Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020319.1 Corchorus olitorius cultivar O-4 contig20352, 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: 28864
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:1310 original size:22 final size:22
Alignment explanation
Indices: 1081--1317 Score: 145
Period size: 22 Copynumber: 10.6 Consensus size: 22
1071 CTCCAACGTA
* **
1081 GAAATATTGATAACCACACTGC
1 GAAATTTTGATAACCACACTAT
* * * *
1103 GAAAATTTGATAACCTCATTGT
1 GAAATTTTGATAACCACACTAT
* * *
1125 GAAATTTCGATAACCTCCCTAT
1 GAAATTTTGATAACCACACTAT
* * * * *
1147 AAAAATTTGATAACCATAATGT
1 GAAATTTTGATAACCACACTAT
* *
1169 GAAATTTTGATAACCATACTGT
1 GAAATTTTGATAACCACACTAT
* * *
1191 GAAGTTTTGATAACCACACAAC
1 GAAATTTTGATAACCACACTAT
* *
1213 GAAGTTTTGATAACCTCATTGTCTAT
1 GAAATTTTGATAACCACA----CTAT
* *
1239 GAAATTTTGATAATCACATTAT
1 GAAATTTTGATAACCACACTAT
* * * *
1261 -AAA-ATTGGTAATCGCACTAT
1 GAAATTTTGATAACCACACTAT
*
1281 GAAAATTTTGATAACCACACCAT
1 G-AAATTTTGATAACCACACTAT
*
1304 GAAATTTCGATAAC
1 GAAATTTTGATAAC
1318 TTCCCTATAA
Statistics
Matches: 165, Mismatches: 43, Indels: 14
0.74 0.19 0.06
Matches are distributed among these distances:
20 13 0.08
21 3 0.02
22 119 0.72
23 13 0.08
26 17 0.10
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (22 bp):
GAAATTTTGATAACCACACTAT
Found at i:1404 original size:22 final size:22
Alignment explanation
Indices: 1103--1692 Score: 118
Period size: 22 Copynumber: 26.4 Consensus size: 22
1093 ACCACACTGC
* ** *
1103 GAAAATTTGATAACCTCATTGT
1 GAAATTTTGATAACCTCCCTAT
*
1125 GAAATTTCGATAACCTCCCTAT
1 GAAATTTTGATAACCTCCCTAT
* * ** *
1147 AAAAATTTGATAACCAT-AATGT
1 GAAATTTTGATAACC-TCCCTAT
* *
1169 GAAATTTTGATAACCAT-ACTGT
1 GAAATTTTGATAACC-TCCCTAT
* * * * *
1191 GAAGTTTTGATAACCACACAAC
1 GAAATTTTGATAACCTCCCTAT
* *
1213 GAAGTTTTGATAACCTCATTGTCTAT
1 GAAATTTTGATAACCTC----CCTAT
* * **
1239 GAAATTTTGATAATCACATTAT
1 GAAATTTTGATAACCTCCCTAT
* * * * *
1261 -AAA-ATTGGTAATCGCACTAT
1 GAAATTTTGATAACCTCCCTAT
*
1281 GAAAATTTTGATAACCACACC-AT
1 G-AAATTTTGATAACCTC-CCTAT
* *
1304 GAAATTTCGATAACTTCCCTATAAGAAT
1 GAAATTTTGATAACCTCCC--T----AT
* ** **
1332 GAAATTGTGATATTCTCTATAT
1 GAAATTTTGATAACCTCCCTAT
*
1354 GTAATTTTGATAACCTCTCC-AT
1 GAAATTTTGATAACCTC-CCTAT
*
1376 -AATATTTTCATAACCTCCCTAT
1 GAA-ATTTTGATAACCTCCCTAT
* *
1398 GAAATTTTGTTAACCAT-CCTAG
1 GAAATTTTGATAACC-TCCCTAT
* *
1420 GAAATTTTGATAA------GAA
1 GAAATTTTGATAACCTCCCTAT
*
1436 CAAATTTTGATAACCTCCCTCCCTAT
1 GAAATTTTGATAA----CCTCCCTAT
* * *
1462 GAAATTTTGTTAACGT-TCTAAT
