Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000564.1 Hibiscus syriacus cultivar Beakdansim tig00001103_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: 98587
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.33
Found at i:1508 original size:20 final size:20
Alignment explanation
Indices: 1483--1520 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1473 CACGTGTTAA
1483 AGAATGCATCGATGCACTAT
1 AGAATGCATCGATGCACTAT
*
1503 AGAATGTATCGATGCACT
1 AGAATGCATCGATGCACT
1521 TCAAAGGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATGCACTAT
Found at i:13023 original size:36 final size:35
Alignment explanation
Indices: 12949--13029 Score: 110
Period size: 36 Copynumber: 2.3 Consensus size: 35
12939 AACACAGTCA
*
12949 TCAATTACATTCTAGACCCCAAATTCCAAAATACT
1 TCAATTACATTCTAGACCCCAAATTCAAAAATACT
* *
12984 TCAATTACATTTTA-ATCCTCAAATTTCAAAAATACT
1 TCAATTACATTCTAGA-CCCCAAA-TTCAAAAATACT
13020 TCAATTACAT
1 TCAATTACAT
13030 GCCCAACCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
34 1 0.02
35 19 0.46
36 21 0.51
ACGTcount: A:0.41, C:0.23, G:0.01, T:0.35
Consensus pattern (35 bp):
TCAATTACATTCTAGACCCCAAATTCAAAAATACT
Found at i:13044 original size:36 final size:36
Alignment explanation
Indices: 12949--13044 Score: 90
Period size: 36 Copynumber: 2.7 Consensus size: 36
12939 AACACAGTCA
* * *
12949 TCAATTACATTCTAGACCC-CAAA-TTCCAAAATACT
1 TCAATTACATCCCA-ACCCTCAAATTTCAAAAATACT
*** *
12984 TCAATTACATTTTAATCCTCAAATTTCAAAAATACT
1 TCAATTACATCCCAACCCTCAAATTTCAAAAATACT
13020 TCAATTACATGCCCAACCCT-AAATT
1 TCAATTACAT-CCCAACCCTCAAATT
13045 CATAATCTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
34 3 0.06
35 17 0.33
36 26 0.51
37 5 0.10
ACGTcount: A:0.40, C:0.26, G:0.02, T:0.32
Consensus pattern (36 bp):
TCAATTACATCCCAACCCTCAAATTTCAAAAATACT
Found at i:13693 original size:148 final size:148
Alignment explanation
Indices: 13529--13797 Score: 484
Period size: 148 Copynumber: 1.8 Consensus size: 148
13519 AGACTATTAA
* * *
13529 AATTAGAATCAAATAATATTATAGTATTATAAATATTTATAATTAAATTTAAACAGAAACTCGAA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAAGTTAAACAGAAACTCGAA
*
13594 AAGTCAATTCAATTCAACTTGATTTAAATTTTCTAAACTCAAATCGAAAAAATTTCGAGTCATCT
66 AAGTCAATTCAATTCAACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTCATCT
13659 ATTTTATAGACTTAACTG
131 ATTTTATAGACTTAACTG
13677 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAAGTTAAACAGAAACTCGAA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAAGTTAAACAGAAACTCGAA
* *
13742 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTC
66 AAGTCAATTCAATTCAACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTC
13798 ATGTAACACC
Statistics
Matches: 115, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
148 115 1.00
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.36
Consensus pattern (148 bp):
AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAAGTTAAACAGAAACTCGAA
AAGTCAATTCAATTCAACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTCATCT
ATTTTATAGACTTAACTG
Found at i:16225 original size:35 final size:35
Alignment explanation
Indices: 16186--16262 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
16176 ATTGGACATG
*
16186 TAATTGAAGTATTTTGGAATTTGAGGTTTAGAATA
1 TAATTGAAGAATTTTGGAATTTGAGGTTTAGAATA
* * *
16221 TAATTGAAGAATTTTGGATTTTGGGGTTTAGAATG
1 TAATTGAAGAATTTTGGAATTTGAGGTTTAGAATA
16256 TAATTGA
1 TAATTGA
16263 TGATTGTGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.25, T:0.43
Consensus pattern (35 bp):
TAATTGAAGAATTTTGGAATTTGAGGTTTAGAATA
Found at i:16575 original size:25 final size:25
Alignment explanation
Indices: 16547--16597 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
16537 TACAGTATAA
*
16547 TTTT-TAAAAATTTAGAAGGAGAAAG
1 TTTTATAAAAATTTAG-AGGAAAAAG
**
16572 TTTTATAAATTTTTAGAGGAAAAAG
1 TTTTATAAAAATTTAGAGGAAAAAG
16597 T
1 T
16598 AAATTATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.37
Consensus pattern (25 bp):
TTTTATAAAAATTTAGAGGAAAAAG
Found at i:17667 original size:5 final size:5
Alignment explanation
