Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr3
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: 26558743
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1281270 characters in sequence are not A, C, G, or T
File 5 of 79
Found at i:1642857 original size:20 final size:20
Alignment explanation
Indices: 1642832--1642871 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1642822 AATGCAAGCA
1642832 ACCTACGGTTCTTGCTCTTC
1 ACCTACGGTTCTTGCTCTTC
1642852 ACCTACGGTTCTTGCTCTTC
1 ACCTACGGTTCTTGCTCTTC
1642872 TATTTACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.35, G:0.15, T:0.40
Consensus pattern (20 bp):
ACCTACGGTTCTTGCTCTTC
Found at i:1646024 original size:12 final size:14
Alignment explanation
Indices: 1645990--1646022 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1645980 CAAATACACC
1645990 TTTTATTAACATTAA
1 TTTT-TTAACATTAA
1646005 TTTTTTAA-ATTAA
1 TTTTTTAACATTAA
1646018 TTTTT
1 TTTTT
1646023 AATACTAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.56
14 4 0.22
15 4 0.22
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTTTAACATTAA
Found at i:1656656 original size:5 final size:5
Alignment explanation
Indices: 1656646--1656673 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1656636 AGTTAAAAAG
1656646 AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAA
1656674 CGGAAGGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:1659732 original size:57 final size:60
Alignment explanation
Indices: 1659663--1659774 Score: 146
Period size: 60 Copynumber: 1.9 Consensus size: 60
1659653 ATTACATTAG
1659663 TAGTCACTTAATTATTAGT-AATTT-T-T-TTGGGTCAC-CTAATTATAAAAAGTTACAAAA
1 TAGTCACTTAATTATTAGTAAATTTCTCTATT-GGTCACTC-AATTATAAAAAGTTACAAAA
*
1659720 TAGTCA-TCTAATTATTAGTAAATTTCTCTATTGGTCACTCAATTATGAAAAGTTA
1 TAGTCACT-TAATTATTAGTAAATTTCTCTATTGGTCACTCAATTATAAAAAGTTA
1659775 TAGTATGGTC
Statistics
Matches: 48, Mismatches: 1, Indels: 9
0.83 0.02 0.16
Matches are distributed among these distances:
56 1 0.02
57 17 0.35
58 5 0.10
59 1 0.02
60 21 0.44
61 3 0.06
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.41
Consensus pattern (60 bp):
TAGTCACTTAATTATTAGTAAATTTCTCTATTGGTCACTCAATTATAAAAAGTTACAAAA
Found at i:1660584 original size:17 final size:19
Alignment explanation
Indices: 1660548--1660586 Score: 64
Period size: 17 Copynumber: 2.2 Consensus size: 19
1660538 TTTTATGAAT
1660548 ATTTTTGTATTTATATTTA
1 ATTTTTGTATTTATATTTA
1660567 ATTTTTGT-TTTA-ATTTA
1 ATTTTTGTATTTATATTTA
1660584 ATT
1 ATT
1660587 ACATATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.40
18 4 0.20
19 8 0.40
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (19 bp):
ATTTTTGTATTTATATTTA
Found at i:1664247 original size:83 final size:83
Alignment explanation
Indices: 1664152--1664401 Score: 500
Period size: 83 Copynumber: 3.0 Consensus size: 83
1664142 TTTATAAGCA
1664152 TTTCTTCCTAGGATAGCTCCAAAAACCCTCGATATCCTCTCCTCTTTTTTAGGTAGATTTTTCTG
1 TTTCTTCCTAGGATAGCTCCAAAAACCCTCGATATCCTCTCCTCTTTTTTAGGTAGATTTTTCTG
1664217 GTACAAATATAGTTGGGC
66 GTACAAATATAGTTGGGC
1664235 TTTCTTCCTAGGATAGCTCCAAAAACCCTCGATATCCTCTCCTCTTTTTTAGGTAGATTTTTCTG
1 TTTCTTCCTAGGATAGCTCCAAAAACCCTCGATATCCTCTCCTCTTTTTTAGGTAGATTTTTCTG
1664300 GTACAAATATAGTTGGGC
66 GTACAAATATAGTTGGGC
1664318 TTTCTTCCTAGGATAGCTCCAAAAACCCTCGATATCCTCTCCTCTTTTTTAGGTAGATTTTTCTG
1 TTTCTTCCTAGGATAGCTCCAAAAACCCTCGATATCCTCTCCTCTTTTTTAGGTAGATTTTTCTG
1664383 GTACAAATATAGTTGGGC
66 GTACAAATATAGTTGGGC
1664401 T
1 T
1664402 GAAACTGGTA
Statistics
Matches: 167, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 167 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.39
Consensus pattern (83 bp):
TTTCTTCCTAGGATAGCTCCAAAAACCCTCGATATCCTCTCCTCTTTTTTAGGTAGATTTTTCTG
GTACAAATATAGTTGGGC
Found at i:1664793 original size:14 final size:14
Alignment explanation
Indices: 1664774--1664800 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1664764 TACCTCTTGA
1664774 AATACCCTATTAGC
1 AATACCCTATTAGC
1664788 AATACCCTATTAG
1 AATACCCTATTAG
1664801 GGAGGCACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.26, G:0.07, T:0.30
Consensus pattern (14 bp):
AATACCCTATTAGC
Found at i:1673100 original size:26 final size:26
Alignment explanation
Indices: 1673067--1673152 Score: 93
Period size: 26 Copynumber: 3.3 Consensus size: 26
1673057 ACTGCAGATC
*
1673067 TTATGAGCGTCTTG-TTATATGGCTCT
1 TTATGAGCGTCTTGATTA-AAGGCTCT
*
1673093 TTATGAGCTTCTTGATTAAAGGCTCT
1 TTATGAGCGTCTTGATTAAAGGCTCT
* * **
1673119 TTGTGAGCTTCCCGATTAAAGGCTCT
1 TTATGAGCGTCTTGATTAAAGGCTCT
*
1673145 TTGTGAGC
1 TTATGAGC
1673153 TTCCCGTTAG
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
26 51 0.94
27 3 0.06
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.41
Consensus pattern (26 bp):
TTATGAGCGTCTTGATTAAAGGCTCT
Found at i:1673153 original size:26 final size:26
Alignment explanation
Indices: 1673087--1673158 Score: 117
Period size: 26 Copynumber: 2.8 Consensus size: 26
1673077 CTTGTTATAT
* **
1673087 GGCTCTTTATGAGCTTCTTGATTAAA
1 GGCTCTTTGTGAGCTTCCCGATTAAA
1673113 GGCTCTTTGTGAGCTTCCCGATTAAA
1 GGCTCTTTGTGAGCTTCCCGATTAAA
1673139 GGCTCTTTGTGAGCTTCCCG
1 GGCTCTTTGTGAGCTTCCCG
1673159 TTAGTGCTTG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.38
Consensus pattern (26 bp):
GGCTCTTTGTGAGCTTCCCGATTAAA
Found at i:1678619 original size:2 final size:2
Alignment explanation
Indices: 1678612--1678637 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1678602 CATATGCATC
1678612 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1678638 TATTGATGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1686568 original size:136 final size:137
Alignment explanation
Indices: 1686403--1686675 Score: 539
Period size: 136 Copynumber: 2.0 Consensus size: 137
1686393 ATAATAAAAT
1686403 ATATTTTTAAAATTTAAATTTAGTTATAAAAATATATAACTTAAAATATAATTTTTATTATTTTT
1 ATATTTTTAAAATTTAAATTTAGTTATAAAAATATATAACTTAAAATATAATTTTTATTATTTTT
1686468 TATTTTTAAATAGTAAAATAAACTTTTTTTGGATCCAAAAATAAACTTGGGTATGAACCAACCCG
66 TATTTTTAAATAGTAAAATAAACTTTTTTTGGATCCAAAAATAAACTTGGGTATGAACCAACCCG
1686533 ACATGAC
131 ACATGAC
1686540 ATATTTTT-AAATTTAAATTTAGTTATAAAAATATATAACTTAAAATATAATTTTTATTATTTTT
1 ATATTTTTAAAATTTAAATTTAGTTATAAAAATATATAACTTAAAATATAATTTTTATTATTTTT
1686604 TATTTTTAAATAGTAAAATAAACTTTTTTTGGATCCAAAAATAAACTTGGGTATGAACCAACCCG
66 TATTTTTAAATAGTAAAATAAACTTTTTTTGGATCCAAAAATAAACTTGGGTATGAACCAACCCG
1686669 ACATGAC
131 ACATGAC
1686676 CCATCACACT
Statistics
Matches: 136, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
136 128 0.94
137 8 0.06
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (137 bp):
ATATTTTTAAAATTTAAATTTAGTTATAAAAATATATAACTTAAAATATAATTTTTATTATTTTT
TATTTTTAAATAGTAAAATAAACTTTTTTTGGATCCAAAAATAAACTTGGGTATGAACCAACCCG
ACATGAC
Found at i:1689340 original size:22 final size:22
Alignment explanation
Indices: 1689306--1689354 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1689296 TTAGTTTACC
* * *
1689306 AAATTGAATTAAAAATGTTGTT
1 AAATTAAACTAAAAATGTTATT
*
1689328 AAATTAAACTAAAAGTGTTATT
1 AAATTAAACTAAAAATGTTATT
1689350 AAATT
1 AAATT
1689355 CTATAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (22 bp):
AAATTAAACTAAAAATGTTATT
Found at i:1690203 original size:24 final size:26
Alignment explanation
Indices: 1690176--1690225 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1690166 TATATCTTTT
1690176 GTTAAA-TCGGTC-TAAATTTTTTAA
1 GTTAAATTCGGTCATAAATTTTTTAA
* *
1690200 GTTAAATTTGGTCATTAATTTTTTAA
1 GTTAAATTCGGTCATAAATTTTTTAA
1690226 AAAGAAGCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 6 0.27
25 5 0.23
26 11 0.50
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.50
Consensus pattern (26 bp):
GTTAAATTCGGTCATAAATTTTTTAA
Found at i:1690368 original size:16 final size:17
Alignment explanation
Indices: 1690347--1690378 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1690337 ATATGTTATA
1690347 TTAAAATATTT-TAAAT
1 TTAAAATATTTATAAAT
1690363 TTAAAATATTTATAAA
1 TTAAAATATTTATAAA
1690379 AAAATTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAAAATATTTATAAAT
Found at i:1694932 original size:12 final size:13
Alignment explanation
Indices: 1694902--1694936 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1694892 ATTGTTTTTA
*
1694902 ATAACTTAATTTG
1 ATAATTTAATTTG
1694915 ATAATTTAATTT-
1 ATAATTTAATTTG
1694927 ATAATTTAAT
1 ATAATTTAAT
1694937 ATCAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (13 bp):
ATAATTTAATTTG
Found at i:1695686 original size:6 final size:6
Alignment explanation
Indices: 1695675--1695709 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
1695665 TCTCCCCTGC
1695675 CAAAAA CAAAAA CAAAAA CAAACAA CACAAAA CAA
1 CAAAAA CAAAAA CAAAAA CAAA-AA CA-AAAA CAA
1695710 CAAAAATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 17 0.63
7 8 0.30
8 2 0.07
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (6 bp):
CAAAAA
Found at i:1700668 original size:18 final size:18
Alignment explanation
Indices: 1700633--1700666 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1700623 ATAAATATAA
*
1700633 TTAAAATATTATTTAAAT
1 TTAAAAGATTATTTAAAT
1700651 TTAAAAGATT-TTTAAA
1 TTAAAAGATTATTTAAA
1700667 ATCAATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
TTAAAAGATTATTTAAAT
Found at i:1721980 original size:23 final size:23
Alignment explanation
Indices: 1721950--1722109 Score: 95
Period size: 23 Copynumber: 7.2 Consensus size: 23
1721940 TATCACGTGT
1721950 AGCTTATGTGATGTATAAGGACC
1 AGCTTATGTGATGTATAAGGACC
* * ***
1721973 AGCTTATG-GCA--TATCACGTGT
1 AGCTTATGTG-ATGTATAAGGACC
1721994 AGCTTATGTGATGTATAAGGACC
1 AGCTTATGTGATGTATAAGGACC
* * ***
1722017 AGCTTATG-GCA--TATCACGTGT
1 AGCTTATGTG-ATGTATAAGGACC
1722038 AGCTTATGTGATGTATAAGGACC
1 AGCTTATGTGATGTATAAGGACC
* * ***
1722061 AGCTTATG-GCA--TATCACGTGT
1 AGCTTATGTG-ATGTATAAGGACC
1722082 AGCTTATGTGATGTATAAGGACC
1 AGCTTATGTGATGTATAAGGACC
1722105 AGCTT
1 AGCTT
1722110 TTAATGGGGA
Statistics
Matches: 95, Mismatches: 30, Indels: 24
0.64 0.20 0.16
Matches are distributed among these distances:
21 42 0.44
22 6 0.06
23 47 0.49
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.32
Consensus pattern (23 bp):
AGCTTATGTGATGTATAAGGACC
Found at i:1721997 original size:44 final size:44
Alignment explanation
Indices: 1721934--1722109 Score: 352
Period size: 44 Copynumber: 4.0 Consensus size: 44
1721924 ACAATGACAC
1721934 ATGGCATATCACGTGTAGCTTATGTGATGTATAAGGACCAGCTT
1 ATGGCATATCACGTGTAGCTTATGTGATGTATAAGGACCAGCTT
1721978 ATGGCATATCACGTGTAGCTTATGTGATGTATAAGGACCAGCTT
1 ATGGCATATCACGTGTAGCTTATGTGATGTATAAGGACCAGCTT
1722022 ATGGCATATCACGTGTAGCTTATGTGATGTATAAGGACCAGCTT
1 ATGGCATATCACGTGTAGCTTATGTGATGTATAAGGACCAGCTT
1722066 ATGGCATATCACGTGTAGCTTATGTGATGTATAAGGACCAGCTT
1 ATGGCATATCACGTGTAGCTTATGTGATGTATAAGGACCAGCTT
1722110 TTAATGGGGA
Statistics
Matches: 132, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 132 1.00
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (44 bp):
ATGGCATATCACGTGTAGCTTATGTGATGTATAAGGACCAGCTT
Found at i:1721999 original size:21 final size:21
