAGCGGCGTTTGTTCAAAAAACGCCACTAAAGTAC-AGTACTTTAGCGGCGTTTG-T
* * *
1857883 TTGAAAACGCCACTAAAG-A
64 ATAAAAACGCCACAAAAGTA
* * * * *
1857902 -TTGTATTTTGGCGGCGTTTG-T-AGAAAAATGCCACTAAAGTACAGT-CTTTAGCGGCGTTTGT
1 CTAGT-CTATAGCGGCGTTTGTTCA-AAAAACGCCACTAAAGTACAGTACTTTAGCGGCGTTTGT
* *
1857963 ATAAAAGCGCCATAAAAGTA
64 ATAAAAACGCCACAAAAGTA
* * *
1857983 TTAGTATTTAGCGGCGTTTGTTCAAAAAACGCCACTA
1 CTAGTCTATAGCGGCGTTTGTTCAAAAAACGCCACTA
1858020 GAAATGCCGC
Statistics
Matches: 240, Mismatches: 33, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
80 14 0.06
81 30 0.12
82 114 0.47
83 65 0.27
84 17 0.07
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (83 bp):
CTAGTCTATAGCGGCGTTTGTTCAAAAAACGCCACTAAAGTACAGTACTTTAGCGGCGTTTGTAT
AAAAACGCCACAAAAGTA
Found at i:1857937 original size:165 final size:164
Alignment explanation
Indices: 1857654--1858019 Score: 459
Period size: 165 Copynumber: 2.2 Consensus size: 164
1857644 TCTGTCATTC
* * * *
1857654 CTAGTCTATAGCAGTGTTTGTTCAAAAAACGCCACTAAAGTACAGTACTTTAGCGGCGTTTGTAT
1 CTAGTCTATAGCGGCGTTTGTTCAAAAAACGCCACTAAAGTACAATACTATAGCGGCGTTTGTAT
* *
1857719 AAAAATGCCACGAAAGTACTAGTCTATAAAGGCGTTTGTTCAAAAACGCCACTAAAGTACAGTAC
66 AAAAACGCCACGAAAGTACTAGTCTATAAAGGCGTTTGTACAAAAACGCCACTAAAGTACAGT-C
1857784 TTTAGCGGCGTTTGTATAAAAACACAACAAAAGTA
130 TTTAGCGGCGTTTGTATAAAAACACAACAAAAGTA
1857819 CTAGTCTATAGCGGCGTTTGTTCAAAAAACGCCACTAAAGTACTAATA-TATAGCGGCGTTTGTT
1 CTAGTCTATAGCGGCGTTTGTTCAAAAAACGCCACTAAAGTAC-AATACTATAGCGGCGTTTG-T
* * * * * * *** * *
1857883 TTGAAAACGCCACTAAAG-A-TTGTATTTTGGCGGCGTTTGTAGAAAAATGCCACTAAAGTACAG
64 ATAAAAACGCCACGAAAGTACTAGT-CTATAAAGGCGTTTGTACAAAAACGCCACTAAAGTACAG
* * * *
1857946 TCTTTAGCGGCGTTTGTATAAAAGCGCCATAAAAGTA
128 TCTTTAGCGGCGTTTGTATAAAAACACAACAAAAGTA
* * *
1857983 TTAGTATTTAGCGGCGTTTGTTCAAAAAACGCCACTA
1 CTAGTCTATAGCGGCGTTTGTTCAAAAAACGCCACTA
1858020 GAAATGCCGC
Statistics
Matches: 174, Mismatches: 24, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
164 69 0.40
165 87 0.50
166 18 0.10
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (164 bp):
CTAGTCTATAGCGGCGTTTGTTCAAAAAACGCCACTAAAGTACAATACTATAGCGGCGTTTGTAT
AAAAACGCCACGAAAGTACTAGTCTATAAAGGCGTTTGTACAAAAACGCCACTAAAGTACAGTCT
TTAGCGGCGTTTGTATAAAAACACAACAAAAGTA
Found at i:1864195 original size:15 final size:16
Alignment explanation
Indices: 1864175--1864204 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1864165 CGCCGACAAA
1864175 AAAATT-ACTATTCAC
1 AAAATTCACTATTCAC
1864190 AAAATTCACTATTCA
1 AAAATTCACTATTCA
1864205 TGTAAATACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATTCACTATTCAC
Found at i:1864966 original size:2 final size:2
Alignment explanation
Indices: 1864961--1864995 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1864951 AAAATTAAAT
1864961 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1864996 TAACTTAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1866010 original size:2 final size:2
Alignment explanation
Indices: 1866003--1866037 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1865993 GTATTATCAT
1866003 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1866038 TAAGCTCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1866669 original size:26 final size:26
Alignment explanation
Indices: 1866640--1866699 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
1866630 TTAAATATTT
* *
1866640 TTATATTTTTAATTTTGTAAAAAAAA
1 TTATAATTTAAATTTTGTAAAAAAAA
* *
1866666 TTATGAATTTAAATTTTTTAAAGAAAA
1 TTAT-AATTTAAATTTTGTAAAAAAAA
1866693 TATATAA
1 T-TATAA
1866700 ATATTTTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 4 0.14
27 21 0.75
28 3 0.11
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (26 bp):
TTATAATTTAAATTTTGTAAAAAAAA
Found at i:1872208 original size:37 final size:37
Alignment explanation
Indices: 1872153--1872228 Score: 98
Period size: 37 Copynumber: 2.1 Consensus size: 37
