Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017771.1 Corchorus olitorius cultivar O-4 contig17804, 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: 59716
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:7783 original size:226 final size:226
Alignment explanation
Indices: 7389--8071 Score: 1366
Period size: 226 Copynumber: 3.0 Consensus size: 226
7379 TGGACCAAAT
7389 CTCTCCATTGCTCTTGATGACAATATGTGGTCTTCCTTTTAGCACCAGTCTCTGATGCTGAAATT
1 CTCTCCATTGCTCTTGATGACAATATGTGGTCTTCCTTTTAGCACCAGTCTCTGATGCTGAAATT
7454 GAACATATTGTCTGGACTTTCAAACCCTTCAAAGCACTTGGGCATGATGGCCTCCACCCAGGTTT
66 GAACATATTGTCTGGACTTTCAAACCCTTCAAAGCACTTGGGCATGATGGCCTCCACCCAGGTTT
7519 TTACCAAAATTGTTGGGCGGTTATCAAAGATAAATTTTGTGCTTTAATTAAAGAGATTTTTCAAA
131 TTACCAAAATTGTTGGGCGGTTATCAAAGATAAATTTTGTGCTTTAATTAAAGAGATTTTTCAAA
7584 GATCATGCCTTCTGATTTTAACTTGTCCCTG
196 GATCATGCCTTCTGATTTTAACTTGTCCCTG
7615 CTCTCCATTGCTCTTGATGACAATATGTGGTCTTCCTTTTAGCACCAGTCTCTGATGCTGAAATT
1 CTCTCCATTGCTCTTGATGACAATATGTGGTCTTCCTTTTAGCACCAGTCTCTGATGCTGAAATT
7680 GAACATATTGTCTGGACTTTCAAACCCTTCAAAGCACTTGGGCATGATGGCCTCCACCCAGGTTT
66 GAACATATTGTCTGGACTTTCAAACCCTTCAAAGCACTTGGGCATGATGGCCTCCACCCAGGTTT
7745 TTACCAAAATTGTTGGGCGGTTATCAAAGATAAATTTTGTGCTTTAATTAAAGAGATTTTTCAAA
131 TTACCAAAATTGTTGGGCGGTTATCAAAGATAAATTTTGTGCTTTAATTAAAGAGATTTTTCAAA
7810 GATCATGCCTTCTGATTTTAACTTGTCCCTG
196 GATCATGCCTTCTGATTTTAACTTGTCCCTG
7841 CTCTCCATTGCTCTTGATGACAATATGTGGTCTTCCTTTTAGCACCAGTCTCTGATGCTGAAATT
1 CTCTCCATTGCTCTTGATGACAATATGTGGTCTTCCTTTTAGCACCAGTCTCTGATGCTGAAATT
7906 GAACATATTGTCTGGACTTTCAAACCCTTCAAAGCACTTGGGCATGATGGCCTCCACCCAGGTTT
66 GAACATATTGTCTGGACTTTCAAACCCTTCAAAGCACTTGGGCATGATGGCCTCCACCCAGGTTT
7971 TTACCAAAATTGTTGGGCGGTTATCAAAGATAAATTTTGTGCTTTAATTAAAGAGATTTTTCAAA
131 TTACCAAAATTGTTGGGCGGTTATCAAAGATAAATTTTGTGCTTTAATTAAAGAGATTTTTCAAA
8036 GATCATGCCTTCTGATTTTAACTTGTCCCTG
196 GATCATGCCTTCTGATTTTAACTTGTCCCTG
8067 CTCTC
1 CTCTC
8072 TCTCATTCCG
Statistics
Matches: 457, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
226 457 1.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.36
Consensus pattern (226 bp):
CTCTCCATTGCTCTTGATGACAATATGTGGTCTTCCTTTTAGCACCAGTCTCTGATGCTGAAATT
GAACATATTGTCTGGACTTTCAAACCCTTCAAAGCACTTGGGCATGATGGCCTCCACCCAGGTTT
TTACCAAAATTGTTGGGCGGTTATCAAAGATAAATTTTGTGCTTTAATTAAAGAGATTTTTCAAA
GATCATGCCTTCTGATTTTAACTTGTCCCTG
Found at i:19564 original size:30 final size:30
Alignment explanation
Indices: 19528--19733 Score: 225
Period size: 30 Copynumber: 6.7 Consensus size: 30
19518 ACTCTCCAAA
19528 TGACACCA-AAGGTTGTCATGATCTTACAAT
1 TGACACCAGAA-GTTGTCATGATCTTACAAT
*