Indices: 17657--17682 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
17647 AAAATTAGTT
17657 AGAAA AGAAA AGAAA AGAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA A
17683 CTAGAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:18330 original size:22 final size:22
Alignment explanation
Indices: 18303--18346 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
18293 CTGAAAGATG
* *
18303 CCAGCTCAGCATAGTTGGTTAT
1 CCAGCTCAACATAGTTAGTTAT
18325 CCAGCTCAACATAGTTAGTTAT
1 CCAGCTCAACATAGTTAGTTAT
18347 TAGGTTAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (22 bp):
CCAGCTCAACATAGTTAGTTAT
Found at i:27950 original size:29 final size:29
Alignment explanation
Indices: 27908--28085 Score: 234
Period size: 29 Copynumber: 6.2 Consensus size: 29
27898 GACCGAGTGT
27908 TATTTTAGTAATTAATTCAAAATGGGTGC
1 TATTTTAGTAATTAATTCAAAATGGGTGC
**
27937 TATTTTAGTAATTAATTTGAAATGGGTGC
1 TATTTTAGTAATTAATTCAAAATGGGTGC
* *
27966 TATTTTAGTAATTAATTCGAAATGGGTGT
1 TATTTTAGTAATTAATTCAAAATGGGTGC
*
27995 TATTTTAGTAATTAATTCAAAATAGGTGC
1 TATTTTAGTAATTAATTCAAAATGGGTGC
* *
28024 TATTTTAGTAATTAATTTGAAAAT--GTGT
1 TATTTTAGTAATTAA-TTCAAAATGGGTGC
* * * *
28052 TATTTTTGTAATTATTTTAAAAAGGGTGC
1 TATTTTAGTAATTAATTCAAAATGGGTGC
28081 TATTT
1 TATTT
28086 CTGTAAAATG
Statistics
Matches: 132, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
27 6 0.05
28 16 0.12
29 103 0.78
30 7 0.05
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (29 bp):
TATTTTAGTAATTAATTCAAAATGGGTGC
Found at i:32334 original size:22 final size:22
Alignment explanation
Indices: 32307--32350 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
32297 CTGGAAGATG
*
32307 CCAGCTCAGCATAATTGGTTAT
1 CCAGCTCACCATAATTGGTTAT
*
32329 CCAGCTCACCATAGTTGGTTAT
1 CCAGCTCACCATAATTGGTTAT
32351 TAGGTTAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (22 bp):
CCAGCTCACCATAATTGGTTAT
Found at i:36625 original size:18 final size:18
Alignment explanation
Indices: 36604--36653 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
36594 ACTATACATA
36604 AGGGTATCGGTACCCTAT
1 AGGGTATCGGTACCCTAT
36622 AGGGTATCGGTACCCTAT
1 AGGGTATCGGTACCCTAT
36640 AGGGTATCGGTACC
1 AGGGTATCGGTACC
36654 ATTGGCTATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.26
Consensus pattern (18 bp):
AGGGTATCGGTACCCTAT
Found at i:36699 original size:81 final size:81
Alignment explanation
Indices: 36562--36716 Score: 283
Period size: 81 Copynumber: 1.9 Consensus size: 81
36552 CAAAGGGGTA
*
36562 GTATCGGTACCATTGGCTATGGTACCGGTACTACTATACATAAGGGTATCGGTACCCTATAGGGT
1 GTATCGGTACCATTGGCTATGGTACCGGTACTACTATACATAAGGGTATCGATACCCTATAGGGT
*
36627 ATCGGTACCCTATAGG
66 ATCAGTACCCTATAGG
*
36643 GTATCGGTACCATTGGCTATGGTATCGGTACTACTATACATAAGGGTATCGATACCCTATAGGGT
1 GTATCGGTACCATTGGCTATGGTACCGGTACTACTATACATAAGGGTATCGATACCCTATAGGGT
36708 ATCAGTACC
66 ATCAGTACC
36717 TCTTTTGCAT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 71 1.00
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.29
Consensus pattern (81 bp):
GTATCGGTACCATTGGCTATGGTACCGGTACTACTATACATAAGGGTATCGATACCCTATAGGGT
ATCAGTACCCTATAGG
Found at i:41243 original size:22 final size:20
Alignment explanation
Indices: 41191--41250 Score: 84
Period size: 20 Copynumber: 2.9 Consensus size: 20
41181 GATATCTGGG
41191 CAAGGAGAATCGGTACCCATT
1 CAAGG-GAATCGGTACCCATT
41212 CAAGGGAATCGGTACCCATT
1 CAAGGGAATCGGTACCCATT
*
41232 CAATGGGGAATCGATACCC
1 CAA--GGGAATCGGTACCC
41251 CTCAAGCGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 18 0.50
21 5 0.14
22 13 0.36
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.18
Consensus pattern (20 bp):
CAAGGGAATCGGTACCCATT
Found at i:42815 original size:103 final size:103
Alignment explanation
Indices: 42634--42830 Score: 349
Period size: 103 Copynumber: 1.9 Consensus size: 103
42624 TCCTTTGGGT
* *
42634 CATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCTTGGCATATG
1 CATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAGCATATG
42699 TATATGATACTTAAGGAATAATATGTGGTCATTCGGGA
66 TATATGATACTTAAGGAATAATATGTGGTCATTCGGGA
*