1872143 TTGACCATAG
*
1872153 TGTACGATCCAAAATTTACATGCGTAGGAAGTGTACC
1 TGTACGATCCAAAATTTACATGCGTAGGAAGCGTACC
* * * * *
1872190 TGTATGATCCAGAATTTACGTGCGTTGGATGCGTACC
1 TGTACGATCCAAAATTTACATGCGTAGGAAGCGTACC
1872227 TG
1 TG
1872229 GTCAAAAGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.30
Consensus pattern (37 bp):
TGTACGATCCAAAATTTACATGCGTAGGAAGCGTACC
Found at i:1872597 original size:18 final size:20
Alignment explanation
Indices: 1872552--1872597 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1872542 CCCTTATAGG
1872552 GAGTATCGATACTTTACCCTT
1 GAGTATCGATAC-TTACCCTT
1872573 G-GTATCGATAC-T-CCCTT
1 GAGTATCGATACTTACCCTT
1872590 GAGTATCG
1 GAGTATCG
1872598 GTACCAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 6 0.25
18 7 0.29
20 10 0.42
21 1 0.04
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.35
Consensus pattern (20 bp):
GAGTATCGATACTTACCCTT
Found at i:1889848 original size:29 final size:29
Alignment explanation
Indices: 1889805--1889887 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
1889795 CTCACCTAAC
*
1889805 TAAATTGATGTAAGCAATGACATCATTATT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
1889835 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
1889864 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
1889888 ATTTAGTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 45 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:1894616 original size:29 final size:29
Alignment explanation
Indices: 1894583--1894655 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
1894573 TAAATTGATA
*
1894583 TAAGCAATGACATCATTATTTAAATGACG
1 TAAGCAATGACATCATTAATTAAATGACG
* *
1894612 TAAGCAATGACATCTTTAATTAAATGATG
1 TAAGCAATGACATCATTAATTAAATGACG
*
1894641 TAAGTAATGACATCA
1 TAAGCAATGACATCA
1894656 ATTTAGTTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (29 bp):
TAAGCAATGACATCATTAATTAAATGACG
Found at i:1903030 original size:21 final size:21
Alignment explanation
Indices: 1903004--1903043 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1902994 CCAGATTCGC
1903004 AACGCGAACTTCGACTATCTT
1 AACGCGAACTTCGACTATCTT
*
1903025 AACGCGAACTTGGACTATC
1 AACGCGAACTTCGACTATC
1903044 GCAATGCGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (21 bp):
AACGCGAACTTCGACTATCTT
Found at i:1903052 original size:21 final size:21
Alignment explanation
Indices: 1903000--1903052 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1902990 GTTTCCAGAT
1903000 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
** *
1903021 TCTTAACGCGAACTTGGACTA
1 TCGCAACGCGAACTTCGACTA
*
1903042 TCGCAATGCGA
1 TCGCAACGCGA
1903053 TTTACATATT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:1903137 original size:40 final size:40
Alignment explanation
Indices: 1903086--1903338 Score: 452
Period size: 40 Copynumber: 6.2 Consensus size: 40
1903076 TCCAAGTTCG
1903086 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
1903126 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
*
1903166 CGTTGTGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
1903208 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
1903248 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
1903288 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
*
1903330 CATTGCGAT
1 CGTTGCGAT
1903339 TTATTCCAAA
Statistics
Matches: 206, Mismatches: 3, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
40 146 0.71
41 6 0.03
42 54 0.26
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.36
Consensus pattern (40 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
Found at i:1903216 original size:82 final size:80
Alignment explanation
Indices: 1903086--1903338 Score: 452
Period size: 82 Copynumber: 3.1 Consensus size: 80
1903076 TCCAAGTTCG
1903086 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
