Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010603.1 Corchorus capsularis cultivar CVL-1 contig10624, 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: 81184
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:745 original size:22 final size:22
Alignment explanation
Indices: 719--765 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
709 ATTTATTCAT
719 TATTAATTAACTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
*
741 TATTAATTAGCTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
763 TAT
1 TAT
766 AATATAATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (22 bp):
TATTAATTAACTATTAATTAGA
Found at i:761 original size:11 final size:11
Alignment explanation
Indices: 719--761 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
709 ATTTATTCAT
*
719 TATTAATTAAC
1 TATTAATTAGC
*
730 TATTAATTAGA
1 TATTAATTAGC
741 TATTAATTAGC
1 TATTAATTAGC
752 TATTAATTAG
1 TATTAATTAG
762 ATATAATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (11 bp):
TATTAATTAGC
Found at i:1164 original size:31 final size:32
Alignment explanation
Indices: 1128--1194 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 32
1118 TTTAGTAATG
*
1128 ACAATTTAGAAATATGTTTTTAAAAA-AA-GGT
1 ACAATTTAGAAATAT-ATTTTAAAAATAAGGGT
*
1159 ACAA-TTGGAAATATATTTTAAAAATAAGGGT
1 ACAATTTAGAAATATATTTTAAAAATAAGGGT
1190 ACAAT
1 ACAAT
1195 CAGAAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 9 0.29
30 11 0.35
31 11 0.35
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.33
Consensus pattern (32 bp):
ACAATTTAGAAATATATTTTAAAAATAAGGGT
Found at i:1171 original size:30 final size:31
Alignment explanation
Indices: 1136--1194 Score: 86
Period size: 29 Copynumber: 1.9 Consensus size: 31
1126 TGACAATTTA
*
1136 GAAATATGTTTTTAAAAA-AA-GGTACAATTG
1 GAAATAT-ATTTTAAAAATAAGGGTACAATTG
1166 GAAATATATTTTAAAAATAAGGGTACAAT
1 GAAATATATTTTAAAAATAAGGGTACAAT
1195 CAGAAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 9 0.35
30 9 0.35
31 8 0.31
ACGTcount: A:0.49, C:0.03, G:0.15, T:0.32
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAGGGTACAATTG
Found at i:3562 original size:11 final size:11
Alignment explanation
Indices: 3530--3564 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
3520 TTTTTCTGTT
*
3530 TTTTATTTTTA
1 TTTTATTTTTG
*
3541 TTTCATTTTTG
1 TTTTATTTTTG
3552 TTTTATTTTTG
1 TTTTATTTTTG
3563 TT
1 TT
3565 GCGCTGTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.11, C:0.03, G:0.06, T:0.80
Consensus pattern (11 bp):
TTTTATTTTTG
Found at i:4492 original size:31 final size:31
Alignment explanation
Indices: 4454--4557 Score: 108
Period size: 31 Copynumber: 3.4 Consensus size: 31
4444 TTAATTTGGC
4454 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
* * * **
4485 CAAATAAGGGCCCGATC-TT-T-TAATTTGGC-
1 CAAATAAGGG-CCTAACGTTATCGAAAAT-GCT
*
4514 CAAATAAGGGCCTAACGTTATCGAAAATACT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
4545 CAAATAAGGGCCT
1 CAAATAAGGGCCT
4558 GGTTTCAGTT
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
28 4 0.07
29 15 0.27
30 5 0.09
31 28 0.50
32 4 0.07
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCT
Found at i:4554 original size:60 final size:60
Alignment explanation
Indices: 4394--4556 Score: 247
