Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008031.1 Hibiscus syriacus cultivar Beakdansim tig00110511_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1788856
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 9
Found at i:1666340 original size:21 final size:21
Alignment explanation
Indices: 1666314--1666360 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
1666304 ACGCTATCAT
1666314 ACGCCTTCTCAAGGTCAATGA
1 ACGCCTTCTCAAGGTCAATGA
1666335 ACGCCTTCTCAAGGTCAATGA
1 ACGCCTTCTCAAGGTCAATGA
1666356 ACGCC
1 ACGCC
1666361 ATGTGAAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.32, G:0.19, T:0.21
Consensus pattern (21 bp):
ACGCCTTCTCAAGGTCAATGA
Found at i:1667146 original size:40 final size:40
Alignment explanation
Indices: 1667027--1667146 Score: 109
Period size: 40 Copynumber: 3.0 Consensus size: 40
1667017 AATCGCGTTG
* * * * *
1667027 CGATTTCCAAATTCGCAACACTGAATTTCAAATTCGCAACT
1 CGATTTTCGAATTCGAAACAC-GAATTTTAATTTCGCAACT
* * * *
1667068 CGA-TTTCTGAATTCAAAACGCGAATTTT-GTTGTAGCAACT
1 CGATTTTC-GAATTCGAAACACGAATTTTAATT-TCGCAACT
*
1667108 CGATTTTCGAATTCGTAACACGAATTTTAATTTCGCAAC
1 CGATTTTCGAATTCGAAACACGAATTTTAATTTCGCAAC
1667147 AGGTTTTAGT
Statistics
Matches: 61, Mismatches: 14, Indels: 9
0.73 0.17 0.11
Matches are distributed among these distances:
39 1 0.02
40 42 0.69
41 18 0.30
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (40 bp):
CGATTTTCGAATTCGAAACACGAATTTTAATTTCGCAACT
Found at i:1667147 original size:20 final size:19
Alignment explanation
Indices: 1667119--1667166 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
1667109 GATTTTCGAA
*
1667119 TTCGTAACACGAATTTTAAT
1 TTCGCAACACG-ATTTTAAT
* *
1667139 TTCGCAACA-GGTTTTAGT
1 TTCGCAACACGATTTTAAT
1667157 TTCGCAACAC
1 TTCGCAACAC
1667167 AAATGTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 15 0.62
19 1 0.04
20 8 0.33
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (19 bp):
TTCGCAACACGATTTTAAT
Found at i:1667958 original size:12 final size:12
Alignment explanation
Indices: 1667937--1667970 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1667927 ACCACATTTC
*
1667937 CAATACCAAACA
1 CAATATCAAACA
1667949 CAATATCAAACA
1 CAATATCAAACA
*
1667961 CAATCTCAAA
1 CAATATCAAA
1667971 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1668118 original size:24 final size:24
Alignment explanation
Indices: 1668090--1668149 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
1668080 TATTCAGTAT
1668090 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
*
1668114 TCGAACTTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
* *
1668138 TCGGATTTTGAT
1 TCGAAATTTGAT
1668150 GATGTTTCAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40
Consensus pattern (24 bp):
TCGAAATTTGATCTTGGTCAATAC
Found at i:1670724 original size:20 final size:20
Alignment explanation
Indices: 1670648--1670722 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 20
1670638 AAATCGCAAC
* *
1670648 GCGAAGTTGACTTTTACGTT
1 GCGAATTTGACTTTCACGTT
*
1670668 GCGAATTTGCCTTTCACGTT
1 GCGAATTTGACTTTCACGTT
*
1670688 GCGAATTTGACTTTCGCGTT
1 GCGAATTTGACTTTCACGTT
*
1670708 GAGAATTTGACTTTC
1 GCGAATTTGACTTTC
1670723 GCAACCATCA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.40
Consensus pattern (20 bp):
GCGAATTTGACTTTCACGTT
Found at i:1670763 original size:20 final size:20
Alignment explanation
Indices: 1670738--1670781 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1670728 CATCACAACT
1670738 CGAATTTGACTTTCGCGTTG
1 CGAATTTGACTTTCGCGTTG
* *
1670758 CGAATTTGATTTTCGTGTTG
1 CGAATTTGACTTTCGCGTTG
1670778 CGAA
1 CGAA
1670782 AGTGTACCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.18, C:0.16, G:0.25, T:0.41
Consensus pattern (20 bp):
CGAATTTGACTTTCGCGTTG
Found at i:1670923 original size:13 final size:14
Alignment explanation
Indices: 1670905--1670938 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
1670895 CATCAATTAA
1670905 ACAAATAAAC-TTT
1 ACAAATAAACTTTT
1670918 ACAAATAAACTTTT
1 ACAAATAAACTTTT
1670932 ACAAATA
1 ACAAATA
1670939 CATCAATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (14 bp):
ACAAATAAACTTTT
Found at i:1672217 original size:21 final size:21
Alignment explanation
Indices: 1672188--1672300 Score: 93
Period size: 21 Copynumber: 5.4 Consensus size: 21
1672178 GTGAATCGGG
* *
1672188 CTCTCGAACGGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGGGC
* ** *
1672209 CTCTTGAACGATGACAAGGGC
1 CTCTTGAACGGTGGGAGGGGC
*
1672230 CTCTTGAACGGTAGGAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
**
1672251 CTCTTGAA-GGATGATAGGGGC
1 CTCTTGAACGG-TGGGAGGGGC
** * *
1672272 CTCTTGAACAATAGGAGAGGC
1 CTCTTGAACGGTGGGAGGGGC
1672293 CTCTTGAA
1 CTCTTGAA
1672301 TGATGAAAGG
Statistics
Matches: 70, Mismatches: 20, Indels: 4
0.74 0.21 0.04
Matches are distributed among these distances:
20 2 0.03
21 68 0.97
ACGTcount: A:0.25, C:0.20, G:0.35, T:0.20
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:1672254 original size:42 final size:41
Alignment explanation
Indices: 1672188--1672310 Score: 147
Period size: 42 Copynumber: 3.0 Consensus size: 41
1672178 GTGAATCGGG
* * *
1672188 CTCTCGAACGGTGGGAGGGACCTCTTGAACGATGACAAGGGC
1 CTCTTGAACGGTAGGAGGGGCCTCTTGAACGATGA-AAGGGC
* *
1672230 CTCTTGAACGGTAGGAGGGGCCTCTTGAAGGATGATAGGGGC
1 CTCTTGAACGGTAGGAGGGGCCTCTTGAACGATGA-AAGGGC
** * *
1672272 CTCTTGAACAATAGGAGAGGCCTCTTGAATGATGAAAGG
1 CTCTTGAACGGTAGGAGGGGCCTCTTGAACGATGAAAGG
1672311 TGCTTCGGGC
Statistics
Matches: 70, Mismatches: 11, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
41 3 0.04
42 67 0.96
ACGTcount: A:0.26, C:0.19, G:0.35, T:0.20
Consensus pattern (41 bp):
CTCTTGAACGGTAGGAGGGGCCTCTTGAACGATGAAAGGGC
Found at i:1672689 original size:21 final size:21
Alignment explanation