1 GAAATTTTGATAACCTCCCT-AT
* * * *
1484 -TAATTTTGATAATCACACTAT
1 GAAATTTTGATAACCTCCCTAT
* ** * * *
1505 AAAATTTCAATAATCTTCGTAT
1 GAAATTTTGATAACCTCCCTAT
** * *
1527 GAAATTTTGATAATTTCCATAA
1 GAAATTTTGATAACCTCCCTAT
* ***
1549 GAGATTTTGATAACCTTTTTTTTAT
1 GAAATTTTGATAACC---TCCCTAT
* **
1574 GAAATTTTGGTAACCTCTGTAT
1 GAAATTTTGATAACCTCCCTAT
* * *
1596 GAAATTTTGATAA-TTACACTAC
1 GAAATTTTGATAACCT-CCCTAT
* *
1618 GAAGTTTTGATAACCTCCATAT
1 GAAATTTTGATAACCTCCCTAT
* *
1640 GAAATTTTGGTAA-CTACACTAT
1 GAAATTTTGATAACCT-CCCTAT
* *
1662 GAAATTTTAATAACCTTCCTAT
1 GAAATTTTGATAACCTCCCTAT
*
1684 GTAATTTTG
1 GAAATTTTG
1693 GTTTGATTGT
Statistics
Matches: 407, Mismatches: 119, Indels: 84
0.67 0.20 0.14
Matches are distributed among these distances:
16 13 0.03
20 13 0.03
21 25 0.06
22 278 0.68
23 18 0.04
24 1 0.00
25 16 0.04
26 29 0.07
28 14 0.03
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (22 bp):
GAAATTTTGATAACCTCCCTAT
Found at i:1693 original size:44 final size:43
Alignment explanation
Indices: 1571--1694 Score: 149
Period size: 44 Copynumber: 2.8 Consensus size: 43
1561 ACCTTTTTTT
* * * *
1571 TATGAAATTTTGGTAACCTCTGTATGAAATTTTGATAATTACAC
1 TATGAAATTTTGATAACCTC-CTATGAAATTTTGGTAACTACAC
* *
1615 TACGAAGTTTTGATAACCTCCATATGAAATTTTGGTAACTACAC
1 TATGAAATTTTGATAACCTCC-TATGAAATTTTGGTAACTACAC
* *
1659 TATGAAATTTTAATAACCTTCCTATGTAATTTTGGT
1 TATGAAATTTTGATAACC-TCCTATGAAATTTTGGT
1695 TTGATTGTCA
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
44 65 0.96
45 3 0.04
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (43 bp):
TATGAAATTTTGATAACCTCCTATGAAATTTTGGTAACTACAC
Found at i:3084 original size:166 final size:166
Alignment explanation
Indices: 2904--3305 Score: 380
Period size: 171 Copynumber: 2.4 Consensus size: 166
2894 CAAAATTTTG
* * * *
2904 AAGTTGAGGTTTTAGGCTTTGAAGAAAAATTTGTTTGGCAAGCCACTTTCCAATGAGCTCTATTG
1 AAGTTGAAGTTTTAGGCTTTGAAGAAAAATTTATTTGGCAAGCCACTTTCCAATAAGCTCTATTC
* * *
2969 ACTCTGAAACATGACATATGAGTGATGGTTACACAAATAATGCA-TTCAGAATTAACATTTT-CT
66 ACTCTGAAACATAACATATGAGCGATGGTTACACAAATAATGCACTT-AGAATGAACATTTTCCT
*
3032 CAAGAACAACGTTCT-GCGCACAAACACGCAAAATCGTA
130 -AAGAACAACGTT-TGGCGCACAAACACGCAAAATCGGA
* * * * * *
3070 AAGTTTAAGTTTTAGGTTTTGAAGAAAGATTTTTTTTTTTTGGCAAACCCACTTTCCAATTAGCT
1 AAGTTGAAGTTTTAGGCTTTGAAGAAA-A----ATTTATTTGGC-AAGCCACTTTCCAATAAGCT
* * * * * * *
3135 -TACTCACTCTGAAACATAACATTTGAGCGTTGGTTCCACAAATAATGTACTTGGAATGAGCATT
60 CTATTCACTCTGAAACATAACATATGAGCGATGGTTACACAAATAATGCACTTAGAATGAACATT
* ** * *