Period size: 60 Copynumber: 2.7 Consensus size: 60
4384 GGTAATTGTT
* * * ** *
4394 CAAATAAGGGCCTAACGTT-TGCCATAATGTTCAAATAAGGATCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTAT-CGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
4454 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
*
4514 CAAATAAGGGCCTAACGTTATCGAAAATACTCAAATAAGGGCC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCC
4557 TGGTTTCAGT
Statistics
Matches: 95, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
60 94 0.99
61 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
Found at i:4619 original size:31 final size:30
Alignment explanation
Indices: 4584--4687 Score: 90
Period size: 31 Copynumber: 3.5 Consensus size: 30
4574 ACGTATGAGA
4584 TAGGCCCTTATTTGAGCATTATGGCAAATGT
1 TAGGCCCTTATTTGAGCATTATGGCAAA-GT
* * *
4615 TAGGCCCTTATTTG-GCCA-AAT-TCAAAGA
1 TAGGCCCTTATTTGAG-CATTATGGCAAAGT
* *
4643 TCGGACCCTTATTTGAGCATTTTGGCAAACGT
1 TAGG-CCCTTATTTGAGCATTATGGCAAA-GT
*
4675 TAGG-CTTTATTTG
1 TAGGCCCTTATTTG
4688 GCCAAATTAA
Statistics
Matches: 57, Mismatches: 10, Indels: 13
0.71 0.12 0.16
Matches are distributed among these distances:
28 4 0.07
29 16 0.28
30 13 0.23
31 20 0.35
32 4 0.07
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (30 bp):
TAGGCCCTTATTTGAGCATTATGGCAAAGT
Found at i:4755 original size:59 final size:60
Alignment explanation
Indices: 4588--4747 Score: 232
Period size: 59 Copynumber: 2.7 Consensus size: 60
4578 ATGAGATAGG
* * * *
4588 CCCTTATTTGAGCATTATGGCAAATGTTAGGCCCTTATTTGGCCAAATTCAAAGATCGGA
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
* *
4648 CCCTTATTTGAGCATTTTGGCAAACGTTAGG-CTTTATTTGGCCAAATTAAAATATCAGA
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
* * *
4707 CCCTTATTTGAACATTTTCGCAAACATTAGGCCCTTATTTG
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
4748 AGCAATTAGC
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
59 52 0.58
60 37 0.42
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
Found at i:5965 original size:13 final size:13
Alignment explanation
Indices: 5947--5972 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5937 ATTTATAGGC
5947 AACGCATATTTCT
1 AACGCATATTTCT
5960 AACGCATATTTCT
1 AACGCATATTTCT
5973 TCTGCTGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
AACGCATATTTCT
Found at i:8520 original size:91 final size:91
Alignment explanation
Indices: 8365--8541 Score: 291
Period size: 91 Copynumber: 1.9 Consensus size: 91
8355 AATGTTTGGA
* * *
8365 ATGACAGATGGCGAGTGCGGCTCCAATCCATTACTATATGTGTCCGATGATTTCCAATGCAGCTT
1 ATGACAGATGGCGAGTGCGGCTCCAATCCATTACTATATGTGTCCAATGACTTCCAATACAGCTT
*
8430 TGGATTGTTGACATGTGTATAATTAT
66 TGCATTGTTGACATGTGTATAATTAT
* * *
8456 ATGACAGATGGCGGGTGTGGCTCCAGTCCATTACTATATGTGTCCAATGACTTCCAATACAGCTT
1 ATGACAGATGGCGAGTGCGGCTCCAATCCATTACTATATGTGTCCAATGACTTCCAATACAGCTT
8521 TGCATTGTTGACATGTGTATA
66 TGCATTGTTGACATGTGTATA
8542 TAATTGGTTT
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 79 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (91 bp):
ATGACAGATGGCGAGTGCGGCTCCAATCCATTACTATATGTGTCCAATGACTTCCAATACAGCTT
TGCATTGTTGACATGTGTATAATTAT
Found at i:9580 original size:32 final size:33
Alignment explanation
Indices: 9544--9608 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 33