Indices: 1672622--1672692 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
1672612 CGTAAAGTAG
1672622 ATACCTCACCACGTAAAGCACC
1 ATACCTCACCACGTAAAG-ACC
** *
1672644 AT-TGTCATCACGTAAA-ACC
1 ATACCTCACCACGTAAAGACC
*
1672663 TCTACCTCACCACGTAAAGACC
1 -ATACCTCACCACGTAAAGACC
*
1672685 GTACCTCA
1 ATACCTCA
1672693 TCACACCATG
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
19 3 0.08
20 1 0.03
21 29 0.76
22 5 0.13
ACGTcount: A:0.34, C:0.37, G:0.10, T:0.20
Consensus pattern (21 bp):
ATACCTCACCACGTAAAGACC
Found at i:1674650 original size:21 final size:21
Alignment explanation
Indices: 1674626--1674710 Score: 143
Period size: 21 Copynumber: 4.0 Consensus size: 21
1674616 TCGCGTTGCA
1674626 AATTTGGAAAATCGCAACGCG
1 AATTTGGAAAATCGCAACGCG
1674647 AATTTGGAAAATCGCAACGCG
1 AATTTGGAAAATCGCAACGCG
* *
1674668 AATTTGGAAAATCGCAATGTG
1 AATTTGGAAAATCGCAACGCG
*
1674689 AATTTGGAAAATCGCAATGCG
1 AATTTGGAAAATCGCAACGCG
1674710 A
1 A
1674711 TTTACATATT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (21 bp):
AATTTGGAAAATCGCAACGCG
Found at i:1676003 original size:4 final size:4
Alignment explanation
Indices: 1675994--1676020 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1675984 ATAGCTGTTT
1675994 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1676021 TTTTAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:1676736 original size:51 final size:49
Alignment explanation
Indices: 1676670--1676866 Score: 190
Period size: 51 Copynumber: 4.1 Consensus size: 49
1676660 AGATATGCAT
* *
1676670 ACTTAAACCGGTGTAAATATGTGTTAAATGCTACATTTTTTTATTTTATTC
1 ACTTACACCGATGTAAATATGTGTTAAATGCTACA--TTTTTATTTTATTC
* *
1676721 ACTTACACCGATGTAAGTATGTGTTAAGTGCTACATTTTTTTATTTTATTC
1 ACTTACACCGATGTAAATATGTGTTAAATGCTACA--TTTTTATTTTATTC
* * * * * *
1676772 TCTTACATCGATG----TGTGTATTAAATGTTACA-CTTT-TTTTATTC
1 ACTTACACCGATGTAAATATGTGTTAAATGCTACATTTTTATTTTATTC
** * *
1676815 ACTTACATTGGTGTAAATATATGTTAAATGCTACATTTTTATTTTATTC
1 ACTTACACCGATGTAAATATGTGTTAAATGCTACATTTTTATTTTATTC
1676864 ACT
1 ACT
1676867 CACATTGTTA
Statistics
Matches: 121, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
43 18 0.15
44 3 0.02
47 28 0.23
48 3 0.02
49 11 0.09
51 58 0.48
ACGTcount: A:0.27, C:0.13, G:0.12, T:0.48
Consensus pattern (49 bp):
ACTTACACCGATGTAAATATGTGTTAAATGCTACATTTTTATTTTATTC
Found at i:1685034 original size:11 final size:12
Alignment explanation
Indices: 1685018--1685050 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1685008 TAAATGGGAG
1685018 TAATTTCAAAC-
1 TAATTTCAAACT
1685029 TAATTTCAAACT
1 TAATTTCAAACT
*
1685041 TGATTTCAAA
1 TAATTTCAAA
1685051 ATCTTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (12 bp):
TAATTTCAAACT
Found at i:1696545 original size:20 final size:20
Alignment explanation
Indices: 1696515--1696569 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
1696505 CGCCACCATC
*
1696515 TGGTT-GGCTCGGTTTTTCT
1 TGGTTCGGCTCGGTTTTGCT
1696534 TGGTTCGGCTCGGTTTTGCT
1 TGGTTCGGCTCGGTTTTGCT
*
1696554 TGGTTCAGCTCGGTTT
1 TGGTTCGGCTCGGTTT
1696570 GTAGTGGTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 5 0.15
20 28 0.85
ACGTcount: A:0.02, C:0.18, G:0.33, T:0.47
Consensus pattern (20 bp):
TGGTTCGGCTCGGTTTTGCT
Found at i:1712781 original size:17 final size:18
Alignment explanation
Indices: 1712755--1712800 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
1712745 TATGGAATTG
* *
1712755 GATTCTAATTCC-TGACA
1 GATTCCAATTCCTTCACA
1712772 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
1712790 GATTCCAATTC
1 GATTCCAATTC
1712801 TCTCAGAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.35
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:1721521 original size:29 final size:30
Alignment explanation
Indices: 1721478--1721565 Score: 126
Period size: 29 Copynumber: 2.9 Consensus size: 30
1721468 CTCACCTAAC
*
1721478 TAAATTGATGTAAGCAATGACATCA-TTACT
1 TAAA-TGATGTAAGCAATGACATCATTTAAT
1721508 TAAATGATGTAAGCAATGACAT-ATTTAAT
1 TAAATGATGTAAGCAATGACATCATTTAAT
*
1721537 TAAATGATGTAAGTAATGACATCAATTTA
1 TAAATGATGTAAGCAATGACATC-ATTTA
1721566 GTTTGGGTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
28 1 0.02
29 43 0.81
30 4 0.08
31 5 0.09
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (30 bp):
TAAATGATGTAAGCAATGACATCATTTAAT
Found at i:1726310 original size:21 final size:21
Alignment explanation
Indices: 1726284--1726336 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1726274 CTTTAATGCA
* *
1726284 TTAATAGTTGTCATTATTGAT
1 TTAATACTTGTCACTATTGAT
1726305 TTAATACTTGTCACTATTGAT
1 TTAATACTTGTCACTATTGAT
*
1726326 ATAATACTTGT
1 TTAATACTTGT
1726337 GCCAGGTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.49
Consensus pattern (21 bp):
TTAATACTTGTCACTATTGAT
Found at i:1730744 original size:2 final size:2
Alignment explanation
Indices: 1730737--1730762 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1730727 ACAATTTAGG
1730737 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
1730763 CTGAGAATTT
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:1733737 original size:21 final size:21
Alignment explanation
Indices: 1733711--1733759 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
1733701 TTTTTAAGGG
1733711 GAGTACCGATAATGTTGAGAT
1 GAGTACCGATAATGTTGAGAT
1733732 GAGTACCGATAATGTTGAGAT
1 GAGTACCGATAATGTTGAGAT
1733753 GAGTACC
1 GAGTACC
1733760 AATACTCCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.27
Consensus pattern (21 bp):
GAGTACCGATAATGTTGAGAT
Found at i:1736041 original size:59 final size:59
Alignment explanation
Indices: 1735944--1736294 Score: 497
Period size: 59 Copynumber: 5.9 Consensus size: 59
1735934 AAATTCATTA
* * * * *
1735944 GGAATTTCATACAATTAGTATGATTTCCGTATCATTTTAGTACACGAAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCTTTTTAGCACACGAAGTGCCCTATCT
* *