3199 TTCCTAAGAACAACGTTTGGCGCTCAAACGTGCTAAATCGGG
125 TTCCTAAGAACAACGTTTGGCGCACAAACACGCAAAATCGGA
* ** ** * * *
3241 AAGTTGAGGTTTTAGGCTTTTCAGAAAGCTTTATTTGGCGAGTCCACTTTACAATAAACTCTATT
1 AAGTTGAAGTTTTAGGCTTTGAAGAAAAATTTATTTGGCAAG-CCACTTTCCAATAAGCTCTATT
3306 TAAATGTAAT
Statistics
Matches: 187, Mismatches: 38, Indels: 21
0.76 0.15 0.09
Matches are distributed among these distances:
165 1 0.01
166 47 0.25
167 4 0.02
170 1 0.01
171 112 0.60
172 22 0.12
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (166 bp):
AAGTTGAAGTTTTAGGCTTTGAAGAAAAATTTATTTGGCAAGCCACTTTCCAATAAGCTCTATTC
ACTCTGAAACATAACATATGAGCGATGGTTACACAAATAATGCACTTAGAATGAACATTTTCCTA
AGAACAACGTTTGGCGCACAAACACGCAAAATCGGA
Found at i:3255 original size:171 final size:166
Alignment explanation
Indices: 2903--3261 Score: 384
Period size: 171 Copynumber: 2.1 Consensus size: 166
2893 ACAAAATTTT
* * *
2903 GAAGTTGAGGTTTTAGGCTTTGAAGAAAAATTTGTTTGGCAAGCCACTTTCCAATGAGCTCTATT
1 GAAGTTGAGGTTTTAGGTTTTGAAGAAAAATTTGTTTGGCAACCCACTTTCCAATGAGCTCTACT
* * * *
2968 GACTCTGAAACATGACATATGAGTGATGGTTACACAAATAATGCATTCAGAATTAACATTTTCTC
66 CACTCTGAAACATAACATATGAGCGATGGTTACACAAATAATGCATTCAGAATGAACATTTTCTC
*
3033 AAGAACAACGTTCTGCGCACAAACACGCAAAATCGT
131 AAGAACAACGTTCTGCGCACAAACACGCAAAATCGG
* * * * * *
3069 AAAGTTTAAGTTTTAGGTTTTGAAGAAAGATTTTTTTTTTTTGGCAAACCCACTTTCCAATTAGC
1 GAAGTTGAGGTTTTAGGTTTTGAAGAAA-A----ATTTGTTTGGC-AACCCACTTTCCAATGAGC
* * * * * *
3134 T-TACTCACTCTGAAACATAACATTTGAGCGTTGGTTCCACAAATAATGTACTT-GGAATGAGCA
60 TCTACTCACTCTGAAACATAACATATGAGCGATGGTTACACAAATAATGCA-TTCAGAATGAACA
* ** *
3197 TTTTC-CTAAGAACAACGTT-TGGCGCTCAAACGTGCTAAATCGG
124 TTTTCTC-AAGAACAACGTTCT-GCGCACAAACACGCAAAATCGG
3240 GAAGTTGAGGTTTTAGGCTTTT
1 GAAGTTGAGGTTTTAGG-TTTT
3262 CAGAAAGCTT
Statistics
Matches: 156, Mismatches: 27, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
166 24 0.15
167 1 0.01
170 2 0.01
171 105 0.67
172 24 0.15
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (166 bp):
GAAGTTGAGGTTTTAGGTTTTGAAGAAAAATTTGTTTGGCAACCCACTTTCCAATGAGCTCTACT
CACTCTGAAACATAACATATGAGCGATGGTTACACAAATAATGCATTCAGAATGAACATTTTCTC
AAGAACAACGTTCTGCGCACAAACACGCAAAATCGG
Found at i:3460 original size:22 final size:21
Alignment explanation
Indices: 3393--3636 Score: 116
Period size: 22 Copynumber: 11.1 Consensus size: 21
3383 TTCCAATGTA
* *
3393 GAAATATTGATAACCACATTTT
1 GAAAT-TTGATAACCACACTAT
*
3415 GCAAATTTGATAACCTCA-TAT
1 G-AAATTTGATAACCACACTAT
* * *
3436 GAAATTTCGATAAACTCCCTAT
1 GAAATTT-GATAACCACACTAT
*
3458 GAAAATTTGATAACCACACTGT
1 G-AAATTTGATAACCACACTAT