19558 TGACACCAGAAGTTGTCATGATCTTACATT
1 TGACACCAGAAGTTGTCATGATCTTACAAT
* *
19588 TGACACCAGAAGTTGTCATGATCCTACACT
1 TGACACCAGAAGTTGTCATGATCTTACAAT
* *
19618 TGACACCAAAAGTTGTCAATGGTCTTACAAT
1 TGACACCAGAAGTTGTC-ATGATCTTACAAT
* *
19649 TGACACCAGAAGTTGTCATGATAAATTTCCAAT
1 TGACACCAGAAGTTGTCATGAT---CTTACAAT
* ** * * *
19682 AGACACTTGAAGATGTCATAATTTTATTCAAT
1 TGACACCAGAAGTTGTCATGATCTTA--CAAT
19714 TGACACCAGAAGTTGTCATG
1 TGACACCAGAAGTTGTCATG
19734 GTTTTACCTT
Statistics
Matches: 147, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
30 77 0.52
31 28 0.19
32 19 0.13
33 23 0.16
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (30 bp):
TGACACCAGAAGTTGTCATGATCTTACAAT
Found at i:40990 original size:14 final size:13
Alignment explanation
Indices: 40971--41009 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
40961 AAATTGTAAA
40971 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
40984 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
40998 ATTTAAAAAATT
1 ATTTAAAAAATT
41010 CTAATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTAAAAAATTT
Found at i:41217 original size:126 final size:127
Alignment explanation
Indices: 40995--41252 Score: 328
Period size: 134 Copynumber: 2.0 Consensus size: 127
40985 ATTTAAGAAA
40995 TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAATAAAATGGTAAAAATAAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAATAAAATGGTAAAAAT---A
* * * *
41060 TAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAG-TTTTAGTTGAGTAAAACTGTAAAA
63 CA-GTATAAGGATATTAGATTTAAATAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAAAA
41124 G
127 G
* * *
41125 TATATTTAAAAAATTCTAATATATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT
1 TATATTTAAAAAATTC---TA-ATATATATAAGTTTTTAAAATAAAATAATAAAATGGTAAAAAT
* *
41190 -CA-TA-AA-GATATTAGATTTAAATAAATAAAATTAGAGTTTTTAGTTGAATAAAATTATAAAA
62 ACAGTATAAGGATATTAGATTTAAATAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAAAA
41251 G
127 G
41252 T
1 T
41253 TTAAACAATG
Statistics
Matches: 114, Mismatches: 9, Indels: 13
0.84 0.07 0.10
Matches are distributed among these distances:
126 28 0.25
127 25 0.22
128 2 0.02
130 17 0.15
133 2 0.02
134 40 0.35
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.37
Consensus pattern (127 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAATAAAATGGTAAAAATACAG
TATAAGGATATTAGATTTAAATAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAAAAG
Found at i:43194 original size:259 final size:260
Alignment explanation
Indices: 42853--43366 Score: 1003
Period size: 259 Copynumber: 2.0 Consensus size: 260
42843 AATATTATCC