1736003 AGAAATTCATACACTTAGTATGACTTCCTTATCTTTTTAGCACACGAAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCTTTTTAGCACACGAAGTGCCCTATCT
*
1736062 GGAAATTCATACACTTAGTATGATTTCCTTATCTTTTTAGCACACGAAGTGCCCTATAT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCTTTTTAGCACACGAAGTGCCCTATCT
* * * *
1736121 GGAAATTCATACACTTAGTATGATTTCCTTATCGTTTTAGCACGCAAAGTGCCGTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCTTTTTAGCACACGAAGTGCCCTATCT
* *
1736180 GGAAATTCATACACTTAGTATGATTTTCTTAT-TGTTTTAGCACACGAAAATGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCT-TTTTAGCACACG-AAGTGCCCTATCT
* ** * **
1736240 AGAAATTCATACACTTAGTACAATTTCCTTATCGTTTTAGCACACTTAGTGCCCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCTTTTTAGCACACGAAGTGCCCT
1736295 TTTTGGTAAT
Statistics
Matches: 260, Mismatches: 29, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
59 210 0.81
60 50 0.19
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.37
Consensus pattern (59 bp):
GGAAATTCATACACTTAGTATGATTTCCTTATCTTTTTAGCACACGAAGTGCCCTATCT
Found at i:1736774 original size:19 final size:18
Alignment explanation
Indices: 1736748--1736783 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1736738 ATACTACCTT
1736748 TCTATGGTACCGATACCC
1 TCTATGGTACCGATACCC
*
1736766 TCTACTGGTATCGATACC
1 TCTA-TGGTACCGATACC
1736784 AAAATTAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.22, C:0.31, G:0.17, T:0.31
Consensus pattern (18 bp):
TCTATGGTACCGATACCC
Found at i:1739892 original size:16 final size:16
Alignment explanation
Indices: 1739871--1739906 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
1739861 ATTCATTAAT
1739871 CCGAGATTATGTTAGC
1 CCGAGATTATGTTAGC
1739887 CCGAGATTATGTTAGC
1 CCGAGATTATGTTAGC
1739903 CCGA
1 CCGA
1739907 TTTTAAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (16 bp):
CCGAGATTATGTTAGC
Found at i:1742024 original size:55 final size:54
Alignment explanation
Indices: 1741891--1742345 Score: 578
Period size: 55 Copynumber: 8.4 Consensus size: 54
1741881 TTTATTAAGA
* * *
1741891 TGCACACGTAGTGCCTATACGG-TAGTTCATCAACTCATGATGAATTCAGTGG-GT
1 TGCACACATAGTGCCTGTACGGTTA-TTCATCAACTCATGATGAATTC-GTGGATT
* * *
1741945 TGCACACGTAGTGCCTATATGGTTATTCATCAACTCATGATGAAATTCGTGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATG-AATTCGTGGATT
*
1742000 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGG-GT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAA-TTCGTGGATT
* * *
1742054 TGCACACATAGTACCTATATGGTTATTCATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATT-CGTGGATT
* * * *
1742109 TGCACACATAGTTCCTGTACGGTTATTCATCAACTCGTGATGAATTCTATGG-GT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTC-GTGGATT
* * *
1742163 TACACACATAGTGTCTATACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATT-CGTGGATT
* * *
1742218 TGTACACATAGTTCTTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAA-TTCGTGGATT
* * * *
1742273 TACACATATAATGCATGTACGGTTATTCATCAACTCATGATGAATTCCGT-GATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATT-CGTGGATT
1742327 TGCACACATAGTGCCTGTA
1 TGCACACATAGTGCCTGTA
1742346 GTACACATGG
Statistics
Matches: 351, Mismatches: 39, Indels: 22
0.85 0.09 0.05
Matches are distributed among these distances:
53 2 0.01
54 158 0.45
55 189 0.54
56 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (54 bp):
TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCGTGGATT
Found at i:1742029 original size:109 final size:109
Alignment explanation
Indices: 1741891--1742345 Score: 650
Period size: 109 Copynumber: 4.2 Consensus size: 109
1741881 TTTATTAAGA
* * * *
1741891 TGCACACGTAGTGCCTATACGG-TAGTTCATCAACTCATGATGAA-TTCAGTGGGTTGCACACGT
1 TGCACACATAGTGCCTGTACGGTTA-TTCATCAACTCATGATGAATTTC-GTGGGTTACACACAT
*
1741954 AGTGCCTATATGGTTATTCATCAACTCATGATGAAATT-CGTGGATT
64 AGTGCCTATACGGTTATTCATCAACTCATGATG-AATTCCGTGGATT
*
1742000 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGGTTGCACACATAG
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGGTTACACACATAG
* *
1742065 TACCTATATGGTTATTCATCAACTCATGATGAATTCCGTGGATT
66 TGCCTATACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * *
1742109 TGCACACATAGTTCCTGTACGGTTATTCATCAACTCGTGATGAA-TTCTATGGGTTACACACATA
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTC-GTGGGTTACACACATA
*
1742173 GTGTCTATACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
65 GTGCCTATACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * * * *
1742218 TGTACACATAGTTCTTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGATTTACACATATA
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGG-GTTACACACATA
* * *
1742283 ATGCATGTACGGTTATTCATCAACTCATGATGAATTCCGT-GATT
65 GTGCCTATACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
1742327 TGCACACATAGTGCCTGTA
1 TGCACACATAGTGCCTGTA
1742346 GTACACATGG
Statistics
Matches: 316, Mismatches: 24, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
108 7 0.02
109 255 0.81
110 54 0.17
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (109 bp):
TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGGTTACACACATAG
TGCCTATACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
Found at i:1742808 original size:19 final size:20
Alignment explanation
Indices: 1742765--1742814 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
1742755 TCTTATCAAT
*
1742765 GGTATCGATACCTTCCTTAC
1 GGTATCGATACCTCCCTTAC
* *
1742785 AGTATCGATACC-CCCTTTC
1 GGTATCGATACCTCCCTTAC
1742804 GGTATCGATAC
1 GGTATCGATAC
1742815 TTATTGAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.22, C:0.30, G:0.16, T:0.32
Consensus pattern (20 bp):
GGTATCGATACCTCCCTTAC
Found at i:1747039 original size:12 final size:11
Alignment explanation
Indices: 1747022--1747056 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
1747012 ATTCCGTTAA
1747022 ATTTTTATTTTT