1903151 GCGATTTTCCAAATT
66 GCGATTTTCCAAATT
*
1903166 CGTTGTGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
1903231 TTGCGATTTTCCAAATT
64 TTGCGATTTTCCAAATT
1903248 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
1903313 GCGATTTATTCCAAATT
66 GCGA-TT-TTCCAAATT
*
1903330 CATTGCGAT
1 CGTTGCGAT
1903339 TTATTCCAAA
Statistics
Matches: 166, Mismatches: 3, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
80 66 0.40
81 6 0.04
82 94 0.57
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.36
Consensus pattern (80 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
GCGATTTTCCAAATT
Found at i:1903234 original size:122 final size:122
Alignment explanation
Indices: 1903086--1903338 Score: 488
Period size: 122 Copynumber: 2.1 Consensus size: 122
1903076 TCCAAGTTCG
1903086 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
*
1903151 GCGATTTTCCAAATTCGTTGTGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
66 GCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1903208 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
1903273 GCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
66 GCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
*
1903330 CATTGCGAT
1 CGTTGCGAT
1903339 TTATTCCAAA
Statistics
Matches: 129, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
122 129 1.00
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.36
Consensus pattern (122 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
GCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:1903335 original size:21 final size:21
Alignment explanation
Indices: 1903311--1903361 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
1903301 GAAGTTCGCG
1903311 TTGCGATTTATTCCAAATTCA
1 TTGCGATTTATTCCAAATTCA
**
1903332 TTGCGATTTATTCCAAATTTG
1 TTGCGATTTATTCCAAATTCA
1903353 TTGCGATTT
1 TTGCGATTT
1903362 TCCCACATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.47
Consensus pattern (21 bp):
TTGCGATTTATTCCAAATTCA
Found at i:1903672 original size:42 final size:42
Alignment explanation
Indices: 1903613--1903729 Score: 220
Period size: 42 Copynumber: 2.8 Consensus size: 42
1903603 TCGTAACGAA
1903613 AATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGG
1 AATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGG
1903655 AATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGG
1 AATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGG
1903697 -A-AAATCGCAACGCGAACTTCGACTATCGCAACG
1 AATAAATCGCAACGCGAACTTCGACTATCGCAACG
1903730 CGAATTTGGA
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
40 32 0.43
41 1 0.01
42 42 0.56
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.18
Consensus pattern (42 bp):
AATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGG
Found at i:1903754 original size:42 final size:40
Alignment explanation
Indices: 1903618--1903754 Score: 202
Period size: 42 Copynumber: 3.3 Consensus size: 40
1903608 ACGAAAATAA
1903618 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAAT
1 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAAT
*
1903658 AAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAAA
1 --ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAAT
* *
1903700 ATCGCAACGCGAACTTCGACTATCGCAACGCGAATTTGGACT
1 ATCGCAACGCGAACTTCGACTATCGCAA--CGAACTTGGAAT
*
1903742 ATCGCAATGCGAA
1 ATCGCAACGCGAA
1903755 TATATAAATC
Statistics
Matches: 88, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
40 28 0.32
42 60 0.68
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (40 bp):
ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAAT
Found at i:1903755 original size:21 final size:21
Alignment explanation
Indices: 1903618--1903754 Score: 156
Period size: 21 Copynumber: 6.6 Consensus size: 21
1903608 ACGAAAATAA
1903618 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* *