42853 TTTTATTTTGCATATTTATAATTTATGTATACATAAATTTTTTTTTGTGAAAATGTATACATAAA
1 TTTTATTTTGCATATTTATAATTTATGTATACATAAATTTTTTTTTGTGAAAATGTATACATAAA
42918 TATTATAAATAAAAAGTAATATAAAAGGGTTTTGTACGAAAACAAAAAAAATAAGAATAAAAGAA
66 TATTATAAATAAAAAGTAATATAAAAGGGTTTTGTACGAAAACAAAAAAAATAAGAATAAAAGAA
42983 AAACCCTAAATTAAAGATAAATCAATTAATTAATAATATATACAATATCTAAATGAGATAAGAAA
131 AAACCCTAAATTAAAGATAAATCAATTAATTAATAATATATACAATATCTAAATGAGATAAGAAA
43048 CATGGGTCATTCCAAATTCCAAATTGAACAAAAGAAATAAGTGGGGTTGGTAGAGTTGGTTTTTT
196 CATGGGTCATTCCAAATTCCAAATTGAACAAAAGAAATAAGTGGGGTTGGTAGAGTTGGTTTTTT
*
43113 TTTTTTTTTGCATATTTATAATTTATGTATACAT-AATTTTTTTTTGTGAAAATGTATACATAAA
1 TTTTATTTTGCATATTTATAATTTATGTATACATAAATTTTTTTTTGTGAAAATGTATACATAAA
43177 TATTATAAATAAAAAGTAATATAAAAGGGTTTTGTACGAAAACAAAAAAAATAAGAATAAAAGAA
66 TATTATAAATAAAAAGTAATATAAAAGGGTTTTGTACGAAAACAAAAAAAATAAGAATAAAAGAA
43242 AAACCCTAAATTAAAGATAAATCAATTAATTAATAATATATACAATATCTAAATGAGATAAGAAA
131 AAACCCTAAATTAAAGATAAATCAATTAATTAATAATATATACAATATCTAAATGAGATAAGAAA
*
43307 CATGGGTCATTCCAAATTCCAAATTGAACAAAAGAAATAGGTGGGGTTGGTAGAGTTGGT
196 CATGGGTCATTCCAAATTCCAAATTGAACAAAAGAAATAAGTGGGGTTGGTAGAGTTGGT
43367 AAAAGTTGAC
Statistics
Matches: 252, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
259 219 0.87
260 33 0.13
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.33
Consensus pattern (260 bp):
TTTTATTTTGCATATTTATAATTTATGTATACATAAATTTTTTTTTGTGAAAATGTATACATAAA
TATTATAAATAAAAAGTAATATAAAAGGGTTTTGTACGAAAACAAAAAAAATAAGAATAAAAGAA
AAACCCTAAATTAAAGATAAATCAATTAATTAATAATATATACAATATCTAAATGAGATAAGAAA
CATGGGTCATTCCAAATTCCAAATTGAACAAAAGAAATAAGTGGGGTTGGTAGAGTTGGTTTTTT
Found at i:45269 original size:50 final size:50
Alignment explanation
Indices: 45193--45287 Score: 147
Period size: 50 Copynumber: 1.9 Consensus size: 50
45183 ACTGCAACTT
45193 CAGTCTTCATTCTTTCTTTTTAAGATTTTACTGGTTCATCAACCTAATTG
1 CAGTCTTCATTCTTTCTTTTTAAGATTTTACTGGTTCATCAACCTAATTG
* * *
45243 CAGTCTTCATTAGTTT-TTTTTTAGATTTTGCTGGTTCATCAACCT
1 CAGTCTTCATT-CTTTCTTTTTAAGATTTTACTGGTTCATCAACCT
45288 TTGAACACTT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
50 38 0.93
51 3 0.07
ACGTcount: A:0.20, C:0.19, G:0.12, T:0.49
Consensus pattern (50 bp):
CAGTCTTCATTCTTTCTTTTTAAGATTTTACTGGTTCATCAACCTAATTG
Found at i:49498 original size:28 final size:27
Alignment explanation
Indices: 49467--49531 Score: 85
Period size: 28 Copynumber: 2.4 Consensus size: 27
49457 GTTTTAAAAA
* * *
49467 AAATAAATAGGTATAGAGAATAATAGAT
1 AAATAAATAGCTAAAAAGAATAATA-AT
*
49495 AAATAAATAGCTAAAAATAATAATAAT
1 AAATAAATAGCTAAAAAGAATAATAAT
49522 AAATAAATAG
1 AAATAAATAG
49532 ATAATAGCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