1 ATTTTT-TTTTT
1747034 ATTTTTTCTTTT
1 ATTTTTT-TTTT
1747046 ATTTTTTTTTT
1 ATTTTTTTTTT
1747057 CCGATTAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 5 0.23
12 17 0.77
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.86
Consensus pattern (11 bp):
ATTTTTTTTTT
Found at i:1747936 original size:17 final size:19
Alignment explanation
Indices: 1747914--1747951 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1747904 AAAAAAAAAC
1747914 AAAAAG-CAG-CTGTTCGA
1 AAAAAGACAGACTGTTCGA
*
1747931 AAAAAGAGAGACTGTTCGA
1 AAAAAGACAGACTGTTCGA
1747950 AA
1 AA
1747952 GAAAAAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 2 0.11
19 10 0.56
ACGTcount: A:0.47, C:0.13, G:0.24, T:0.16
Consensus pattern (19 bp):
AAAAAGACAGACTGTTCGA
Found at i:1753854 original size:95 final size:94
Alignment explanation
Indices: 1753749--1753924 Score: 253
Period size: 95 Copynumber: 1.9 Consensus size: 94
1753739 GGTAATATTG
* * *
1753749 ATACCATGGTAAGGGTATCGATACCAAGCATCATCAAAGCTAAAATTGGTATCGATACCAGATAG
1 ATACCATGGTAAGGGTATCGATACCAAGAAACATCAAAGCTAAAATTGGTATCGATACC-GAAAG
1753814 GGGTATCAGTACCATAGCATTAAAGTATCT
65 GGGTATCAGTACCATAGCATTAAAGTATCT
* * * * * *
1753844 ATACCATGGTAAGGGTATTGATACTAGGAAACATCGAATCTAAAATTGGTATTGATACCGAAAGG
1 ATACCATGGTAAGGGTATCGATACCAAGAAACATCAAAGCTAAAATTGGTATCGATACCGAAAGG
*
1753909 GGTATCGGTACCATAG
66 GGTATCAGTACCATAG
1753925 TATAGAAGTA
Statistics
Matches: 71, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
94 20 0.28
95 51 0.72
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (94 bp):
ATACCATGGTAAGGGTATCGATACCAAGAAACATCAAAGCTAAAATTGGTATCGATACCGAAAGG
GGTATCAGTACCATAGCATTAAAGTATCT
Found at i:1753961 original size:94 final size:95
Alignment explanation
Indices: 1753748--1753963 Score: 240
Period size: 95 Copynumber: 2.3 Consensus size: 95
1753738 AGGTAATATT
* * * * * * * * *
1753748 GATACCATGGTAAGGGTATCGATACCAAGCATCATCAAAGCTAAAATTGGTATCGATACCAGATA
1 GATACCAGGGTAAGAGTATCGATACTAGGAAACATCGAATCTAAAATTGGTATCGATACCAGAAA
1753813 GGGGTATCAGTACCATAGCATTAAAGTATC
66 GGGGTATCAGTACCATAGCATTAAAGTATC
* * * * *
1753843 TATACCATGGTAAGGGTATTGATACTAGGAAACATCGAATCTAAAATTGGTATTGATACC-GAAA
1 GATACCAGGGTAAGAGTATCGATACTAGGAAACATCGAATCTAAAATTGGTATCGATACCAGAAA
* *
1753907 GGGGTATCGGTACCATAGTA-TAGAAGTATC
66 GGGGTATCAGTACCATAGCATTA-AAGTATC
*
1753937 GGTACCAGGGT-AGTAGTATCGATACTA
1 GATACCAGGGTAAG-AGTATCGATACTA
1753964 TTGAGCTTAG
Statistics
Matches: 102, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
93 4 0.04
94 47 0.46
95 51 0.50
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (95 bp):
GATACCAGGGTAAGAGTATCGATACTAGGAAACATCGAATCTAAAATTGGTATCGATACCAGAAA
GGGGTATCAGTACCATAGCATTAAAGTATC
Found at i:1754473 original size:34 final size:34
Alignment explanation
Indices: 1754425--1754548 Score: 108
Period size: 34 Copynumber: 3.6 Consensus size: 34
1754415 CCATAGCTGA
* *
1754425 AATGGATATGGGTGCATTATCGACATAAAGGAAT
1 AATGCATATGGGTGCATTATCGACATAAAAGAAT
* ** ***
1754459 AATGCATATGGGTGCATGAAAGGATGCCATAGCTG-A-
1 AATGCATATGGGTGCAT-TATCGA---CATAAAAGAAT
**
1754495 AATGCATATGGGTGCATTATCGGGATAAAAGAAT
1 AATGCATATGGGTGCATTATCGACATAAAAGAAT
1754529 AATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTAT
1754549 TGGCAAGAAA
Statistics
Matches: 69, Mismatches: 15, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
32 4 0.06
33 1 0.01
34 36 0.52
35 5 0.07
36 17 0.25
37 1 0.01
38 5 0.07
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.27
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATCGACATAAAAGAAT
Found at i:1754580 original size:45 final size:45
Alignment explanation
Indices: 1754529--1754673 Score: 143
Period size: 45 Copynumber: 3.5 Consensus size: 45
1754519 ATAAAAGAAT
1754529 AATGCATATGGGTGCATTATTGGCAAGAAAAGATGCCATAGATGA
1 AATGCATATGGGTGCATTATTGGCAAGAAAAGATGCCATAGATGA
* * *
1754574 AATGCATATAGGTGCATTATCGGC-ATAAAA-A----ATA-ATG-
1 AATGCATATGGGTGCATTATTGGCAAGAAAAGATGCCATAGATGA
* * * *
1754611 --T--ATATGGGTGCATTATAGGCATGAAAGGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCAAGAAAAGATGCCATAGATGA
1754652 AATGCATATGGGTGCATTATTG
1 AATGCATATGGGTGCATTATTG
1754674 ACATAAAAGA
Statistics
Matches: 78, Mismatches: 10, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
33 17 0.22
34 3 0.04
35 2 0.03
38 3 0.04
39 6 0.08
40 2 0.03
43 2 0.03
44 5 0.06
45 38 0.49
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.28
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATTGGCAAGAAAAGATGCCATAGATGA
Found at i:1754686 original size:157 final size:156
Alignment explanation
Indices: 1754370--1754804 Score: 580
Period size: 157 Copynumber: 2.8 Consensus size: 156
1754360 GAACGAATGA
* * * *
1754370 ATAAAAAAATAATGCATATGGGTGCATTATTGGCATGAAAGGAGGCCATAGCTGAAATGGATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAAGATGCCATAGCTGAAATGCATATG
*
1754435 GGTGCATTATCGACATAAAGGAATAATGCATAT-GG-G-----T-GCATGAAAGGATGCCATAGC
66 GGTGCATTATCGACATAAA-AAATAATGCATATGGGTGCATTATGGCATGAAAGGATGCCATAGC
**
1754492 TGAAATGCATATGGGTGCATTATCGGG
130 TGAAATGCATATGGGTGCATTATCGAC
* * *
1754519 ATAAAAGAATAATGCATATGGGTGCATTATTGGCAAGAAAAGATGCCATAGATGAAATGCATATA
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAAGATGCCATAGCTGAAATGCATATG
* *
1754584 GGTGCATTATCGGCATAAAAAATAATGTATATGGGTGCATTATAGGCATGAAAGGATGCCATAGC
66 GGTGCATTATCGACATAAAAAATAATGCATATGGGTGCATTAT-GGCATGAAAGGATGCCATAGC
*
1754649 TGAAATGCATATGGGTGCATTATTGAC
130 TGAAATGCATATGGGTGCATTATCGAC
* * * * *
1754676 ATAAAAGAATAATGCATATGGGTGCATTATTGGGATGAAATGATACCATAGCTGAAATACTTATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAAGATGCCATAGCTGAAATGCATATG
* * * *
1754741 GGTGCATTATCAACATAAAAGAATAATACATTTGGGTGCATTATTGGCATGATAGGATGCCATA
66 GGTGCATTATCGACATAAAA-AATAATGCATATGGGTGCATTA-TGGCATGAAAGGATGCCATA
1754805 AATAAAAATG
Statistics