42737 CATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAGTATATG
1 CATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAGCATATG
* *
42802 TATATGATTCTTAAGGAATGATATGTGGT
66 TATATGATACTTAAGGAATAATATGTGGT
42831 GCTTATGGAC
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 89 1.00
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.36
Consensus pattern (103 bp):
CATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAGCATATG
TATATGATACTTAAGGAATAATATGTGGTCATTCGGGA
Found at i:42877 original size:23 final size:23
Alignment explanation
Indices: 42851--42918 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
42841 AATATTATAT
*
42851 GGCACTACGGTGCAATTCTATGC
1 GGCACTACGGTGCAATTCTACGC
* *
42874 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
42897 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
42919 AGCTGCGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:45673 original size:16 final size:16
Alignment explanation
Indices: 45652--45694 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
45642 GGTAATTAAA
45652 GATTGATAAGGAATTT
1 GATTGATAAGGAATTT
* *
45668 GATTGATTAATGATTTT
1 GATTGA-TAAGGAATTT
*
45685 GAGTGATAAG
1 GATTGATAAG
45695 AACTGATGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.40
Consensus pattern (16 bp):
GATTGATAAGGAATTT
Found at i:46688 original size:23 final size:22
Alignment explanation
Indices: 46643--46688 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
46633 GAATCTCATA
*
46643 AGGGAACCGAATCCCCCACAGG
1 AGGGAACCGAATCCCCCAAAGG
* *
46665 AGGGAATCGATTCCCCCTAAAGG
1 AGGGAACCGAATCCCCC-AAAGG
46688 A
1 A
46689 AAAATGTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.33, C:0.30, G:0.26, T:0.11
Consensus pattern (22 bp):
AGGGAACCGAATCCCCCAAAGG
Found at i:50146 original size:16 final size:16
Alignment explanation
Indices: 50125--50167 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
50115 GGTAATTAAA
50125 GATTGATAAGGAATTT
1 GATTGATAAGGAATTT
* *
50141 GATTGATTAATGATTTT
1 GATTGA-TAAGGAATTT
*
50158 GAGTGATAAG
1 GATTGATAAG
50168 AACTGATGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.40
Consensus pattern (16 bp):
GATTGATAAGGAATTT
Found at i:51112 original size:22 final size:20
Alignment explanation
Indices: 51055--51096 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
51045 TATTTGGGCA
51055 AAGGGAATCGGTACCCATTC
1 AAGGGAATCGGTACCCATTC
51075 AAGGGAATCGGTACCCATTC
1 AAGGGAATCGGTACCCATTC
51095 AA
1 AA
51097 TGGGGAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.19
Consensus pattern (20 bp):
AAGGGAATCGGTACCCATTC
Found at i:51189 original size:22 final size:22
Alignment explanation
Indices: 51146--51189 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
51136 AATCTCATAG
*
51146 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
* *
51168 GGGAATCGATTCCCCTAAAGGA
1 GGGAACCGATTCCCCCAAAGGA
51190 AAAATGTGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.30, G:0.27, T:0.14
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:52647 original size:103 final size:103
Alignment explanation
Indices: 52459--52676 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
52449 GTCGAGGGTC
* *
52459 TATGCGGTACTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
52524 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
52562 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
52627 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
52665 TATGTGGTCCTT
1 TATGTGGTCCTT
52677 ATAGACATTA
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:52727 original size:23 final size:23
Alignment explanation
Indices: 52701--52760 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
52691 ATGGCACTAT
52701 GGTGCAATTCTACGCGGCACTCC
1 GGTGCAATTCTACGCGGCACTCC
* *
52724 GGTGCAATTCTACGTGGCACTTC
1 GGTGCAATTCTACGCGGCACTCC
*
52747 GGTGCAATTATACG
1 GGTGCAATTCTACG
52761 AGCTGCGGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGTGCAATTCTACGCGGCACTCC
Found at i:55515 original size:16 final size:16
Alignment explanation
