Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014033.1 Corchorus capsularis cultivar CVL-1 contig14054, 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: 166900
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:83 original size:34 final size:34
Alignment explanation
Indices: 12--112 Score: 102
Period size: 33 Copynumber: 3.0 Consensus size: 34
2 TGAGGGCGGC
* * *
12 CTGCCTTGGC-GAAGCCGGCCCCGGTGGGGCGGC-
1 CTGCCATGGCTGAAGCC-GCCCCAGTGGGGAGGCT
45 CTGCCCATGG-TGAAGCCGCCCCAGTGGGGAGGCT
1 CTG-CCATGGCTGAAGCCGCCCCAGTGGGGAGGCT
* * *
79 CTGCCGTGGCTG-AGCCGTCCTAGTGGGGAGGCT
1 CTGCCATGGCTGAAGCCGCCCCAGTGGGGAGGCT
112 C
1 C
113 AGTGTAAAAG
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
33 42 0.72
34 16 0.28
ACGTcount: A:0.10, C:0.33, G:0.42, T:0.16
Consensus pattern (34 bp):
CTGCCATGGCTGAAGCCGCCCCAGTGGGGAGGCT
Found at i:5075 original size:178 final size:177
Alignment explanation
Indices: 4695--5141 Score: 499
Period size: 178 Copynumber: 2.5 Consensus size: 177
4685 TATCCGATCA
* * * *
4695 AGGTGATTCAAGTGTCTATTAAAAGGTTGTTCCATCATCTACAACTTTCATGTAAGACTCGAAAA
1 AGGTGATTCAAGTGTCTATTAAAAGGTTGTTTCATGATCTACAACTTTCATGTAGGACTCGAAAG
* ** * * * * **
4760 CTAAATCTAATGTTTTAAATATCAAAAAACTTCCGAATAATTAGTTGTTTCGGTTACCGGGAATG
66 CTAAATTTAATAATTCAAATATCAAAAAACTTCCAAAAAATTAATTGTTTCGGTTACCAAGAATG
* * * *
4825 GACGATCCACTTAATATAACATTACTTTTGCTGCACATGTCTTATTG
131 AACGATCCACTTAATATAACATAACTTTTGCTCCACATGTCTGATTG
* * * *
4872 AGCTGATTCAATTGTCTCA-TAAAAGGTTATTTTATGATCTACAACTTTCATGTAGGACTCGAAA
1 AGGTGATTCAAGTGTCT-ATTAAAAGGTTGTTTCATGATCTACAACTTTCATGTAGGACTCGAAA
* * *
4936 GCTAAATTTAATAATTCAAGTAT-AAAAAATGCTTCCAAAAAATTAATTTTTTCGGTTAGCAAGA
65 GCTAAATTTAATAATTCAAATATCAAAAAA--CTTCCAAAAAATTAATTGTTTCGGTTACCAAGA
* * * *
5000 ATGAACGATCCACTTAATA-ATACATAATTTTTGTTCCAGATAT-TCGATTG
128 ATGAACGATCCACTTAATATA-ACATAACTTTTGCTCCACATGTCT-GATTG
* * * *
5050 AGGTGATTCAAGTGTCTGTTAAAAGGTTGTTTCGTGATCTTCAACTTTCATGTAGGACTTGAAAG
1 AGGTGATTCAAGTGTCTATTAAAAGGTTGTTTCATGATCTACAACTTTCATGTAGGACTCGAAAG
* * *
5115 CTAAATTTGAT-TTTCAAATACCAAAAA
66 CTAAATTTAATAATTCAAATATCAAAAA
5142 TGCTTATGAA
Statistics
Matches: 223, Mismatches: 40, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
176 6 0.03
177 81 0.36
178 136 0.61
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (177 bp):
AGGTGATTCAAGTGTCTATTAAAAGGTTGTTTCATGATCTACAACTTTCATGTAGGACTCGAAAG
CTAAATTTAATAATTCAAATATCAAAAAACTTCCAAAAAATTAATTGTTTCGGTTACCAAGAATG
AACGATCCACTTAATATAACATAACTTTTGCTCCACATGTCTGATTG
Found at i:8062 original size:26 final size:23
Alignment explanation
Indices: 8033--8093 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 23
8023 ATTAAAATAC
*
8033 TTTTGGATTTTTATCTTTTATCTTTT
1 TTTTGGATTTTT-T-TTTT-TCATTT
*
8059 TTTTGGATTCTTTTTTTTCATTT
1 TTTTGGATTTTTTTTTTTCATTT
*
8082 TTTTGAATTTTT
1 TTTTGGATTTTT
8094 GGGAAGTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 15 0.48
24 4 0.13
25 1 0.03
26 11 0.35
ACGTcount: A:0.11, C:0.07, G:0.08, T:0.74
Consensus pattern (23 bp):
TTTTGGATTTTTTTTTTTCATTT
Found at i:9291 original size:8 final size:8
Alignment explanation
Indices: 9278--9305 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
9268 GGTGGCTTGT
9278 TGATGTTG
1 TGATGTTG
9286 TGATGTTG
1 TGATGTTG
9294 TGATGTTG
1 TGATGTTG
9302 TGAT
1 TGAT
9306 TTCTCTCTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.14, C:0.00, G:0.36, T:0.50
Consensus pattern (8 bp):
TGATGTTG
Found at i:11127 original size:2 final size:2
Alignment explanation
Indices: 11120--11155 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
11110 AATTGTTAGG
11120 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
11156 ATGATAGTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16847 original size:109 final size:109