27 12 0.36
28 21 0.64
ACGTcount: A:0.63, C:0.02, G:0.11, T:0.25
Consensus pattern (27 bp):
AAATAAATAGCTAAAAAGAATAATAAT
Found at i:49528 original size:31 final size:30
Alignment explanation
Indices: 49485--49640 Score: 92
Period size: 31 Copynumber: 5.0 Consensus size: 30
49475 AGGTATAGAG
*
49485 AATAATAGATAAATAAATAGCTAAAAATAAT
1 AATAATAAATAAATAAATAG-TAAAAATAAT
*
49516 AATAATAAATAAATAGATAATAGCT-AAATTAAT
1 AATAATAAATAAAT--A-AATAG-TAAAAATAAT
49549 -A-AATAAA-AAGATAAATAGTAAATAGATAGAT
1 AATAATAAATAA-ATAAATAGTAAA-A-ATA-AT
*
49580 AATAATTAAATTAATAAAT-G-AAAAGATAAAT
1 AATAA-TAAATAAATAAATAGTAAAA-AT-AAT
* *
49611 AGTAAATAAATAGAT-AATAGTTAAAAATAA
1 AAT-AATAAATAAATAAATAG-TAAAAATAA
49641 AAAAAGGGAT
Statistics
Matches: 101, Mismatches: 7, Indels: 34
0.71 0.05 0.24
Matches are distributed among these distances:
27 1 0.01
28 7 0.07
29 2 0.02
30 7 0.07
31 41 0.41
32 10 0.10
33 15 0.15
34 17 0.17
35 1 0.01
ACGTcount: A:0.63, C:0.01, G:0.08, T:0.27
Consensus pattern (30 bp):
AATAATAAATAAATAAATAGTAAAAATAAT
Found at i:49543 original size:19 final size:18
Alignment explanation
Indices: 49500--49550 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
49490 TAGATAAATA
49500 AATAGCT-AA-AAATAAT
1 AATAGCTAAATAAATAAT
*
49516 AATA-ATAAATAAATAGAT
1 AATAGCTAAATAAATA-AT
*
49534 AATAGCTAAATTAATAA
1 AATAGCTAAATAAATAA
49551 ATAAAAAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 1 0.04
16 6 0.21
17 5 0.18
18 7 0.25
19 9 0.32
ACGTcount: A:0.63, C:0.04, G:0.06, T:0.27
Consensus pattern (18 bp):
AATAGCTAAATAAATAAT
Found at i:49548 original size:27 final size:27
Alignment explanation
Indices: 49518--49627 Score: 87
Period size: 27 Copynumber: 4.4 Consensus size: 27
49508 AAAATAATAA
*
49518 TAATAAATAAATAGAT-AATAGCTAAAT
1 TAATAAATAAAAAGATAAATAG-TAAAT
49545 TAATAAATAAAAAGATAAATAGTAAA-
1 TAATAAATAAAAAGATAAATAGTAAAT
*
49571 TAGATAGAT----A-AT-AAT--TAAAT
1 TA-ATAAATAAAAAGATAAATAGTAAAT
*
49591 TAATAAATGAAAAGATAAATAGTAAAT
1 TAATAAATAAAAAGATAAATAGTAAAT
* *
49618 AAATAGATAA
1 TAATAAATAA
49628 TAGTTAAAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 22
0.70 0.06 0.23
Matches are distributed among these distances:
19 9 0.14
20 2 0.03
21 3 0.05
22 2 0.03
23 2 0.03
24 2 0.03
25 3 0.05
26 2 0.03
27 36 0.55
28 5 0.08
ACGTcount: A:0.63, C:0.01, G:0.09, T:0.27
Consensus pattern (27 bp):
TAATAAATAAAAAGATAAATAGTAAAT
Found at i:49556 original size:46 final size:47
Alignment explanation
Indices: 49486--49753 Score: 267
Period size: 46 Copynumber: 6.0 Consensus size: 47
49476 GGTATAGAGA
* * ** * *
49486 ATAATAGATAAATAAATAGCTAAAAATAAT-AATAATAAATAAATAG