1903639 ATCGCAA--CGAACTTGGAAT
1 ATCGCAACGCGAACTTCGACT
1903658 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
* **
1903681 ATCGCAA--CGAACTTGGAAA
1 ATCGCAACGCGAACTTCGACT
1903700 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* *
1903721 ATCGCAACGCGAATTTGGACT
1 ATCGCAACGCGAACTTCGACT
*
1903742 ATCGCAATGCGAA
1 ATCGCAACGCGAA
1903755 TATATAAATC
Statistics
Matches: 97, Mismatches: 13, Indels: 12
0.80 0.11 0.10
Matches are distributed among these distances:
19 26 0.27
21 61 0.63
23 10 0.10
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:1904359 original size:30 final size:31
Alignment explanation
Indices: 1904325--1904391 Score: 79
Period size: 30 Copynumber: 2.2 Consensus size: 31
1904315 AACAAAATGC
1904325 TAATAAAT-AAA-AAA-AATATAAAAAAAATAA
1 TAATAAATGAAAGAAAGAA-AT-AAAAAAATAA
*
1904355 TAAT-AATGAAAGAAAGAAATAATAAAATAA
1 TAATAAATGAAAGAAAGAAATAAAAAAATAA
1904385 TAATAAA
1 TAATAAA
1904392 AGGTTAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
29 3 0.09
30 20 0.62
31 7 0.22
32 2 0.06
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (31 bp):
TAATAAATGAAAGAAAGAAATAAAAAAATAA
Found at i:1905538 original size:11 final size:11
Alignment explanation
Indices: 1905522--1905558 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
1905512 GTTTGGACCC
1905522 TAAAAA-AAACA
1 TAAAAAGAAA-A
1905533 TAAAAAGAAAA
1 TAAAAAGAAAA
1905544 TAAAAAGAAAA
1 TAAAAAGAAAA
1905555 TAAA
1 TAAA
1905559 TAATAATACT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 22 0.88
12 3 0.12
ACGTcount: A:0.81, C:0.03, G:0.05, T:0.11
Consensus pattern (11 bp):
TAAAAAGAAAA
Found at i:1905596 original size:23 final size:22
Alignment explanation
Indices: 1905554--1905597 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
1905544 TAAAAAGAAA
1905554 ATAAATAATAATACTGATATAAT
1 ATAAATAATAATAC-GATATAAT
1905577 ATAAATTATATAATAC-ATATA
1 ATAAA-TA-ATAATACGATATA
1905598 TTTCAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 10 0.53
24 2 0.11
25 7 0.37
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (22 bp):
ATAAATAATAATACGATATAAT
Found at i:1905651 original size:30 final size:32
Alignment explanation
Indices: 1905594--1905754 Score: 99
Period size: 30 Copynumber: 5.2 Consensus size: 32
1905584 ATATAATACA
* ** *
1905594 TATATTTCAAAAATATTTTTTAAACTATATAT
1 TATATTTAAAAAACGTTTTTAAAACTATATAT
*
1905626 TATATTT-AAAAA-GTTTTCAAAACTAT-TA-
1 TATATTTAAAAAACGTTTTTAAAACTATATAT
** *
1905654 TATAGTTTTCAAAATG-TTTTAAAA--ATATAT
1 TATA-TTTAAAAAACGTTTTTAAAACTATATAT
*
1905684 AAGT-TTTAAAAAACGTTTTTAAAA-TATAT-T
1 TA-TATTTAAAAAACGTTTTTAAAACTATATAT
* *
1905714 ATATAATTTATTCAAAATGTTTTTAAAACTATATAT
1 -TAT-ATTTA--AAAAACGTTTTTAAAACTATATAT
1905750 TATAT
1 TATAT
1905755 AAGTTTTTAA
Statistics
Matches: 102, Mismatches: 12, Indels: 28
0.72 0.08 0.20
Matches are distributed among these distances:
28 6 0.06
29 15 0.15
30 33 0.32
31 12 0.12
32 11 0.11
34 16 0.16
35 8 0.08
36 1 0.01
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.47
Consensus pattern (32 bp):
TATATTTAAAAAACGTTTTTAAAACTATATAT
Found at i:1905683 original size:27 final size:29
Alignment explanation
Indices: 1905633--1905712 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 29
1905623 TATTATATTT
*
1905633 AAAAA-GTTTTCAAAACTATTATATAGTTTT-
1 AAAAACGTTTT-AAAAATA-TATA-AGTTTTA
* *
1905663 CAAAATGTTTTAAAAATATATAAGTTTTA
1 AAAAACGTTTTAAAAATATATAAGTTTTA
*
1905692 AAAAACGTTTTTAAAATATAT
1 AAAAACGTTTTAAAAATATAT
1905713 TATATAATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
28 6 0.14
29 22 0.51
30 10 0.23
31 5 0.12
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.41
Consensus pattern (29 bp):
AAAAACGTTTTAAAAATATATAAGTTTTA
Found at i:1905753 original size:37 final size:36
Alignment explanation
Indices: 1905707--1905879 Score: 148
Period size: 37 Copynumber: 4.8 Consensus size: 36