Alignment explanation
Indices: 16706--16938 Score: 376
Period size: 109 Copynumber: 2.1 Consensus size: 109
16696 CTCTGGAAAC
* * * * *
16706 CGTCCCCTAATTAAAAGGTATCTATCAAATAAAAGACAGTTTTTTGTAGTTTATACCTATTGAAA
1 CGTCTCCTAATTAAAAGATATCTATCAAATAAAAGACAATTTTTTGTAATTTATACCTATTCAAA
16771 TAGGTATAACCAAATTTTCTTAAGGAAAATAAAAAATAAAAAAT
66 TAGGTATAACCAAATTTTCTTAAGGAAAATAAAAAATAAAAAAT
* * * *
16815 CGTCTCCTAATTAAAATATATCTATCATATAAAAGATAATTTTTTGTAATTTATAGCTATTCAAA
1 CGTCTCCTAATTAAAAGATATCTATCAAATAAAAGACAATTTTTTGTAATTTATACCTATTCAAA
*
16880 TAGGTATAACCAAATTTTCTTAAGGAAAATAAAAGATAAAAAAT
66 TAGGTATAACCAAATTTTCTTAAGGAAAATAAAAAATAAAAAAT
16924 CGTCTCCTAATTAAA
1 CGTCTCCTAATTAAA
16939 TAAAAGGTAT
Statistics
Matches: 114, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
109 114 1.00
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (109 bp):
CGTCTCCTAATTAAAAGATATCTATCAAATAAAAGACAATTTTTTGTAATTTATACCTATTCAAA
TAGGTATAACCAAATTTTCTTAAGGAAAATAAAAAATAAAAAAT
Found at i:25026 original size:24 final size:24
Alignment explanation
Indices: 24999--25049 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
24989 TTTGGTTAGA
24999 ATTAAAACCATGGTACTTTAAAAT
1 ATTAAAACCATGGTACTTTAAAAT
*
25023 ATTAAAACCATGGTACTTTAAAGT
1 ATTAAAACCATGGTACTTTAAAAT
25047 ATT
1 ATT
25050 TTGGTTAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (24 bp):
ATTAAAACCATGGTACTTTAAAAT
Found at i:25160 original size:48 final size:48
Alignment explanation
Indices: 25089--25186 Score: 160
Period size: 48 Copynumber: 2.0 Consensus size: 48
25079 ATGTTAATTT
* * * *
25089 AATACCAAATTATTATGAGATTAGAGCAAATCATAACACTTATGAATC
1 AATACAAAAATATTATGAGATTAGAGCAAATCATAAAACTCATGAATC
25137 AATACAAAAATATTATGAGATTAGAGCAAATCATAAAACTCATGAATC
1 AATACAAAAATATTATGAGATTAGAGCAAATCATAAAACTCATGAATC
25185 AA
1 AA
25187 ATTAGTTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.50, C:0.13, G:0.10, T:0.27
Consensus pattern (48 bp):
AATACAAAAATATTATGAGATTAGAGCAAATCATAAAACTCATGAATC
Found at i:25646 original size:26 final size:27
Alignment explanation
Indices: 25597--25648 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
25587 AATATATAAT
*
25597 AATTATTATTATAATAAGAAGTTTAAG
1 AATTATTATCATAATAAGAAGTTTAAG
* *
25624 AATTA-TATCATACTAAGATGTTTAA
1 AATTATTATCATAATAAGAAGTTTAA
25649 CGTAATATCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (27 bp):
AATTATTATCATAATAAGAAGTTTAAG
Found at i:25670 original size:27 final size:29
Alignment explanation
Indices: 25638--25708 Score: 110
Period size: 27 Copynumber: 2.5 Consensus size: 29
25628 ATATCATACT
25638 AAGATGTTTAACGTAATATCT-AAAA-AA
1 AAGATGTTTAACGTAATATCTAAAAAGAA
*
25665 AAGATGTTTAATGTAATATCTAAAAAAGAA
1 AAGATGTTTAACGTAATATCT-AAAAAGAA
25695 AAGATGTTTAACGT
1 AAGATGTTTAACGT
25709 GTAAAAATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
27 20 0.51
29 4 0.10
30 15 0.38
ACGTcount: A:0.49, C:0.06, G:0.14, T:0.31
Consensus pattern (29 bp):
AAGATGTTTAACGTAATATCTAAAAAGAA
Found at i:25863 original size:2 final size:2
Alignment explanation
Indices: 25858--25896 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
25848 AATTTAGACT
* *
25858 TA TA TA -A TA TA AA GA 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
25897 CTAGTTAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (2 bp):
TA
Found at i:27278 original size:60 final size:59
Alignment explanation
Indices: 27183--27343 Score: 216
Period size: 60 Copynumber: 2.7 Consensus size: 59
27173 CGCGATCTAG
27183 CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAAGTAAAAGATCATA
1 CCCTTATTTGAGCATTTTC-ATAACGTTAGGCCCTTATTTGGCCAAAGTAAAAGATCATA
* * * * *
27243 CTCTTATTTGAGCATTTTCAATAATGTTAGGCCCTTATTTGGCCAAATTAAAATATCATG