Alignment explanation
Indices: 1721973--1722089 Score: 76
Period size: 21 Copynumber: 5.4 Consensus size: 21
1721963 TATAAGGACC
1721973 AGCTTATGGCATATCACGTGT
1 AGCTTATGGCATATCACGTGT
* * ***
1721994 AGCTTATGTG-ATGTATAAGGACC
1 AGCTTATG-GCA--TATCACGTGT
1722017 AGCTTATGGCATATCACGTGT
1 AGCTTATGGCATATCACGTGT
* * ***
1722038 AGCTTATGTG-ATGTATAAGGACC
1 AGCTTATG-GCA--TATCACGTGT
1722061 AGCTTATGGCATATCACGTGT
1 AGCTTATGGCATATCACGTGT
1722082 AGCTTATG
1 AGCTTATG
1722090 TGATGTATAA
Statistics
Matches: 68, Mismatches: 20, Indels: 16
0.65 0.19 0.15
Matches are distributed among these distances:
21 36 0.53
22 4 0.06
23 28 0.41
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.32
Consensus pattern (21 bp):
AGCTTATGGCATATCACGTGT
Found at i:1730967 original size:18 final size:19
Alignment explanation
Indices: 1730921--1730984 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 19
1730911 TTCTTTTATT
* * *
1730921 AAATGTATATACATATTAA
1 AAATATATATAAATAATAA
1730940 AAA-A-ATATAAA-AATAA
1 AAATATATATAAATAATAA
*
1730956 AAATATATATAAATTCATAA
1 AAATATATATAAA-TAATAA
1730976 AAATATATA
1 AAATATATA
1730985 ATNNNNNNNN
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
16 7 0.19
17 7 0.19
18 7 0.19
19 3 0.08
20 13 0.35
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (19 bp):
AAATATATATAAATAATAA
Found at i:1733143 original size:16 final size:17
Alignment explanation
Indices: 1733119--1733167 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 17
1733109 GGCAGTGACC
*
1733119 ATATCTATTT-TGTATT
1 ATATTTATTTATGTATT
*
1733135 ATATTTATTTATTTATT
1 ATATTTATTTATGTATT
*
1733152 -TATTTATTTATTTATT
1 ATATTTATTTATGTATT
1733168 TTTCATTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 25 0.83
17 5 0.17
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (17 bp):
ATATTTATTTATGTATT
Found at i:1733145 original size:4 final size:4
Alignment explanation
Indices: 1733131--1733168 Score: 67
Period size: 4 Copynumber: 9.2 Consensus size: 4
1733121 ATCTATTTTG
1733131 TATT ATATT TATT TATT TATT TATT TATT TATT TATT T
1 TATT -TATT TATT TATT TATT TATT TATT TATT TATT T
1733169 TTCATTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 29 0.88
5 4 0.12
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:1733949 original size:64 final size:64
Alignment explanation
Indices: 1733842--1733961 Score: 159
Period size: 64 Copynumber: 1.9 Consensus size: 64
1733832 CCTATATCGA
* * * * * *
1733842 GACGCTTATAAAGAGTTGCAGTATGTCCGCAATATATGTAGGATCAATACCGATCATATAACAG
1 GACGCTCACAAAGAGATGCAGTATGTCCGCAACACATGCAGGATCAATACCGATCATATAACAG
* * *
1733906 GACGCTCACAAAGAGATGCGGTATGTTCGCAACACATGCAGGATCAATACTGATCA
1 GACGCTCACAAAGAGATGCAGTATGTCCGCAACACATGCAGGATCAATACCGATCA
1733962 AGATGCTAGC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
64 47 1.00
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (64 bp):
GACGCTCACAAAGAGATGCAGTATGTCCGCAACACATGCAGGATCAATACCGATCATATAACAG
Found at i:1738355 original size:33 final size:33
Alignment explanation
Indices: 1738308--1738373 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1738298 AAAGTATTTA
1738308 CGTATTTACATATGTTTTGGTCTTATGATCATT
1 CGTATTTACATATGTTTTGGTCTTATGATCATT
** *
1738341 CGTATTTATGTATGTTTTGGTCTTGTGATCATT
1 CGTATTTACATATGTTTTGGTCTTATGATCATT
1738374 AGTTTTCAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.18, C:0.11, G:0.18, T:0.53
Consensus pattern (33 bp):
CGTATTTACATATGTTTTGGTCTTATGATCATT
Found at i:1742573 original size:31 final size:31
Alignment explanation
Indices: 1742538--1742600 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
1742528 ATGTCTGTTA
1742538 TATCTTTATTTATTCCTAGTTTGTGTGGCTT
1 TATCTTTATTTATTCCTAGTTTGTGTGGCTT
1742569 TATCTTTATTTATTCCTAGTTTGTGTGGCTT
1 TATCTTTATTTATTCCTAGTTTGTGTGGCTT
1742600 T
1 T
1742601 CTTTATACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.13, C:0.13, G:0.16, T:0.59
Consensus pattern (31 bp):
TATCTTTATTTATTCCTAGTTTGTGTGGCTT
Found at i:1749110 original size:98 final size:97
Alignment explanation
Indices: 1748878--1749290 Score: 410
Period size: 109 Copynumber: 4.0 Consensus size: 97
1748868 AAAAATTTTT
**
1748878 TTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTTAAAAAAAAATTCTTTTTTTTT
1 TTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAA-TTT------AAATT-TTTTTTTCG
*
1748943 TGTCAGAGTCAGATATCAGTATAC----AAAA-AAAAAAA
58 TGTCAGAATCAGATATCAGTATACGAAAAAAATAAAAAAA
* *
1748978 -TTTGGGTGTTGGCCTGTCAATGGCCGGCACCCAGTACAATTT-AA-TTTTTTTTCGTGTTAGAA
1 TTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAATTTTTTTTTCGTGTCAGAA
1749040 TCAGATATCAGTATACGAAAAAAATTTTAAAAAAA
66 TCAGATATCAGTATACGAAAAAAA---TAAAAAAA
*
1749075 TTTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTTAAAAAAAAATTTCTTTTTTTT
1 TTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAA-TTT------AAA--T-TTTTTTTT
1749140 CGTGTCAGAATCAGATATCAGTATACGAAAAAAATAATAAAAA
56 CGTGTCAGAATCAGATATCAGTATACGAAAAAAATAA-AAAAA
*
1749183 TTTTCGGGTGCTGGCTTGTCAATGGCCGGCACCCAGTACAATTTTAAAAAAAAATTTCTTTTTTT
1 TTTT-GGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAA-TTT------AAA--T-TTTTTTT
1749248 TCGTGTCAGAATCAGATATCAGTATACGAAAAAAATAAAAAAA
55 TCGTGTCAGAATCAGATATCAGTATACGAAAAAAATAAAAAAA
1749291 ATAAATGAGA
Statistics
Matches: 280, Mismatches: 10, Indels: 38
0.85 0.03 0.12
Matches are distributed among these distances:
89 29 0.10
90 1 0.00
91 2 0.01
93 4 0.01
97 7 0.03
98 40 0.14
99 41 0.15
106 2 0.01
107 3 0.01
108 14 0.05
109 96 0.34
110 41 0.15
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Consensus pattern (97 bp):
TTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAATTTTTTTTTCGTGTCAGAA
TCAGATATCAGTATACGAAAAAAATAAAAAAA
Found at i:1749291 original size:109 final size:108
Alignment explanation
Indices: 1749022--1749292 Score: 470
Period size: 109 Copynumber: 2.5 Consensus size: 108
1749012 TACAATTTAA
* * *
1749022 TTTTTTTTCGTGTTAGAATCAGATATCAGTATACGAAAAAAATTTTAAAAAAATTTTTGGTGCTG
1 TTTTTTTTCGTGTCAGAATCAGATATCAGTATACGAAAAAAA--TAAAAAAAATTTTGGGTGCTG
1749087 GCCTGTCAATGGCCGGCACCCAGTACAATTTTAAAAAAAAATTTC
64 GCCTGTCAATGGCCGGCACCCAGTACAATTTTAAAAAAAAATTTC
*
1749132 TTTTTTTTCGTGTCAGAATCAGATATCAGTATACGAAAAAAATAATAAAAATTTTCGGGTGCTGG
1 TTTTTTTTCGTGTCAGAATCAGATATCAGTATACGAAAAAAATAAAAAAAATTTT-GGGTGCTGG
*
1749197 CTTGTCAATGGCCGGCACCCAGTACAATTTTAAAAAAAAATTTC
65 CCTGTCAATGGCCGGCACCCAGTACAATTTTAAAAAAAAATTTC
1749241 TTTTTTTTCGTGTCAGAATCAGATATCAGTATACGAAAAAAATAAAAAAAAT
1 TTTTTTTTCGTGTCAGAATCAGATATCAGTATACGAAAAAAATAAAAAAAAT
1749293 AAATGAGATT
Statistics
Matches: 154, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
108 11 0.07
109 102 0.66
110 41 0.27
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (108 bp):
TTTTTTTTCGTGTCAGAATCAGATATCAGTATACGAAAAAAATAAAAAAAATTTTGGGTGCTGGC
CTGTCAATGGCCGGCACCCAGTACAATTTTAAAAAAAAATTTC
Found at i:1749541 original size:98 final size:100
Alignment explanation
Indices: 1749430--1749704 Score: 358
Period size: 98 Copynumber: 2.6 Consensus size: 100
1749420 GAAAAAAAAA
1749430 AGAAA-TTTTTTTTAAATTGTACTGGGTGCCGGCCATTGACAGGCCAACACCAAAATTTTTTTTT
1 AGAAATTTTTTTTTAAATTGTACTGGGTGCCGGCCATTGACAGGCCAACACCAAAATTTTTTTTT
*
1749494 -ATTTTTTTCATATACTGATATCTGATTCTGACAC
66 GATTTTTTTCATATACTGATATCTGACTCTGACAC
1749528 -GAAATTTTTTTTTAAATTGTACTGGGTGCCGGCCATTGACAGGCCAACACCCAAAAGATTTTTA
1 AGAAATTTTTTTTTAAATTGTACTGGGTGCCGGCCATTGACAGGCCAACA-CC-AAA-A-TTTT-
*
1749592 TTTTTGATTTTTTTCGTATACTGATATCTGACTCTGACAC
61 TTTTTGATTTTTTTCATATACTGATATCTGACTCTGACAC
** * *
1749632 AAAAAAAAGAAATTTTTTTAAAAAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAT
1 -------AGAAATTTTTTT-TTAAATTGTACTGGGTGCCGGCCATTGACAGGCCAACACCAAAAT
1749697 TTTTTTTT
58 TTTTTTTT
1749705 TTTCGTTTTT
Statistics
Matches: 155, Mismatches: 6, Indels: 22
0.85 0.03 0.12
Matches are distributed among these distances:
97 4 0.03
98 44 0.28
99 2 0.01
100 3 0.02
101 1 0.01
102 4 0.03
103 5 0.03
104 32 0.21
108 5 0.03
109 4 0.03
110 1 0.01
111 2 0.01
112 13 0.08
113 35 0.23
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (100 bp):
AGAAATTTTTTTTTAAATTGTACTGGGTGCCGGCCATTGACAGGCCAACACCAAAATTTTTTTTT
GATTTTTTTCATATACTGATATCTGACTCTGACAC
Found at i:1751839 original size:11 final size:10
Alignment explanation
Indices: 1751800--1751838 Score: 53
Period size: 11 Copynumber: 3.9 Consensus size: 10
1751790 TGAAGATTAG
1751800 AAATATATAA
1 AAATATATAA
1751810 AAGATATATAA
1 AA-ATATATAA
*
1751821 AAAAATAT-A
1 AAATATATAA
1751830 AAATATATA
1 AAATATATA
1751839 TTTATGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 8 0.32
10 7 0.28
11 10 0.40
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (10 bp):
AAATATATAA
Found at i:1751883 original size:21 final size:22
Alignment explanation
Indices: 1751798--1751884 Score: 63
Period size: 23 Copynumber: 3.9 Consensus size: 22
1751788 TATGAAGATT
1751798 AGAAATATATAAA-AGATATATA
1 AGAAA-ATATAAATAGATATATA
* * *
1751820 AAAAAATATAAAATATATATTTA
1 AGAAAATAT-AAATAGATATATA
* *
1751843 TGAAAAT-TAAAAATGCATATATA
1 AGAAAATATAAATA-G-ATATATA
*
1751866 AGAATATATAAATA-ATATA
1 AGAAAATATAAATAGATATA
1751885 AGGTATAGAA
Statistics
Matches: 49, Mismatches: 11, Indels: 11
0.69 0.15 0.15
Matches are distributed among these distances:
21 13 0.27
22 8 0.16
23 23 0.47
24 5 0.10
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.31
Consensus pattern (22 bp):
AGAAAATATAAATAGATATATA
Found at i:1753400 original size:354 final size:354
Alignment explanation
Indices: 1752752--1753458 Score: 1362
Period size: 354 Copynumber: 2.0 Consensus size: 354
1752742 AGATTCCGGC
*
1752752 GTGGGGATCACCGTCGGCCGCCACGCCGGCCATCGTGCGCGGTGGCCGGAAACTTCAAAAAAGGT
1 GTGGGGATCACCGTCGGCCGCCACGCCGGCCACCGTGCGCGGTGGCCGGAAACTTCAAAAAAGGT
1752817 AATTTTTTCTTTTTTCCTTTTTTATATATATTATACGTATATAAATAAATGAACAAAAAAATAAA
66 AATTTTTTCTTTTTTCCTTTTTTATATATATTATACGTATATAAATAAATGAACAAAAAAATAAA
1752882 AAATAAAAAAGGGGTTAGAATATGTAAAAATGAAAACAAAAAGAGCCAGAAATCACCTTTGATTT
131 AAATAAAAAAGGGGTTAGAATATGTAAAAATGAAAACAAAAAGAGCCAGAAATCACCTTTGATTT
1752947 TTGTGTTTCTTATTTCTAAAAAACGTTACAAATAGTAAAGGAAAAGAAAAATGAAAAAAACCCCC
196 TTGTGTTTCTTATTTCTAAAAAACGTTACAAATAGTAAAGGAAAAGAAAAATGAAAAAAACCCCC
1753012 CGATCCAAGGTTTCAATCGGTTTGTATGCCGATTTTAAAGAAACAAAAGT-CCCCCTCTTTTCAT
261 CGATCCAAGGTTTCAATCGGTTTGTATGCCGATTTTAAAGAAACAAAAGTCCCCCCTCTTTTCAT
1753076 TTTTTGCGGCCTTTATAGCCGATTTTACT
326 TTTTTGCGGCCTTTATAGCCGATTTTACT
* **
1753105 GTGGGGATCGCCGTCGGCCGCTGCGCCGGCCACCGTGCGCGGTGGCCGGAAACTTCAAAAAAGGT
1 GTGGGGATCACCGTCGGCCGCCACGCCGGCCACCGTGCGCGGTGGCCGGAAACTTCAAAAAAGGT
1753170 AATTTTTTCTTTTTTCCTTTTTTTATATATATTATACGTATATAAATAAATGAACAAAAAAATAA
66 AATTTTTTCTTTTTTCC-TTTTTTATATATATTATACGTATATAAATAAATGAACAAAAAAATAA
1753235 AAAATAAAAAAGGGGTTAGAATATGTAAAAATGAAAACAAAAAGAGCCAGAAATCACCTTTGATT
130 AAAATAAAAAAGGGGTTAGAATATGTAAAAATGAAAACAAAAAGAGCCAGAAATCACCTTTGATT
1753300 TTTGTGTTTCTTATTTCTAAAAAACGTTACAAATAGTAAAGGAAAAGAAAAATGAAAAAAACCCC
195 TTTGTGTTTCTTATTTCTAAAAAACGTTACAAATAGTAAAGGAAAAGAAAAATGAAAAAAACCCC
1753365 CCGATCCAAGGTTTCAATCGGTTTGTATGCCGATTTTAAAGAAACAAAAGTCCCCCCTCTTTTCA