Matches: 248, Mismatches: 27, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
148 11 0.04
149 78 0.31
150 1 0.00
155 1 0.00
157 119 0.48
158 37 0.15
159 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.27
Consensus pattern (156 bp):
ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAAGATGCCATAGCTGAAATGCATATG
GGTGCATTATCGACATAAAAAATAATGCATATGGGTGCATTATGGCATGAAAGGATGCCATAGCT
GAAATGCATATGGGTGCATTATCGAC
Found at i:1754725 original size:79 final size:79
Alignment explanation
Indices: 1754472--1754804 Score: 488
Period size: 79 Copynumber: 4.2 Consensus size: 79
1754462 GCATATGGGT
**
1754472 GCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTATCGGGATAAAAGAATAATGCATA
1 GCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTATCGACATAAAAGAATAATGCATA
1754537 TGGGTGCATTATTG
66 TGGGTGCATTATTG
* * * * * *
1754551 GCAAGAAAAGATGCCATAGATGAAATGCATATAGGTGCATTATCGGCATAAAA-AATAATGTATA
1 GCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTATCGACATAAAAGAATAATGCATA
*
1754615 TGGGTGCATTATAG
66 TGGGTGCATTATTG
*
1754629 GCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTATTGACATAAAAGAATAATGCATA
1 GCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTATCGACATAAAAGAATAATGCATA
1754694 TGGGTGCATTATTG
66 TGGGTGCATTATTG
* * * * * * * *
1754708 GGATGAAATGATACCATAGCTGAAATACTTATGGGTGCATTATCAACATAAAAGAATAATACATT
1 GCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTATCGACATAAAAGAATAATGCATA
1754773 TGGGTGCATTATTG
66 TGGGTGCATTATTG
*
1754787 GCATGATAGGATGCCATA
1 GCATGAAAGGATGCCATA
1754805 AATAAAAATG
Statistics
Matches: 225, Mismatches: 28, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
78 70 0.31
79 155 0.69
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.27
Consensus pattern (79 bp):
GCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTATCGACATAAAAGAATAATGCATA
TGGGTGCATTATTG
Found at i:1756428 original size:55 final size:55
Alignment explanation
Indices: 1756344--1756845 Score: 516
Period size: 55 Copynumber: 9.3 Consensus size: 55
1756334 TTTATTAAGA
* * *
1756344 TGCACACGTAGTGCCTATAC-GGTAGTTCATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCCTGTACAGTTA-TTCATCAACTCATGATGAATTCCGTGGATT
** * * * * *
1756399 TGCACACATAACGCCTCTATAGTTATTCATCAACTCATAATGAATTACGTGG-GT
1 TGCACACATAGTGCCTGTACAGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * * *
1756453 TGCACACATAGTGCCTATAC-GATTATTCGTCTACTCATGATGAATTTCGTGGATT
1 TGCACACATAGTGCCTGTACAG-TTATTCATCAACTCATGATGAATTCCGTGGATT
* * ** * *
1756508 TGCACACATAGTGACTGTACGGTTATTCATTTACTCATGATGAATTTCGTGG-GT
1 TGCACACATAGTGCCTGTACAGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * * * * *
1756562 TGAAAACATAGTGGCTATACGGTTATTCATCAACTCATGATGAATTCAGTGGATT
1 TGCACACATAGTGCCTGTACAGTTATTCATCAACTCATGATGAATTCCGTGGATT
* *
1756617 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCA-GATGAATTTCGT-G-TGT
1 TGCACACATAGTGCCTGTACAGTTATTCATCAACTCATGATGAATTCCGTGGAT-T
* * *
1756670 TGGACACATAGTGCCTATAC-G--ATT-AT----TCATGATGAATTCCGTAGATT
1 TGCACACATAGTGCCTGTACAGTTATTCATCAACTCATGATGAATTCCGTGGATT
* *
1756717 TGCACACATAGTGCATGTACAGTTATTCATCAACTCATGATGAATTCCATGGATT
1 TGCACACATAGTGCCTGTACAGTTATTCATCAACTCATGATGAATTCCGTGGATT
* *
1756772 TGTACACATAGTGCCTGTAC-GATTATTCATCAAGTCATGATGAATTCTC-TGGATT
1 TGCACACATAGTGCCTGTACAG-TTATTCATCAACTCATGATGAATTC-CGTGGATT
*
1756827 TGCACACATAGTGTCTGTA
1 TGCACACATAGTGCCTGTA
1756846 GTACACATCA
Statistics
Matches: 377, Mismatches: 51, Indels: 38
0.81 0.11 0.08
Matches are distributed among these distances:
45 3 0.01
46 11 0.03
47 19 0.05
48 2 0.01
49 2 0.01
50 6 0.02
51 2 0.01
52 2 0.01
53 21 0.06
54 99 0.26
55 205 0.54
56 5 0.01
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (55 bp):
TGCACACATAGTGCCTGTACAGTTATTCATCAACTCATGATGAATTCCGTGGATT
Found at i:1756494 original size:109 final size:109
Alignment explanation
Indices: 1756344--1756845 Score: 612
Period size: 109 Copynumber: 4.7 Consensus size: 109
1756334 TTTATTAAGA
* *
1756344 TGCACACGTAGTGCCTATACG-GTAGTTCATCAACTCATGATGAATTCCGTGGATTTGCACACAT
1 TGCACACATAGTGCCTATACGATTA-TTCATCAACTCATGATGAATTCCGTGGATTTGCACACAT
** * * * *
1756408 AACGCCTCTATAGTTATTCATCAACTCATAATGAATTACGTGGGT
65 AGTGCCTGTACAGTTATTCATCAACTCATGATGAATTTCGTGGGT
* * *
1756453 TGCACACATAGTGCCTATACGATTATTCGTCTACTCATGATGAATTTCGTGGATTTGCACACATA
1 TGCACACATAGTGCCTATACGATTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATA
* * **
1756518 GTGACTGTACGGTTATTCATTTACTCATGATGAATTTCGTGGGT
66 GTGCCTGTACAGTTATTCATCAACTCATGATGAATTTCGTGGGT
* * * * *
1756562 TGAAAACATAGTGGCTATACGGTTATTCATCAACTCATGATGAATTCAGTGGATTTGCACACATA
1 TGCACACATAGTGCCTATACGATTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATA
* *
1756627 GTGCCTGTACGGTTATTCATCAACTCA-GATGAATTTCGTGTGT
66 GTGCCTGTACAGTTATTCATCAACTCATGATGAATTTCGTGGGT
* *
1756670 TGGACACATAGTGCCTATACG---ATT-AT----TCATGATGAATTCCGTAGATTTGCACACATA
1 TGCACACATAGTGCCTATACGATTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATA
* * * *
1756727 GTGCATGTACAGTTATTCATCAACTCATGATGAATTCCATGGATT
66 GTGCCTGTACAGTTATTCATCAACTCATGATGAATTTCGTGG-GT
* * *
1756772 TGTACACATAGTGCCTGTACGATTATTCATCAAGTCATGATGAATTCTC-TGGATTTGCACACAT
1 TGCACACATAGTGCCTATACGATTATTCATCAACTCATGATGAATTC-CGTGGATTTGCACACAT
*
1756836 AGTGTCTGTA
65 AGTGCCTGTA
1756846 GTACACATCA
Statistics
Matches: 338, Mismatches: 43, Indels: 23
0.84 0.11 0.06
Matches are distributed among these distances:
100 54 0.16
101 11 0.03
102 20 0.06
104 2 0.01
105 6 0.02
106 2 0.01
108 33 0.10
109 172 0.51
110 37 0.11
111 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (109 bp):
TGCACACATAGTGCCTATACGATTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATA
GTGCCTGTACAGTTATTCATCAACTCATGATGAATTTCGTGGGT
Found at i:1756762 original size:155 final size:159
Alignment explanation
Indices: 1756344--1756839 Score: 537