1 CCCTTATTTGAGCATTTTC-ATAACGTTAGGCCCTTATTTGGCCAAAGTAAAAGATCATA
* *
27303 CCCTTGTTTAAGCATTTTGTCA-AACGTTAGGCCCTTATTTG
1 CCCTTATTTGAGCA-TTT-TCATAACGTTAGGCCCTTATTTG
27344 AACAATTAGC
Statistics
Matches: 89, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
60 83 0.93
61 4 0.04
62 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (59 bp):
CCCTTATTTGAGCATTTTCATAACGTTAGGCCCTTATTTGGCCAAAGTAAAAGATCATA
Found at i:30458 original size:2 final size:2
Alignment explanation
Indices: 30451--30484 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
30441 TAATGTAAAG
30451 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
30485 CTGGGAAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31187 original size:19 final size:19
Alignment explanation
Indices: 31151--31221 Score: 76
Period size: 19 Copynumber: 3.8 Consensus size: 19
31141 CCCGCCCCTA
*
31151 TTTTCTTTT-TTCTCTTCC
1 TTTTCTTTTCTTCTTTTCC
31169 TTTTCTTTTCTTCTTTTCC
1 TTTTCTTTTCTTCTTTTCC
*
31188 TTGTATATTTTC-T-TTTTCC
1 TT-T-TCTTTTCTTCTTTTCC
*
31207 TTCTCTTTTCTTCTT
1 TTTTCTTTTCTTCTT
31222 CAAAACAAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
17 6 0.14
18 10 0.23
19 20 0.45
20 2 0.05
21 6 0.14
ACGTcount: A:0.03, C:0.24, G:0.01, T:0.72
Consensus pattern (19 bp):
TTTTCTTTTCTTCTTTTCC
Found at i:31860 original size:30 final size:30
Alignment explanation
Indices: 31824--31883 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
31814 ATTGATCTTG
31824 GAATTAAGTAAGCTTCCACTCTTTTGAAAC
1 GAATTAAGTAAGCTTCCACTCTTTTGAAAC
*
31854 GAATTAATTAAGCTTCCACTCTTTTGAAAC
1 GAATTAAGTAAGCTTCCACTCTTTTGAAAC
31884 TCATTAGTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (30 bp):
GAATTAAGTAAGCTTCCACTCTTTTGAAAC
Found at i:34800 original size:22 final size:21
Alignment explanation
Indices: 34756--34797 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
34746 TGAACAACAC
34756 GCGCCATTAAACCCATTTTTT
1 GCGCCATTAAACCCATTTTTT
*
34777 GCGCCGTTAAACCCATTTTTT
1 GCGCCATTAAACCCATTTTTT
34798 TGCCTACGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.29, G:0.12, T:0.38
Consensus pattern (21 bp):
GCGCCATTAAACCCATTTTTT
Found at i:42549 original size:15 final size:15
Alignment explanation
Indices: 42529--42559 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
42519 GACCGAATAA
42529 TGATTATCTATGTAC
1 TGATTATCTATGTAC
42544 TGATTATCTATGTAC
1 TGATTATCTATGTAC
42559 T
1 T
42560 ATGGAAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (15 bp):
TGATTATCTATGTAC
Found at i:54979 original size:129 final size:129
Alignment explanation
Indices: 54745--54990 Score: 402
Period size: 129 Copynumber: 1.9 Consensus size: 129
54735 TGAATTGACC
* *
54745 CAGGAGAGGGTCGATGTATCATAGACTATACCCGATAACTACATTGGATCCTGACTAATCCATAG
1 CAGGAGAAGGTCGATGTATCATAGACTATACCCGATAACTACATTGGATCCTGACTAATCCATAC
*
54810 TTGAGCCATGTTGAACCCTATACGGGGGAAACTCTTTCCGTGCCTATTTTTTTATAAATTCACG
66 TTGAGCCATGTTGAACCCTATACGGGGGAAACTCTCTCCGTGCCTATTTTTTTATAAATTCACG
* * ***
54874 CAGGAGAAGGTCGATGTATCATAGAGTATACCCGATAGCTACATTGGATCCTGACTAATTTGTAC
1 CAGGAGAAGGTCGATGTATCATAGACTATACCCGATAACTACATTGGATCCTGACTAATCCATAC
* *
54939 TTGAGCCATGTTGGACCCTATATGGGGGAAACTCTCTCCGTGCCTATTTTTT
66 TTGAGCCATGTTGAACCCTATACGGGGGAAACTCTCTCCGTGCCTATTTTTT
54991 GCATCTGCAA
Statistics
Matches: 107, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
129 107 1.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (129 bp):
CAGGAGAAGGTCGATGTATCATAGACTATACCCGATAACTACATTGGATCCTGACTAATCCATAC
TTGAGCCATGTTGAACCCTATACGGGGGAAACTCTCTCCGTGCCTATTTTTTTATAAATTCACG
Found at i:59790 original size:19 final size:19
Alignment explanation
Indices: 59761--59800 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