9534 CCTCACTCAA
*
9544 CAAAATGTAAC-AAAAAATACCAGGAAAATCAG
1 CAAAATGTAACAAAAAAATACCAGCAAAATCAG
*
9576 CAAAATTTAACAAAAAAAATACCAGCAAAATCA
1 CAAAATGTAAC-AAAAAAATACCAGCAAAATCA
9609 ACTCAAACCC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 10 0.34
34 19 0.66
ACGTcount: A:0.62, C:0.17, G:0.08, T:0.14
Consensus pattern (33 bp):
CAAAATGTAACAAAAAAATACCAGCAAAATCAG
Found at i:9766 original size:85 final size:85
Alignment explanation
Indices: 9667--9826 Score: 311
Period size: 85 Copynumber: 1.9 Consensus size: 85
9657 AAACCCGTAG
*
9667 CAAAAAATTCCAACAAAATCAAATGAAAAAATAACAAACAAATTCCTAGATTGTTGCTCTTTCCA
1 CAAAAAATTCCAACAAAATCAAATGAAAAAATAACAAACAAATTCCAAGATTGTTGCTCTTTCCA
9732 GTGAAAATATCCAATAGCAA
66 GTGAAAATATCCAATAGCAA
9752 CAAAAAATTCCAACAAAATCAAATGAAAAAATAACAAACAAATTCCAAGATTGTTGCTCTTTCCA
1 CAAAAAATTCCAACAAAATCAAATGAAAAAATAACAAACAAATTCCAAGATTGTTGCTCTTTCCA
9817 GTGAAAATAT
66 GTGAAAATAT
9827 TTGAGTTATT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 74 1.00
ACGTcount: A:0.50, C:0.18, G:0.08, T:0.24
Consensus pattern (85 bp):
CAAAAAATTCCAACAAAATCAAATGAAAAAATAACAAACAAATTCCAAGATTGTTGCTCTTTCCA
GTGAAAATATCCAATAGCAA
Found at i:21461 original size:151 final size:151
Alignment explanation
Indices: 21187--21477 Score: 573
Period size: 151 Copynumber: 1.9 Consensus size: 151
21177 ACTATGAGCC
21187 TTTTAGCATTTTTAGATTGTAGTAGGTTTCTATGTTTGCAATGTAGAGGATTGCAGCCTTTACGT
1 TTTTAGCATTTTTAGATTGTAGTAGGTTTCTATGTTTGCAATGTAGAGGATTGCAGCCTTTACGT
21252 GATCCCCAATCTGATATTGTACTATATATAAACGTTGCAACAGGAAAGAAATCAAGAAGAATGTT
66 GATCCCCAATCTGATATTGTACTATATATAAACGTTGCAACAGGAAAGAAATCAAGAAGAATGTT
21317 AAGGAAAAAAGCCTTTTAGCA
131 AAGGAAAAAAGCCTTTTAGCA
21338 TTTTAGCATTTTTAGATTGTAGTAGGTTTCTATGTTTGCAATGTAGAGGATTGCAGCCTTTACGT
1 TTTTAGCATTTTTAGATTGTAGTAGGTTTCTATGTTTGCAATGTAGAGGATTGCAGCCTTTACGT
*
21403 GATCCCCAATCTGATATTGTATTATATATAAACGTTGCAACAGGAAAGAAATCAAGAAGAATGTT
66 GATCCCCAATCTGATATTGTACTATATATAAACGTTGCAACAGGAAAGAAATCAAGAAGAATGTT
21468 AAGGAAAAAA
131 AAGGAAAAAA
21478 ATCTAGTTTC
Statistics
Matches: 139, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
151 139 1.00
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.33
Consensus pattern (151 bp):
TTTTAGCATTTTTAGATTGTAGTAGGTTTCTATGTTTGCAATGTAGAGGATTGCAGCCTTTACGT
GATCCCCAATCTGATATTGTACTATATATAAACGTTGCAACAGGAAAGAAATCAAGAAGAATGTT
AAGGAAAAAAGCCTTTTAGCA
Found at i:24005 original size:2 final size:2
Alignment explanation
Indices: 23956--23988 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
23946 TATGCTTTAT
23956 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
23989 GGAGAATGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28480 original size:2 final size:2
Alignment explanation
Indices: 28473--28511 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
28463 ATTTCTTTTA
28473 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
28512 ATCATTAGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:32039 original size:30 final size:30
Alignment explanation
Indices: 32005--32090 Score: 163
Period size: 30 Copynumber: 2.9 Consensus size: 30
31995 CAGCTTTATC
*
32005 TTCTGCAATTCGCTCTTTACAATCATTCTT
1 TTCTGCAATTCGCTCCTTACAATCATTCTT
32035 TTCTGCAATTCGCTCCTTACAATCATTCTT
1 TTCTGCAATTCGCTCCTTACAATCATTCTT