*
3480 GAAATTTGGGTAACCACACTAT
1 GAAATTT-GATAACCACACTAT
* * * *
3502 GAAATTTCGATAAGCTCAGTGT
1 GAAATTT-GATAACCACACTAT
* **
3524 GAAATTTTGGTAATCTGC-CTAT
1 GAAA-TTTGATAA-CCACACTAT
* * *
3546 AAAATTTTAATAATCACACTAAAT
1 GAAA-TTTGATAACCACACT--AT
* * **
3570 -AAAATTGGTAACTGCACTAT
1 GAAATTTGATAACCACACTAT
*
3590 GAAAATTTTGATAACCACACCAT
1 G-AAA-TTTGATAACCACACTAT
* *
3613 GAAATTTCGATAACCTCTCTAT
1 GAAATTT-GATAACCACACTAT
3635 GA
1 GA
3637 GAATGAAACT
Statistics
Matches: 166, Mismatches: 42, Indels: 28
0.70 0.18 0.12
Matches are distributed among these distances:
20 8 0.05
21 21 0.13
22 105 0.63
23 30 0.18
24 2 0.01
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (21 bp):
GAAATTTGATAACCACACTAT
Found at i:3502 original size:44 final size:43
Alignment explanation
Indices: 3393--3619 Score: 131
Period size: 44 Copynumber: 5.2 Consensus size: 43
3383 TTCCAATGTA
* * * * *
3393 GAAATATTGATAACCACATTTTGCAAATTTGATAACCTCA-TAT
1 GAAAT-TTGGTAACCACACTATGAAAATTTGATAACCACACTAT
* * * * *
3436 GAAATTTCGATAAACTCCCTATGAAAATTTGATAACCACACTGT
1 GAAATTT-GGTAACCACACTATGAAAATTTGATAACCACACTAT
* * * *
3480 GAAATTTGGGTAACCACACTATG-AAATTTCGATAAGCTCAGTGT
1 GAAATTT-GGTAACCACACTATGAAAATTT-GATAACCACACTAT
** * *
3524 GAAATTTTGGTAATCTGC-CTAT-AAAATTTTAATAATCACACTAAAT
1 GAAA-TTTGGTAA-CCACACTATGAAAA-TTTGATAACCACACT--AT
* ** *
3570 -AAAATTGGTAACTGCACTATGAAAATTTTGATAACCACACCAT
1 GAAATTTGGTAACCACACTATGAAAA-TTTGATAACCACACTAT
3613 GAAATTT
1 GAAATTT
3620 CGATAACCTC
Statistics
Matches: 144, Mismatches: 28, Indels: 23
0.74 0.14 0.12
Matches are distributed among these distances:
42 2 0.01
43 42 0.29
44 71 0.49
45 28 0.19
46 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.32
Consensus pattern (43 bp):
GAAATTTGGTAACCACACTATGAAAATTTGATAACCACACTAT
Found at i:3777 original size:22 final size:22
Alignment explanation
Indices: 3752--3875 Score: 110
Period size: 22 Copynumber: 5.6 Consensus size: 22
3742 CCTCCCTCCC
* *
3752 TATGAAATTTTGGTAACCTCTG
1 TATGAAATTTTGATAACCTCTA
3774 TATGAAATTTTGATAA-CTAC-A
1 TATGAAATTTTGATAACCT-CTA
*
3795 CTATGAAGTTTTGATAACCTCTA
1 -TATGAAATTTTGATAACCTCTA
*
3818 TATGAAATTTTGATAACCAC-A
1 TATGAAATTTTGATAACCTCTA
** * * *
3839 CTACCAAATTTTGATAATCTTTC
1 -TATGAAATTTTGATAACCTCTA
*
3862 TATGTAATTTTGAT
1 TATGAAATTTTGAT
3876 TTGATAATCA
Statistics
Matches: 82, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
21 3 0.04
22 76 0.93
23 3 0.04
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCTA
Found at i:3813 original size:44 final size:44