59751 TTCTCTCTCA
59761 TAAAAAAAAATTATT-TTT
1 TAAAAAAAAATTATTATTT
59779 TAAAATAAAAATTATTATTT
1 TAAAA-AAAAATTATTATTT
59799 TA
1 TA
59801 TTTCTCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 5 0.25
19 10 0.50
20 5 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TAAAAAAAAATTATTATTT
Found at i:69810 original size:32 final size:32
Alignment explanation
Indices: 69769--69835 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
69759 CTCGTGTTCG
**
69769 AATTCTAGGATGGATGGGATGAGATTATGGGA
1 AATTCTAGGATGGACAGGATGAGATTATGGGA
69801 AATTCTAGGATGGACAGGATGAGATTATGGGA
1 AATTCTAGGATGGACAGGATGAGATTATGGGA
69833 AAT
1 AAT
69836 GAGAGGGCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.34, C:0.04, G:0.34, T:0.27
Consensus pattern (32 bp):
AATTCTAGGATGGACAGGATGAGATTATGGGA
Found at i:72497 original size:2 final size:2
Alignment explanation
Indices: 72490--72529 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
72480 ATTATAAAAC
* *
72490 AT AT AT AT AT AT AT AT AC AT AC 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
72530 CCCATGTAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:72656 original size:21 final size:21
Alignment explanation
Indices: 72632--72672 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
72622 TTAATTCCTA
* *
72632 TAAATATATTTGTAATTTATT
1 TAAATAAATGTGTAATTTATT
*
72653 TAAATAAATGTGTTATTTAT
1 TAAATAAATGTGTAATTTAT
72673 ACTAATTAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (21 bp):
TAAATAAATGTGTAATTTATT
Found at i:76121 original size:1 final size:1
Alignment explanation
Indices: 76117--76144 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
76107 TTTTTTTCAA
76117 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
76145 CACTTTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:84420 original size:110 final size:110
Alignment explanation
Indices: 84227--84447 Score: 442
Period size: 110 Copynumber: 2.0 Consensus size: 110
84217 TGATAGCTTG
84227 TACATAAGAATATCATACGGACCAATAATTTCATGTACAAATAATCATTCCATTCATGTATCATG
1 TACATAAGAATATCATACGGACCAATAATTTCATGTACAAATAATCATTCCATTCATGTATCATG
84292 TGGGATTATGGGATTTCAGTAGTGTATTGTATAATTTACCTATTA
66 TGGGATTATGGGATTTCAGTAGTGTATTGTATAATTTACCTATTA
84337 TACATAAGAATATCATACGGACCAATAATTTCATGTACAAATAATCATTCCATTCATGTATCATG
1 TACATAAGAATATCATACGGACCAATAATTTCATGTACAAATAATCATTCCATTCATGTATCATG
84402 TGGGATTATGGGATTTCAGTAGTGTATTGTATAATTTACCTATTA
66 TGGGATTATGGGATTTCAGTAGTGTATTGTATAATTTACCTATTA
84447 T
1 T
84448 TATTATTTTT
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
110 111 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (110 bp):
TACATAAGAATATCATACGGACCAATAATTTCATGTACAAATAATCATTCCATTCATGTATCATG
TGGGATTATGGGATTTCAGTAGTGTATTGTATAATTTACCTATTA
Found at i:85613 original size:23 final size:23
Alignment explanation
Indices: 85560--85613 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
85550 CAAAATGGCC
85560 ATTGAAAGGGTTAAATTGTCCCA
1 ATTGAAAGGGTTAAATTGTCCCA
* *
85583 AATCAAAGGGCTT-AATTGTCCCA
1 ATTGAAAGGG-TTAAATTGTCCCA
85606 ATTGAAAG
1 ATTGAAAG
85614 CTCAATAACC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 24 0.92
24 2 0.08
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (23 bp):
ATTGAAAGGGTTAAATTGTCCCA
Found at i:90967 original size:15 final size:15
Alignment explanation
Indices: 90947--90975 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
90937 TTATGTAGTT
90947 GAAGAAGAAGATGAA
1 GAAGAAGAAGATGAA
90962 GAAGAAGAAGATGA
1 GAAGAAGAAGATGA
90976 TAGTTTGGAA
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:0.59, C:0.00, G:0.34, T:0.07
Consensus pattern (15 bp):
GAAGAAGAAGATGAA
Found at i:105379 original size:27 final size:27
Alignment explanation