1905697 CGTTTTTAAA
*
1905707 ATATATTATATAATTTATTC-AAAATGTTTTTAAAACT
1 ATATATTATAT-ATTT-TTCAAAAATGTTTTAAAAACT
1905744 ATATATTATATAAGTTTTT--AAAATGATTTT-AAAAC-
1 ATATATTATAT-A-TTTTTCAAAAATG-TTTTAAAAACT
*
1905779 -TATATTATATA-TTTTCTAAAATGTTTTAAAAACT
1 ATATATTATATATTTTTCAAAAATGTTTTAAAAACT
* * *
1905813 ATATGTTATATAGTTTTCAAAAAATATTTTAAAAAACT
1 ATATATTATATATTTTTC-AAAAATGTTTT-AAAAACT
*
1905851 ATATATTACCCATA-TTTTC-AAAATGTTTT
1 ATATATTA--TATATTTTTCAAAAATGTTTT
1905880 CCTTTTAAAA
Statistics
Matches: 118, Mismatches: 6, Indels: 24
0.80 0.04 0.16
Matches are distributed among these distances:
31 4 0.03
32 4 0.03
33 12 0.10
34 10 0.08
35 10 0.08
36 16 0.14
37 37 0.31
38 17 0.14
39 5 0.04
40 3 0.03
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (36 bp):
ATATATTATATATTTTTCAAAAATGTTTTAAAAACT
Found at i:1905754 original size:71 final size:70
Alignment explanation
Indices: 1905679--1905846 Score: 211
Period size: 69 Copynumber: 2.4 Consensus size: 70
1905669 GTTTTAAAAA
* *
1905679 TATATAAGTTTTAAAAAACGTTTTTAAAA-TATATTATATAATTTAT-TCAAAATGTTTTTAAAA
1 TATATAAGTTTTAAAAAACGATTTTAAAACTATATTATAT-ATTT-TCT-AAAATGTTTTAAAAA
1905742 CTATATAT
63 CTATATAT
* *
1905750 TATATAAGTTTT-TAAAATGATTTTAAAACTATATTATATATTTTCTAAAATGTTTTAAAAACTA
1 TATATAAGTTTTAAAAAACGATTTTAAAACTATATTATATATTTTCTAAAATGTTTTAAAAACTA
*
1905814 TATGT
66 TATAT
*
1905819 TATAT-AGTTTTCAAAAAA-TATTTTAAAA
1 TATATAAGTTTT-AAAAAACGATTTTAAAA
1905847 AACTATATAT
Statistics
Matches: 86, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
68 6 0.07
69 36 0.42
70 22 0.26
71 22 0.26
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (70 bp):
TATATAAGTTTTAAAAAACGATTTTAAAACTATATTATATATTTTCTAAAATGTTTTAAAAACTA
TATAT
Found at i:1906684 original size:20 final size:20
Alignment explanation
Indices: 1906659--1906697 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1906649 TTTTTGTTTG
*
1906659 GCCGCCGATGAACGACGGCC
1 GCCGCCGATCAACGACGGCC
*
1906679 GCCGCCGATCAACGGCGGC
1 GCCGCCGATCAACGACGGC
1906698 GGTGAGGCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.41, G:0.36, T:0.05
Consensus pattern (20 bp):
GCCGCCGATCAACGACGGCC
Found at i:1908340 original size:10 final size:10
Alignment explanation
Indices: 1908325--1908358 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1908315 TTCATTTACC
1908325 ATTTATTTTT
1 ATTTATTTTT
1908335 ATTTATTTTT
1 ATTTATTTTT
* *
1908345 ATCTATTTCT
1 ATTTATTTTT
1908355 ATTT
1 ATTT
1908359 TACTAACGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:1918945 original size:106 final size:106
Alignment explanation
Indices: 1918567--1919024 Score: 805
Period size: 105 Copynumber: 4.3 Consensus size: 106
1918557 AGGTTTTACC
*
1918567 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
1918632 ACGAAGGGACCGCTGGTTGTCAACAAA-TATTTCTCAATGT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTT
1918672 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1918737 ACGAAGGGACCGCTGCTTGTCAACAAAC-ATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTT
*
1918777 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1918842 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTT
* *
1918883 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAATGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1918948 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTC-CAAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTC-AATTT
*
1918989 CGGAGCCAATTTCAACTTCACAACGAAGGATATTGG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
1919025 CCTCGGAACA
Statistics
Matches: 339, Mismatches: 11, Indels: 5
0.95 0.03 0.01
Matches are distributed among these distances:
105 193 0.57
106 146 0.43
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (106 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTT
Found at i:1918972 original size:211 final size:211