260 CCGATCCAAGGTTTCAATCGGTTTGTATGCCGATTTTAAAGAAACAAAAGTCCCCCCTCTTTTCA
1753430 TTTTTTGCGGCCTTTATAGCCGATTTTAC
325 TTTTTTGCGGCCTTTATAGCCGATTTTAC
1753459 ACTTTTTTCT
Statistics
Matches: 348, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
353 78 0.22
354 228 0.66
355 42 0.12
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (354 bp):
GTGGGGATCACCGTCGGCCGCCACGCCGGCCACCGTGCGCGGTGGCCGGAAACTTCAAAAAAGGT
AATTTTTTCTTTTTTCCTTTTTTATATATATTATACGTATATAAATAAATGAACAAAAAAATAAA
AAATAAAAAAGGGGTTAGAATATGTAAAAATGAAAACAAAAAGAGCCAGAAATCACCTTTGATTT
TTGTGTTTCTTATTTCTAAAAAACGTTACAAATAGTAAAGGAAAAGAAAAATGAAAAAAACCCCC
CGATCCAAGGTTTCAATCGGTTTGTATGCCGATTTTAAAGAAACAAAAGTCCCCCCTCTTTTCAT
TTTTTGCGGCCTTTATAGCCGATTTTACT
Found at i:1757494 original size:24 final size:24
Alignment explanation
Indices: 1757479--1757530 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1757469 AATCAAAGTC
1757479 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* * *
1757503 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATGCT
1757527 AAAT
1 AAAT
1757531 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:1764366 original size:24 final size:23
Alignment explanation
Indices: 1764325--1764374 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
1764315 ATCAAAGTCG
* *
1764325 AATATATTATGCTAATAAATGCTA
1 AATATATTATACTAAT-AATACTA
*
1764349 AATATATTATACTCATAATACTA
1 AATATATTATACTAATAATACTA
1764372 AAT
1 AAT
1764375 CTTCTAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.38
Consensus pattern (23 bp):
AATATATTATACTAATAATACTA
Found at i:1768980 original size:36 final size:36
Alignment explanation
Indices: 1768936--1769008 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
1768926 ACCAACGTCT
*
1768936 CATCCAAGTTCGTTTTACGGTTTATAGAATATAATC
1 CATCCAAGTCCGTTTTACGGTTTATAGAATATAATC
1768972 CATCCAAGTCCGTTTTACGGTTTATAGAATATAATC
1 CATCCAAGTCCGTTTTACGGTTTATAGAATATAATC
1769008 C
1 C
1769009 TTTTGAGGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (36 bp):
CATCCAAGTCCGTTTTACGGTTTATAGAATATAATC
Found at i:1772676 original size:19 final size:18
Alignment explanation
Indices: 1772647--1772688 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
1772637 TATAATCTGA
1772647 ATAATTATACTCAATATT-
1 ATAATTATACTC-ATATTC
1772665 ATAATATATACTCATATTC
1 ATAAT-TATACTCATATTC
1772684 ATAAT
1 ATAAT
1772689 CGAAATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (18 bp):
ATAATTATACTCATATTC
Found at i:1778694 original size:75 final size:76
Alignment explanation
Indices: 1778594--1778744 Score: 268
Period size: 75 Copynumber: 2.0 Consensus size: 76
1778584 AATTAGCTAA
* * *
1778594 TATTATTATAATTTTTTAAAAGATTAAATTAAAATCTCAAAATGAATTTTATCATTACAAATTTA
1 TATTATTATAATTTTTTAAAAGATTAAATTAAAATCTCAAAATGAAATTTAACAATACAAATTTA
1778659 TAATATTATAT
66 TAATATTATAT
1778670 TATTATTAT-ATTTTTTAAAAGATTAAATTAAAATCTCAAAATGAAATTTAACAATACAAATTTA
1 TATTATTATAATTTTTTAAAAGATTAAATTAAAATCTCAAAATGAAATTTAACAATACAAATTTA
1778734 TAATATTATAT
66 TAATATTATAT
1778745 ATTTTAAAGG
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
75 63 0.88
76 9 0.12
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (76 bp):
TATTATTATAATTTTTTAAAAGATTAAATTAAAATCTCAAAATGAAATTTAACAATACAAATTTA
TAATATTATAT
Found at i:1786033 original size:58 final size:58
Alignment explanation
Indices: 1785968--1786084 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
1785958 CGAAGTTGAA
1785968 AGTACCAAATATTCCTAGAGCCATACCATCAGAAAAACTTCCTTGACCACTTGAATAG
1 AGTACCAAATATTCCTAGAGCCATACCATCAGAAAAACTTCCTTGACCACTTGAATAG
1786026 AGTACCAAATATTCCTAGAGCCATACCATCAGAAAAACTTCCTTGACCACTTGAATAG
1 AGTACCAAATATTCCTAGAGCCATACCATCAGAAAAACTTCCTTGACCACTTGAATAG
1786084 A
1 A
1786085 TTAAGAAAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (58 bp):
AGTACCAAATATTCCTAGAGCCATACCATCAGAAAAACTTCCTTGACCACTTGAATAG
Found at i:1788246 original size:19 final size:19
Alignment explanation
Indices: 1788195--1788247 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 19
1788185 TTTCTAAATT
1788195 TATAATATAGTATAATATATTA
1 TATAATATA-TAT--TATATTA
* *
1788217 TGTTATATATATTATATTA
1 TATAATATATATTATATTA
*
1788236 TATAATTTATAT
1 TATAATATATAT
1788248 CACATATAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (19 bp):
TATAATATATATTATATTA
Found at i:1788247 original size:14 final size:14
Alignment explanation
Indices: 1788195--1788239 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1788185 TTTCTAAATT
* *
1788195 TATAATATAGTATAA
1 TATATTATATTAT-A
*
1788210 TATATTATGTTATA
1 TATATTATATTATA
1788224 TATATTATATTATA
1 TATATTATATTATA
1788238 TA
1 TA
1788240 ATTTATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 16 0.62
15 10 0.38
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
TATATTATATTATA
Found at i:1788373 original size:23 final size:23
Alignment explanation
Indices: 1788342--1788385 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1788332 TTAATGAATG
1788342 AAAATATAAAAA-ATGTTAAATT
1 AAAATATAAAAATATGTTAAATT
*
1788364 AAAATGATAAAAATATTTTAAA
1 AAAAT-ATAAAAATATGTTAAA
1788386 ATTTTAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 7 0.37
24 7 0.37
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (23 bp):
AAAATATAAAAATATGTTAAATT
Found at i:1800147 original size:22 final size:22
Alignment explanation
Indices: 1800103--1800147 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1800093 TCCTGACTTG
* * **
1800103 TAGGTTTTTGGATTTTAGGGTT
1 TAGGGTTTAGGATTTTAAAGTT
1800125 TAGGGTTTAGGATTTTAAAGTT
1 TAGGGTTTAGGATTTTAAAGTT
1800147 T
1 T
1800148 TTAGGATTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (22 bp):
TAGGGTTTAGGATTTTAAAGTT
Found at i:1800166 original size:17 final size:17
Alignment explanation
Indices: 1800123--1800166 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1800113 GATTTTAGGG
1800123 TTTAGGG-TTTAGGATT
1 TTTAGGGTTTTAGGATT
* * *
1800139 TTAAAGTTTTTAGGATT
1 TTTAGGGTTTTAGGATT
1800156 TTTAGGGTTTT
1 TTTAGGGTTTT
1800167 GGAGAAAAAA
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.20, C:0.00, G:0.25, T:0.55
Consensus pattern (17 bp):
TTTAGGGTTTTAGGATT
Found at i:1802731 original size:55 final size:55
Alignment explanation
Indices: 1802643--1802766 Score: 158
Period size: 55 Copynumber: 2.3 Consensus size: 55
1802633 TGATTTTGGA
* * * * *
1802643 TTGAATCGATTATTTTTATGTTTAAATCAATTGTTATGCTAGAATATTGCTTCGT
1 TTGAATCGATTGTTTATATGTTTAAATCAATTGTCATGCTAGAACACTGCTTCGT
** * * *
1802698 TTGAATCGATTGTTTATATGTTTAAATTGATTGTCATGTTAGAACGCTGCTTCTT
1 TTGAATCGATTGTTTATATGTTTAAATCAATTGTCATGCTAGAACACTGCTTCGT
1802753 TTGAATCGATTGTT
1 TTGAATCGATTGTT
1802767 ATGTTGGAAT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 59 1.00
ACGTcount: A:0.25, C:0.10, G:0.17, T:0.48
Consensus pattern (55 bp):
TTGAATCGATTGTTTATATGTTTAAATCAATTGTCATGCTAGAACACTGCTTCGT
Found at i:1802771 original size:34 final size:34
Alignment explanation
Indices: 1802726--1802800 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 34
1802716 TGTTTAAATT
* *
1802726 GATTGTCATGTTAGAACGCTGCTTCTTTTGAATC
1 GATTGTTATGTTAGAACACTGCTTCTTTTGAATC
* * * *
1802760 GATTGTTATGTTGGAATATTGTTTCTTTTGAATC
1 GATTGTTATGTTAGAACACTGCTTCTTTTGAATC
1802794 GATTGTT
1 GATTGTT
1802801 TATATGTTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.20, C:0.11, G:0.21, T:0.48
Consensus pattern (34 bp):
GATTGTTATGTTAGAACACTGCTTCTTTTGAATC
Found at i:1802815 original size:55 final size:55
Alignment explanation
Indices: 1802756--1802932 Score: 266
Period size: 55 Copynumber: 3.2 Consensus size: 55
1802746 GCTTCTTTTG
* *
1802756 AATCGATTGTTATGTTGGAATATTGTTTCTTTTGAATCGATTGTTTATATGTTTA
1 AATCGATTGTTATGTTGGAATACTGCTTCTTTTGAATCGATTGTTTATATGTTTA
* *
1802811 AATCGATTGTTATGTTGGAATACTGCTTCTTTTGAATTGATTGTTTATATGTTCA
1 AATCGATTGTTATGTTGGAATACTGCTTCTTTTGAATCGATTGTTTATATGTTTA
* * * *
1802866 AATCGATTGTTATATTGGATTGCTGCTTCTTTTGAATCGGTTGTTTATATGTTTA
1 AATCGATTGTTATGTTGGAATACTGCTTCTTTTGAATCGATTGTTTATATGTTTA
1802921 AAT-GAATTGTTA
1 AATCG-ATTGTTA
1802933 CGTAGCATGT
Statistics
Matches: 111, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
54 1 0.01
55 110 0.99
ACGTcount: A:0.24, C:0.07, G:0.19, T:0.50
Consensus pattern (55 bp):
AATCGATTGTTATGTTGGAATACTGCTTCTTTTGAATCGATTGTTTATATGTTTA
Found at i:1802826 original size:18 final size:18
Alignment explanation
Indices: 1802658--1802831 Score: 69
Period size: 18 Copynumber: 9.7 Consensus size: 18
1802648 TCGATTATTT
* *
1802658 TTATGTTTAAATCAATTG
1 TTATGTTTGAATCGATTG
* *
1802676 TTATGCTAGAAT--ATTG
1 TTATGTTTGAATCGATTG
*
1802692 CTT-CGTTTGAATCGATTG
1 -TTATGTTTGAATCGATTG
* *
1802710 TTTATATGTTTAAATTGATTG
1 --T-TATGTTTGAATCGATTG
* * *
1802731 TCATGTTAGAA-CG-CTG
1 TTATGTTTGAATCGATTG
*
1802747 CTTCT-TTTGAATCGATTG
1 -TTATGTTTGAATCGATTG
*
1802765 TTATGTTGGAAT--ATTG
1 TTATGTTTGAATCGATTG
*
1802781 TT-TCTTTTGAATCGATTG
1 TTAT-GTTTGAATCGATTG
*
1802799 TTTATATGTTTAAATCGATTG
1 --T-TATGTTTGAATCGATTG
*
1802820 TTATGTTGGAAT
1 TTATGTTTGAAT
1802832 ACTGCTTCTT
Statistics
Matches: 112, Mismatches: 27, Indels: 34
0.65 0.16 0.20
Matches are distributed among these distances:
15 1 0.01
16 29 0.26
17 10 0.09
18 41 0.37
19 3 0.03
20 2 0.02
21 25 0.22
22 1 0.01
ACGTcount: A:0.25, C:0.08, G:0.18, T:0.49
Consensus pattern (18 bp):
TTATGTTTGAATCGATTG
Found at i:1802826 original size:89 final size:89
Alignment explanation
Indices: 1802667--1802855 Score: 279
Period size: 89 Copynumber: 2.1 Consensus size: 89
1802657 TTTATGTTTA
* *
1802667 AATCAATTGTTATGCTAGAATATTGCTTCGTTTGAATCGATTGTTTATATGTTTAAATTGATTGT
1 AATCGATTGTTATGCTAGAATATTGCTTCGTTTGAATCGATTGTTTATATGTTTAAATCGATTGT
*
1802732 CATGTTAGAACGCTGCTTCTTTTG
66 CATGTTAGAACACTGCTTCTTTTG
* * * *
1802756 AATCGATTGTTATGTTGGAATATTGTTTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTGT
1 AATCGATTGTTATGCTAGAATATTGCTTCGTTTGAATCGATTGTTTATATGTTTAAATCGATTGT
* * *
1802821 TATGTTGGAATACTGCTTCTTTTG
66 CATGTTAGAACACTGCTTCTTTTG
*
1802845 AATTGATTGTT
1 AATCGATTGTT
1802856 TATATGTTCA
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.24, C:0.09, G:0.19, T:0.49
Consensus pattern (89 bp):
AATCGATTGTTATGCTAGAATATTGCTTCGTTTGAATCGATTGTTTATATGTTTAAATCGATTGT
CATGTTAGAACACTGCTTCTTTTG
Found at i:1802903 original size:144 final size:144
Alignment explanation
Indices: 1802643--1802910 Score: 392
Period size: 144 Copynumber: 1.9 Consensus size: 144
1802633 TGATTTTGGA
* *
1802643 TTGAATCGATTATTTTTATGTTTAAATCAATTGTTATGCTAGAATATTGCTTCGTTTGAATCGAT
1 TTGAATCGATTATTTATATGTTTAAATCAATTGTTATGCTAGAATACTGCTTCGTTTGAATCGAT
* * *
1802708 TGTTTATATGTTTAAATTGATTGTCATGTTAGAACGCTGCTTCTTTTGAATCGATTGTTATGTTG
66 TGTTTATATGTTCAAATCGATTGTCATATTAGAACGCTGCTTCTTTTGAATCGATTGTTATGTTG
1802773 GAATATTGTTTCTT
131 GAATATTGTTTCTT
* * * * * *
1802787 TTGAATCGATTGTTTATATGTTTAAATCGATTGTTATGTTGGAATACTGCTTCTTTTGAATTGAT
1 TTGAATCGATTATTTATATGTTTAAATCAATTGTTATGCTAGAATACTGCTTCGTTTGAATCGAT
* * ** *
1802852 TGTTTATATGTTCAAATCGATTGTTATATTGGATTGCTGCTTCTTTTGAATCGGTTGTT
66 TGTTTATATGTTCAAATCGATTGTCATATTAGAACGCTGCTTCTTTTGAATCGATTGTT
1802911 TATATGTTTA
Statistics
Matches: 108, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