Indices: 105341--105394 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
105331 GATAATGAGA
* *
105341 CTTTTGATTATTGTATTCCCCAAAAAT
1 CTTTCGATTATTGTATTCCCAAAAAAT
105368 CTTTCGATTATTGTATTCCCAAAAAAT
1 CTTTCGATTATTGTATTCCCAAAAAAT
105395 AATTAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.43
Consensus pattern (27 bp):
CTTTCGATTATTGTATTCCCAAAAAAT
Found at i:108152 original size:30 final size:29
Alignment explanation
Indices: 108100--108165 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 29
108090 TGAGCCGGTA
*
108100 AAAATAATCAAAAAATACAAAAATATATTT
1 AAAA-AATCAAAAAATACAAAAAAATATTT
* *
108130 AAAAAATTAAAAAATAATAAAAAAATATTT
1 AAAAAATCAAAAAAT-ACAAAAAAATATTT
108160 AAAAAA
1 AAAAAA
108166 GCCACGTAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 10 0.31
30 22 0.69
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (29 bp):
AAAAAATCAAAAAATACAAAAAAATATTT
Found at i:108270 original size:31 final size:31
Alignment explanation
Indices: 108235--108337 Score: 88
Period size: 31 Copynumber: 3.4 Consensus size: 31
108225 GGTTGAAAAA
108235 GTACCAAATTGAACCATTTATAAAAGGTTTG
1 GTACCAAATTGAACCATTTATAAAAGGTTTG
* * * *
108266 GTACCAAATCGGACGA--AATAAAAGGTTTG
1 GTACCAAATTGAACCATTTATAAAAGGTTTG
* * * *
108295 GTACCGAGTTG--CGCTTTTCATGAAAGGTTTG
1 GTACCAAATTGAAC-CATTT-ATAAAAGGTTTG
108326 GTACCAAATTGA
1 GTACCAAATTGA
108338 GATTTCAGCC
Statistics
Matches: 54, Mismatches: 13, Indels: 9
0.71 0.17 0.12
Matches are distributed among these distances:
27 1 0.02
29 20 0.37
31 33 0.61
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (31 bp):
GTACCAAATTGAACCATTTATAAAAGGTTTG
Found at i:108548 original size:3 final size:3
Alignment explanation
Indices: 108540--108568 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
108530 TTTATCCAAA
108540 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
108569 ACTATTAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:108828 original size:21 final size:21
Alignment explanation
Indices: 108802--108854 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
108792 ATTGTTTTTG
108802 TTTCCTGTTTTCTGTTGTCAA
1 TTTCCTGTTTTCTGTTGTCAA
*
108823 TTTCCTGTTTTCTGTTGTTAA
1 TTTCCTGTTTTCTGTTGTCAA
108844 TTTCCTGTTTT
1 TTTCCTGTTTT
108855 TGAAAACAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.08, C:0.17, G:0.13, T:0.62
Consensus pattern (21 bp):
TTTCCTGTTTTCTGTTGTCAA
Found at i:109141 original size:11 final size:11
Alignment explanation
Indices: 109117--109151 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
109107 TTGACAGCGC
109117 AACAAAAACAA
1 AACAAAAACAA
* *
109128 AACGAAAACGA
1 AACAAAAACAA
109139 AACAAAAACAA
1 AACAAAAACAA
109150 AA
1 AA
109152 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:121368 original size:4 final size:4
Alignment explanation
Indices: 121359--121384 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
121349 TCTTACTATA
121359 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
121385 TTATCTATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:122653 original size:17 final size:18
Alignment explanation
Indices: 122628--122661 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
122618 TGTATGGTTC
122628 TCCTGGATAA-ATTCTTT
1 TCCTGGATAATATTCTTT
*
122645 TCCTTGATAATATTCTT
1 TCCTGGATAATATTCTT
122662 AATCATTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.24, C:0.18, G:0.09, T:0.50
Consensus pattern (18 bp):
TCCTGGATAATATTCTTT
Found at i:128473 original size:185 final size:176
Alignment explanation
Indices: 128170--128530 Score: 641
Period size: 185 Copynumber: 2.0 Consensus size: 176
128160 CACCTTGAAT
128170 CCCCCAAGTTGAAATTAGCCTAGAAATCTAGAATTCATCTAGAATTCTCCTAAGTAGCTTATCTT