Alignment explanation
Indices: 1918567--1919024 Score: 803
Period size: 211 Copynumber: 2.2 Consensus size: 211
1918557 AGGTTTTACC
*
1918567 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
1918632 ACGAAGGGACCGCTGGTTGTCAACAAATATTTCTCAATGTCAGAGCCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAACAAAAACTTCTCAATGTCAGAGCCAATTTCAACTTCACAACG
1918697 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACA
131 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACA
1918762 AAC-ATTTCTC-AATTT
196 AACAATTTC-CAAATTT
*
1918777 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1918842 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAAC
66 ACGAAGGGACCGCTGGTTGTCAACAAA-AACTTCTCAATGTCAGAGCCAATTTCAACTTCACAAC
* * *
1918907 GAAGGATATTGGACTCGAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
130 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC
1918972 AAACAATTTCCAAATTT
195 AAACAATTTCCAAATTT
*
1918989 CGGAGCCAATTTCAACTTCACAACGAAGGATATTGG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
1919025 CCTCGGAACA
Statistics
Matches: 235, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
210 90 0.38
211 101 0.43
212 44 0.19
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (211 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAAAACTTCTCAATGTCAGAGCCAATTTCAACTTCACAACG
AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACA
AACAATTTCCAAATTT
Found at i:1920412 original size:20 final size:20
Alignment explanation
Indices: 1920387--1920425 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1920377 TTTTTGTTTG
*
1920387 GCCGCCGATGAACGACGGCC
1 GCCGCCGATCAACGACGGCC
*
1920407 GCCGCCGATCAACGGCGGC
1 GCCGCCGATCAACGACGGC
1920426 GGTGAGGCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.41, G:0.36, T:0.05
Consensus pattern (20 bp):
GCCGCCGATCAACGACGGCC
Found at i:1921040 original size:32 final size:32
Alignment explanation
Indices: 1920982--1921042 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
1920972 TTTTTCTCGT
1920982 TATACATATATTTATTATTTTACTTTATTTAC
1 TATACATATATTTATTATTTTACTTTATTTAC
* * *
1921014 TATATATATATTGT-TTCTTTTCCTTTATT
1 TATACATATATT-TATTATTTTACTTTATT
1921043 ATATTCATCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 24 0.96
33 1 0.04
ACGTcount: A:0.26, C:0.10, G:0.02, T:0.62
Consensus pattern (32 bp):
TATACATATATTTATTATTTTACTTTATTTAC
Found at i:1922412 original size:21 final size:21
Alignment explanation
Indices: 1922386--1922427 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1922376 CTACCCTTGC
1922386 TCAAACAGAGAGAATGAACGT
1 TCAAACAGAGAGAATGAACGT
1922407 TCAAACAGAGAGAATGAACGT
1 TCAAACAGAGAGAATGAACGT
1922428 GTTGCATGGC
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:0.48, C:0.14, G:0.24, T:0.14
Consensus pattern (21 bp):
TCAAACAGAGAGAATGAACGT
Found at i:1922490 original size:29 final size:29
Alignment explanation
Indices: 1922457--1922512 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
1922447 TCCCAACACA
*
1922457 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
1922486 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCACTCCGGGCGACCT
1922513 ACCCTCGCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.12, C:0.38, G:0.30, T:0.20
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:1922604 original size:14 final size:14
Alignment explanation
Indices: 1922582--1922635 Score: 99
Period size: 14 Copynumber: 3.9 Consensus size: 14
1922572 CCTCGCATAG
*
1922582 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
1922596 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
1922610 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
1922624 CTCGGTCGGATG
1 CTCGGTCGGATG
1922636 CCCAGCGTGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
14 39 1.00
ACGTcount: A:0.07, C:0.28, G:0.41, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:1924306 original size:86 final size:86