Alignment explanation
Indices: 3420--3875 Score: 169
Period size: 44 Copynumber: 10.1 Consensus size: 44
3410 ATTTTGCAAA
* * * ** *
3420 TTTGATAACCTCA-TATGAAATTTCGATAAACTCCCTATGAAAA
1 TTTGATAACCACACTATGAAATTTTGATAACCTCTATATGAAAT
* * * *
3463 TTTGATAACCACACTGTGAAATTTGGGTAACCAC-ACTATGAAAT
1 TTTGATAACCACACTATGAAATTTTGATAACCTCTA-TATGAAAT
* * * * * * *
3507 TTCGATAAGCTCAGTGTGAAATTTTGGTAATCTGCCTATA--AAAT
1 TTTGATAACCACACTATGAAATTTTGATAACCT--CTATATGAAAT
* * * *
3551 TTTAATAATCACACTAAAT-AAA-ATTGGTAA-CTGC-ACTATGAAAAT
1 TTTGATAACCACACT--ATGAAATTTTGATAACCT-CTA-TATG-AAAT
* * *
3596 TTTGATAACCACACCATGAAATTTCGATAACCTCTCTATGAGAATGAAAC
1 TTTGATAACCACACTATGAAATTTTGATAA-C-CTCTAT----ATGAAAT
* * * * * *
3646 TGTGATATCCTCTCTATG-TATTTTCGATAACCTCTCA-ATAAAAT
1 TTTGATAACCACACTATGAAATTTT-GATAACCTCT-ATATGAAAT
** * * * * * * * *
3690 GATCATAACCTCCCTATAAAATTTTGTTGACCTCTAGCA-CAAAT
1 TTTGATAACCACACTATGAAATTTTGATAACCTCTA-TATGAAAT
* * * * *
3734 TTTGGTAACCTCCCTCCCTATGAAATTTTGGTAACCTCTGTATGAAAT
1 TTTGATAA----CCACACTATGAAATTTTGATAACCTCTATATGAAAT
* *
3782 TTTGATAACTACACTATGAAGTTTTGATAACCTCTATATGAAAT
1 TTTGATAACCACACTATGAAATTTTGATAACCTCTATATGAAAT
** * * * *
3826 TTTGATAACCACACTACCAAATTTTGATAATCTTTCTATGTAAT
1 TTTGATAACCACACTATGAAATTTTGATAACCTCTATATGAAAT
3870 TTTGAT
1 TTTGAT
3876 TTGATAATCA
Statistics
Matches: 308, Mismatches: 74, Indels: 61
0.70 0.17 0.14
Matches are distributed among these distances:
41 1 0.00
42 3 0.01
43 17 0.06
44 177 0.57
45 30 0.10
46 4 0.01
47 4 0.01
48 42 0.14
49 6 0.02
50 21 0.07
51 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (44 bp):
TTTGATAACCACACTATGAAATTTTGATAACCTCTATATGAAAT
Found at i:5635 original size:26 final size:26
Alignment explanation
Indices: 5591--5648 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
5581 TTCGTAATAG
5591 TAAGAT-ATATAGTAGTAAGATAAAA
1 TAAGATAATATAGTAGTAAGATAAAA
*
5616 TAAGATAATA-AGATAGTAAGATAAGA
1 TAAGATAATATAG-TAGTAAGATAAAA
5642 TAAGATA
1 TAAGATA
5649 TAATATATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 8 0.27
26 22 0.73
ACGTcount: A:0.57, C:0.00, G:0.17, T:0.26
Consensus pattern (26 bp):
TAAGATAATATAGTAGTAAGATAAAA
Found at i:22799 original size:16 final size:16
Alignment explanation
Indices: 22761--22799 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
22751 AATAAGCAAC
*
22761 TGAAAAATAAATAAAA
1 TGAAAAAGAAATAAAA
22777 T-AGAAAAGAAATAAAA
1 TGA-AAAAGAAATAAAA
22793 TGAAAAA
1 TGAAAAA
22800 AGTTAGACCT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
15 1 0.05
16 18 0.90
17 1 0.05