1 CCCCCAAGTTGAAATTAGCCTAGAAATCTAGAATTCATCTAGAATTCTCCTAAGTAGCTTATCTT
128235 GAGTTCATTTATTTTCCTTAATGAAAATGAAAGCAAAGAGCAATGGAATTTCATTTTAGGACAAT
66 GAGTTCATTTATTTTCCTTAATGAAAATGAAAGCAAAGAGCAATGGAATTTCATTTTAGGACAAT
128300 GGTAGCAAATTTGCTACTCCCCCAATTAGGGTAAGTAAAAGAGGGC
131 GGTAGCAAATTTGCTACTCCCCCAATTAGGGTAAGTAAAAGAGGGC
128346 CCCCCAAGTTGAAATTAGCCTAGAAATCTAGAATTCATCTAGAATTCTCCTATGTAGCTTATCTA
1 CCCCCAAGTTGAAATTAGCCTAGAAATCTAGAATTCATCTAGAATTCTCCTA---AG------TA
128411 GCTTATCTTGAGTTCATTTATTTTCCTTAATGAAAATGAAAGCAAAGAGCAATGGAATTTCATTT
57 GCTTATCTTGAGTTCATTTATTTTCCTTAATGAAAATGAAAGCAAAGAGCAATGGAATTTCATTT
128476 TAGGACAATGGTAGCAAATTTGCTACTCCCCCAATTAGGGTAAGTAAAAGAGGGC
122 TAGGACAATGGTAGCAAATTTGCTACTCCCCCAATTAGGGTAAGTAAAAGAGGGC
128531 TAAGTAAGTA
Statistics
Matches: 176, Mismatches: 0, Indels: 9
0.95 0.00 0.05
Matches are distributed among these distances:
176 52 0.30
179 2 0.01
185 122 0.69
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (176 bp):
CCCCCAAGTTGAAATTAGCCTAGAAATCTAGAATTCATCTAGAATTCTCCTAAGTAGCTTATCTT
GAGTTCATTTATTTTCCTTAATGAAAATGAAAGCAAAGAGCAATGGAATTTCATTTTAGGACAAT
GGTAGCAAATTTGCTACTCCCCCAATTAGGGTAAGTAAAAGAGGGC
Found at i:128539 original size:19 final size:19
Alignment explanation
Indices: 128515--128552 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
128505 CCCAATTAGG
128515 GTAAGTAAAAGAGGGCTAA
1 GTAAGTAAAAGAGGGCTAA
128534 GTAAGTAAAAGAGGGCTAA
1 GTAAGTAAAAGAGGGCTAA
128553 TAGAGGGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.32, T:0.16
Consensus pattern (19 bp):
GTAAGTAAAAGAGGGCTAA
Found at i:128617 original size:41 final size:41
Alignment explanation
Indices: 128572--128717 Score: 175
Period size: 41 Copynumber: 3.7 Consensus size: 41
128562 AATCCCAAGT
128572 TATCACATGCTGCCATTCAAATAGTAGCCATTCCAAAACTA
1 TATCACATGCTGCCATTCAAATAGTAGCCATTCCAAAACTA
* *
128613 TATCACATGCTGCCATTCAAATAGTAGCCATATTC---A-TC
1 TATCACATGCTGCCATTCAAATAGTAGCCAT-TCCAAAACTA
128651 TA--A-A--CTGCCATTCAAATAGTAGCCATTCCAAAACTAA
1 TATCACATGCTGCCATTCAAATAGTAGCCATTCCAAAACT-A
128688 GTTATCACATGCTGCCATTCAAATAGTAGC
1 --TATCACATGCTGCCATTCAAATAGTAGC
128718 ATATTCATCT
Statistics
Matches: 88, Mismatches: 4, Indels: 23
0.77 0.03 0.20
Matches are distributed among these distances:
32 2 0.02
33 22 0.25
35 2 0.02
36 2 0.02
38 3 0.03
39 3 0.03
41 32 0.36
42 3 0.03
44 19 0.22
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.28
Consensus pattern (41 bp):
TATCACATGCTGCCATTCAAATAGTAGCCATTCCAAAACTA
Found at i:130439 original size:8 final size:8
Alignment explanation
Indices: 130426--130451 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
130416 TGCGCAAGAG
130426 GGGTTTTA
1 GGGTTTTA
130434 GGGTTTTA
1 GGGTTTTA
130442 GGGTTTTA
1 GGGTTTTA
130450 GG
1 GG
130452 AACAGGAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.42, T:0.46
Consensus pattern (8 bp):
GGGTTTTA
Found at i:137286 original size:50 final size:51
Alignment explanation
Indices: 137202--137304 Score: 181
Period size: 50 Copynumber: 2.0 Consensus size: 51
137192 TCCAAATGCC
*
137202 ACCACAATTAAGCATATATATAGTTCTCTAAGATTTCCCATAAGCGAAACAA
1 ACCACAATTAAGCA-ATATATAGTTCTCTAAGATTTCCCATAAGCAAAACAA
137254 ACCACAATTAAGC-ATATATAGTTCTCTAAGATTTCCCATAAGCAAAACAA
1 ACCACAATTAAGCAATATATAGTTCTCTAAGATTTCCCATAAGCAAAACAA
137304 A
1 A
137305 GTAGTACGTA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
50 37 0.74
52 13 0.26
ACGTcount: A:0.44, C:0.21, G:0.09, T:0.26
Consensus pattern (51 bp):
ACCACAATTAAGCAATATATAGTTCTCTAAGATTTCCCATAAGCAAAACAA
Found at i:139238 original size:16 final size:17
Alignment explanation
Indices: 139203--139242 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
139193 TCTTGAGGGT
139203 CTAAAATTCATTGGAAA
