Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017222.1 Corchorus olitorius cultivar O-4 contig17255, 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: 74605
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:171 original size:20 final size:21
Alignment explanation
Indices: 148--186 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
138 ACCCCAATAT
148 ACATAAAAATCCA-AAAAAAG
1 ACATAAAAATCCATAAAAAAG
*
168 ACATAAACATCCATAAAAA
1 ACATAAAAATCCATAAAAA
187 TCCCAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.67, C:0.18, G:0.03, T:0.13
Consensus pattern (21 bp):
ACATAAAAATCCATAAAAAAG
Found at i:1992 original size:20 final size:20
Alignment explanation
Indices: 1963--2004 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1953 ATAATTTATT
*
1963 TAATTTATTTCAATTTATAA
1 TAATTAATTTCAATTTATAA
1983 TAATTAATTTCAATTTATAA
1 TAATTAATTTCAATTTATAA
2003 TA
1 TA
2005 TCACATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (20 bp):
TAATTAATTTCAATTTATAA
Found at i:2308 original size:26 final size:26
Alignment explanation
Indices: 2277--2343 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 26
2267 AGCACCAGCG
2277 GCAGCCTC-CCTCTCCGGATA-ATCCGA
1 GCAGCCTCACCTC-CC-GATACATCCGA
*
2303 GCAGCCTCAGCCTCCCTATACATCCGA
1 GCAGCCTCA-CCTCCCGATACATCCGA
2330 GCAGCCTCAGCCTC
1 GCAGCCTCA-CCTC
2344 TTTCTCCCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
26 11 0.30
27 22 0.59
28 4 0.11
ACGTcount: A:0.19, C:0.45, G:0.18, T:0.18
Consensus pattern (26 bp):
GCAGCCTCACCTCCCGATACATCCGA
Found at i:5562 original size:19 final size:18
Alignment explanation
Indices: 5526--5567 Score: 61
Period size: 16 Copynumber: 2.4 Consensus size: 18
5516 TAAAATTTAT
5526 TAATTATTTATTAAATAA
1 TAATTATTTATTAAATAA
*
5544 TAATTATTT-TTCAA-AA
1 TAATTATTTATTAAATAA
5560 TAATTATT
1 TAATTATT
5568 ATTTGTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.43
17 4 0.17
18 9 0.39
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATTATTTATTAAATAA
Found at i:30215 original size:132 final size:131
Alignment explanation
Indices: 29801--30313 Score: 546
Period size: 131 Copynumber: 3.9 Consensus size: 131
29791 TCGTTGTCTT
* * * * * * *
29801 AGTGATTTTGATGTTATTTTACCCAACAATTTTTCTAATTGTTGCCAATGTTTATAGTTTTCGTA
1 AGTGATTTTGATGGTATTTTACACAACACTTTTT-TAGTTGTTGCCAATGTTTACAATATTCGTA
** * * *
29866 ACAATAAA-AATAAAGTCGTTATGAAATCATAATATATTCGTAACAATTTTAT-AAAGTCGTTGC
65 ACAATAAATAATAAAGTCGTTACAAAATCATAAAATATTCGTAACAACTTTATAAAAAT-GTTGC
*
29929 ATA
129 CTA
* * * ** * * * *