1 ATAATAGTTAAATTAATAAATAAAAATGATAAATAGTAAATAAATAG
* *
49532 ATAATAGCTAAATTAATAAATAAAAA-GATAAATAGTAAATAGATAG
1 ATAATAGTTAAATTAATAAATAAAAATGATAAATAGTAAATAAATAG
* *
49578 ATAATAATTAAATTAATAAATGAAAA-GATAAATAGTAAATAAATAG
1 ATAATAGTTAAATTAATAAATAAAAATGATAAATAGTAAATAAATAG
**
49624 ATAATAGTTAAA--AATAAA-AAAAGGGATAAATAGTAAATAAATAG
1 ATAATAGTTAAATTAATAAATAAAAATGATAAATAGTAAATAAATAG
**
49668 ATAATAGTTAAA--AAT-AA-AAAAGGGATAAATAGTAAATAAATA-
1 ATAATAGTTAAATTAATAAATAAAAATGATAAATAGTAAATAAATAG
* * * *
49710 AGTAATAGTTAAA--AATAAGTAAATA-GATAAATAATGAATAAATA
1 A-TAATAGTTAAATTAATAAATAAAAATGATAAATAGTAAATAAATA
49754 AAAAAAAATC
Statistics
Matches: 198, Mismatches: 19, Indels: 12
0.86 0.08 0.05
Matches are distributed among these distances:
42 1 0.01
43 44 0.22
44 59 0.30
45 5 0.03
46 89 0.45
ACGTcount: A:0.63, C:0.01, G:0.10, T:0.26
Consensus pattern (47 bp):
ATAATAGTTAAATTAATAAATAAAAATGATAAATAGTAAATAAATAG
Found at i:49701 original size:43 final size:43
Alignment explanation
Indices: 49558--49727 Score: 245
Period size: 43 Copynumber: 3.9 Consensus size: 43
49548 TAAATAAAAA
* * *
49558 GATAAATAGTAAATAGATAGATAATAATTAAATTAATAAATGAAA-A
1 GATAAATAGTAAATAAATAGATAATAGTTAAA--AATAAA--AAAGG
49604 GATAAATAGTAAATAAATAGATAATAGTTAAAAATAAAAAAAGG
1 GATAAATAGTAAATAAATAGATAATAGTTAAAAAT-AAAAAAGG
49648 GATAAATAGTAAATAAATAGATAATAGTTAAAAATAAAAAAGG
1 GATAAATAGTAAATAAATAGATAATAGTTAAAAATAAAAAAGG
49691 GATAAATAGTAAATAAATA-AGTAATAGTTAAAAATAA
1 GATAAATAGTAAATAAATAGA-TAATAGTTAAAAATAA
49728 GTAAATAGAT
Statistics
Matches: 118, Mismatches: 3, Indels: 9
0.91 0.02 0.07
Matches are distributed among these distances:
42 1 0.01
43 46 0.39
44 38 0.32
45 3 0.03
46 30 0.25
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (43 bp):
GATAAATAGTAAATAAATAGATAATAGTTAAAAATAAAAAAGG
Found at i:49716 original size:18 final size:19
Alignment explanation
Indices: 49559--49743 Score: 73
Period size: 19 Copynumber: 9.2 Consensus size: 19
49549 AAATAAAAAG
*
49559 ATAAAT-AGTAAATAGATAG
1 ATAAATAAGTAAATAG-TAA
* *
49578 AT-AATAATTAAATTAATAA
1 ATAAATAAGTAAA-TAGTAA
*
49597 ATGAA-AAGATAAATAGTAA
1 ATAAATAAG-TAAATAGTAA
49616 ATAAAT-AG-ATAATAGTTAAAA
1 ATAAATAAGTA-AATAG-T--AA
*
49637 ATAAAAAAAGGGATAAATAGTAA
1 AT-AAATAA--G-TAAATAGTAA
49660 ATAAAT-AG-ATAATAGTTAAAA
1 ATAAATAAGTA-AATAG-T--AA
*
49681 ATAAAAAAGGGATAAATAGTAA
1 ATAAATAA--G-TAAATAGTAA
*
49703 ATAAATAAGT-AATAGTTA
1 ATAAATAAGTAAATAGTAA
49721 A-AAATAAGTAAATAGATAA
1 ATAAATAAGTAAATAG-TAA
49740 ATAA
1 ATAA
49744 TGAATAAATA
Statistics
Matches: 127, Mismatches: 12, Indels: 53
0.66 0.06 0.28
Matches are distributed among these distances:
17 10 0.08
18 26 0.20
19 31 0.24
20 11 0.09
21 12 0.09
22 16 0.13
23 5 0.04
24 2 0.02
25 7 0.06
26 6 0.05
27 1 0.01
ACGTcount: A:0.63, C:0.00, G:0.12, T:0.25
Consensus pattern (19 bp):
ATAAATAAGTAAATAGTAA
Found at i:49727 original size:17 final size:18
Alignment explanation
Indices: 49695--49743 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
49685 AAAAGGGATA
49695 AATAGTAAATAAATAAGT
1 AATAGTAAATAAATAAGT
*
49713 AATAGTTAA-AAATAAGT
1 AATAGTAAATAAATAAGT
49730 AAATAGATAAATAA
1 -AATAG-TAAATAA
49744 TGAATAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 8 0.31
18 13 0.50
19 3 0.12
20 2 0.08
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (18 bp):
AATAGTAAATAAATAAGT
Found at i:49739 original size:87 final size:88
Alignment explanation
Indices: 49516--49753 Score: 295
Period size: 87 Copynumber: 2.7 Consensus size: 88
49506 TAAAAATAAT
* * *
49516 AATAATAAATAAATAGATAATAGCTAAATTAATAAATAAAAAGATAAATAGTAAATAGATAGATA
1 AATAGTAAATAAATAGATAATAGTTAAA--AATAAATAAAAAGATAAATAGTAAATAAATAGATA
49581 ATAATTAAATTAATAAATGAAAAGATA
64 ATAATTAAA-TAATAAA-GAAAAGATA
*
49608 AATAGTAAATAAATAGATAATAGTTAAAAATAAA-AAAAGGGATAAATAGTAAATAAATAGATAA
1 AATAGTAAATAAATAGATAATAGTTAAAAATAAATAAAA-AGATAAATAGTAAATAAATAGATAA
* *
49672 TAGTTAAA-AATAAA-AAAGGGATA
65 TAATTAAATAATAAAGAAA-AGATA
* * * *
49695 AATAGTAAATAAATA-AGTAATAGTTAAAAATAAGTAAATAGATAAATAATGAATAAATA
1 AATAGTAAATAAATAGA-TAATAGTTAAAAATAAATAAAAAGATAAATAGTAAATAAATA
49754 AAAAAAAATC
Statistics
Matches: 131, Mismatches: 11, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
86 4 0.03
87 52 0.40
88 9 0.07
89 4 0.03
90 36 0.27
92 26 0.20
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (88 bp):
AATAGTAAATAAATAGATAATAGTTAAAAATAAATAAAAAGATAAATAGTAAATAAATAGATAAT
AATTAAATAATAAAGAAAAGATA
Found at i:51128 original size:35 final size:35
Alignment explanation
Indices: 51082--51543 Score: 570
Period size: 35 Copynumber: 13.0 Consensus size: 35
51072 ATCAATGTGA
*
51082 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* *
51117 AGATCAACTCTGATCATAAAAAAAACTTCTTGAAAGG
1 AGATCAACTCTGATCAT--CAAAAACTTCTTGAAATG
* *
51154 AGATCAACTCTGACCATATAAAAAACTTCTTGAAATG
1 AGATCAACTCTGATC--ATCAAAAACTTCTTGAAATG
* *
51191 AGATCAACTCTGACCATATAAAAAACTTCTTGAAATG
1 AGATCAACTCTGATC--ATCAAAAACTTCTTGAAATG
* *
51228 AGATCAACTCTGATCAACAAAAAC-TCTTTGAAACG
1 AGATCAACTCTGATCATCAAAAACTTC-TTGAAATG
*
51263 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* * *
51298 AGATCAATTCTGACCAT-AAAAACATCTTGAAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTG-AAATG
* * *
51333 AGATCAACTCTGATCATAAAAAACTTCCTGAAAGG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* *
51368 AGATCAACTCTGATCACCGAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* *
51403 AGATCAACTCTGACCAT-AAAAACATCTTGAAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTG-AAATG
* * *
51438 AGATCAACTCTGATCATAAAAAACTTCCTGAAAGG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* * *
51473 AGATCAACTCTGATCACCGAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* *
51508 AGATCAACTCTGATCATCGAAAACTTCTTGGAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
51543 A
1 A
51544 CCGCACTGGA
Statistics
Matches: 375, Mismatches: 42, Indels: 20
0.86 0.10 0.05
Matches are distributed among these distances:
34 22 0.06
35 232 0.62
36 22 0.06
37 97 0.26
39 2 0.01
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.25
Consensus pattern (35 bp):
AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
Found at i:51590 original size:54 final size:54
Alignment explanation
Indices: 51508--51616 Score: 191
Period size: 54 Copynumber: 2.0 Consensus size: 54
51498 TCTTGAAACG
* *
51508 AGATCAACTCTGATCATCGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
1 AGATCAACTCTGACCATCGAAAACTTCTTGGAATGACCGCAATGGATCATCTGA
*
51562 AGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCAATGGATCATCTGA
1 AGATCAACTCTGACCATCGAAAACTTCTTGGAATGACCGCAATGGATCATCTGA
51616 A
1 A
51617 CACCTGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (54 bp):
AGATCAACTCTGACCATCGAAAACTTCTTGGAATGACCGCAATGGATCATCTGA
Found at i:52453 original size:15 final size:15
Alignment explanation
Indices: 52427--52458 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
52417 ACTTGAACCC
52427 TTCCCTTTTTTTCTTT
1 TTCCCTTTTTTT-TTT
52443 TTCCCTTTTTTTTTT
1 TTCCCTTTTTTTTTT
52458 T
1 T
52459 GAAACTTCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTCCCTTTTTTTTTT
Found at i:55953 original size:4 final size:4
Alignment explanation
Indices: 55946--55971 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
55936 TACCAAAGGA
55946 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
55972 GTGAATGAAA
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:59696 original size:21 final size:21
Alignment explanation
Indices: 59640--59696 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
59630 TTTATAACAC
*
59640 CTTGTTCCTGCCTCATCTCAT
1 CTTGTGCCTGCCTCATCTCAT
* ** * * *
59661 CTTGCGAATGTCTCATTTCTT
1 CTTGTGCCTGCCTCATCTCAT
59682 CTTGTGCCTGCCTCA
1 CTTGTGCCTGCCTCA
59697 GTTGTTCGAT
Statistics
Matches: 25, Mismatches: 11, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.11, C:0.33, G:0.14, T:0.42
Consensus pattern (21 bp):
CTTGTGCCTGCCTCATCTCAT
Done.