1 CTAAAATTCATTGGAAA
*
139220 CTAAAATTCATT-TAAA
1 CTAAAATTCATTGGAAA
139236 CTAAAAT
1 CTAAAAT
139243 ATTTTACAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.33
Consensus pattern (17 bp):
CTAAAATTCATTGGAAA
Found at i:141484 original size:24 final size:24
Alignment explanation
Indices: 141433--141482 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
141423 TTAGTAGAAT
*
141433 AATTGTAAAAATTTATTTCTAAAA
1 AATTGTAAAAATATATTTCTAAAA
141457 AATTGTAAAAGAATATATTT-TAAAA
1 AATTGT-AAA-AATATATTTCTAAAA
141482 A
1 A
141483 TTCTAATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 6 0.26
25 9 0.39
26 8 0.35
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (24 bp):
AATTGTAAAAATATATTTCTAAAA
Found at i:147266 original size:22 final size:22
Alignment explanation
Indices: 147241--147283 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
147231 CCAAACAAAC
147241 AATTCGAAGAGAAAATGATTAT
1 AATTCGAAGAGAAAATGATTAT
*
147263 AATTTGAAGAGAAAATGATTA
1 AATTCGAAGAGAAAATGATTA
147284 CTTTCAGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.02, G:0.19, T:0.28
Consensus pattern (22 bp):
AATTCGAAGAGAAAATGATTAT
Found at i:148047 original size:29 final size:29
Alignment explanation
Indices: 148015--148076 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 29
148005 TTTTGGTTAT
148015 AAAAATATAT-AAAGTAATATAATTTTTTA
1 AAAAATATATAAAAGTAATATAA-TTTTTA
*
148044 AAAAATATATAAAAGTAATCTAATTTTTA
1 AAAAATATATAAAAGTAATATAATTTTTA
148073 AAAA
1 AAAA
148077 TAACACTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 20 0.65
30 11 0.35
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (29 bp):
AAAAATATATAAAAGTAATATAATTTTTA
Found at i:148355 original size:15 final size:15
Alignment explanation
Indices: 148335--148368 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
148325 ATAGTTCAAG
* *
148335 GCTGTGGCGATGCAC
1 GCTGTGGCAATGCAA
148350 GCTGTGGCAATGCAA
1 GCTGTGGCAATGCAA
148365 GCTG
1 GCTG
148369 GAGCCAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.24, G:0.38, T:0.21
Consensus pattern (15 bp):
GCTGTGGCAATGCAA
Found at i:155665 original size:31 final size:31
Alignment explanation
Indices: 155624--155697 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
155614 AAATTTATAT
*
155624 TTTTCGATTGTACCCTTATTT-TTAAAACATA
1 TTTTCAATTGTACCCTT-TTTCTTAAAACATA
155655 TTTTCAATTGTACCCTTTTTCTTAAAACATA
1 TTTTCAATTGTACCCTTTTTCTTAAAACATA
*
155686 TTTCTAAATTGT
1 TTT-TCAATTGT
155698 CATTACTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
30 3 0.08
31 29 0.74
32 7 0.18
ACGTcount: A:0.28, C:0.16, G:0.05, T:0.50
Consensus pattern (31 bp):
TTTTCAATTGTACCCTTTTTCTTAAAACATA
Found at i:160115 original size:31 final size:31
Alignment explanation
Indices: 160077--160170 Score: 145
Period size: 31 Copynumber: 3.0 Consensus size: 31
160067 TTAAGTGCCA
160077 AACGTTGCAAAATCGGCTCAAATCAGTCCCT
1 AACGTTGCAAAATCGGCTCAAATCAGTCCCT
160108 AACGTTGCAAAATCGG-TCCAAATCAGTCCCT
1 AACGTTGCAAAATCGGCT-CAAATCAGTCCCT
* * *
160139 AACGTTTCAAAATCGGCTTAAATAAGTCCCT
1 AACGTTGCAAAATCGGCTCAAATCAGTCCCT
160170 A
1 A
160171 TAGTCAATTT
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
30 1 0.02
31 56 0.97
32 1 0.02
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (31 bp):
AACGTTGCAAAATCGGCTCAAATCAGTCCCT
Found at i:160420 original size:21 final size:21
Alignment explanation
Indices: 160375--160414 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
160365 TCAATTTGGG
**
160375 TTTTGCTATTTACCGCCCCCC
1 TTTTGCTAAATACCGCCCCCC
160396 TTTTGCTAAATACCGCCCC
1 TTTTGCTAAATACCGCCCC
160415 TTTTTTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.40, G:0.10, T:0.35
Consensus pattern (21 bp):
TTTTGCTAAATACCGCCCCCC