Indices: 55494--55536 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
55484 GGTAATTAAA
55494 GATTGATAAGGAATTT
1 GATTGATAAGGAATTT
* *
55510 GATTGATTAATGATTTT
1 GATTGA-TAAGGAATTT
*
55527 GAGTGATAAG
1 GATTGATAAG
55537 AACTTATGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.40
Consensus pattern (16 bp):
GATTGATAAGGAATTT
Found at i:56472 original size:22 final size:21
Alignment explanation
Indices: 56420--56479 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
56410 GATATCTGGG
56420 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
56441 CAA-GGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
*
56461 CAATGGGGAATCGATACCC
1 CAA-GGGGAATCGGTACCC
56480 CTCAAGCGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 20 0.56
21 3 0.08
22 13 0.36
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (21 bp):
CAAGGGGAATCGGTACCCATT
Found at i:56557 original size:23 final size:22
Alignment explanation
Indices: 56513--56557 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
56503 AATCTCATAG
*
56513 GGGAATCGATTCCCCCACAGGA
1 GGGAATCGATTCCCCCAAAGGA
56535 GGGAATCGATTCCCCCTAAAGGA
1 GGGAATCGATTCCCCC-AAAGGA
56558 AAAATGTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.29, C:0.29, G:0.27, T:0.16
Consensus pattern (22 bp):
GGGAATCGATTCCCCCAAAGGA
Found at i:58015 original size:103 final size:103
Alignment explanation
Indices: 57836--58044 Score: 366
Period size: 103 Copynumber: 2.0 Consensus size: 103
57826 CTACGCGGTT
* *
57836 CTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCTT
1 CTTCGGGACATATATGTATTCATTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCTA
57901 GCCATATGTATATGATTCTTAAGGAATGATATGTGGTC
66 GCCATATGTATATGATTCTTAAGGAATGATATGTGGTC
*
57939 CTTCGGGACATATATGTATTCATTGGAACATGTGTGAAGTCTGTTGAGACACATACTTGATCCCT
1 CTTCGGGACATATATGTATTCATTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT-CCT
*
58004 AG-TATATGTATATGATTCTTAAGGAATGATATGTGGTC
65 AGCCATATGTATATGATTCTTAAGGAATGATATGTGGTC
58042 CTT
1 CTT
58045 ATGTACATTA
Statistics
Matches: 101, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
103 97 0.96
104 4 0.04
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.36
Consensus pattern (103 bp):
CTTCGGGACATATATGTATTCATTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCTA
GCCATATGTATATGATTCTTAAGGAATGATATGTGGTC
Found at i:58087 original size:23 final size:22
Alignment explanation
Indices: 58061--58128 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 22
58051 ATTATTATAT
58061 GGCACTATGGTGCAATTCTACGC
1 GGCACT-TGGTGCAATTCTACGC
* * *
58084 GGCACTCCGATGCAATTCTACGT
1 GGCACT-TGGTGCAATTCTACGC
*
58107 GGCACTTCGGTGCAATTATACG
1 GGCACTT-GGTGCAATTCTACG
58129 AGCTACGGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.26
Consensus pattern (22 bp):
GGCACTTGGTGCAATTCTACGC
Found at i:60881 original size:16 final size:16
Alignment explanation
Indices: 60860--60902 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
60850 GGTAATTAAA
60860 GATTGATAAGGAATTT
1 GATTGATAAGGAATTT
* *
60876 GATTGATTAATGATTTT
1 GATTGA-TAAGGAATTT
*
60893 GAGTGATAAG
1 GATTGATAAG
60903 AACTGATGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.40
Consensus pattern (16 bp):
GATTGATAAGGAATTT
Found at i:61738 original size:22 final size:21
Alignment explanation
Indices: 61686--61745 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
61676 GATATATGGG
61686 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
61707 CAA-GGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
*
61727 CAATGGGGAATCGATACCC
1 CAA-GGGGAATCGGTACCC
61746 CTCAAGCGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 20 0.56
21 3 0.08
22 13 0.36
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (21 bp):
CAAGGGGAATCGGTACCCATT
Found at i:61823 original size:23 final size:22
Alignment explanation
Indices: 61779--61823 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
61769 AATCTCATAG
*
61779 GGGAACCGATTCCCCCATAGGA
1 GGGAACCGATTCCCCCAAAGGA
*
61801 GGGAATCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