29932 AGTGATTTTGATAGTATTTTACGCAACATTTTTTTAGACGTTGCCAATGCTTACAATTTTTGCAA
1 AGTGATTTTGATGGTATTTTACACAACACTTTTTTAGTTGTTGCCAATGTTTACAATATTCGTAA
* * * * * ** *
29997 CAATAAAAAAAAAAGTCATTGCAAAATCATAAACTATTCGTAACAACTTTATAAAAACATTGTCT
66 CAATAAATAATAAAGTCGTTACAAAATCATAAAATATTCGTAACAACTTTATAAAAATGTTGCCT
*
30062 T
131 A
*
30063 AGTGATTTTGATGATATTTTACACAACACTTTTTTAGTTGTTGCCAATGTTTACAATATTCGTAA
1 AGTGATTTTGATGGTATTTTACACAACACTTTTTTAGTTGTTGCCAATGTTTACAATATTCGTAA
* ** * * *
30128 CAACAAATTCTTAAGTTGTTACGAAATCATAAAACTATTCGTAACAACTTTATAAAAATGTTGCC
66 CAATAAATAATAAAGTCGTTACAAAATCATAAAA-TATTCGTAACAACTTTATAAAAATGTTGCC
30193 TA
130 TA
* * *
30195 AGTGATTTTGATGGTATTTTACACAACACTTTTTTGGTTGTTGCCAATCTTTACTATATTCGTAA
1 AGTGATTTTGATGGTATTTTACACAACACTTTTTTAGTTGTTGCCAATGTTTACAATATTCGTAA
* ** * * *
30260 CAAAAAATTCTTAAA-TTGTTGCAAAATCATAATATATTCGTAACAACTTTATAA
66 CAATAAA-TAATAAAGTCGTTACAAAATCATAAAATATTCGTAACAACTTTATAA
30314 GTTGTTGCGC
Statistics
Matches: 316, Mismatches: 62, Indels: 8
0.82 0.16 0.02
Matches are distributed among these distances:
130 30 0.09
131 168 0.53
132 114 0.36
133 4 0.01
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.39
Consensus pattern (131 bp):
AGTGATTTTGATGGTATTTTACACAACACTTTTTTAGTTGTTGCCAATGTTTACAATATTCGTAA
CAATAAATAATAAAGTCGTTACAAAATCATAAAATATTCGTAACAACTTTATAAAAATGTTGCCT
A
Found at i:30284 original size:263 final size:262
Alignment explanation
Indices: 29794--30313 Score: 647
Period size: 263 Copynumber: 2.0 Consensus size: 262
29784 TTAATACTCG
* * * *
29794 TTGTCTTAGTGATTTTGATGTTATTTTACCCAACAATTTTTCTAATTGTTGCCAATGTTTATAGT
1 TTGTCTTAGTGATTTTGATGATATTTTACACAACAATTTTTCTAATTGTTGCCAATGTTTACAAT
* * * * * *
29859 TTTCGTAACAATAAAAATAAAGTCGTTATGAAATCATAATATATTCGTAACAATTTTATAAAGTC
66 ATTCGTAACAACAAAAATAAAGTCGTTACGAAATCATAAAATATTCGTAACAACTTTATAAAATC
* *
29924 GTTGCATAAGTGATTTTGATAGTATTTTACGCAACATTTTTTTAGACGTTGCCAATGCTTACAAT
131 GTTGCATAAGTGATTTTGATAGTATTTTACACAACACTTTTTTAGACGTTGCCAATGCTTACAAT
* *
29989 TTTTGCAACAATAAAAAAAAAAGTCATTGCAAAATCATAA-ACTATTCGTAACAACTTTATAAAA
196 ATTCGCAACAATAAAAAAAAAAGTCATTGCAAAATCATAATA-TATTCGTAACAACTTTATAAAA
30053 ACA
260 ACA
* *
30056 TTGTCTTAGTGATTTTGATGATATTTTACACAACACTTTTT-TAGTTGTTGCCAATGTTTACAAT
1 TTGTCTTAGTGATTTTGATGATATTTTACACAACAATTTTTCTAATTGTTGCCAATGTTTACAAT
** * *
30120 ATTCGTAACAACAAATTCTTAAGTTGTTACGAAATCATAAAACTATTCGTAACAACTTTATAAAA
66 ATTCGTAACAACAAA-AATAAAGTCGTTACGAAATCATAAAA-TATTCGTAACAACTTTAT-AAA
* * * **
30185 AT-GTTGCCTAAGTGATTTTGATGGTATTTTACACAACACTTTTTTGGTTGTTGCCAAT-CTTTA