144 108 1.00
ACGTcount: A:0.23, C:0.09, G:0.18, T:0.50
Consensus pattern (144 bp):
TTGAATCGATTATTTATATGTTTAAATCAATTGTTATGCTAGAATACTGCTTCGTTTGAATCGAT
TGTTTATATGTTCAAATCGATTGTCATATTAGAACGCTGCTTCTTTTGAATCGATTGTTATGTTG
GAATATTGTTTCTT
Found at i:1810569 original size:78 final size:78
Alignment explanation
Indices: 1810334--1810621 Score: 220
Period size: 78 Copynumber: 3.7 Consensus size: 78
1810324 ATTGACTTCT
* * * * *** * * * *
1810334 ATCTGTCGAAAGAAATGGTTCTTATTTATACTCATTCTTGTAAGATAGAAGTGCCATCAGGATCT
1 ATCTGTCGAAAGAAACGGTTCCTATTCACACTCATTCTCACAAGATAGAAGTGTCGTAAGGATCG
**
1810399 GATCCTATCCATA
66 GATATTATCCATA
* * *** * * **
1810412 ATCTTTC-AAGAGAAACGATTCCTATTCGTGCTCGTTCTCGCAAGATAGAAGTGTCGTTGGGATC
1 ATCTGTCGAA-AGAAACGGTTCCTATTCACACTCATTCTCACAAGATAGAAGTGTCGTAAGGATC
* *
1810476 GGATGTTA-CATATA
65 GGATATTATC-CATA
* *
1810490 ATCTGCCGAAAGAAACGGTTCCTATTCACACTCATTCTCACAAGATAGAAGTGTCGTAAGGACCG
1 ATCTGTCGAAAGAAACGGTTCCTATTCACACTCATTCTCACAAGATAGAAGTGTCGTAAGGATCG
1810555 GATATTATCCATA
66 GATATTATCCATA
* * * ** ** * *
1810568 ATCCGTTGAAAAAAAATAGTTCCTATTCACACTTGTTCTTATAAGATAGAAGTG
1 ATCTGTCG-AAAGAAACGGTTCCTATTCACACTCATTCTCACAAGATAGAAGTG
1810622 CCATCAAGAG
Statistics
Matches: 164, Mismatches: 41, Indels: 9
0.77 0.19 0.04
Matches are distributed among these distances:
77 3 0.02
78 120 0.73
79 41 0.25
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (78 bp):
ATCTGTCGAAAGAAACGGTTCCTATTCACACTCATTCTCACAAGATAGAAGTGTCGTAAGGATCG
GATATTATCCATA
Found at i:1810669 original size:157 final size:156
Alignment explanation
Indices: 1810500--1810786 Score: 335
Period size: 157 Copynumber: 1.8 Consensus size: 156
1810490 ATCTGCCGAA
* * *
1810500 AGAAACGGTTCCTATTCACACTCATTCTCACAAGATAGAAGTGTCGTAAGGACCGGATATTATCC
1 AGAAACGGTTCCTATGCACACTCATTCTCACAAGATAGAAGTGCCGTAAGGACCGGATACTATCC
** *
1810565 ATAATCCGTTGAAAAAAAATAG-TTCCTATTCACACTTGTTCTTATAAGATAGAAGTGCCATCAA
66 ATAATCC-TCCAAAAAAAA-AGATTCCTATTCACACTTGTTCTTATAAGATAGAAGTACCATCAA
1810629 GAGTGAATCCCATTCGTAATCCTTCGAG
129 GAGTGAATCCCATTCGTAATCCTTCGAG
* ** * * * * * *
1810657 AGAAA-GGATTCCTATGCACATTTGTTCTCGCAAGTTAGACGTGCCGTCAGGACTGGATCCTATC
1 AGAAACGG-TTCCTATGCACACTCATTCTCACAAGATAGAAGTGCCGTAAGGACCGGATACTATC
* * * * * * *
1810721 CATAATTCTCCAAGAGAAACGATTCCTATTTACACTTGTTCTTTTAAGATCGAAGTACCATCAAG
65 CATAATCCTCCAAAAAAAAAGATTCCTATTCACACTTGTTCTTATAAGATAGAAGTACCATCAAG
1810786 A
130 A
1810787 CCGAATCCTA
Statistics
Matches: 106, Mismatches: 22, Indels: 5
0.80 0.17 0.04
Matches are distributed among these distances:
155 1 0.01
156 49 0.46
157 56 0.53
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (156 bp):
AGAAACGGTTCCTATGCACACTCATTCTCACAAGATAGAAGTGCCGTAAGGACCGGATACTATCC
ATAATCCTCCAAAAAAAAAGATTCCTATTCACACTTGTTCTTATAAGATAGAAGTACCATCAAGA
GTGAATCCCATTCGTAATCCTTCGAG
Found at i:1810795 original size:78 final size:78
Alignment explanation
Indices: 1810587--1810803 Score: 227
Period size: 78 Copynumber: 2.8 Consensus size: 78
1810577 AAAAAAATAG
* * * *
1810587 TTCCTATTCACACTTGTTCTTATAAGATAGAAGTGCCATCAAGAGTGAATCCCATTCGTAATCCT
1 TTCCTATTCACACTTGTTCTTATAAGATAGAAGTGCCATCAAGACTGAATCCTATCCATAATCCT
* * *
1810652 TCGAGAGAAAGGA
66 CCAAGAGAAACGA
* * *** * * * * * *
1810665 TTCCTATGCACATTTGTTCTCGCAAGTTAGACGTGCCGTCAGGACTGGATCCTATCCATAATTCT
1 TTCCTATTCACACTTGTTCTTATAAGATAGAAGTGCCATCAAGACTGAATCCTATCCATAATCCT
1810730 CCAAGAGAAACGA
66 CCAAGAGAAACGA
* * * * *
1810743 TTCCTATTTACACTTGTTCTTTTAAGATCGAAGTACCATCAAGACCGAATCCTATCCATAA
1 TTCCTATTCACACTTGTTCTTATAAGATAGAAGTGCCATCAAGACTGAATCCTATCCATAA
1810804 CCTGCCGAAG
Statistics
Matches: 107, Mismatches: 32, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
78 107 1.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (78 bp):
TTCCTATTCACACTTGTTCTTATAAGATAGAAGTGCCATCAAGACTGAATCCTATCCATAATCCT
CCAAGAGAAACGA
Found at i:1811136 original size:19 final size:20
Alignment explanation
Indices: 1811112--1811156 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
1811102 CTCTATTGTA
1811112 GTTTTTAGGGTTTTT-TCTT
1 GTTTTTAGGGTTTTTGTCTT
*
1811131 GTTTTTATGGTTTTTGTCTT
1 GTTTTTAGGGTTTTTGTCTT
1811151 GTTTTT
1 GTTTTT
1811157 GCTTTCCGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.04, C:0.04, G:0.20, T:0.71
Consensus pattern (20 bp):
GTTTTTAGGGTTTTTGTCTT
Found at i:1811145 original size:20 final size:19
Alignment explanation
Indices: 1811112--1811156 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1811102 CTCTATTGTA
*
1811112 GTTTTTAGGGTTTTTTCTT
1 GTTTTTAGGGTTTTGTCTT
*
1811131 GTTTTTATGGTTTTTGTCTT
1 GTTTTTA-GGGTTTTGTCTT
1811151 GTTTTT
1 GTTTTT
1811157 GCTTTCCGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.04, C:0.04, G:0.20, T:0.71
Consensus pattern (19 bp):
GTTTTTAGGGTTTTGTCTT
Found at i:1822463 original size:29 final size:29
Alignment explanation
Indices: 1822407--1822492 Score: 95
Period size: 29 Copynumber: 2.9 Consensus size: 29
1822397 ATATCAAAAT
* * *
1822407 TATACTTGAACTTTGATTTAATGAGTAATT-
1 TATACATGAATTTTGATTTGAT--GTAATTA
1822437 TGATACATGAATTTTGATTTGATGTAATTA
1 T-ATACATGAATTTTGATTTGATGTAATTA
*
1822467 TATACATGAATTTTGA-TTGATTTAAT
1 TATACATGAATTTTGATTTGATGTAAT
1822493 GAGTATTATA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
28 9 0.18
29 21 0.42
30 2 0.04
31 18 0.36
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.48
Consensus pattern (29 bp):
TATACATGAATTTTGATTTGATGTAATTA
Found at i:1826243 original size:23 final size:23
Alignment explanation
Indices: 1826198--1826242 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
1826188 TTTTCATTAG
1826198 AACTTTTTAAATTAATTAATTTT
1 AACTTTTTAAATTAATTAATTTT
1826221 AACTTTTT-AATTAATTAATTTT
1 AACTTTTTAAATTAATTAATTTT
1826243 TCAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (23 bp):
AACTTTTTAAATTAATTAATTTT
Found at i:1828429 original size:18 final size:19
Alignment explanation
Indices: 1828408--1828444 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1828398 TTAAAAAATA
1828408 TATAAAT-TTTAAATTTTT
1 TATAAATATTTAAATTTTT
1828426 TATAAATACTTTAAATTTT
1 TATAAATA-TTTAAATTTT
1828445 AAAAATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
TATAAATATTTAAATTTTT
Found at i:1828440 original size:27 final size:27
Alignment explanation
Indices: 1828387--1828447 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
1828377 TTATATATTC
1828387 TTTAGAATTTTTTAAAAAATATATAAAT
1 TTTA-AATTTTTTAAAAAATATATAAAT
* *
1828415 TTTAAATTTTTT-ATAAATACTTTAAAT
1 TTTAAATTTTTTAAAAAATA-TATAAAT
1828442 TTTAAA
1 TTTAAA
1828448 AATTATTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 6 0.20
27 20 0.67
28 4 0.13
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (27 bp):
TTTAAATTTTTTAAAAAATATATAAAT
Found at i:1828898 original size:19 final size:18
Alignment explanation
Indices: 1828856--1828898 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
1828846 AAATTTTAGA
* *
1828856 ATTTTTATAAATATTTTT
1 ATTTTTAAAAATATTTTG
*
1828874 AATTTTAAAAATTATTTTG
1 ATTTTTAAAAA-TATTTTG
1828893 ATTTTT
1 ATTTTT
1828899 TTTTTGTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
ATTTTTAAAAATATTTTG
Found at i:1830756 original size:20 final size:19
Alignment explanation
Indices: 1830727--1830767 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1830717 AAGTAATTTT
*
1830727 TTTTAATATTATATATTCAG
1 TTTTAATATT-CATATTCAG
*
1830747 TTTTATTATTCATATTCAG
1 TTTTAATATTCATATTCAG
1830766 TT
1 TT
1830768 AATGAAATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.59
Consensus pattern (19 bp):
TTTTAATATTCATATTCAG
Found at i:1836610 original size:15 final size:15
Alignment explanation
Indices: 1836590--1836618 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1836580 CTGAATTAAG
1836590 ATTTTTTTTAAATAA
1 ATTTTTTTTAAATAA
1836605 ATTTTTTTTAAATA
1 ATTTTTTTTAAATA
1836619 TATATATTTG
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTTTTTTTAAATAA
Found at i:1841115 original size:13 final size:13
Alignment explanation
Indices: 1841097--1841169 Score: 50
Period size: 13 Copynumber: 6.1 Consensus size: 13
1841087 GAAAATTTCA
1841097 TATAATTTATATT
1 TATAATTTATATT
1841110 TATAATTTAT-TT
1 TATAATTTATATT
*
1841122 TA-AA-TTATAAT
1 TATAATTTATATT
* ** *
1841133 TGTACGTTAT-TA
1 TATAATTTATATT
*
1841145 T-TAATTT-TAAT
1 TATAATTTATATT
1841156 TATAATTTATATT
1 TATAATTTATATT
1841169 T
1 T
1841170 TTTTAAGTAC
Statistics
Matches: 44, Mismatches: 10, Indels: 12
0.67 0.15 0.18
Matches are distributed among these distances:
10 5 0.11
11 9 0.20
12 12 0.27
13 18 0.41
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (13 bp):
TATAATTTATATT
Found at i:1841129 original size:23 final size:23
Alignment explanation
Indices: 1841103--1841165 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
1841093 TTCATATAAT
*
1841103 TTATATTTATAATTTATT-TTAAA
1 TTATAATTATAATTTATTATT-AA
* **
1841126 TTATAATTGTACGTTATTATTAA
1 TTATAATTATAATTTATTATTAA
*
1841149 TTTTAATTATAATTTAT
1 TTATAATTATAATTTAT
1841166 ATTTTTTTAA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
23 29 0.94
24 2 0.06
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.59
Consensus pattern (23 bp):
TTATAATTATAATTTATTATTAA
Found at i:1844156 original size:7 final size:7
Alignment explanation
Indices: 1844144--1844179 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
1844134 ATTTCATCTC
1844144 ATAATAA
1 ATAATAA
1844151 ATAATAA
1 ATAATAA
1844158 ATAATAA
1 ATAATAA
1844165 ATAATAA
1 ATAATAA
1844172 ATAATAA
1 ATAATAA
1844179 A
1 A
1844180 GAGAGCATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
ATAATAA
Found at i:1850930 original size:59 final size:59
Alignment explanation
Indices: 1850864--1850982 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 59
1850854 AATTTTTATT
1850864 TGACATGAAATGAAAACCTAATTCAATTGATTCAATTTAAATTTGATTTAACTCGATTA
1 TGACATGAAATGAAAACCTAATTCAATTGATTCAATTTAAATTTGATTTAACTCGATTA
*
1850923 TGACATGAAATGAGAACCTAATTCAATTGATTCAATTTAAATTTGATTTAACTCGATTA
1 TGACATGAAATGAAAACCTAATTCAATTGATTCAATTTAAATTTGATTTAACTCGATTA
1850982 T
1 T
1850983 CTTAAATATA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (59 bp):
TGACATGAAATGAAAACCTAATTCAATTGATTCAATTTAAATTTGATTTAACTCGATTA
Found at i:1855595 original size:3 final size:3
Alignment explanation
Indices: 1855589--1855644 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
1855579 CTCCATCATC
1855589 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1855637 ATT ATT AT
1 ATT ATT AT
1855645 GCAGTTGAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1855711 original size:3 final size:3
Alignment explanation
Indices: 1855703--1855736 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1855693 CTGAAAAGTT
1855703 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1855737 GCAGTTGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1855768 original size:92 final size:92
Alignment explanation
Indices: 1855611--1855793 Score: 366
Period size: 92 Copynumber: 2.0 Consensus size: 92
1855601 ATTATTATTA
1855611 TTATTATTATTATTATTATTATTATTATTATTATGCAGTTGAATAATAAGAGGGTAAGAATAGCC
1 TTATTATTATTATTATTATTATTATTATTATTATGCAGTTGAATAATAAGAGGGTAAGAATAGCC