61824 AAAATATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.29, C:0.29, G:0.27, T:0.16
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:63296 original size:103 final size:103
Alignment explanation
Indices: 63117--63326 Score: 357
Period size: 103 Copynumber: 2.0 Consensus size: 103
63107 GGGTCTACGC
* *
63117 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTTTAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* * * *
63182 CCTTGGCATATGTATATGATTTTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAAGAATGATATGT
63220 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
*
63285 CCCTAGTATATGTATATGATTCTTAAAGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAAGAATGATATGT
63323 GGTC
1 GGTC
63327 TTTATGGACA
Statistics
Matches: 100, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 100 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAAGAATGATATGT
Found at i:63379 original size:23 final size:23
Alignment explanation
Indices: 63346--63413 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
63336 ATTATTATAT
63346 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
63369 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* * *
63392 GGCACTTCGGTGTAATTATACG
1 GGCACTACGGTGCAATTCTACG
63414 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:70368 original size:312 final size:305
Alignment explanation
Indices: 69810--70392 Score: 934
Period size: 312 Copynumber: 1.9 Consensus size: 305
69800 GACTTCCAAC
* *
69810 ATTATCGAGTTAACACTAGTTTTGATGGCTCAAGCATCACTCCCGTTTCGGTTTAGTCGTATGCG
1 ATTATCGAGTTAACACTAGTTTTGATGGATCAAGCATCACTCCCGTTTCGGTTTAGTCGTATGCA
69875 GTATGCACTGCGATTCATCTTATAAATCATCTTCACACTCATGTTTTGCAAGGGAAGTCTCCATT
66 GTATGCACTGCGATTCATCTTATAAATCATCTTCACACTCATGTTTTGCAAGGGAAGTCTCCATT
*
69940 TGAGGCTTTGTTTAATAAGGTGCCTGATTATGGGTTTTTAAAGGTCTTTGGGTGTCGATGTTTTC
131 TGAGGCTTTGTTTAATAAGGTGCCTGATTATGGGTTTTTAAAGGTCTTTGGGTGCCGATGTTTTC
* *
70005 CGCATTTGCATCCATATTAGAACCACAAGCTGAGTTATTGATCTTAACCGTGCACCTTCCTTGGA
196 CGCATTTGCATCCATATCAGAACCACAAGCTGAGTTATCGATCTTAACCGTGCACCTTCCTTGGA
70070 TATAGCCCACAGTAAAATGGTGTGGTTGAACAAAAACATCGACAT
261 TATAGCCCACAGTAAAATGGTGTGGTTGAACAAAAACATCGACAT
* * * * * *
70115 ATTATCGAGTTAGCACTGGTTTTGATTGATCAAGCATCGCTCTCGTTTCGTTTTAGTAGTATGCA
1 ATTATCGAGTTAACACTAGTTTTGATGGATCAAGCATCACTCCCGTTTCG-GTT--TAG--T-C-
* * *
70180 GTATGCAGTATGCATTGCGGTTCATCTTATAAAT-AGTCTTCCCACTCATGTTTTGCAAGGGAAG
59 GTATGCAGTATGCACTGCGATTCATCTTATAAATCA-TCTTCACACTCATGTTTTGCAAGGGAAG
*
70244 TCTCCGTTTGAGGCTTTGTTTAATAAGGTGCCTGATTATGGGTTTTTAAAGGTCTTTGGGTGCCG
123 TCTCCATTTGAGGCTTTGTTTAATAAGGTGCCTGATTATGGGTTTTTAAAGGTCTTTGGGTGCCG
* *
70309 ATGTTTTCTGCATTTGCATCCATATCAGAACCACAAGCTGAGTTATCGGTCTTAACCGTGCACCT
188 ATGTTTTCCGCATTTGCATCCATATCAGAACCACAAGCTGAGTTATCGATCTTAACCGTGCACCT
70374 TCCTTGGATATAGCCCACA
253 TCCTTGGATATAGCCCACA
70393 ACATAAGGGT
Statistics
Matches: 253, Mismatches: 17, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
305 44 0.17
306 2 0.01
308 3 0.01
310 1 0.00
311 2 0.01
312 201 0.79
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (305 bp):
ATTATCGAGTTAACACTAGTTTTGATGGATCAAGCATCACTCCCGTTTCGGTTTAGTCGTATGCA
GTATGCACTGCGATTCATCTTATAAATCATCTTCACACTCATGTTTTGCAAGGGAAGTCTCCATT
TGAGGCTTTGTTTAATAAGGTGCCTGATTATGGGTTTTTAAAGGTCTTTGGGTGCCGATGTTTTC
CGCATTTGCATCCATATCAGAACCACAAGCTGAGTTATCGATCTTAACCGTGCACCTTCCTTGGA
TATAGCCCACAGTAAAATGGTGTGGTTGAACAAAAACATCGACAT
Found at i:70938 original size:29 final size:29
Alignment explanation
Indices: 70904--70963 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
70894 CGACACAACA
70904 GAACAAAGTTAGCACAAGAA-AACAAGATC
1 GAACAAAGTTAGCACAA-AACAACAAGATC
*
70933 GAACAAAGTTAGCACAAAACTACAAGATC
1 GAACAAAGTTAGCACAAAACAACAAGATC
70962 GA
1 GA
70964 CCAATCAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 2 0.07
29 27 0.93
ACGTcount: A:0.53, C:0.18, G:0.17, T:0.12
Consensus pattern (29 bp):
GAACAAAGTTAGCACAAAACAACAAGATC
Found at i:72162 original size:37 final size:37
Alignment explanation
Indices: 72112--72183 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
72102 GACTTGTAGT