128 ATCGTTGCATAAGTGATTTTGATAGTATTTTACACAACACTTTTTTAGACGTTGCCAATGC-TTA
* * *** **
30248 CTATATTCGTAACAA-AAAATTCTTAAA-TTGTTGCAAAATCATAATATATTCGTAACAACTTTA
192 CAATATTCGCAACAATAAAA--AAAAAAGTCATTGCAAAATCATAATATATTCGTAACAACTTTA
30311 TAA
255 TAA
30314 GTTGTTGCGC
Statistics
Matches: 219, Mismatches: 32, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
261 33 0.15
262 63 0.29
263 115 0.53
264 8 0.04
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (262 bp):
TTGTCTTAGTGATTTTGATGATATTTTACACAACAATTTTTCTAATTGTTGCCAATGTTTACAAT
ATTCGTAACAACAAAAATAAAGTCGTTACGAAATCATAAAATATTCGTAACAACTTTATAAAATC
GTTGCATAAGTGATTTTGATAGTATTTTACACAACACTTTTTTAGACGTTGCCAATGCTTACAAT
ATTCGCAACAATAAAAAAAAAAGTCATTGCAAAATCATAATATATTCGTAACAACTTTATAAAAA
CA
Found at i:31654 original size:75 final size:75
Alignment explanation
Indices: 31552--31699 Score: 226
Period size: 75 Copynumber: 2.0 Consensus size: 75
31542 AATATATGTT
* * *
31552 GTTGTTAAAATATTTTTACGCCATAATATTCAGTTGTTGCGTAAAATACAATTCTTTTAA-CAAC
1 GTTGTTAAAATACTTTTACGCAATAATATTCAGTTGTCGCGTAAAATACAATTC-TTTAAGCAAC
31616 AATAAAATGAC
65 AATAAAATGAC
* * *
31627 GTTGTTAAAATACTTTTATGCAATAATATTGAGTTGTCGCGTAAAATATAATTCTTTAAGCAACA
1 GTTGTTAAAATACTTTTACGCAATAATATTCAGTTGTCGCGTAAAATACAATTCTTTAAGCAACA
31692 ATAAAATG
66 ATAAAATG
31700 GTGTAACGAA
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
74 5 0.08
75 61 0.92
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.37
Consensus pattern (75 bp):
GTTGTTAAAATACTTTTACGCAATAATATTCAGTTGTCGCGTAAAATACAATTCTTTAAGCAACA
ATAAAATGAC
Found at i:32161 original size:6 final size:7
Alignment explanation
Indices: 32144--32170 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
32134 CCTATCTCAA
32144 AAAAAAT
1 AAAAAAT
32151 AAAAAAT
1 AAAAAAT
32158 AAAAAAT
1 AAAAAAT
32165 AAAAAA
1 AAAAAA
32171 CTAGCATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:37892 original size:30 final size:30
Alignment explanation
Indices: 37858--37919 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
37848 ATTTTTATCT
37858 TGACTTTCCTCTTATACCCTCAAATTTTAA
1 TGACTTTCCTCTTATACCCTCAAATTTTAA
*
37888 TGACTTTTCTCTTATACCCTCAAATTTTAA
1 TGACTTTCCTCTTATACCCTCAAATTTTAA
37918 TG
1 TG
37920 GCTTATTAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.24, G:0.05, T:0.45
Consensus pattern (30 bp):
TGACTTTCCTCTTATACCCTCAAATTTTAA
Found at i:38867 original size:18 final size:18
Alignment explanation
Indices: 38844--38927 Score: 66
Period size: 18 Copynumber: 4.5 Consensus size: 18