Found at i:160730 original size:26 final size:26
Alignment explanation
Indices: 160701--160768 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
160691 TTTTTAGTTT
160701 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAGTATCTA
*
160727 ATTAGTTTAT-TATTAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAGTATCTA
*
160753 ATTAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
160769 AATGAAGGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 1 0.03
26 37 0.97
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAGTATCTA
Found at i:160768 original size:15 final size:13
Alignment explanation
Indices: 160671--160762 Score: 52
Period size: 13 Copynumber: 7.1 Consensus size: 13
160661 TATGATTAGT
*
160671 TTTAATTAGTTAA
1 TTTAATTAGTTTA
* *
160684 TTAAAATT-TTTTA
1 TT-TAATTAGTTTA
160697 GTTT-ATTAGTTTA
1 -TTTAATTAGTTTA
160710 TGTTTAATTAG--TA
1 --TTTAATTAGTTTA
*
160723 TCTAATTAGTTTA
1 TTTAATTAGTTTA
160736 TTATTAATTAG--TA
1 -T-TTAATTAGTTTA
160749 TTTAATTAGTTTA
1 TTTAATTAGTTTA
160762 T
1 T
160763 GATTAAAATG
Statistics
Matches: 61, Mismatches: 7, Indels: 22
0.68 0.08 0.24
Matches are distributed among these distances:
11 16 0.26
12 4 0.07
13 18 0.30
14 11 0.18
15 12 0.20
ACGTcount: A:0.33, C:0.01, G:0.09, T:0.58
Consensus pattern (13 bp):
TTTAATTAGTTTA
Found at i:160812 original size:24 final size:25
Alignment explanation
Indices: 160778--160836 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
160768 AAATGAAGGA
*
160778 AAATGAA-TTTGAAG-ATTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
160801 AAATGAAGTTTGAAGAAGTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
160826 AAATGAAGTTT
1 AAATGAAGTTT
160837 AGGGTTTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 7 0.21
24 7 0.21
25 19 0.58
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.36
Consensus pattern (25 bp):
AAATGAAGTTTGAAGAAGTTGTTAG
Found at i:162318 original size:29 final size:30
Alignment explanation
Indices: 162254--162325 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
162244 TTCTTTACTT
162254 GAAACTTGAAAGAAGTAAAAAAAAAAAATCCA
1 GAAACTTGAAAGAAGT--AAAAAAAAAATCCA
* * *
162286 GAAACTTGAAATAAGT-AAAAAAAATTCCG
1 GAAACTTGAAAGAAGTAAAAAAAAAATCCA
162315 GAAACTTGAAA
1 GAAACTTGAAA
162326 AACTAGGAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 22 0.59
32 15 0.41
ACGTcount: A:0.60, C:0.10, G:0.14, T:0.17
Consensus pattern (30 bp):
GAAACTTGAAAGAAGTAAAAAAAAAATCCA
Found at i:165999 original size:6 final size:6
Alignment explanation
Indices: 165984--166017 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
165974 AAAAAAAAGG
*
165984 GAAAAA GAAAAT GAAAAA -AAAAA GAAAAA GAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAA
166018 TAAAAAGTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (6 bp):
GAAAAA
Found at i:166004 original size:23 final size:22
Alignment explanation
Indices: 165973--166023 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 22
165963 GCATTTAAGT
**
165973 TAAAAAAAAGGGAAAAAGAAAA
1 TAAAAAAAAAAGAAAAAGAAAA
165995 TGAAAAAAAAAAGAAAAAGAAAA
1 T-AAAAAAAAAAGAAAAAGAAAA
166018 TAAAAA
1 TAAAAA
166024 GTGATCTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 6 0.23
23 20 0.77
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (22 bp):
TAAAAAAAAAAGAAAAAGAAAA
Found at i:166005 original size:17 final size:17
Alignment explanation
Indices: 165985--166024 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
165975 AAAAAAAGGG
*
165985 AAAAAGAAAATGAAAAA
1 AAAAAGAAAAAGAAAAA
*
166002 AAAAAGAAAAAGAAAAT
1 AAAAAGAAAAAGAAAAA
166019 AAAAAG
1 AAAAAG
166025 TGATCTTCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.05
Consensus pattern (17 bp):
AAAAAGAAAAAGAAAAA
Done.