Period size: 155 Copynumber: 3.1 Consensus size: 159
1756334 TTTATTAAGA
* * *
1756344 TGCACACGTAGTGCCTATACGGTAGTTCATCAACTCATGATGAATTCCGTGGATTTGCACACATA
1 TGCACACATAGTGACTATACGGTA-TTCAT-TA-TCATGATGAATTCCGT-GATTTGCACACATA
** * * * * *
1756409 ACGCCTCTATAGTTATTCATCAACTCATAATGAATT-ACGTGG-GTTGCACACATAGTGCCTATA
62 GTG-CTATACAGTTATTCATCAACTCATGATGAATTCA-GTGGATTTGCACACATAGTGCCTGTA
* *
1756472 CGATTATTCGTCTACTCATGATGAATTTCGTGGATT
125 CGATTATTCATCAACTCATGATGAATTTCGTGGA-T
* * ** * *
1756508 TGCACACATAGTGACTGTACGGTTATTCATTTACTCATGATGAATTTCGTGGGTTGAAAACATAG
1 TGCACACATAGTGACTATACGG-TATTCA-TTA-TCATGATGAATTCCGTGATTTGCACACATAG
*
1756573 TGGCTATACGGTTATTCATCAACTCATGATGAATTCAGTGGATTTGCACACATAGTGCCTGTACG
63 T-GCTATACAGTTATTCATCAACTCATGATGAATTCAGTGGATTTGCACACATAGTGCCTGTACG
*
1756638 GTTATTCATCAACTCA-GATGAATTTCGTGTG-T
127 ATTATTCATCAACTCATGATGAATTTCGTG-GAT
* *
1756670 TGGACACATAGTGCCTATAC-G-ATT-A-T-TCATGATGAATTCCGTAGATTTGCACACATAGTG
1 TGCACACATAGTGACTATACGGTATTCATTATCATGATGAATTCCGT-GATTTGCACACATAGTG
* *
1756730 CATGTACAGTTATTCATCAACTCATGATGAATTCCA-TGGATTTGTACACATAGTGCCTGTACGA
65 C-TATACAGTTATTCATCAACTCATGATGAATT-CAGTGGATTTGCACACATAGTGCCTGTACGA
*
1756794 TTATTCATCAAGTCATGATGAATTCTC-TGGATT
128 TTATTCATCAACTCATGATGAATT-TCGTGGA-T
1756827 TGCACACATAGTG
1 TGCACACATAGTG
1756840 TCTGTAGTAC
Statistics
Matches: 285, Mismatches: 34, Indels: 33
0.81 0.10 0.09
Matches are distributed among these distances:
154 17 0.06
155 82 0.29
156 13 0.05
157 15 0.05
158 1 0.00
159 3 0.01
161 1 0.00
162 18 0.06
163 55 0.19
164 77 0.27
165 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (159 bp):
TGCACACATAGTGACTATACGGTATTCATTATCATGATGAATTCCGTGATTTGCACACATAGTGC
TATACAGTTATTCATCAACTCATGATGAATTCAGTGGATTTGCACACATAGTGCCTGTACGATTA
TTCATCAACTCATGATGAATTTCGTGGAT
Found at i:1757237 original size:19 final size:22
Alignment explanation
Indices: 1757187--1757238 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 22
1757177 CCCCTACCAT
*
1757187 GGTATCGATACTACTACACTAT
1 GGTATCGATACTACTACACTAC
1757209 GGTA-CTGATACT-CTA-A-TAC
1 GGTATC-GATACTACTACACTAC
1757228 GGTATCGATAC
1 GGTATCGATAC
1757239 CATTTTTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 11 0.41
20 2 0.07
21 4 0.15
22 10 0.37
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (22 bp):
GGTATCGATACTACTACACTAC
Found at i:1759754 original size:18 final size:18
Alignment explanation
Indices: 1759727--1759762 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1759717 GAGGGTTTTA
1759727 GGTTGAGTAGGTATCGAT
1 GGTTGAGTAGGTATCGAT
*
1759745 GGTTGGGTAGGTATCGAT
1 GGTTGAGTAGGTATCGAT
1759763 ACCATGTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.42, T:0.33
Consensus pattern (18 bp):
GGTTGAGTAGGTATCGAT
Found at i:1760256 original size:22 final size:22
Alignment explanation
Indices: 1760202--1760324 Score: 133
Period size: 22 Copynumber: 5.7 Consensus size: 22
1760192 TACTCCAATC
* * *
1760202 AGTGCTAAGGCTCTTTAGTATT
1 AGTGCTAATGCACTTTCGTATT
1760224 AGTG--AATGCACTTTCGTATT
1 AGTGCTAATGCACTTTCGTATT
1760244 AGTGCTAATGCACTTTCGTATT
1 AGTGCTAATGCACTTTCGTATT
*
1760266 AGTGCTAATGCACTTTCGTATC
1 AGTGCTAATGCACTTTCGTATT
* * * * **
1760288 AATGCTGAGGCACTTTAGTACC
1 AGTGCTAATGCACTTTCGTATT
*
1760310 AGTGCTAAAGCACTT
1 AGTGCTAATGCACTT
1760325 CAGTTAGTCG
Statistics
Matches: 87, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.20
22 70 0.80
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (22 bp):
AGTGCTAATGCACTTTCGTATT
Found at i:1760301 original size:44 final size:44
Alignment explanation
Indices: 1760199--1760324 Score: 157
Period size: 44 Copynumber: 2.9 Consensus size: 44
1760189 ACATACTCCA
*
1760199 ATCAGTGCTAAGGCTCTTTAGTATTAGTG--AATGCACTTTCGT
1 ATCAGTGCTAAGGCACTTTAGTATTAGTGCTAATGCACTTTCGT
* * *
1760241 ATTAGTGCTAATGCACTTTCGTATTAGTGCTAATGCACTTTCGT
1 ATCAGTGCTAAGGCACTTTAGTATTAGTGCTAATGCACTTTCGT
* * ** *
1760285 ATCAATGCTGAGGCACTTTAGTACCAGTGCTAAAGCACTT
1 ATCAGTGCTAAGGCACTTTAGTATTAGTGCTAATGCACTT
1760325 CAGTTAGTCG
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
42 25 0.36
44 45 0.64
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (44 bp):
ATCAGTGCTAAGGCACTTTAGTATTAGTGCTAATGCACTTTCGT
Found at i:1763817 original size:41 final size:41
Alignment explanation
Indices: 1763736--1763818 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
1763726 CAAGTCCTTA
* *
1763736 TATGATGGAATTGAGCGAAATGTTAATGCTAACCCGACTCC
1 TATGATGGAATTGAGCGAAATGTTAATACTAACCCAACTCC
* * * *
1763777 TATGATGGAATTGAGCGAAATGTTGATATTGATCCAACTCC
1 TATGATGGAATTGAGCGAAATGTTAATACTAACCCAACTCC
1763818 T
1 T
1763819 TATGTGATGG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (41 bp):
TATGATGGAATTGAGCGAAATGTTAATACTAACCCAACTCC
Found at i:1764010 original size:13 final size:13
Alignment explanation
Indices: 1763992--1764016 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1763982 AATCTTCTTC
1763992 TTGAATTGAAATA
1 TTGAATTGAAATA
1764005 TTGAATTGAAAT
1 TTGAATTGAAAT
1764017 CTTTGTTGAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (13 bp):
TTGAATTGAAATA
Found at i:1765608 original size:90 final size:89
Alignment explanation
Indices: 1765436--1765613 Score: 232
Period size: 90 Copynumber: 2.0 Consensus size: 89
1765426 TCGACCGATA
* *
1765436 ACCATCATACACCAAGAATACCAATTACATACATAGTGTGTAGTACACAAAGTACTAATACAATA
1 ACCATCATACACCAAGAATACCAATTACATACATAATGTGTAATACACAAAGTACTAATACAATA
*
1765501 CCACCTTATTTATGGTATTACAAC
66 CCACCTTATTTACGGTATTACAAC
* * * * * *
1765525 ACCATCATACATCAAGTATGCCAATTACATACATAATGCT-TCAATAGACAAAGTAGTACTACAA
1 ACCATCATACACCAAGAATACCAATTACATACATAATG-TGT-AATACACAAAGTACTAATACAA
* *
1765589 TACCACTTTATTTCCGGTATTACAA
64 TACCACCTTATTTACGGTATTACAA
1765614 TTGAACCTAC
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
89 35 0.46
90 41 0.54