1855676 GAAAGGGCAAGTCTTGACTGAAAAGTT
66 GAAAGGGCAAGTCTTGACTGAAAAGTT
1855703 TTATTATTATTATTATTATTATTATTATTATTATGCAGTTGAATAATAAGAGGGTAAGAATAGCC
1 TTATTATTATTATTATTATTATTATTATTATTATGCAGTTGAATAATAAGAGGGTAAGAATAGCC
1855768 GAAAGGGCAAGTCTTGACTGAAAAGT
66 GAAAGGGCAAGTCTTGACTGAAAAGT
1855794 GAAAGCATTT
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 91 1.00
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.38
Consensus pattern (92 bp):
TTATTATTATTATTATTATTATTATTATTATTATGCAGTTGAATAATAAGAGGGTAAGAATAGCC
GAAAGGGCAAGTCTTGACTGAAAAGTT
Found at i:1857169 original size:19 final size:19
Alignment explanation
Indices: 1857118--1857169 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
1857108 CTCGTTAATG
* *
1857118 GTGTTTGATTAGTAGAATT
1 GTGTCTGATTAGTGGAATT
1857137 GTGTCTGATTAGTGGAATT
1 GTGTCTGATTAGTGGAATT
1857156 GTGTCTGATTAGTG
1 GTGTCTGATTAGTG
1857170 AAACCGTGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.21, C:0.04, G:0.31, T:0.44
Consensus pattern (19 bp):
GTGTCTGATTAGTGGAATT
Found at i:1857178 original size:19 final size:19
Alignment explanation
Indices: 1857137--1857178 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1857127 TAGTAGAATT
* **
1857137 GTGTCTGATTAGTGGAATT
1 GTGTCTGATTAGTGAAACC
1857156 GTGTCTGATTAGTGAAACC
1 GTGTCTGATTAGTGAAACC
1857175 GTGT
1 GTGT
1857179 GTGCATATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.10, G:0.31, T:0.38
Consensus pattern (19 bp):
GTGTCTGATTAGTGAAACC
Found at i:1859348 original size:19 final size:21
Alignment explanation
Indices: 1859311--1859355 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
1859301 TAGTTTTAAG
1859311 TTTTAAAAGTATTTATTTA-T
1 TTTTAAAAGTATTTATTTAGT
1859331 TTTTAAAA-T-TTTATTTTAGT
1 TTTTAAAAGTATTTA-TTTAGT
1859351 TTTTA
1 TTTTA
1859356 TTTCAAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.17
19 5 0.22
20 14 0.61
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (21 bp):
TTTTAAAAGTATTTATTTAGT
Found at i:1860742 original size:37 final size:38
Alignment explanation
Indices: 1860688--1860779 Score: 91
Period size: 38 Copynumber: 2.4 Consensus size: 38
1860678 TTCCACCATT
* * *
1860688 TGTGGTGTG-TAGAGTGGATG-GACCTAACAT-GGTCCTA
1 TGTGGTGTGCAAG-GTGGATGAG-CCTAACATAGCTCATA
* *
1860725 TGTGGTGTGCAAGGTGGATGAGCTTAATATAGCTCATA
1 TGTGGTGTGCAAGGTGGATGAGCCTAACATAGCTCATA
*
1860763 TGTGGTGTGCAAAGTGG
1 TGTGGTGTGCAAGGTGG
1860780 TCGGAGTGGC
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
37 22 0.48
38 24 0.52
ACGTcount: A:0.23, C:0.11, G:0.36, T:0.30
Consensus pattern (38 bp):
TGTGGTGTGCAAGGTGGATGAGCCTAACATAGCTCATA
Found at i:1862929 original size:188 final size:188
Alignment explanation
Indices: 1862596--1862980 Score: 576
Period size: 188 Copynumber: 2.0 Consensus size: 188
1862586 CACTGAAATT
* * *
1862596 AAAATTTATTGTAATTACTAGAAGATATAATTACTACATATTAATAGTTAAACTTTCTTACAACT
1 AAAATTTTTTGTAATTACAAGAAGATATAATTACTACA-ATTAATAATTAAACTTTCTTACAACT
* *
1862661 ACTCTATGGTCTCTAAAAACAACAACTCATAAAAGAAACTCAAATTTACCTCGATAATTGCAAAG
65 ACTCTATGATCTCTAAAAACAACAACTCATAAAAGAAACTCAAATTTACCTCCATAATTGCAAAG
*
1862726 TCAAGCTTGAACTCAAAG-AGCTTGAGCTATCAAATAAGTCAAATTAAAGTACAGGGATTG
130 TCAAGCTTAAACTC-AAGTAGCTTGAGCTATCAAATAAGTCAAA-TAAAGTACAGGGATTG
* * * * * *
1862786 AAATTTTTTTGTAATTACAAGAAGATATAATTACTAC-CTTAATAATTCAATTTTCTTATAATTA
1 AAAATTTTTTGTAATTACAAGAAGATATAATTACTACAATTAATAATTAAACTTTCTTACAACTA
** *
1862850 CTCTATGATCTCTAAAAACAACAACTCATAAAAGAATTTCAAATTTAGCTCCATAATTGCAAAGT
66 CTCTATGATCTCTAAAAACAACAACTCATAAAAGAAACTCAAATTTACCTCCATAATTGCAAAGT
* *
1862915 CAAGTTTAAACTCAAGTAGCTTGGGCTATCAAATAAGTCAAATAAAGTACAGGGATTG
131 CAAGCTTAAACTCAAGTAGCTTGAGCTATCAAATAAGTCAAATAAAGTACAGGGATTG
1862973 AAAATTTT
1 AAAATTTT
1862981 AAAATTGAAA
Statistics
Matches: 176, Mismatches: 18, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
187 26 0.15
188 116 0.66
190 34 0.19
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (188 bp):
AAAATTTTTTGTAATTACAAGAAGATATAATTACTACAATTAATAATTAAACTTTCTTACAACTA
CTCTATGATCTCTAAAAACAACAACTCATAAAAGAAACTCAAATTTACCTCCATAATTGCAAAGT
CAAGCTTAAACTCAAGTAGCTTGAGCTATCAAATAAGTCAAATAAAGTACAGGGATTG
Found at i:1866643 original size:22 final size:23
Alignment explanation
Indices: 1866618--1866661 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
1866608 CCCAAACAAA
* *
1866618 AAAACCAAATCAAAAA-TAAAAT
1 AAAACAAAACCAAAAATTAAAAT
*
1866640 AAAATAAAACCAAAAATTAAAA
1 AAAACAAAACCAAAAATTAAAA
1866662 GTCCATTACA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.75, C:0.11, G:0.00, T:0.14
Consensus pattern (23 bp):
AAAACAAAACCAAAAATTAAAAT
Found at i:1868076 original size:4 final size:4
Alignment explanation
Indices: 1868067--1868118 Score: 59
Period size: 4 Copynumber: 13.0 Consensus size: 4
1868057 TTTGTTTTGT
* ** * *
1868067 TTTA TTTA TTTA TTTA TTTA TTTA TGTA TCCA TTCA TTTA TTTA TTTC
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1868115 TTTA
1 TTTA
1868119 CTCTTTTTGT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:1877765 original size:47 final size:47
Alignment explanation
Indices: 1877696--1877788 Score: 186
Period size: 47 Copynumber: 2.0 Consensus size: 47
1877686 AAGTCGTTAG
1877696 AGTTGCTCATAGATTAGGTCGGGTCAAGCTTAAAGCATGATATTTAA
1 AGTTGCTCATAGATTAGGTCGGGTCAAGCTTAAAGCATGATATTTAA
1877743 AGTTGCTCATAGATTAGGTCGGGTCAAGCTTAAAGCATGATATTTA
1 AGTTGCTCATAGATTAGGTCGGGTCAAGCTTAAAGCATGATATTTA
1877789 CACACTTTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.32
Consensus pattern (47 bp):
AGTTGCTCATAGATTAGGTCGGGTCAAGCTTAAAGCATGATATTTAA
Found at i:1877962 original size:31 final size:31
Alignment explanation
Indices: 1877914--1877972 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1877904 TTTTTAATTT
* *
1877914 TTTAAAAAATATTTATATTTTTTATTTAATA
1 TTTAAAAAATATTTATATTCTTCATTTAATA
*
1877945 TTTAATAAAT-TTATATATTCTTCATTTA
1 TTTAAAAAATATT-TATATTCTTCATTTA
1877973 TTAAAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 2 0.08
31 22 0.92
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (31 bp):
TTTAAAAAATATTTATATTCTTCATTTAATA
Found at i:1878090 original size:19 final size:21
Alignment explanation
Indices: 1878066--1878105 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
1878056 GTTATAAATT
1878066 ATATAATATA-TAT-AACATA
1 ATATAATATATTATAAACATA
1878085 ATATAATATATTATAAACATA
1 ATATAATATATTATAAACATA
1878106 TAAAATTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.53
20 3 0.16
21 6 0.32
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATAATATATTATAAACATA
Found at i:1894124 original size:23 final size:24
Alignment explanation
Indices: 1894098--1894142 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1894088 TAAATTTATT
1894098 TAAAA-TTAAAAAAAATAAAATGG
1 TAAAATTTAAAAAAAATAAAATGG
* *
1894121 TAAAATTTAAAAACATTAAAAT
1 TAAAATTTAAAAAAAATAAAAT
1894143 TCATTTAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (24 bp):
TAAAATTTAAAAAAAATAAAATGG
Found at i:1894558 original size:18 final size:18
Alignment explanation
Indices: 1894523--1894563 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
1894513 TTTATAGTGT
*
1894523 TTTTTTAGAAATTTTTAA
1 TTTTTTAGAAATTATTAA
1894541 TATTTTTAGAAA-TATTAA
1 T-TTTTTAGAAATTATTAA
1894559 TTTTT
1 TTTTT
1894564 AAATTCATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 7 0.33
19 10 0.48
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (18 bp):
TTTTTTAGAAATTATTAA
Found at i:1894649 original size:27 final size:26
Alignment explanation
Indices: 1894619--1894671 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
1894609 TTTTTTTTAA
* *
1894619 ATTTGAATTCTTTATAAAATTATAATT
1 ATTTGAATTCCTTAAAAAATTA-AATT
1894646 ATTTGAATTCCTTAAAAAATTAAATT
1 ATTTGAATTCCTTAAAAAATTAAATT
1894672 TTAAATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (26 bp):
ATTTGAATTCCTTAAAAAATTAAATT
Found at i:1898871 original size:3 final size:3
Alignment explanation
Indices: 1898863--1898897 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1898853 GTAGCGTCTT
1898863 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1898898 TAAATTTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1899484 original size:12 final size:12
Alignment explanation
Indices: 1899467--1899533 Score: 59
Period size: 12 Copynumber: 5.5 Consensus size: 12
1899457 TTTTATGTTC
1899467 ATTTATGTATTT
1 ATTTATGTATTT
1899479 ATTTATATGTCCA-TT
1 A-TT-TATGT--ATTT
1899494 -TTTATGT-TTT
1 ATTTATGTATTT
*
1899504 ATTTATTTATTT
1 ATTTATGTATTT
*
1899516 ATTTATTTATTT
1 ATTTATGTATTT
1899528 ATTTAT
1 ATTTAT
1899534 TTGTTATGGT
Statistics
Matches: 47, Mismatches: 1, Indels: 14
0.76 0.02 0.23
Matches are distributed among these distances:
10 2 0.04
11 6 0.13
12 27 0.57
13 4 0.09
14 5 0.11
15 2 0.04
16 1 0.02
ACGTcount: A:0.24, C:0.03, G:0.04, T:0.69
Consensus pattern (12 bp):
ATTTATGTATTT
Found at i:1899510 original size:4 final size:4
Alignment explanation
Indices: 1899501--1899535 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
1899491 ATTTTTATGT
1899501 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1899536 GTTATGGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:1903140 original size:65 final size:65
Alignment explanation
Indices: 1903065--1903198 Score: 259
Period size: 65 Copynumber: 2.1 Consensus size: 65
1903055 AAGTAACCTA
*
1903065 TTCAATCTCATTTCATTCATGAATATGGAAATCACATACTATGCCAAAACTTTATATTCAAATAG
1 TTCAATCTCATTTCATTCATGAATATGGAAATCACATACTATGCCAAAACTTCATATTCAAATAG
1903130 TTCAATCTCATTTCATTCATGAATATGGAAATCACATACTATGCCAAAACTTCATATTCAAATAG
1 TTCAATCTCATTTCATTCATGAATATGGAAATCACATACTATGCCAAAACTTCATATTCAAATAG
1903195 TTCA
1 TTCA
1903199 CTAACAATTT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 68 1.00
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.35
Consensus pattern (65 bp):
TTCAATCTCATTTCATTCATGAATATGGAAATCACATACTATGCCAAAACTTCATATTCAAATAG
Found at i:1909224 original size:6 final size:6
Alignment explanation
Indices: 1909213--1909240 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1909203 GGCAACGGGC
1909213 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1909241 GTAAAATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTAT
Found at i:1911154 original size:18 final size:18
Alignment explanation
Indices: 1911116--1911154 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1911106 TTTTAATTTG
* **
1911116 ATTTTTTTATTTTTTGGT
1 ATTTTTTAATTTTTTAAT
1911134 ATTTTTTAATTTTTTAAT
1 ATTTTTTAATTTTTTAAT
1911152 ATT
1 ATT
1911155 ATTTGGATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (18 bp):
ATTTTTTAATTTTTTAAT
Found at i:1913742 original size:29 final size:30
Alignment explanation
Indices: 1913710--1913794 Score: 68
Period size: 29 Copynumber: 2.8 Consensus size: 30
1913700 AATATTTTTT
* * *
1913710 TAATATTATATATTTT-ATCAATTTAGTTA
1 TAATATTAAAAATTTTAATCAATTTAATTA
* *
1913739 TAATTTTAAAAATTTTAATTAATTTAATTA
1 TAATATTAAAAATTTTAATCAATTTAATTA
*
1913769 TCAATGTTTACAAAA-TTT-ATCAATTT
1 T-AAT-ATTA-AAAATTTTAATCAATTT
1913795 TCTCTTAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