72112 TAAAGGATTTTCGCAGATTACTGGACAGGATTTTCCC
1 TAAAGGATTTTCGCAGATTACTGGACAGGATTTTCCC
* *
72149 TAAAGGATTTTCGCAGGTTCCTGGACAGGATTTTC
1 TAAAGGATTTTCGCAGATTACTGGACAGGATTTTC
72184 ACGATACCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (37 bp):
TAAAGGATTTTCGCAGATTACTGGACAGGATTTTCCC
Found at i:73739 original size:23 final size:23
Alignment explanation
Indices: 73713--73760 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
73703 ATAAAGTACA
*
73713 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
** *
73736 ATAATGTAATAGGTAGCGTTTAT
1 ATAACATAATAGGTAGCGCTTAT
73759 AT
1 AT
73761 TTACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:74004 original size:30 final size:29
Alignment explanation
Indices: 73964--74030 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
73954 TCATTTGCAC
* * *
73964 AAAAAATTATTT-GATTTTTTGATATTTTAT
1 AAAATATTATTTAGAATTTTT-A-ATTTAAT
73994 AAAATATTATTTAGAATTTTTAATTTAAT
1 AAAATATTATTTAGAATTTTTAATTTAAT
74023 AATAATAT
1 AA-AATAT
74031 ATATCGTAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.25
30 17 0.53
31 7 0.22
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (29 bp):
AAAATATTATTTAGAATTTTTAATTTAAT
Found at i:74212 original size:23 final size:23
Alignment explanation
Indices: 74186--74248 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
74176 ATATAACCAC
74186 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
74209 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
74232 TACCTATTACATCATAT
1 TACCTATTACATTATAT
74249 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:74423 original size:430 final size:429
Alignment explanation
Indices: 73827--74880 Score: 2002
Period size: 430 Copynumber: 2.5 Consensus size: 429
73817 TATTACATTA
*
73827 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTATTTTAAAGTTATGTAAT
73892 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
66 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
73957 TTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
131 TTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
74022 TAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCT
196 TAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCT
*
74087 TAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCCCAGTGAAAAAAGTATGGACACTTT
261 TAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTT
74152 TATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATT
326 TATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATT
*
74217 ACATTATATAAGCGCTACCTATTACATCATATTTTTACC
391 ACATTATATAAGCGCTACCTATTACATCATATGTTTACC
74256 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTATTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTATTTTAAAGTTATGTAAT
*
74321 TTATGTTTCAATTTTTTTTAATAGTGTTTCATATTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
*
74386 ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
130 ATTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
*
74451 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGATGCCTATAATTACTAAATTAATATC
195 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
74516 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
260 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
74581 TTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTAT
325 TTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTAT
74646 TACATTATATAAGCGCTACCTATTACATCATATGTTTACC
390 TACATTATATAAGCGCTACCTATTACATCATATGTTTACC
74686 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTATTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTATTTTAAAGTTATGTAAT
74751 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
66 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
* * *
74816 TTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTATAA-TTTAAATTTA
131 TTTGCACAAAAAATTATTTGATT-TTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
74880 A
195 A
74881 CAACATTAAC
Statistics
Matches: 612, Mismatches: 11, Indels: 4
0.98 0.02 0.01
Matches are distributed among these distances:
429 161 0.26