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.28
Consensus pattern (89 bp):
ACCATCATACACCAAGAATACCAATTACATACATAATGTGTAATACACAAAGTACTAATACAATA
CCACCTTATTTACGGTATTACAAC
Found at i:1765770 original size:11 final size:11
Alignment explanation
Indices: 1765743--1765777 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
1765733 GGCACTCGAG
1765743 GTTCAAAATAT
1 GTTCAAAATAT
*
1765754 -TTCAAAATGT
1 GTTCAAAATAT
1765764 GTTCAAAATAT
1 GTTCAAAATAT
1765775 GTT
1 GTT
1765778 TAATAAGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (11 bp):
GTTCAAAATAT
Found at i:1772731 original size:2 final size:2
Alignment explanation
Indices: 1772724--1773145 Score: 293
Period size: 2 Copynumber: 221.5 Consensus size: 2
1772714 TCTGACCTTT
*
1772724 TA TA TA TA TA T- TA TA TA GTA TA TA TA T- TA TA TA TA T- TA CA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* *
1772764 -A TA TA T- TA TA TA -A TA T- TA TA T- TA TA TA CA TG T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1772800 TA T- TA TA TA T- TA TA T- TA GA TA -A TA TA TA TA T- TA GTC T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
*
1772837 TA TA T- TA TA GTA CTA TA T- TA TA TA CTA TA TA GTG TA TA TA TA
1 TA TA TA TA TA -TA -TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA
*
1772879 TA TA TA TA TT TA TA T- TA TA T- TA TA TA T- TA TA T- TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1772916 TA TA GTA T- TA TA T- TA TA TA TT TA TA T- TA TA TA GTT TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * * *
1772957 TA TA T- TC TA T- TA T- TA T- TA TA TA GTG T- TA TA T- TG TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * *
1772994 TT TA TA TA TA TA GTG TG TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1773037 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
** * *
1773079 TA TA TA CTA TA GGG TA T- TA TA T- TA TA TA TA TT TA TA T- TA TG
1 TA TA TA -TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1773120 TA TA T- TA TA TA TA TCA TA CTA TA TA T
1 TA TA TA TA TA TA TA T-A TA -TA TA TA T
1773146 TTTTATATTA
Statistics
Matches: 340, Mismatches: 32, Indels: 96
0.73 0.07 0.21
Matches are distributed among these distances:
1 35 0.10
2 284 0.84
3 21 0.06
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1773115 original size:52 final size:50
Alignment explanation
Indices: 1772722--1773230 Score: 288
Period size: 48 Copynumber: 10.5 Consensus size: 50
1772712 CGTCTGACCT
*
1772722 TTTATATATATAT-TATATAGTATATATA-T-TA-TA-TATATTACA-ATA
1 TTTATATATATATATATATA-TATATATATTATAGTATTATATTATATATA
* *
1772767 TATTATATA-ATAT-TATATTATATACATGTTATA-TATTATA-TAT-TATA
1 T-TTATATATATATATATA-TATATATATATTATAGTATTATATTATATATA
* * *
1772814 -TTAGATA-ATATATATAT-TAGTCTTATATTATAGTACTATATTATATACTA
1 TTTATATATATATATATATATA-T-ATATATTATAGTATTATATTATATA-TA
* * * *
1772864 TATAGTGTATATATATATATATATTTATATTATATTA-TATATTATAT-TA
1 TTTA-TATATATATATATATATATATATATTATAGTATTATATTATATATA
*
1772913 -TTATATAGTAT-TATATTATATATTTATATTATA-TAGTT-TA-TATATATA
1 TTTATATA-TATATATA-TATATATATATATTATAGTA-TTATATTATATATA
* * *
1772961 TTCTAT-TAT-TAT-TATATAGTGT-TATATTGTATGT-TTATA-TATATAGTG
1 TT-TATATATATATATATATA-TATATATATTATA-GTATTATATTATATA-TA
*
1773009 TGTATATATATATATATATATATATATA-TATA-TA-TATATATATATATA
1 TTTATATATATATATATATATATATATATTATAGTATTATAT-TATATATA
* *
1773057 TATATATATATATATATATATATATATACTATAGGGTATTATATTATATATA
1 TTTATATATATATATATATATATATATATTATA--GTATTATATTATATATA
* * *
1773109 TTTATAT-TATGTATATTATATATATCATACTATATATTTTTATATTATA-AT-
1 TTTATATATATATATA-TATATATAT-ATA-T-TATAGTATTATATTATATATA
* * *
1773160 TTTTTATATA-AGAGTATATAT-TATTAATATTAT--TATTATAATT-TATACA
1 TTTATATATATATA-TATATATATA-T-ATATTATAGTATTAT-ATTATATATA
*
1773209 TATTATTTAT-TATAT-TATATAT
1 T-TTATATATATATATATATATAT
1773231 TTATTTAATT
Statistics
Matches: 373, Mismatches: 36, Indels: 106
0.72 0.07 0.21
Matches are distributed among these distances:
44 2 0.01
45 27 0.07
46 35 0.09
47 57 0.15
48 78 0.21
49 32 0.09
50 26 0.07
51 35 0.09
52 45 0.12
53 30 0.08
54 2 0.01
55 4 0.01
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (50 bp):
TTTATATATATATATATATATATATATATTATAGTATTATATTATATATA
Found at i:1773221 original size:16 final size:16
Alignment explanation
Indices: 1772724--1773239 Score: 89
Period size: 15 Copynumber: 31.1 Consensus size: 16
1772714 TCTGACCTTT
*
1772724 TATATATATATTAT-A
1 TATATATTTATTATAA
*
1772739 TAGTATATATATTATATA
1 TA-TATATTTATTATA-A
* *
1772757 TATTACAATATATTAT-A
1 TA-TA-TATTTATTATAA
1772774 TA-ATATTATATTAT-A
1 TATATATT-TATTATAA
* * *
1772789 TACAT-GTTA-TATAT
1 TATATATTTATTATAA
1772803 TATATATTATATTAGATAA
1 TATATATT-TATT--ATAA
*
1772822 TATATATATTAGTCTTATAT
1 TATATAT-TTA---TTATAA
*
1772842 TATAGTACTATATTATATA
1 TATA-TA-TTTATTATA-A
*
1772861 CTATATAGTGTATATATATA
1 -TATATA-TTTAT-TATA-A
*
1772881 TATATATTTATATTATAT
1 TATATA-TT-TATTATAA
1772899 TATATATTATATTAT--
1 TATATATT-TATTATAA
* *
1772914 TATATA-GTATTATAT
1 TATATATTTATTATAA
1772929 TATATATTTA-TAT--
1 TATATATTTATTATAA
1772942 TATATAGTTTA-TAT-A
1 TATATA-TTTATTATAA
* *
1772957 TATAT-TCTATTATTA
1 TATATATTTATTATAA
* * *
1772972 T-TATATAGTGTTATAT
1 TATATAT-TTATTATAA
* *
1772988 TGTATGTTTA-TAT-A
1 TATATATTTATTATAA
* *
1773002 TATAGTGTGTA-TAT-A
1 TATA-TATTTATTATAA
*
1773017 TATATATATA-TATATA
1 TATATATTTATTATA-A
*
1773033 TATATATATATATATATA
1 TATATATTTAT-TATA-A
*
1773051 TATATATATATATATATA
1 TATATATTTAT-TATA-A
* *
1773069 TATATATATATATATAC
1 TATATATTTAT-TATAA
1773086 TATAGGGTATTATATTAT-A
1 TATA---TATT-TATTATAA
*
1773105 TATAT-TTATATTATGTA
1 TATATATT-TATTAT-AA
* * *
1773122 TATTATATATATCATAC
1 TA-TATATTTATTATAA
*
1773139 TATATATTT-TTATAT
1 TATATATTTATTATAA
*
1773154 TATA-ATTTTTTAT-A
1 TATATATTTATTATAA
* *
1773168 TAAGAGTATATATTATTAA
1 T-ATA-TATTTATTA-TAA
1773187 TATTATTATTATAATTTATACA