32065 TTCTGCAATTCGCTCCTTACAATCAT
1 TTCTGCAATTCGCTCCTTACAATCAT
32091 AGAAATATAG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 55 1.00
ACGTcount: A:0.21, C:0.29, G:0.07, T:0.43
Consensus pattern (30 bp):
TTCTGCAATTCGCTCCTTACAATCATTCTT
Found at i:40945 original size:3 final size:3
Alignment explanation
Indices: 40937--40977 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
40927 GAGTTGTGTG
40937 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
40978 AACCACCGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:41011 original size:27 final size:27
Alignment explanation
Indices: 40962--41014 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
40952 ATTATTATTA
* *
40962 TTATTATTATTATTATAACCACCGTAG
1 TTATGATTATTATAATAACCACCGTAG
* *
40989 TTATGATTATTATAATCATCACCGTA
1 TTATGATTATTATAATAACCACCGTA
41015 CTTCAGTACC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (27 bp):
TTATGATTATTATAATAACCACCGTAG
Found at i:50490 original size:30 final size:32
Alignment explanation
Indices: 50456--50515 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
50446 TAAAAAAAGA
50456 GAAGA-AAGA-CAAGGCAAGAAGAAGAAGAAG
1 GAAGAGAAGATCAAGGCAAGAAGAAGAAGAAG
*
50486 GAAGATGATGATCAAGGCAAGAAGAAGAAG
1 GAAGA-GAAGATCAAGGCAAGAAGAAGAAG
50516 GAAGATGATG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 5 0.19
32 3 0.12
33 18 0.69
ACGTcount: A:0.55, C:0.07, G:0.33, T:0.05
Consensus pattern (32 bp):
GAAGAGAAGATCAAGGCAAGAAGAAGAAGAAG
Found at i:51134 original size:27 final size:28
Alignment explanation
Indices: 51079--51135 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
51069 TAATTATTCA
*
51079 TTTTGGGACAAATTGACCCCTTAAGTTT
1 TTTTGGAACAAATTGACCCCTTAAGTTT
*
51107 TTTTGGAACAAATTGGCCCCTTAA-TTT
1 TTTTGGAACAAATTGACCCCTTAAGTTT
51134 TT
1 TT
51136 AAAAACGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.42
Consensus pattern (28 bp):
TTTTGGAACAAATTGACCCCTTAAGTTT
Found at i:51897 original size:31 final size:28
Alignment explanation
Indices: 51828--51899 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
51818 TCTCATTTTT
*
51828 AAAAGTTAAGGGGCCAAATTGTCCCATA
1 AAAAGTTAAGGGGCCAAATTGTCCCAAA
* *
51856 AAAAGTTAAGGGGCCAATTTGTTCCAAA
1 AAAAGTTAAGGGGCCAAATTGTCCCAAA
51884 ATAGATAGTTAAGGGG
1 A-A-A-AGTTAAGGGG
51900 TTAATTTGGG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 26 0.68
29 1 0.03
30 1 0.03
31 10 0.26
ACGTcount: A:0.39, C:0.12, G:0.25, T:0.24
Consensus pattern (28 bp):
AAAAGTTAAGGGGCCAAATTGTCCCAAA
Found at i:51954 original size:23 final size:23
Alignment explanation
Indices: 51919--51962 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
51909 GTATTAAGCC
51919 TTTTTCTTCTGATAATAGTGCGA
1 TTTTTCTTCTGATAATAGTGCGA
* *
51942 TTTTTGTTTTGATAATAGTGC
1 TTTTTCTTCTGATAATAGTGC
51963 ATCTCGAGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.52
Consensus pattern (23 bp):
TTTTTCTTCTGATAATAGTGCGA
Found at i:53509 original size:6 final size:6
Alignment explanation
Indices: 53500--53529 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
53490 AACAAACTCC
53500 CCCTAT CCCTAT CCCTAT CCCTAT CCCTAT
1 CCCTAT CCCTAT CCCTAT CCCTAT CCCTAT
53530 GGTTACTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.50, G:0.00, T:0.33
Consensus pattern (6 bp):
CCCTAT