430 451 0.74
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.42
Consensus pattern (429 bp):
TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTATTTTAAAGTTATGTAAT
TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
TTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
TAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCT
TAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTT
TATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATT
ACATTATATAAGCGCTACCTATTACATCATATGTTTACC
Found at i:74642 original size:23 final size:23
Alignment explanation
Indices: 74616--74678 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
74606 ATATAACCAC
74616 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
74639 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
74662 TACCTATTACATCATAT
1 TACCTATTACATTATAT
74679 GTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:75154 original size:39 final size:39
Alignment explanation
Indices: 75100--75185 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 39
75090 CAAGTTGTAG
*
75100 ATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTGA
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
* *
75139 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGG
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
75178 ATTTTGAT
1 ATTTTGAT
75186 GAGCATCGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.49
Consensus pattern (39 bp):
ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
Found at i:75467 original size:18 final size:18
Alignment explanation
Indices: 75444--75480 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
75434 CGAAATATAT
75444 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
75462 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
75480 A
1 A
75481 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:75939 original size:23 final size:23
Alignment explanation
Indices: 75913--75975 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
75903 ATATAACCAC
75913 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
75936 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
75959 TACCTATTACATCATAT
1 TACCTATTACATTATAT
75976 GTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:77837 original size:17 final size:18
Alignment explanation
Indices: 77815--77857 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
77805 ATATATCCGG
77815 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
77832 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
77852 TATCAT
1 TATCAT
77858 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:77875 original size:20 final size:19
Alignment explanation
Indices: 77820--77866 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
77810 TCCGGTATCA
77820 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
77839 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
77860 TTTTACC
1 TTTTACC
77867 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:78024 original size:20 final size:20
Alignment explanation
Indices: 78001--78047 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
77991 TCCGGTAACG
*
78001 TTTTACCGGTTTTATCATTT
1 TTTTACCGGTTTTATCATAT
78021 TTTTACCGGTTTTATCATAT
1 TTTTACCGGTTTTATCATAT
78041 TTTTACC
1 TTTTACC
78048 TGGTATATCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.17, C:0.17, G:0.09, T:0.57
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:78056 original size:20 final size:20
Alignment explanation
Indices: 78001--78056 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
77991 TCCGGTAACG
* *
78001 TTTTACCGGTTTTATCATTT
1 TTTTACCGGTTATATCATAT
*
78021 TTTTACCGGTTTTATCATAT
1 TTTTACCGGTTATATCATAT
78041 TTTTACCTGG-TATATC
1 TTTTACC-GGTTATATC
78057 GTTTTGGATC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 31 0.94
21 2 0.06
ACGTcount: A:0.18, C:0.16, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTATATCATAT
Found at i:78100 original size:181 final size:182
Alignment explanation
Indices: 77787--78259 Score: 696
Period size: 181 Copynumber: 2.6 Consensus size: 182