Alignment explanation
Indices: 1924159--1924324 Score: 280
Period size: 86 Copynumber: 1.9 Consensus size: 86
1924149 GAAGACTTTT
* *
1924159 ATATTTAATTTATATATAGTTTAAATATTTTTTTCTCCAACCAATCACCATATGAGGAAAGGAAA
1 ATATTTAATTTATAAATAATTTAAATA-TTTTTTCTCCAACCAATCACCATATGAGGAAAGGAAA
1924224 ATAAACATGAGAGAAAGAAGCAG
65 ATAAA-ATGAGAGAAAGAAGCAG
*
1924247 ATATTTAATTTATAAATAATTTAAATA-TTTTTCTCCAACCAATCACTATATGAGGAAAGGAAAA
1 ATATTTAATTTATAAATAATTTAAATATTTTTTCTCCAACCAATCACCATATGAGGAAAGGAAAA
1924311 TAAAATGAGAGAAA
66 TAAAATGAGAGAAA
1924325 AAAAAAGCTA
Statistics
Matches: 75, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
85 10 0.13
86 40 0.53
88 25 0.33
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.31
Consensus pattern (86 bp):
ATATTTAATTTATAAATAATTTAAATATTTTTTCTCCAACCAATCACCATATGAGGAAAGGAAAA
TAAAATGAGAGAAAGAAGCAG
Found at i:1924607 original size:25 final size:26
Alignment explanation
Indices: 1924564--1924613 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
1924554 CCATATAATA
*
1924564 TTTAAAATAAAAATAAGTTTAATATC
1 TTTAAAATAAAAATAAGTTCAATATC
*
1924590 TTTAAACT-AAAATAAGTTCAATAT
1 TTTAAAATAAAAATAAGTTCAATAT
1924614 AATACTTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (26 bp):
TTTAAAATAAAAATAAGTTCAATATC
Found at i:1924966 original size:17 final size:18
Alignment explanation
Indices: 1924944--1924989 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
1924934 GGATTATGAC
**
1924944 TTAGGGTTTTTAT-TTAT
1 TTAGGGTTTTTATAGAAT
1924961 TTAGGGTTTTT-TAGAAT
1 TTAGGGTTTTTATAGAAT
1924978 TTAGGGTTTTTA
1 TTAGGGTTTTTA
1924990 GGACATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 1 0.04
17 24 0.96
ACGTcount: A:0.20, C:0.00, G:0.22, T:0.59
Consensus pattern (18 bp):
TTAGGGTTTTTATAGAAT
Found at i:1927103 original size:126 final size:124
Alignment explanation
Indices: 1926844--1927251 Score: 614
Period size: 126 Copynumber: 3.4 Consensus size: 124
1926834 ATTTCGTATT
1926844 TTTTTTTCATAATAAGAGGTGTA-TTATACATTAATAATATATTTTCATATATTTTAACATGTTT
1 TTTTTTTCATAATAAGAGGTGTATTTATACATTAATAATATATTTTCATATATTTTAACATGTTT
1926908 G--TA-TAT-TTATAT-T-ATATAATATTATTTTTATTATTTCGTGGTGTGTCGAATTA
66 GTATATTATATTATATATAATATAATATTATTTTTATTATTTCGTGGTGTGTCGAATTA
1926961 TTTTTTTCATAATAAGAGGTGTATTTATACATTAATAATATATTTTCATATATTTTAACATGTTT
1 TTTTTTTCATAATAAGAGGTGTATTTATACATTAATAATATATTTTCATATATTTTAACATGTTT
1927026 GTATATTTATATTATAATATAATATAATATTATTTTTATTATTTCGTGGTGTGTCGAATTA
66 GTATA-TTATATTAT-ATATAATATAATATTATTTTTATTATTTCGTGGTGTGTCGAATTA
* *
1927087 TTTTTTTCATAATAAGAGGTGTATTTATACATTAATAATATATTTACATATATTTTGACATGTTT
1 TTTTTTTCATAATAAGAGGTGTATTTATACATTAATAATATATTTTCATATATTTTAACATGTTT
*
1927152 GTATATT-TA-TAT-TATAATATAATATTATTTTTATTATTTCGTGGTGTGTCTAA-TA
66 GTATATTATATTATATATAATATAATATTATTTTTATTATTTCGTGGTGTGTCGAATTA
* * * * *
1927207 ---ATCTAATAATAAGAGGTGTATTTATA-A-TAATATTATTTTTTCATA
1 TTTTTTTCATAATAAGAGGTGTATTTATACATTAATAATATATTTTCATA
1927252 ATAAGAGGTG
Statistics
Matches: 273, Mismatches: 9, Indels: 20
0.90 0.03 0.07
Matches are distributed among these distances:
115 15 0.05
116 1 0.00
117 46 0.17
118 42 0.15
120 4 0.01
121 40 0.15
122 3 0.01
123 7 0.03
124 4 0.01
125 3 0.01
126 108 0.40
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.52
Consensus pattern (124 bp):
TTTTTTTCATAATAAGAGGTGTATTTATACATTAATAATATATTTTCATATATTTTAACATGTTT
GTATATTATATTATATATAATATAATATTATTTTTATTATTTCGTGGTGTGTCGAATTA
Found at i:1927235 original size:18 final size:18
Alignment explanation
Indices: 1927212--1927269 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
1927202 TAATAATCTA
1927212 ATAATAAGAGGTGTATTT
1 ATAATAAGAGGTGTATTT
* * * *
1927230 ATAATAATA-TTATTTTTT
1 ATAATAAGAGGT-GTATTT
1927248 CATAATAAGAGGTGTATTT
1 -ATAATAAGAGGTGTATTT
1927267 ATA
1 ATA
1927270 CATTAATAAT
Statistics