1 TA-TA-TATT-T-A-TTATA-A
*
1773209 TAT-TATTTATTATAT
1 TATATATTTATTATAA
1773224 TATATATTTATT-TAA
1 TATATATTTATTATAA
1773239 T
1 T
1773240 TATTATTCAG
Statistics
Matches: 393, Mismatches: 51, Indels: 114
0.70 0.09 0.20
Matches are distributed among these distances:
13 18 0.05
14 36 0.09
15 82 0.21
16 56 0.14
17 33 0.08
18 67 0.17
19 53 0.13
20 28 0.07
21 11 0.03
22 9 0.02
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (16 bp):
TATATATTTATTATAA
Found at i:1777282 original size:21 final size:21
Alignment explanation
Indices: 1777256--1777296 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1777246 AAAAGGAACT
*
1777256 AGCACTGGACACCCCTCATCA
1 AGCACTGGACACACCTCATCA
1777277 AGCACTGGACACACCTCATC
1 AGCACTGGACACACCTCATC
1777297 CTCAAAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.41, G:0.15, T:0.15
Consensus pattern (21 bp):
AGCACTGGACACACCTCATCA
Found at i:1780744 original size:21 final size:21
Alignment explanation
Indices: 1780720--1780766 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
1780710 GCAATTTTCC
*
1780720 TTTCTAGCAAACATTTCTTCA
1 TTTCAAGCAAACATTTCTTCA
*
1780741 TTTCAAGCAAACATTTCTTCC
1 TTTCAAGCAAACATTTCTTCA
1780762 TTTCA
1 TTTCA
1780767 CTTCTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.28, C:0.26, G:0.04, T:0.43
Consensus pattern (21 bp):
TTTCAAGCAAACATTTCTTCA
Found at i:1784740 original size:5 final size:5
Alignment explanation
Indices: 1784725--1784898 Score: 101
Period size: 5 Copynumber: 33.8 Consensus size: 5
1784715 CATAAAATAT
* ** ** * *
1784725 TTATA -TATA TTATA TTATA TTATA -TATA ATGGA GGATA TACATG TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA T-TATA TTATA
*
1784774 -TATTA T-ATA TTATA TTATA TATAGTA TTGTA -TATA TTTATA TTATA
1 TTA-TA TTATA TTATA TTATA T-TA-TA TTATA TTATA -TTATA TTATA
* *
1784820 ATATA TTATTA TTATTA TTATTA TTATTA TTATA TTTTA TATATA TTATTTA
1 TTATA TTA-TA TTA-TA TTA-TA TTA-TA TTATA TTATA T-TATA TTA--TA
1784872 TTATA TTATA TTATA TTAT- TTA-A TTAT
1 TTATA TTATA TTATA TTATA TTATA TTAT
1784899 TCAGGTCCAG
Statistics
Matches: 136, Mismatches: 17, Indels: 32
0.74 0.09 0.17
Matches are distributed among these distances:
4 22 0.16
5 69 0.51
6 37 0.27
7 8 0.06
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.57
Consensus pattern (5 bp):
TTATA
Found at i:1784750 original size:12 final size:12
Alignment explanation
Indices: 1784721--1784887 Score: 101
Period size: 12 Copynumber: 14.3 Consensus size: 12
1784711 CGATCATAAA
1784721 ATAT-TTATATAT
1 ATATATTATAT-T
1784733 ATTATATTATATT
1 A-TATATTATATT
* **
1784746 ATATATAATGGAGG
1 ATATATTAT--ATT
* *
1784760 ATATA-CATGTT
1 ATATATTATATT
1784771 ATATATTATA-T
1 ATATATTATATT
1784782 ATTATATTATA-T
1 A-TATATTATATT
*
1784794 ATAGTATTGTA-T
1 ATA-TATTATATT
1784806 ATAT-TTATATT
1 ATATATTATATT
1784817 ATA-A-TATATT
1 ATATATTATATT
1784827 AT-TATTATTATT
1 ATATATTA-TATT
1784839 AT-TATTATTATT
1 ATATATTA-TATT
1784851 ATAT-TT-TA-T
1 ATATATTATATT
1784860 ATATATTAT-TT
1 ATATATTATATT
1784871 ATTATATTATATT
1 A-TATATTATATT
1784884 ATAT
1 ATAT
1784888 TATTTAATTA
Statistics
Matches: 126, Mismatches: 11, Indels: 36
0.73 0.06 0.21
Matches are distributed among these distances:
9 5 0.04
10 17 0.13
11 19 0.15
12 62 0.49
13 11 0.09
14 12 0.10
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (12 bp):
ATATATTATATT
Found at i:1784808 original size:44 final size:42
Alignment explanation
Indices: 1784723--1784891 Score: 128
Period size: 44 Copynumber: 3.8 Consensus size: 42
1784713 ATCATAAAAT
* *** *
1784723 ATTTATATA-TATTATATTATATTATATATAATGGAGGATATA
1 ATTTATATATTA-TATATTATATTATATATATTATTGTATATA
*
1784765 CATGTTATATATTATATATTATATTATATATAGTATTGTATAT-
1 -AT-TTATATATTATATATTATATTATATATATTATTGTATATA
* *
1784808 ATTTATATTATAATATATTATTATTAT-TATTATTATTATTATTATA
1 ATTTATA-TATTATATATTA-TATTATATA-TATTATT-GTA-TATA
* *
1784854 TTTTATATATATTATTTATTATATTATATTATATTATT
1 -ATT-TATATATTATATATTATATTATA-TATATTATT
1784892 TAATTATTCA
Statistics
Matches: 103, Mismatches: 11, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
41 5 0.05
42 15 0.15
43 14 0.14
44 33 0.32
45 5 0.05
46 6 0.06
47 19 0.18
48 6 0.06
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (42 bp):
ATTTATATATTATATATTATATTATATATATTATTGTATATA
Found at i:1784831 original size:3 final size:3
Alignment explanation
Indices: 1784813--1784891 Score: 80
Period size: 3 Copynumber: 27.3 Consensus size: 3
1784803 TATATATTTA
*
1784813 TAT TAT AAT ATAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT T-T
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1784857 TA- TAT ATAT TATT TAT TA- TAT TA- TAT TA- TAT TAT T
1 TAT TAT -TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT T
1784892 TAATTATTCA
Statistics
Matches: 65, Mismatches: 2, Indels: 18
0.76 0.02 0.21
Matches are distributed among these distances:
2 12 0.18
3 45 0.69
4 8 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1784897 original size:8 final size:9
Alignment explanation
Indices: 1784783--1784899 Score: 72
Period size: 9 Copynumber: 13.1 Consensus size: 9
1784773 ATATTATATA
1784783 TTATATTAT
1 TTATATTAT
* *
1784792 ATATAGTAT
1 TTATATTAT
1784801 TGTATA-TAT
1 T-TATATTAT
1784810 TTATATTAT
1 TTATATTAT
*
1784819 AATATATTA-
1 -TTATATTAT
1784828 TTATTATTA-
1 TTA-TATTAT
1784837 TTATTATTA-
1 TTA-TATTAT
1784846 TTAT-TATAT
1 TTATAT-TAT
1784855 TT-TATATAT
1 TTATAT-TAT
1784864 ATTAT-TTA-
1 -TTATATTAT
1784872 TTATATTAT
1 TTATATTAT
1784881 ATTATATTAT
1 -TTATATTAT
1784891 TTA-ATTAT
1 TTATATTAT
1784899 T
1 T
1784900 CAGGTCCAGA
Statistics
Matches: 91, Mismatches: 5, Indels: 25
0.75 0.04 0.21
Matches are distributed among these distances:
7 5 0.05
8 19 0.21
9 43 0.47
10 23 0.25
11 1 0.01
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (9 bp):
TTATATTAT
Done.