29 13 0.28
30 12 0.26
31 10 0.22
32 7 0.15
33 4 0.09
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (30 bp):
TAATATTAAAAATTTTAATCAATTTAATTA
Found at i:1913752 original size:20 final size:21
Alignment explanation
Indices: 1913715--1913753 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1913705 TTTTTTAATA
**
1913715 TTATATATTTTATCAATTTAG
1 TTATATATTTTAAAAATTTAG
1913736 TTATA-ATTTTAAAAATTT
1 TTATATATTTTAAAAATTT
1913754 TAATTAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (21 bp):
TTATATATTTTAAAAATTTAG
Found at i:1914129 original size:232 final size:233
Alignment explanation
Indices: 1913712--1914179 Score: 929
Period size: 232 Copynumber: 2.0 Consensus size: 233
1913702 TATTTTTTTA
1913712 ATATTATATATTTTATCAATTTAGTTATAATTTTAAAAATTTTAATTAATTTAATTATCAATGTT
1 ATATTATATATTTTATCAATTTAGTTATAATTTTAAAAATTTTAATTAATTTAATTATCAATGTT
1913777 TACAAAATTTATCAATTTTCTCTTAAAAAATTTAAAAATAGAAAATTACTTCAAAAAATGATTTG
66 TACAAAATTTATCAATTTTCTCTTAAAAAATTTAAAAATAGAAAATTACTTCAAAAAATGATTTG
1913842 CTTCAACTACAGTTTCTTGTTGCAGTGTTCATTTTCTTGTTCTGTTTCTGAAACATTTTCTTCAA
131 CTTCAACTACAGTTTCTTGTTGCAGTGTTCATTTTCTTGTTCTGTTTCTGAAACATTTTCTTCAA
1913907 CCTCAAGCTTGTTAAAATCAAATGAATCTTGGGGCAAC
196 CCTCAAGCTTGTTAAAATCAAATGAATCTTGGGGCAAC
1913945 ATATTATATA-TTTATCAATTTAGTTATAATTTTAAAAATTTTAATTAATTTAATTATCAATGTT
1 ATATTATATATTTTATCAATTTAGTTATAATTTTAAAAATTTTAATTAATTTAATTATCAATGTT
1914009 TACAAAATTTATCAATTTTCTCTTAAAAAATTTAAAAATAGAAAATTACTTCAAAAAATGATTTG
66 TACAAAATTTATCAATTTTCTCTTAAAAAATTTAAAAATAGAAAATTACTTCAAAAAATGATTTG
1914074 CTTCAACTACAGTTTCTTGTTGCAGTGTTCATTTTCTTGTTCTGTTTCTGAAACATTTTCTTCAA
131 CTTCAACTACAGTTTCTTGTTGCAGTGTTCATTTTCTTGTTCTGTTTCTGAAACATTTTCTTCAA
1914139 CCTCAAGCTTGTTAAAATCAAATGAATCTTGGGGCAAC
196 CCTCAAGCTTGTTAAAATCAAATGAATCTTGGGGCAAC
1914177 ATA
1 ATA
1914180 ATTTCTTCTT
Statistics
Matches: 235, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
232 225 0.96
233 10 0.04
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (233 bp):
ATATTATATATTTTATCAATTTAGTTATAATTTTAAAAATTTTAATTAATTTAATTATCAATGTT
TACAAAATTTATCAATTTTCTCTTAAAAAATTTAAAAATAGAAAATTACTTCAAAAAATGATTTG
CTTCAACTACAGTTTCTTGTTGCAGTGTTCATTTTCTTGTTCTGTTTCTGAAACATTTTCTTCAA
CCTCAAGCTTGTTAAAATCAAATGAATCTTGGGGCAAC
Found at i:1919348 original size:20 final size:20
Alignment explanation
Indices: 1919306--1919350 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1919296 TTTATTTTCT
**
1919306 ATTTTTCTTAAATCCCATTA
1 ATTTTTCTTAAATCCCAGAA
*
1919326 ATTTTTCTTAAATCCTAGAA
1 ATTTTTCTTAAATCCCAGAA
1919346 ATTTT
1 ATTTT
1919351 ATACTTCTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.16, G:0.02, T:0.51
Consensus pattern (20 bp):
ATTTTTCTTAAATCCCAGAA
Found at i:1927637 original size:28 final size:27
Alignment explanation
Indices: 1927597--1927650 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
1927587 TTGTAATTTT
1927597 TTTAAAACTTACAAAAAAAATATTAAAAC
1 TTTAAAACTTAC-AAAAAAATA-TAAAAC
1927626 TTTAAAA-TTACAAAAAAATATAAAA
1 TTTAAAACTTACAAAAAAATATAAAA
1927651 TATAAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 5 0.20
27 9 0.36
28 4 0.16
29 7 0.28
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (27 bp):
TTTAAAACTTACAAAAAAATATAAAAC
Found at i:1928157 original size:29 final size:27
Alignment explanation
Indices: 1928125--1928179 Score: 83
Period size: 29 Copynumber: 2.0 Consensus size: 27
1928115 TTGTAATTTT
1928125 TTTAAAACTTACAAAAAAAATATTAAAAC
1 TTTAAAACTTAC-AAAAAAATA-TAAAAC
*
1928154 TTTAAAATTTACAAAAAAATATAAAA
1 TTTAAAACTTACAAAAAAATATAAAA
1928180 TATAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 5 0.20
28 9 0.36
29 11 0.44
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (27 bp):
TTTAAAACTTACAAAAAAATATAAAAC
Found at i:1928537 original size:529 final size:528
Alignment explanation
Indices: 1927540--1928590 Score: 2093
Period size: 529 Copynumber: 2.0 Consensus size: 528
1927530 CATGCCATAC
1927540 CATGACATCACTGTGACACCATCATTTGAAAAAAAAAACCTTAAAATTTGTAATTTTTTTAAAAC
1 CATGACATCACTGTGACACCATCATTTGAAAAAAAAAACCTTAAAATTTGTAATTTTTTTAAAAC
1927605 TTACAAAAAAAATATTAAAACTTTAAAATTACAAAAAAATATAAAATATAAAAATACTGGATTTG
66 TTACAAAAAAAATATTAAAACTTTAAAATTACAAAAAAATATAAAATATAAAAATACTGGATTTG
1927670 ACTATTTAAAAAATTAGAAATTTTAGTTTTTTTTTTAGATTTTTATAAATCACATTTACTAAAGC
131 ACTATTTAAAAAATTAGAAATTTTAGTTTTTTTTTTAGATTTTTATAAATCACATTTACTAAAGC
1927735 TTGAACATGAGATCATTGTCTTTTGGAATGATATTACTTATGGTAGTTGTTTTATAATTTAATTA
196 TTGAACATGAGATCATTGTCTTTTGGAATGATATTACTTATGGTAGTTGTTTTATAATTTAATTA
1927800 ATCGAAACTTATAGTTGGTAGTTTTTTTCGGTAATAAATTTGGATAAGTTTTTTTTTCAAATTAT
261 ATCGAAACTTATAGTTGGTAGTTTTTTTCGGTAATAAATTTGGATAAGTTTTTTTTTCAAATTAT
1927865 TTAAATAATGAAAAAAAATACTATTTTAATTAACATGATGGGAAAAAAATAACATTATTTTTCAT
326 TTAAATAATGAAAAAAAATACTATTTTAATTAACATGATGGGAAAAAAATAACATTATTTTTCAT
1927930 TATTTAAATAATTAAAAAACTTATCCTAAATTTATCACCTAAATATTTTAAAATATTTAAATTTC
391 TATTTAAATAATTAAAAAACTTATCCTAAATTTATCACCTAAATATTTTAAAATATTTAAATTTC
1927995 TATTTTTAAAAAAATAATTATTTAATTATTATATTTTTGTATTGTTTTTGTAGCTTTGTTTTTTT
456 TATTTTTAAAAAAATAATTATTTAATTATTATATTTTTGTATTGTTTTTGTAGCTTTGTTTTTTT
1928060 TTTCCCAT
521 TTTCCCAT
1928068 CATGACATCACTGTGACACCATCATTTGAAAAAAAAAACCTTAAAATTTGTAATTTTTTTAAAAC
1 CATGACATCACTGTGACACCATCATTTGAAAAAAAAAACCTTAAAATTTGTAATTTTTTTAAAAC
1928133 TTACAAAAAAAATATTAAAACTTTAAAATTTACAAAAAAATATAAAATATAAAAATACTGGATTT
66 TTACAAAAAAAATATTAAAACTTTAAAA-TTACAAAAAAATATAAAATATAAAAATACTGGATTT
1928198 GACTATTTAAAAAATTAGAAATTTTAGTTTTTTTTTTAGATTTTTATAAATCACATTTACTAAAG
130 GACTATTTAAAAAATTAGAAATTTTAGTTTTTTTTTTAGATTTTTATAAATCACATTTACTAAAG
1928263 CTTGAACATGAGATCATTGTCTTTTGGAATGATATTACTTATGGTAGTTGTTTTATAATTTAATT
195 CTTGAACATGAGATCATTGTCTTTTGGAATGATATTACTTATGGTAGTTGTTTTATAATTTAATT
1928328 AATCGAAACTTATAGTTGGTAGTTTTTTTCGGTAATAAATTTGGATAAGTTTTTTTTTCAAATTA
260 AATCGAAACTTATAGTTGGTAGTTTTTTTCGGTAATAAATTTGGATAAGTTTTTTTTTCAAATTA
1928393 TTTAAATAATGAAAAAAAATACTATTTTAATTAACATGATGGGAAAAAAATAACATTATTTTTCA
325 TTTAAATAATGAAAAAAAATACTATTTTAATTAACATGATGGGAAAAAAATAACATTATTTTTCA
1928458 TTATTTAAATAATTAAAAAACTTATCCTAAATTTATCACCTAAATATTTTAAAATATTTAAATTT
390 TTATTTAAATAATTAAAAAACTTATCCTAAATTTATCACCTAAATATTTTAAAATATTTAAATTT
1928523 CTATTTTTAAAAAAATAATTATTTAATTATTATATTTTTGTATTGTTTTTGTAGCTTTGTTTTTT
455 CTATTTTTAAAAAAATAATTATTTAATTATTATATTTTTGTATTGTTTTTGTAGCTTTGTTTTTT
1928588 TTT
520 TTT
1928591 CCCCCTATTT
Statistics
Matches: 522, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
528 93 0.18
529 429 0.82
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (528 bp):
CATGACATCACTGTGACACCATCATTTGAAAAAAAAAACCTTAAAATTTGTAATTTTTTTAAAAC
TTACAAAAAAAATATTAAAACTTTAAAATTACAAAAAAATATAAAATATAAAAATACTGGATTTG
ACTATTTAAAAAATTAGAAATTTTAGTTTTTTTTTTAGATTTTTATAAATCACATTTACTAAAGC
TTGAACATGAGATCATTGTCTTTTGGAATGATATTACTTATGGTAGTTGTTTTATAATTTAATTA
ATCGAAACTTATAGTTGGTAGTTTTTTTCGGTAATAAATTTGGATAAGTTTTTTTTTCAAATTAT
TTAAATAATGAAAAAAAATACTATTTTAATTAACATGATGGGAAAAAAATAACATTATTTTTCAT
TATTTAAATAATTAAAAAACTTATCCTAAATTTATCACCTAAATATTTTAAAATATTTAAATTTC
TATTTTTAAAAAAATAATTATTTAATTATTATATTTTTGTATTGTTTTTGTAGCTTTGTTTTTTT
TTTCCCAT
Found at i:1932106 original size:142 final size:144
Alignment explanation
Indices: 1931780--1932097 Score: 452
Period size: 142 Copynumber: 2.2 Consensus size: 144
1931770 TGGTAGTGGG
1931780 GAGATGAAGTTGGTGAGGAAGA--CTTTAGCTTTCCAAAACCATACAAATATAGACGCTTTAGAG
1 GAGATGAAGTTGGTGAGGAAGACTCTTTAGCTTTCCAAAACCATACAAATATAGACGCTTTAGAG
* * * * *
1931843 AAGAGAGATTTCCCAACCGCTCTGGAAAGGCTTCTATTCCTTGAAACCCCATGAATGTCAAATCT
66 AAGAGAGATTTCCCAACCACTCTGGAAAGGCTTCTACTCCTTCAAACCCCATCAATCTCAAATCT
* **
1931908 TCAAGGGCATTGGG
131 TCAAGGGCAGTGAA
1931922 GAGATGAAGTTGGTGAGGAAGACTCTTTAGCTTTCCAAAACCACT-CAAATATAGACGCTTTAGA
1 GAGATGAAGTTGGTGAGGAAGACTCTTTAGCTTTCCAAAACCA-TACAAATATAGACGCTTTAGA
* * *
1931986 G-A-AGAGATTTCCCAACCACTCTGGAAAGGCTTCTACTCCTTCAAA-CCCTTCCATCCTCAATT
65 GAAGAGAGATTTCCCAACCACTCTGGAAAGGCTTCTACTCCTTCAAACCCCATCAAT-CTCAAAT
*
1932048 CTTCGAGGGCAGTGAA
129 CTTCAAGGGCAGTGAA
1932064 GA-ACTGAAGTTGGTGAGGAAGACTCTTTAGCTTT
1 GAGA-TGAAGTTGGTGAGGAAGACTCTTTAGCTTT
1932098 TCCCAACCAG
Statistics
Matches: 159, Mismatches: 12, Indels: 10
0.88 0.07 0.06
Matches are distributed among these distances:
141 7 0.04
142 111 0.70
143 1 0.01
144 39 0.25
145 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (144 bp):
GAGATGAAGTTGGTGAGGAAGACTCTTTAGCTTTCCAAAACCATACAAATATAGACGCTTTAGAG
AAGAGAGATTTCCCAACCACTCTGGAAAGGCTTCTACTCCTTCAAACCCCATCAATCTCAAATCT
TCAAGGGCAGTGAA
Found at i:1932826 original size:210 final size:210
Alignment explanation
Indices: 1932484--1933702 Score: 2151
Period size: 210 Copynumber: 5.8 Consensus size: 210
1932474 CACAGCCATC
* * *
1932484 AACTGATAGATTTTGAAGAGATGAAAATCCTTCCAAATTTGGGATCGAACTTAAATCAGGACAA-
1 AACTGACAGATATTGAAGAGAGGAAAATCCTTCCAAATTTGGGATCGAACTTAAATCAGGACAAT
*
1932548 CAGTATAGA-CGTAATTCTTTGAGACAAGTGGAGGTAGATAATCCATCTCCAATCTTGCTTAATT
66 C-GTCTAGATC-TAATTCTTTGAGACAAGTGGAGGTAGATAATCCATCTCCAATCTTGCTTAATT
* *
1932612 TTTCACAACCGACAATGCAAAGCTTTTCAAGAGATGAACACCCTCCAGTTATTGGAAGAACTTCC
129 TTTCACAACCGACAATGCGAAGCTTTTCAAGAGATGAACATCCTCCAGTTATTGGAAGAACTTCC
1932677 AATTTGTTGCACCATTT
194 AATTTGTTGCACCATTT
1932694 AACTGACAGATATTGAAGAGAGGAAAATCCTTCCAAATTTGGGATCGAACTTAAATCAGGACAAT
1 AACTGACAGATATTGAAGAGAGGAAAATCCTTCCAAATTTGGGATCGAACTTAAATCAGGACAAT
1932759 CGTCTAGATCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCATCTCCAATCTTGCTTAATTTT
66 CGTCTAGATCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCATCTCCAATCTTGCTTAATTTT
*
1932824 TCACAACCGCCAATGCGAAGCTTTTCAAGAGATGAACATCCTCCAGTTATTGGAAGAACTTCCAA
131 TCACAACCGACAATGCGAAGCTTTTCAAGAGATGAACATCCTCCAGTTATTGGAAGAACTTCCAA
1932889 TTTGTTGCACCATTT
196 TTTGTTGCACCATTT
*
1932904 AACTAACAGATATTGAAGAGAGGAAAATCCTTCCAAATTTGGGATCGAACTTAAATCAGGACAAT
1 AACTGACAGATATTGAAGAGAGGAAAATCCTTCCAAATTTGGGATCGAACTTAAATCAGGACAAT
1932969 CGTCTAGATCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCATCTCCAATCTTGCTTAATTTT
66 CGTCTAGATCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCATCTCCAATCTTGCTTAATTTT
* * *
1933034 CCACAACCGCCAATGTGAAGCTTTTCAAGAGATGAACATCCTCCAGTTATTGGAAGAACTTCCAA
131 TCACAACCGACAATGCGAAGCTTTTCAAGAGATGAACATCCTCCAGTTATTGGAAGAACTTCCAA
* * *
1933099 TTTGTCGCACCAATA
196 TTTGTTGCACCATTT
* *
1933114 AACTGACAAATATTGAAGAGAGGAAAATCCTTCCAAATTTGGGATCAAACTTAAATCAGGACAAT
1 AACTGACAGATATTGAAGAGAGGAAAATCCTTCCAAATTTGGGATCGAACTTAAATCAGGACAAT
*
1933179 TGTCTAGA-CATAATTCTTTGAGACAAGTGGAGGTAGATAATCCATCTCCAATCTTGCTTAATTT
66 CGTCTAGATC-TAATTCTTTGAGACAAGTGGAGGTAGATAATCCATCTCCAATCTTGCTTAATTT
* *
1933243 TTCACAATCGATAATGCGAAGCTTTTCAAGAGATGAACATCCTCCAGTTATTGGAAGAACTTCCA
130 TTCACAACCGACAATGCGAAGCTTTTCAAGAGATGAACATCCTCCAGTTATTGGAAGAACTTCCA
1933308 ATTTGTTGCA-CATTT
195 ATTTGTTGCACCATTT
1933323 CAACTGACAGATATTGAAGAGAGGAAAATCCTTCCAAATTTGGGATCGAACTTAAATCAGGACAA
1 -AACTGACAGATATTGAAGAGAGGAAAATCCTTCCAAATTTGGGATCGAACTTAAATCAGGACAA
1933388 TCGTCTAGATCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCATCTCCAATCTTGCTTAATTT
65 TCGTCTAGATCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCATCTCCAATCTTGCTTAATTT
* *
1933453 TTCACAATCGATAATGCGAAGCTTTTCAAGAGATGAACATCCTCCAGTTATTGGAAGAACTTCCA
130 TTCACAACCGACAATGCGAAGCTTTTCAAGAGATGAACATCCTCCAGTTATTGGAAGAACTTCCA
1933518 ATTTGTTGCACC-TTT
195 ATTTGTTGCACCATTT
1933533 GAACTGACAGATATTGAAGAGAGGAAAATCCTTCCAAATTTGGGATCGAACTTAAATCAGGACAA
1 -AACTGACAGATATTGAAGAGAGGAAAATCCTTCCAAATTTGGGATCGAACTTAAATCAGGACAA
1933598 TCGTCTAGATCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCATCTCCAATCTTGCTTAATTT
65 TCGTCTAGATCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCATCTCCAATCTTGCTTAATTT
* *
1933663 TCCACAACCGACAATGTGAAGCTTTTCAAGAGATGAACAT
130 TTCACAACCGACAATGCGAAGCTTTTCAAGAGATGAACAT
1933703 TGTCCCGTTA
Statistics
Matches: 970, Mismatches: 33, Indels: 12
0.96 0.03 0.01
Matches are distributed among these distances:
209 4 0.00
210 962 0.99
211 4 0.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.29
Consensus pattern (210 bp):
AACTGACAGATATTGAAGAGAGGAAAATCCTTCCAAATTTGGGATCGAACTTAAATCAGGACAAT
CGTCTAGATCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCATCTCCAATCTTGCTTAATTTT
TCACAACCGACAATGCGAAGCTTTTCAAGAGATGAACATCCTCCAGTTATTGGAAGAACTTCCAA
TTTGTTGCACCATTT
Found at i:1936437 original size:13 final size:13
Alignment explanation
Indices: 1936421--1936452 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
1936411 TCCAGGAACC
1936421 GAAATGGAGAGAA
1 GAAATGGAGAGAA
1936434 GAAATGGAGAGAA
1 GAAATGGAGAGAA
1936447 GAAATG
1 GAAATG
1936453 AAGATGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.38, T:0.09
Consensus pattern (13 bp):
GAAATGGAGAGAA
Found at i:1939508 original size:17 final size:17
Alignment explanation
Indices: 1939467--1939513 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
1939457 TATTAAGATG
**
1939467 ATTATATATTAAATTTTA
1 ATTA-ATATTAAATTAAA
*
1939485 ATAAATATTAAATTAAA
1 ATTAATATTAAATTAAA
1939502 ATTAATA-TAAAT
1 ATTAATATTAAAT
1939514 AAATTTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 5 0.20
17 17 0.68
18 3 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTAATATTAAATTAAA
Found at i:1941272 original size:31 final size:31
Alignment explanation
Indices: 1941236--1941300 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
1941226 TACAAAATGA
1941236 TTACTAAACTATTCAAAAGTTTTCATTTAAG
1 TTACTAAACTATTCAAAAGTTTTCATTTAAG
* *
1941267 TTACTAAACTATTCGAAAGTTTTTATTTAAG
1 TTACTAAACTATTCAAAAGTTTTCATTTAAG
1941298 TTA
1 TTA
1941301 TTAGATTGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.45
Consensus pattern (31 bp):
TTACTAAACTATTCAAAAGTTTTCATTTAAG
Found at i:1942644 original size:55 final size:56
Alignment explanation
Indices: 1942567--1942678 Score: 181
Period size: 55 Copynumber: 2.0 Consensus size: 56
1942557 ATGGTATGTT
*
1942567 TTTTTAATGCCGCCTATCTGACAGGCGCTAATGAATTTTTTATATT-ATTTTTTTC
1 TTTTTAATGCCGCCTATCTGACAGGCGCCAATGAATTTTTTATATTAATTTTTTTC
* *
1942622 TTTTTAATGGCGCCTCTCTGACAGGCGCCAATGAATTTTTTATATTAAATTTTTTTC
1 TTTTTAATGCCGCCTATCTGACAGGCGCCAATGAATTTTTTATATT-AATTTTTTTC
1942679 AAATTATTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
55 43 0.83
57 9 0.17
ACGTcount: A:0.22, C:0.17, G:0.13, T:0.47
Consensus pattern (56 bp):
TTTTTAATGCCGCCTATCTGACAGGCGCCAATGAATTTTTTATATTAATTTTTTTC
Found at i:1943399 original size:8 final size:9
Alignment explanation
Indices: 1943378--1943428 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
1943368 TTTATGTTAG
1943378 TTTTTATAA
1 TTTTTATAA
1943387 TTTTTATAA
1 TTTTTATAA
*
1943396 TTTTTCT-A
1 TTTTTATAA
*
1943404 TTTTAAATAA
1 TTTT-TATAA
*
1943414 TTTTAATAA
1 TTTTTATAA
1943423 CTTTTT
1 -TTTTT
1943429 TTTTGTAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 5 0.14
9 21 0.60
10 9 0.26
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTTTATAA
Found at i:1943508 original size:13 final size:13
Alignment explanation
Indices: 1943490--1943514 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1943480 TGACATGTAG
1943490 TAACATATGATTA
1 TAACATATGATTA
1943503 TAACATATGATT
1 TAACATATGATT
1943515 GGATGAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
TAACATATGATTA
Found at i:1943760 original size:23 final size:23
Alignment explanation
Indices: 1943711--1943761 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
1943701 TTTTGATATT
*
1943711 AAATTTATTGAATTAGGTTTTTC
1 AAATTTATTGAATTAGGTTTTTA
* *
1943734 AAATTTATTG-ATTTGTTTTTTGA
1 AAATTTATTGAATTAGGTTTTT-A
1943757 AAATT
1 AAATT
1943762 AATCTTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.55
Consensus pattern (23 bp):
AAATTTATTGAATTAGGTTTTTA
Found at i:1945525 original size:46 final size:46
Alignment explanation
Indices: 1945453--1945637 Score: 246
Period size: 46 Copynumber: 4.0 Consensus size: 46
1945443 ACAATGCTAT
* * * *
1945453 AACTCAGTATGATTTTCTTCACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACGTTCCAC
* *
1945499 AACTTAGTATGGTTTTCTTTACTGAAATATCATACCTACGTTCCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACGTTCCAC
* * * **
1945545 AATTCAATATGGTTTTCTTTACT-ATAATATCATATTTACGTTCCAC
1 AACTCAGTATGGTTTTCTTTACTGA-AATACCATACCTACGTTCCAC
*
1945591 AACTCAGTATGGTTTTCTTTACTGAAATGCCATACCTACGTTCCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACGTTCCAC
1945637 A
1 A
1945638 CTTTACCATG
Statistics
Matches: 120, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
45 1 0.01
46 118 0.98
47 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.39
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACGTTCCAC
Found at i:1947970 original size:31 final size:31
Alignment explanation
Indices: 1947932--1947999 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
1947922 TACAAAATGA
*
1947932 TCACTAAACTATTCAAAAGTTTTCATTTAAG
1 TCACTAAACTATGCAAAAGTTTTCATTTAAG
* * *
1947963 TTACTAAACTATGCGAAAGTTTTTATTTAAG
1 TCACTAAACTATGCAAAAGTTTTCATTTAAG
1947994 TCACTA
1 TCACTA
1948000 GGTTGTTAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.40
Consensus pattern (31 bp):
TCACTAAACTATGCAAAAGTTTTCATTTAAG
Found at i:1949016 original size:18 final size:18
Alignment explanation
Indices: 1948982--1949015 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1948972 ATAAAATAAT
1948982 AATAAAAAAATTTTTTTG
1 AATAAAAAAATTTTTTTG
*
1949000 AAT-AAAATATTTTTTT
1 AATAAAAAAATTTTTTT
1949016 TTACTTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
AATAAAAAAATTTTTTTG
Found at i:1949101 original size:27 final size:27
Alignment explanation
Indices: 1949068--1949139 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 27
1949058 TTGGCGCCTA
1949068 TCTGGGAGGCGCCAATGGTGGTGCCTAC
1 TCTGGGAGGCGCCAATGGTGGTGCC-AC
*
1949096 T-TGGGAGGCGCCAATGGTGGTGCCAT
1 TCTGGGAGGCGCCAATGGTGGTGCCAC
*
1949122 TCTGAGAGGCGCCAATGG
1 TCTGGGAGGCGCCAATGG
1949140 GCCGGGCCAG
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 2 0.05
27 38 0.93
28 1 0.02
ACGTcount: A:0.17, C:0.22, G:0.40, T:0.21
Consensus pattern (27 bp):
TCTGGGAGGCGCCAATGGTGGTGCCAC
Found at i:1949375 original size:19 final size:19
Alignment explanation
Indices: 1949353--1949390 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1949343 AATTTAATTT
*
1949353 ATTAGTAATAAATTACTAA
1 ATTACTAATAAATTACTAA
*
1949372 ATTACTAATAAGTTACTAA
1 ATTACTAATAAATTACTAA
1949391 TAAATTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (19 bp):
ATTACTAATAAATTACTAA
Found at i:1949541 original size:22 final size:22
Alignment explanation
Indices: 1949486--1949572 Score: 129
Period size: 22 Copynumber: 3.7 Consensus size: 22
1949476 ATATACCGAC
1949486 ATTACAATATTCATACAAAATTATAA
1 ATTACAATATTCATAC-AAA--A-AA
1949512 TATTACAATATTCATACAAAAAA
1 -ATTACAATATTCATACAAAAAA
1949535 ATTACAATATTCATACAAAAAA
1 ATTACAATATTCATACAAAAAA
1949557 ATTACAATATTCATAC
1 ATTACAATATTCATAC
1949573 TAAATATAGA
Statistics
Matches: 60, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
22 38 0.63
23 2 0.03
24 1 0.02
26 3 0.05
27 16 0.27
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (22 bp):
ATTACAATATTCATACAAAAAA
Found at i:1950365 original size:23 final size:24
Alignment explanation
Indices: 1950339--1950391 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
1950329 ATTTGTGAAG
1950339 ATTTAAATAAAA-AAATTAGAT-TT
1 ATTTAAATAAAATAAATTA-ATCTT
* *
1950362 ATTT-TATAAAATTAATTAATCTT
1 ATTTAAATAAAATAAATTAATCTT
1950385 ATTTAAA
1 ATTTAAA
1950392 ATATAAATCG
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
22 8 0.33
23 15 0.62
24 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (24 bp):
ATTTAAATAAAATAAATTAATCTT
Found at i:1951459 original size:12 final size:11
Alignment explanation
Indices: 1951431--1951456 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1951421 AATTTTTTAA
1951431 TTTTAAAATAT
1 TTTTAAAATAT
1951442 TTTTAAAATAT
1 TTTTAAAATAT
1951453 TTTT
1 TTTT
1951457 TAATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:1952041 original size:31 final size:31
Alignment explanation
Indices: 1952005--1952063 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1951995 ACAAAATGAC
1952005 CACTAAACTATTCAAAAGTTTTCATTTAAAT
1 CACTAAACTATTCAAAAGTTTTCATTTAAAT
* *
1952036 CACTAAACTATTCGAAAGTTTTTATTTA
1 CACTAAACTATTCAAAAGTTTTCATTTA
1952064 GTCAGTAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.15, G:0.05, T:0.41
Consensus pattern (31 bp):
CACTAAACTATTCAAAAGTTTTCATTTAAAT
Found at i:1952802 original size:15 final size:16
Alignment explanation
Indices: 1952782--1952819 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
1952772 TATGTATCAC
*
1952782 CAAATTATTA-TAGAA
1 CAAATTACTACTAGAA
1952797 CAAATTACTAGCTAGAA
1 CAAATTACTA-CTAGAA
1952814 CAAATT
1 CAAATT
1952820 CAAACTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
17 11 0.55
ACGTcount: A:0.50, C:0.13, G:0.08, T:0.29
Consensus pattern (16 bp):
CAAATTACTACTAGAA
Found at i:1955764 original size:25 final size:25
Alignment explanation
Indices: 1955730--1955796 Score: 116
Period size: 25 Copynumber: 2.7 Consensus size: 25
1955720 GACTTTCTAA
* *
1955730 TATTTAATACCCATATTTTTGACTT
1 TATTTGATACCCATATCTTTGACTT
1955755 TATTTGATACCCATATCTTTGACTT
1 TATTTGATACCCATATCTTTGACTT
1955780 TATTTGATACCCATATC
1 TATTTGATACCCATATC
1955797 AAATATCTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.27, C:0.19, G:0.06, T:0.48
Consensus pattern (25 bp):
TATTTGATACCCATATCTTTGACTT
Found at i:1955828 original size:122 final size:123
Alignment explanation
Indices: 1955673--1955918 Score: 476
Period size: 122 Copynumber: 2.0 Consensus size: 123
1955663 CCAAATATTG
1955673 CAAATATCTCAGATTTCTTATGCCAATATCTCGATACCGATATCTTTGACTTTCTAATATTTAAT
1 CAAATATCTCAGATTTCTTATGCCAATATCTCGATACCGATATCTTTGACTTTCTAATATTTAAT
*
1955738 ACCCATATTTTTGACTTTATTTGATACCCATATCTTTGACTTTATTTGATACCCATAT
66 ACCCATATTTTTGACTTTATTTGATACCCAAATCTTTGACTTTATTTGATACCCATAT
1955796 CAAATATCTCA-ATTTCTTATGCCAATATCTCGATACCGATATCTTTGACTTTCTAATATTTAAT
1 CAAATATCTCAGATTTCTTATGCCAATATCTCGATACCGATATCTTTGACTTTCTAATATTTAAT
1955860 ACCCATATTTTTGACTTTATTTGATACCCAAATCTTTGACTTTATTTGATACCCATAT
66 ACCCATATTTTTGACTTTATTTGATACCCAAATCTTTGACTTTATTTGATACCCATAT
1955918 C
1 C
1955919 TTTGACTTTC
Statistics
Matches: 122, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