Matches: 29, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
17 1 0.03
18 15 0.52
19 12 0.41
20 1 0.03
ACGTcount: A:0.40, C:0.02, G:0.14, T:0.45
Consensus pattern (18 bp):
ATAATAAGAGGTGTATTT
Found at i:1927253 original size:37 final size:39
Alignment explanation
Indices: 1927212--1927290 Score: 126
Period size: 37 Copynumber: 2.1 Consensus size: 39
1927202 TAATAATCTA
* *
1927212 ATAATAAGAGGTGTATTTATA-A-TAATATTATTTTTTC
1 ATAATAAGAGGTGTATTTATACATTAATAATATATTTTC
1927249 ATAATAAGAGGTGTATTTATACATTAATAATATATTTTC
1 ATAATAAGAGGTGTATTTATACATTAATAATATATTTTC
1927288 ATA
1 ATA
1927291 TATTTTGACA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 21 0.55
38 1 0.03
39 16 0.42
ACGTcount: A:0.41, C:0.04, G:0.10, T:0.46
Consensus pattern (39 bp):
ATAATAAGAGGTGTATTTATACATTAATAATATATTTTC
Found at i:1927254 original size:154 final size:151
Alignment explanation
Indices: 1927083--1927504 Score: 741
Period size: 154 Copynumber: 2.8 Consensus size: 151
1927073 GGTGTGTCGA
1927083 ATTATTTTTTTCATAATAAGAGGTGTATTTATACATTAATAATATATTTACATATATTTTGACAT
1 ATTA-TTTTTTCATAATAAGAGGTGTATTTATACATTAATAATATATTT-CATATATTTTGACAT
*
1927148 GTTTGTATATTTATATTATAATATAATATTATTTTTATTATTTCGTGGTGTGTCTAATAATCTAA
64 GTTTGTATAATTATATTATAATATAATATTATTTTTATTATTTCGTGGTGTGTCTAAT--TCTAA
1927213 TAATAAGAGGTGTATTTATAATAAT
127 TAATAAGAGGTGTATTTATAATAAT
1927238 ATTATTTTTTCATAATAAGAGGTGTATTTATACATTAATAATATATTTTCATATATTTTGACATG
1 ATTATTTTTTCATAATAAGAGGTGTATTTATACATTAATAATATA-TTTCATATATTTTGACATG
1927303 TTTGTATAATTATATTATAATATAATATTATTTTTATTATTTCGTGGTGTG------TCTAATAA
65 TTTGTATAATTATATTATAATATAATATTATTTTTATTATTTCGTGGTGTGTCTAATTCTAATAA
1927362 TAAGAGGTGTATTTATAATAAT
130 TAAGAGGTGTATTTATAATAAT
1927384 ATTATTTTTTCATAAT-AGAGGTGTATTTATACATTAATAATATATTTCATATATTTTGACATGT
1 ATTATTTTTTCATAATAAGAGGTGTATTTATACATTAATAATATATTTCATATATTTTGACATGT
1927448 TTGTATAATTATATTATAATATAATATTATTTTTATTATTTCGTGGTGTGTCTAATT
66 TTGTATAATTATATTATAATATAATATTATTTTTATTATTTCGTGGTGTGTCTAATT
1927505 ATTGTCAGAT
Statistics
Matches: 259, Mismatches: 1, Indels: 19
0.93 0.00 0.07
Matches are distributed among these distances:
144 70 0.27
145 28 0.11
146 46 0.18
150 1 0.00
154 107 0.41
155 7 0.03
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.51
Consensus pattern (151 bp):
ATTATTTTTTCATAATAAGAGGTGTATTTATACATTAATAATATATTTCATATATTTTGACATGT
TTGTATAATTATATTATAATATAATATTATTTTTATTATTTCGTGGTGTGTCTAATTCTAATAAT
AAGAGGTGTATTTATAATAAT
Found at i:1927432 original size:37 final size:37
Alignment explanation
Indices: 1927358--1927434 Score: 104
Period size: 36 Copynumber: 2.1 Consensus size: 37
1927348 GGTGTGTCTA
* *
1927358 ATAATAAGAGGTGTATTTATAATAATATTATTTTTTC
1 ATAATAAGAGGTGTATTTATAATAATAATATTATTTC
1927395 ATAAT-AGAGGTGTATTTATACATTAATAATA-TATTTC
1 ATAATAAGAGGTGTATTTATA-A-TAATAATATTATTTC
1927432 ATA
1 ATA
1927435 TATTTTGACA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
36 15 0.42
37 14 0.39
38 7 0.19
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.45
Consensus pattern (37 bp):
ATAATAAGAGGTGTATTTATAATAATAATATTATTTC
Found at i:1927520 original size:2 final size:2
Alignment explanation
Indices: 1927513--1927539 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1927503 TTATTGTCAG
1927513 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1927540 AATGCAAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1935705 original size:30 final size:30
Alignment explanation
Indices: 1935669--1935727 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
1935659 ATGGCTAGGT
1935669 AGGTTGTCGTGTGCTCCTGGAGACCTATGA
1 AGGTTGTCGTGTGCTCCTGGAGACCTATGA
*
1935699 AGGTTGTCGTGTGCTCCTGGAGACTTATG
1 AGGTTGTCGTGTGCTCCTGGAGACCTATG
1935728 GAAGTCACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.15, C:0.19, G:0.34, T:0.32
Consensus pattern (30 bp):
AGGTTGTCGTGTGCTCCTGGAGACCTATGA
Done.