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.15
Consensus pattern (16 bp):
TGAAAAAGAAATAAAA
Found at i:24675 original size:57 final size:57
Alignment explanation
Indices: 24592--24707 Score: 205
Period size: 57 Copynumber: 2.0 Consensus size: 57
24582 TTTATTTTGT
*
24592 AGAATAATTAAGTAGAAATAGGGGGGATAAGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAAATAGAGGGGATAAGATTTATTATAACATTTATTGTGTGAA
* *
24649 AGAATAATTAAGTAGAGATAGAGGGGATATGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAAATAGAGGGGATAAGATTTATTATAACATTTATTGTGTGAA
24706 AG
1 AG
24708 GAAACAGATA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.41, C:0.02, G:0.23, T:0.34
Consensus pattern (57 bp):
AGAATAATTAAGTAGAAATAGAGGGGATAAGATTTATTATAACATTTATTGTGTGAA
Found at i:26157 original size:109 final size:109
Alignment explanation
Indices: 25966--26183 Score: 382
Period size: 109 Copynumber: 2.0 Consensus size: 109
25956 TAGTCATTTT
* * *
25966 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGGTATGTGTGCTT
1 GGTGCTTGTAGTTTTCTTTAAATCCAATAATTCATTGCACTTTGTATTGTTTGGTATATGTGCTT
26031 ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA
66 ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA
*
26075 GGTGCTTGTAGTTTTCTTTAAATCCAATAATTCATTGCATTTTGTATTGTTTGGTATATGTGCTT
1 GGTGCTTGTAGTTTTCTTTAAATCCAATAATTCATTGCACTTTGTATTGTTTGGTATATGTGCTT
* *
26140 ATTTAATAGGTTCAATTGAATAAACCACACAATTAATAGTAATA
66 ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA
26184 TATATAATAG
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
109 103 1.00
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (109 bp):
GGTGCTTGTAGTTTTCTTTAAATCCAATAATTCATTGCACTTTGTATTGTTTGGTATATGTGCTT
ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA
Found at i:27713 original size:61 final size:61
Alignment explanation
Indices: 27618--27764 Score: 163
Period size: 61 Copynumber: 2.4 Consensus size: 61
27608 TTTTTTCCAT
* * * * * * ** * *
27618 CGTTTGCGGAAATGCTTAAATAAGGGCTCAAAGAAAAAAAAATGCTTGAATCATGGCCCAA
1 CGTTTGTGAAAATGCTCAAATAAGTGCCCAAAGAAAAAAAAAAGCTCAAATAAGGGCCCAA
*
27679 CGTTTGTGAAAATGCTCAAATAAGTGCCCAAAGAAAAAAAAAAGCTCAAATAAGGGTCCAA
1 CGTTTGTGAAAATGCTCAAATAAGTGCCCAAAGAAAAAAAAAAGCTCAAATAAGGGCCCAA
27740 C-TTT-TAGAAAATTGCTCAAATAAGT
1 CGTTTGT-GAAAA-TGCTCAAATAAGT
27765 CCTTGTTGTC
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
59 1 0.01
60 8 0.11
61 64 0.88
ACGTcount: A:0.44, C:0.16, G:0.18, T:0.22
Consensus pattern (61 bp):
CGTTTGTGAAAATGCTCAAATAAGTGCCCAAAGAAAAAAAAAAGCTCAAATAAGGGCCCAA
Done.