122 111 0.91
123 11 0.09
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (123 bp):
CAAATATCTCAGATTTCTTATGCCAATATCTCGATACCGATATCTTTGACTTTCTAATATTTAAT
ACCCATATTTTTGACTTTATTTGATACCCAAATCTTTGACTTTATTTGATACCCATAT
Found at i:1955886 original size:25 final size:25
Alignment explanation
Indices: 1955852--1955927 Score: 125
Period size: 25 Copynumber: 3.0 Consensus size: 25
1955842 GACTTTCTAA
* *
1955852 TATTTAATACCCATATTTTTGACTT
1 TATTTGATACCCATATCTTTGACTT
*
1955877 TATTTGATACCCAAATCTTTGACTT
1 TATTTGATACCCATATCTTTGACTT
1955902 TATTTGATACCCATATCTTTGACTT
1 TATTTGATACCCATATCTTTGACTT
1955927 T
1 T
1955928 CCATAAATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.49
Consensus pattern (25 bp):
TATTTGATACCCATATCTTTGACTT
Found at i:1960424 original size:30 final size:27
Alignment explanation
Indices: 1960390--1960465 Score: 111
Period size: 25 Copynumber: 2.8 Consensus size: 27
1960380 CTAATATCTC
1960390 GATACCCATATCTTTGACTTTTCGATATTT
1 GATACCCATATCTTTGACTTTT---TATTT
1960420 GATACCCATATCTTTGAC--TTTATTT
1 GATACCCATATCTTTGACTTTTTATTT
1960445 GATACCCATATCTTTGACTTT
1 GATACCCATATCTTTGACTTT
1960466 CCATAAATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
25 23 0.52
27 1 0.02
28 2 0.05
30 18 0.41
ACGTcount: A:0.24, C:0.21, G:0.09, T:0.46
Consensus pattern (27 bp):
GATACCCATATCTTTGACTTTTTATTT
Found at i:1970447 original size:144 final size:143
Alignment explanation
Indices: 1970177--1970670 Score: 639
Period size: 144 Copynumber: 3.4 Consensus size: 143
1970167 ATTGATATGC
* * * * *
1970177 AGACGCCTTAGGGAAGAGAGATTTCCCAACAACTCTGGCAAGGCTTCTATTTCATGAAACATCGA
1 AGACGCCTTAGAGAAGAGAGATTTCCCAACCACTCCGGAAAGGCTTCTATTCCATGAAAC-TCGA
* * **
1970242 CATAGTCAAATCTTCAAGGGCACTGGGGAGATGAAGTTGGTGAGGAAGGCTCTTTAGCTTTCCAA
65 CATAGTCAAATCTTCAAGGGCAGTGAGGAGATGAAGTTGGTGAGGAAAACTCTTTAGCTTTCCAA
1970307 AACCACTCAAATAT
130 AACCACTCAAATAT
** * * * **
1970321 AGATACCTTAGCGAAGAGAGCTTTCCCAACCACTCCGGAAAGGCTTCTATTCCTTGAAACTCTTC
1 AGACGCCTTAGAGAAGAGAGATTTCCCAACCACTCCGGAAAGGCTTCTATTCCATGAAACTCGAC
* * * ** * * *
1970386 TATAGTCAAATATTTAAGGGTAGAAAGGAGCTGAAGTTGGTGAGGAAAACTCTTTAACTTTCGAA
66 -ATAGTCAAATCTTCAAGGGCAGTGAGGAGATGAAGTTGGTGAGGAAAACTCTTTAGCTTTCCAA
1970451 AACCACTCAAATAT
130 AACCACTCAAATAT
* * * * *
1970465 AGACGCTTTAGAGAAGAGAGATTTCCCAACCACTCTGGCAAGGCTTCTATTTCATGAAACCCCGA
1 AGACGCCTTAGAGAAGAGAGATTTCCCAACCACTCCGGAAAGGCTTCTATTCCATGAAA-CTCGA
* *
1970530 CATAGTCAAATCTTCAAGGGCAGTGAGGTGTTGAAGTTGGTGAGGAAAACTCTTTAGCTTTCCAA
65 CATAGTCAAATCTTCAAGGGCAGTGAGGAGATGAAGTTGGTGAGGAAAACTCTTTAGCTTTCCAA
*
1970595 AACCAATCAAACT-T
130 AACCACTCAAA-TAT
* *
1970609 AGACGCCATAGAGAAGAGAGATTTCCCAACCACTCCGGAAAGGCTTCTATTCCTTGAAACTC
1 AGACGCCTTAGAGAAGAGAGATTTCCCAACCACTCCGGAAAGGCTTCTATTCCATGAAACTC
1970671 TTGTATCAGA
Statistics
Matches: 295, Mismatches: 52, Indels: 7
0.83 0.15 0.02
Matches are distributed among these distances:
143 5 0.02
144 286 0.97
145 4 0.01
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.25
Consensus pattern (143 bp):
AGACGCCTTAGAGAAGAGAGATTTCCCAACCACTCCGGAAAGGCTTCTATTCCATGAAACTCGAC
ATAGTCAAATCTTCAAGGGCAGTGAGGAGATGAAGTTGGTGAGGAAAACTCTTTAGCTTTCCAAA
ACCACTCAAATAT
Found at i:1971061 original size:210 final size:210
Alignment explanation
Indices: 1970674--1971924 Score: 1564
Period size: 210 Copynumber: 6.0 Consensus size: 210
1970664 GAAACTCTTG
* *
1970674 TATCAGAAGAACTTCCAATTCATTGCAGCTATCAATTGACAG-ATCTTGAAGAGAGGAAAATCCT
1 TATCGGAAGAACTTCCAATTCGTTGCAGCTATCAATTGACAGAAT-TTGAAGAGAGGAAAATCCT
* * *
1970738 TCCAAATTTGGAATCCAACTTAAATTAGGACAATTCTTTAGACCTAATTCCTTGAGACAAATGAA
65 TCCAAATTTGGAATCCAACTTAAATTAGGACAATTCTTTAGACCTAATTCTTTGAGACAAGTGGA
* ** * * * * * *
1970803 GGTAGACAATTTGTCTCCAATCTTTCTTAGTTTTTCACAATTGAAAATGCTAAGCTTTTTAATAG
130 GGTAGATAATCCGTCTCCAATCTTGCTTAATTTTTCGCAATCGAAAATGCTAAGCTTTTCAAGAG
1970868 ATGAACACCTTCCAGT
195 ATGAACACCTTCCAGT
*
1970884 TATCGCAAGAACTTCCAATTCGTTGCAGCTATCAATTGACAGAATTTGAAGAGAGGAAAATCCTT
1 TATCGGAAGAACTTCCAATTCGTTGCAGCTATCAATTGACAGAATTTGAAGAGAGGAAAATCCTT
* *
1970949 CCAAATTTGGAATCCAACTTAAATTAGGACAATTCTTTAGACCTAATTCTCTGAGACAAGTAGAG
66 CCAAATTTGGAATCCAACTTAAATTAGGACAATTCTTTAGACCTAATTCTTTGAGACAAGTGGAG
* * * * *
1971014 TTAGATAATCCGTCTCCAATTTTGCTTAATTTTTTGCAGTCGAAAATGCTAAGCTTTTCGAGAGA
131 GTAGATAATCCGTCTCCAATCTTGCTTAATTTTTCGCAATCGAAAATGCTAAGCTTTTCAAGAGA
*
1971079 TGAACACCTTCCAAT
196 TGAACACCTTCCAGT
* * * * * *
1971094 TATTGGAAGAACTTCCAA-TCTGTTGCAGCTATCAATCGAGATATTTTGAAGACAGGAAAATCCT
1 TATCGGAAGAACTTCCAATTC-GTTGCAGCTATCAATTGACAGAATTTGAAGAGAGGAAAATCCT
* **
1971158 TCCAAATTTGGGATTAAACTTAAATTAGGACAATTCTTTAGACCTAATTCTTTGAGACAAGTGGA
65 TCCAAATTTGGAATCCAACTTAAATTAGGACAATTCTTTAGACCTAATTCTTTGAGACAAGTGGA
* * *
1971223 GGTAGACAATCCGTCTCCAATCTTGCTTAATTTTTCGCAACCGAAAATGTTAAGCTTTTCAAGAG
130 GGTAGATAATCCGTCTCCAATCTTGCTTAATTTTTCGCAATCGAAAATGCTAAGCTTTTCAAGAG
* * *
1971288 ATGAGCATGC-TCCAAT
195 ATGAACA-CCTTCCAGT
* * * * * * *
1971304 TATCGGAAGAACTTCCAATCCGTTGCAGGTATGAATTGACAGATTTTGGAGACACGAAAATCCTT
1 TATCGGAAGAACTTCCAATTCGTTGCAGCTATCAATTGACAGAATTTGAAGAGAGGAAAATCCTT
* * ** *
1971369 TCAAATTTGGAATCGAACTTAAATTAGGACAA-TCTTCTAGATTTAATTCTTTGAGACAAGTGTA
66 CCAAATTTGGAATCCAACTTAAATTAGGACAATTCTT-TAGACCTAATTCTTTGAGACAAGTGGA
* * * ** * * * * *
1971433 GGTAAATAATCTGTCTCCAGTCTTGGATAATGTTTT-ACACTTGGAAATGCTAAGCTTTTCAAAA
130 GGTAGATAATCCGTCTCCAATCTTGCTTAAT-TTTTCGCAATCGAAAATGCTAAGCTTTTCAAGA
* * *
1971497 GCTGAACATCC-TCCGGA
194 GATGAACA-CCTTCCAGT
** * * * * *
1971514 TATCTCAAGAACTTCCAATTTGATGCAGCTATCAATTGACAGATTTTGAATAGACGAAAATCCTT
1 TATCGGAAGAACTTCCAATTCGTTGCAGCTATCAATTGACAGAATTTGAAGAGAGGAAAATCCTT
* ** * *** ** *
1971579 CCAATTTTGGAATGGAAGTTAAATTAGGACACCACAATAG-CTCTAATTCTTTAAGACAAGTGGA
66 CCAAATTTGGAATCCAACTTAAATTAGGACAATTCTTTAGAC-CTAATTCTTTGAGACAAGTGGA
* * * * *
1971643 GGTAGATAAACCGTCCCCAATCTTTCTTAATTTCTCGCAATCGAGAATGCTAAGCTTTTCAAGAG
130 GGTAGATAATCCGTCTCCAATCTTGCTTAATTTTTCGCAATCGAAAATGCTAAGCTTTTCAAGAG
*
1971708 ATGAACACCTCCCAGT
195 ATGAACACCTTCCAGT
* * *
1971724 TATTGGAAGAGCTTCCAATTCATTGCAGCTATCAATTGACAGAATTTGAAGAGAGGAAAATCCTT
1 TATCGGAAGAACTTCCAATTCGTTGCAGCTATCAATTGACAGAATTTGAAGAGAGGAAAATCCTT
*
1971789 CCAAATTTGGAATCCAACTTAAATTAGGACAATTCTTTAGAGCTAATTCTTTGAGACAAGTGGAG
66 CCAAATTTGGAATCCAACTTAAATTAGGACAATTCTTTAGACCTAATTCTTTGAGACAAGTGGAG
1971854 GTAGATAATCCGTCTCCAATCTTGCTTAAGTTTTT-GCAATCGAAAATGCTAAGCTTTTCAAGAG
131 GTAGATAATCCGTCTCCAATCTTGCTTAA-TTTTTCGCAATCGAAAATGCTAAGCTTTTCAAGAG
1971918 ATGAACA
195 ATGAACA
1971925 TTGTCCCGTA
Statistics
Matches: 882, Mismatches: 147, Indels: 24
0.84 0.14 0.02
Matches are distributed among these distances:
209 11 0.01
210 858 0.97
211 13 0.01
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (210 bp):
TATCGGAAGAACTTCCAATTCGTTGCAGCTATCAATTGACAGAATTTGAAGAGAGGAAAATCCTT
CCAAATTTGGAATCCAACTTAAATTAGGACAATTCTTTAGACCTAATTCTTTGAGACAAGTGGAG
GTAGATAATCCGTCTCCAATCTTGCTTAATTTTTCGCAATCGAAAATGCTAAGCTTTTCAAGAGA
TGAACACCTTCCAGT
Found at i:1971881 original size:630 final size:630
Alignment explanation
Indices: 1970674--1971921 Score: 1727
Period size: 630 Copynumber: 2.0 Consensus size: 630
1970664 GAAACTCTTG
* * *
1970674 TATCAGAAGAACTTCCAATTCATTGCAGCTATCAATTGACAGATCTTGAAGAGAGGAAAATCCTT
1 TATCAGAAGAACTTCCAATCCATTGCAGCTATCAATTGACAGATCTTGAAGACACGAAAATCCTT
1970739 CCAAATTTGGAATCCAACTTAAATTAGGACAATTCTTTAGACCTAATTCCTTGAGACAAATGAAG
66 CCAAATTTGGAATCCAACTTAAATTAGGACAATTCTTTAGACCTAATTCCTTGAGACAAATGAAG
* * * * * * *
1970804 GTAGACAATTTGTCTCCAATCTTTCTTAGTTTTTCACAATTGAAAATGCTAAGCTTTTTAATAGA
131 GTAAACAATCTGTCTCCAATCTTGCATAATTTTTCACAATTGAAAATGCTAAGCTTTTCAAAAGA
* *
1970869 TGAACACCTTCCAGTTATCGCAAGAACTTCCAATTCGTTGCAGCTATCAATTGACAGAATTTGAA
196 TGAACACCTTCCAGATATCGCAAGAACTTCCAATTCGATGCAGCTATCAATTGACAGAATTTGAA
* ** **
1970934 GAGAGGAAAATCCTTCCAAATTTGGAATCCAACTTAAATTAGGACAATTCTTTAGACCTAATTCT
261 GAGACGAAAATCCTTCCAAATTTGGAATCCAACTTAAATTAGGACAACACAATAGACCTAATTCT
* * * * * * *
1970999 CTGAGACAAGTAGAGTTAGATAATCCGTCTCCAATTTTGCTTAATTTTTTGCAGTCGAAAATGCT
326 CTAAGACAAGTAGAGGTAGATAAACCGTCCCCAATTTTGCTTAATTTCTCGCAATCGAAAATGCT
* * *
1971064 AAGCTTTTCGAGAGATGAACACCTTCCAATTATTGGAAGAACTTCCAATCTGTTGCAGCTATCAA
391 AAGCTTTTCAAGAGATGAACACCTCCCAATTATTGGAAGAACTTCCAATCTATTGCAGCTATCAA
* * * * *
1971129 TCGAGATATTTTGAAGACAGGAAAATCCTTCCAAATTTGGGATTAAACTTAAATTAGGACAATTC
456 TCGACAGAATTTGAAGACAGGAAAATCCTTCCAAATTTGGAATCAAACTTAAATTAGGACAATTC
1971194 TTTAGACCTAATTCTTTGAGACAAGTGGAGGTAGACAATCCGTCTCCAATCTTGCTTAA-TTTTT
521 TTTAGACCTAATTCTTTGAGACAAGTGGAGGTAGACAATCCGTCTCCAATCTTGCTTAAGTTTTT
*
1971258 CGCAACCGAAAATGTTAAGCTTTTCAAGAGATGAGCATGCTCCAAT
586 -GCAACCGAAAATGCTAAGCTTTTCAAGAGATGAGCATGCTCCAAT
* * * * * *
1971304 TATCGGAAGAACTTCCAATCCGTTGCAGGTATGAATTGACAGATTTTGGAGACACGAAAATCCTT
1 TATCAGAAGAACTTCCAATCCATTGCAGCTATCAATTGACAGATCTTGAAGACACGAAAATCCTT
* * ** * * *
1971369 TCAAATTTGGAATCGAACTTAAATTAGGACAA-TCTTCTAGATTTAATTCTTTGAGACAAGTGTA
66 CCAAATTTGGAATCCAACTTAAATTAGGACAATTCTT-TAGACCTAATTCCTTGAGACAAATGAA
* * * * *
1971433 GGTAAATAATCTGTCTCCAGTCTTGGATAATGTTTT-ACACTTGGAAATGCTAAGCTTTTCAAAA
130 GGTAAACAATCTGTCTCCAATCTTGCATAAT-TTTTCACAATTGAAAATGCTAAGCTTTTCAAAA
* * * * *
1971497 GCTGAACATCC-TCCGGATATCTCAAGAACTTCCAATTTGATGCAGCTATCAATTGACAGATTTT
194 GATGAACA-CCTTCCAGATATCGCAAGAACTTCCAATTCGATGCAGCTATCAATTGACAGAATTT
* * ** * *
1971561 GAATAGACGAAAATCCTTCCAATTTTGGAATGGAAGTTAAATTAGGACACCACAATAG-CTCTAA
258 GAAGAGACGAAAATCCTTCCAAATTTGGAATCCAACTTAAATTAGGACAACACAATAGAC-CTAA
* * *
1971625 TTCTTTAAGACAAGTGGAGGTAGATAAACCGTCCCCAATCTTT-CTTAATTTCTCGCAATCGAGA
322 TTCTCTAAGACAAGTAGAGGTAGATAAACCGTCCCCAAT-TTTGCTTAATTTCTCGCAATCGAAA
* *
1971689 ATGCTAAGCTTTTCAAGAGATGAACACCTCCCAGTTATTGGAAGAGCTTCCAAT-TCATTGCAGC
386 ATGCTAAGCTTTTCAAGAGATGAACACCTCCCAATTATTGGAAGAACTTCCAATCT-ATTGCAGC
* * *
1971753 TATCAATTGACAGAATTTGAAGAGAGGAAAATCCTTCCAAATTTGGAATCCAACTTAAATTAGGA
450 TATCAATCGACAGAATTTGAAGACAGGAAAATCCTTCCAAATTTGGAATCAAACTTAAATTAGGA
* *
1971818 CAATTCTTTAGAGCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTCTCCAATCTTGCTTAA
515 CAATTCTTTAGACCTAATTCTTTGAGACAAGTGGAGGTAGACAATCCGTCTCCAATCTTGCTTAA
*
1971883 GTTTTTGCAATCGAAAATGCTAAGCTTTTCAAGAGATGA
580 GTTTTTGCAACCGAAAATGCTAAGCTTTTCAAGAGATGA
1971922 ACATTGTCCC
Statistics
Matches: 538, Mismatches: 73, Indels: 14
0.86 0.12 0.02
Matches are distributed among these distances:
629 6 0.01
630 518 0.96
631 14 0.03
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Consensus pattern (630 bp):
TATCAGAAGAACTTCCAATCCATTGCAGCTATCAATTGACAGATCTTGAAGACACGAAAATCCTT
CCAAATTTGGAATCCAACTTAAATTAGGACAATTCTTTAGACCTAATTCCTTGAGACAAATGAAG
GTAAACAATCTGTCTCCAATCTTGCATAATTTTTCACAATTGAAAATGCTAAGCTTTTCAAAAGA
TGAACACCTTCCAGATATCGCAAGAACTTCCAATTCGATGCAGCTATCAATTGACAGAATTTGAA
GAGACGAAAATCCTTCCAAATTTGGAATCCAACTTAAATTAGGACAACACAATAGACCTAATTCT
CTAAGACAAGTAGAGGTAGATAAACCGTCCCCAATTTTGCTTAATTTCTCGCAATCGAAAATGCT
AAGCTTTTCAAGAGATGAACACCTCCCAATTATTGGAAGAACTTCCAATCTATTGCAGCTATCAA
TCGACAGAATTTGAAGACAGGAAAATCCTTCCAAATTTGGAATCAAACTTAAATTAGGACAATTC
TTTAGACCTAATTCTTTGAGACAAGTGGAGGTAGACAATCCGTCTCCAATCTTGCTTAAGTTTTT
GCAACCGAAAATGCTAAGCTTTTCAAGAGATGAGCATGCTCCAAT
Done.