Found at i:54621 original size:27 final size:28
Alignment explanation
Indices: 54564--54622 Score: 84
Period size: 30 Copynumber: 2.1 Consensus size: 28
54554 GGACCGGCTA
54564 AAGAAGAAGAAGGAAGATGATCAAGGCAAG
1 AAGAAGAAGAAGGAAGATGATCAA-G-AAG
*
54594 AAGAAGAAGAAGGAAGATGATGAA-AAG
1 AAGAAGAAGAAGGAAGATGATCAAGAAG
54621 AA
1 AA
54623 AGTTGGTGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 5 0.18
30 23 0.82
ACGTcount: A:0.58, C:0.03, G:0.32, T:0.07
Consensus pattern (28 bp):
AAGAAGAAGAAGGAAGATGATCAAGAAG
Found at i:72888 original size:37 final size:37
Alignment explanation
Indices: 72847--72918 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 37
72837 CCAAAATAGG
72847 ACGTTGG-AGACAAAGACAAAAAG-CAAAAATAAATACA
1 ACGTTGGAAG-CAAAGAC-AAAAGTCAAAAATAAATACA
*
72884 ACGTTGGAAGCAAAGACAAAAGTCAAAATTAAATA
1 ACGTTGGAAGCAAAGACAAAAGTCAAAAATAAATA
72919 GGACATTAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 5 0.16
37 25 0.78
38 2 0.06
ACGTcount: A:0.57, C:0.12, G:0.17, T:0.14
Consensus pattern (37 bp):
ACGTTGGAAGCAAAGACAAAAGTCAAAAATAAATACA
Found at i:73118 original size:29 final size:30
Alignment explanation
Indices: 73086--73145 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
73076 ATTTATTAAT
*
73086 ATAT-TTTTAAAAAAAGGGTACAATCGAAA
1 ATATGTTTTAAAAAAAGGATACAATCGAAA
73115 ATATGTTTTAAAAAAAGGATACAATCGAAA
1 ATATGTTTTAAAAAAAGGATACAATCGAAA
73145 A
1 A
73146 ACATAAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.53, C:0.07, G:0.13, T:0.27
Consensus pattern (30 bp):
ATATGTTTTAAAAAAAGGATACAATCGAAA
Found at i:74303 original size:21 final size:22
Alignment explanation
Indices: 74249--74304 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 22
74239 CGTACGTTTA
*
74249 AAAATAAATAAATATTTCGCCTT
1 AAAATAAATAAATATTTCACC-T
**
74272 TCAA-AAA-AAATATTTCACC-
1 AAAATAAATAAATATTTCACCT
74291 AAAATAAATAAATA
1 AAAATAAATAAATA
74305 AATAAAATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 6
0.70 0.14 0.16
Matches are distributed among these distances:
19 2 0.08
20 3 0.12
21 16 0.62
22 3 0.12
23 2 0.08
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAATAAATAAATATTTCACCT
Found at i:74989 original size:21 final size:19
Alignment explanation
Indices: 74962--75020 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
74952 CGCTGCTCTA
*
74962 ATAATCTCATCTGTATAGT
1 ATAATCTCATCTGTACAGT
*
74981 ATCTAATCTAATCTGTACAGT
1 A--TAATCTCATCTGTACAGT
*
75002 ATAATCTCATTTGTACAGT
1 ATAATCTCATCTGTACAGT
75021 TGCTAAACAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (19 bp):
ATAATCTCATCTGTACAGT
Found at i:76342 original size:16 final size:16
Alignment explanation
Indices: 76321--76351 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
76311 GAAGTATGGA
76321 AAAGACAAGAGAATAG
1 AAAGACAAGAGAATAG
*
76337 AAAGACAATAGAATA
1 AAAGACAAGAGAATA
76352 TGGAGAAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.06, G:0.19, T:0.10
Consensus pattern (16 bp):
AAAGACAAGAGAATAG
Found at i:77156 original size:2 final size:2
Alignment explanation
Indices: 77149--77187 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
77139 TAATGTCAAA
77149 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
77188 GTAAGAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Done.