77777 CGTACTTACG
* * * *
77787 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTTATACCGGTTT
* * *
77852 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
* *
77917 AGGCGCTATAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* *
77968 AAAGTATCGACACTTTTAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTTTTACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTTATACCGGTTT
* * *
78033 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATTGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** *
78098 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * * * *
78150 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTGACCGGTTTTATCATTTCTATACCGATTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTTATACCGGTTT
* * *
78215 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
78260 AATTTGGATC
Statistics
Matches: 262, Mismatches: 29, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
181 164 0.63
182 98 0.37
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (182 bp):
AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTTATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:82298 original size:26 final size:26
Alignment explanation
Indices: 82249--82344 Score: 68
Period size: 26 Copynumber: 3.7 Consensus size: 26
82239 AATGGGCTGG
* *
82249 TCAAACGTGTACAGTCAATAGGTCAA
1 TCAAACGCGTACAATCAATAGGTCAA
* * *
82275 TCAAACGCGTACAATCAGTGGGTCGA
1 TCAAACGCGTACAATCAATAGGTCAA
* * * * * *
82301 TGAAAAGGGTACATTTAACTA-GTCGA
1 TCAAACGCGTACAATCAA-TAGGTCAA
*
82327 TCAAACGCGTACTATCAA
1 TCAAACGCGTACAATCAA
82345 CGGGTCAAGC
Statistics
Matches: 51, Mismatches: 18, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
26 50 0.98
27 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (26 bp):
TCAAACGCGTACAATCAATAGGTCAA
Found at i:83366 original size:3 final size:3
Alignment explanation
Indices: 83358--83395 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
83348 CATATCATTA
83358 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
83396 AAGTTGTCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:87552 original size:40 final size:41
Alignment explanation
Indices: 87497--87583 Score: 133
Period size: 40 Copynumber: 2.1 Consensus size: 41
87487 CACTTTGTCA
87497 GAAAATACACTTGAATTTTCTAGAGAAAGTAAACTAGAAA-G
1 GAAAATACACTTGAATTTTCTAGAGAAAGTAAACTA-AAAGG
* *
87538 GAAAATA-GCTTGAATTTTCTCGAGAAAGTAAACTAAAAGG
1 GAAAATACACTTGAATTTTCTAGAGAAAGTAAACTAAAAGG
87578 GAAAAT
1 GAAAAT
87584 CTAAAAGAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
39 3 0.07
40 33 0.77
41 7 0.16
ACGTcount: A:0.48, C:0.09, G:0.18, T:0.24
Consensus pattern (41 bp):
GAAAATACACTTGAATTTTCTAGAGAAAGTAAACTAAAAGG
Found at i:89196 original size:19 final size:19
Alignment explanation
Indices: 89172--89221 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
89162 ATGAAATTAA
89172 TGCATCGATGCATAAGGAG
1 TGCATCGATGCATAAGGAG
*
89191 TGCATCGATACATAAGGAG
1 TGCATCGATGCATAAGGAG
89210 TGCATCGATGCA
1 TGCATCGATGCA
89222 CATGTTAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.22
Consensus pattern (19 bp):
TGCATCGATGCATAAGGAG
Found at i:90350 original size:2 final size:2
Alignment explanation
Indices: 90345--90467 Score: 246
Period size: 2 Copynumber: 61.5 Consensus size: 2
90335 GTAGGAAAAA
90345 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
90387 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
90429 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
90468 GGAAGATGAA
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 121 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:90926 original size:23 final size:23
Alignment explanation
Indices: 90893--90960 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
90883 AACCTTATAT
90893 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * * **
90916 GGCACTACGGTACAATTCTACAT
1 GGCACTTCGGTGCATTTCTACGC
* *
90939 GGCATTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
90961 AGCTGTGGTG
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Done.