38834 TAATTTGGAC
38844 TTATTATTATTATAATAA
1 TTATTATTATTATAATAA
*
38862 TTATTAAACTTATTAT--TAG
1 TTATT--A-TTATTATAATAA
*
38881 TGGTATTATAATTATTAA-AA
1 T--TATTATTATTA-TAATAA
*
38901 TTATTATTATAATAATAA
1 TTATTATTATTATAATAA
38919 TTATTATTA
1 TTATTATTA
38928 GTGGTATGTA
Statistics
Matches: 52, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
17 3 0.06
18 30 0.58
19 5 0.10
20 3 0.06
21 11 0.21
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (18 bp):
TTATTATTATTATAATAA
Found at i:38892 original size:30 final size:27
Alignment explanation
Indices: 38842--38924 Score: 112
Period size: 30 Copynumber: 3.0 Consensus size: 27
38832 GTTAATTTGG
38842 ACTTATTATTATTATAATAATTATTAA
1 ACTTATTATTATTATAATAATTATTAA
*
38869 ACTTATTATTAGTGGTATTATAATTATTAA
1 ACTTATTATTA-T--TATAATAATTATTAA
* *
38899 AATTATTATTATAATAATAATTATTA
1 ACTTATTATTATTATAATAATTATTA
38925 TTAGTGGTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
27 23 0.47
28 1 0.02
29 1 0.02
30 24 0.49
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (27 bp):
ACTTATTATTATTATAATAATTATTAA
Found at i:42555 original size:274 final size:273
Alignment explanation
Indices: 42067--42886 Score: 1460
Period size: 273 Copynumber: 3.0 Consensus size: 273
42057 TGGAACTAGC
*
42067 ACTGATATCTACAACAAAATTTTGTTCTCTTAAATTTAATAATTTTGGTTAAGATGCCGAGTTAA
1 ACTGATATCTACAACAAAATTTTGTTCTCTTAAAGTTAATAATTTTGGTTAAGATGCCGAGTTAA
42132 TCAAAGAAATTGCAAAATTACAAATTTGAAGATGAAGAAAATGTTGACACATCTCAACATTTTCG
66 TCAAAGAAATTGCAAAATTACAAATTTGAAGATGAAGAAAATGTTGACACATCTCAACATTTTCG
* * *
42197 TGGAAAAGAGAAAACTCAAGAAGAGCCAAAAGGTTGATGGAAATAAAGATGGAAATGTAGATGCA
131 TGGAAAAGAGAAAGCTCAAGAAGAGGCAAAAGGTTGATGGAAGTAAAGATGGAAATGTAGATGCA
* * *
42262 TACTTAATTATGCTCGATGGATGATTTGCCAAGATAAGCATATGAAAAACCAAAACGAAAAAAGG
196 GACTTAATTATGCTCGATGGATGATTTGCCAAGACAAGCATATGAAAAACCAAAAAGAAAAAAGG
42327 AGTTGCAAGAAAA
261 AGTTGCAAGAAAA
* *
42340 ACTGATATCTGCAACAAAATTTTGTTCTCTTAAAGTTAATAATTTTGGTTAAAATGCCGAGTTAA
1 ACTGATATCTACAACAAAATTTTGTTCTCTTAAAGTTAATAATTTTGGTTAAGATGCCGAGTTAA
42405 TCAAAGAAATTGCAAAATTACAAATTTTGAAGATGAAGAAAATGTTGACACATCTCAACATTTTC
66 TCAAAGAAATTGCAAAATTACAAA-TTTGAAGATGAAGAAAATGTTGACACATCTCAACATTTTC
* *
42470 GTGGAAAAGAGAAAGCTCAAGAAGAGGCAAAAGGTTGATGTAAGTAAAGATGAAAATGTAGATGC
130 GTGGAAAAGAGAAAGCTCAAGAAGAGGCAAAAGGTTGATGGAAGTAAAGATGGAAATGTAGATGC
*
42535 AGACTTAATTATGCTCGATGGATGATTTGCCAAGACAAGCATATGGAAAACCAAAAAGAAAAAAG
195 AGACTTAATTATGCTCGATGGATGATTTGCCAAGACAAGCATATGAAAAACCAAAAAGAAAAAAG
42600 GAGTTGCAAGAAAA
260 GAGTTGCAAGAAAA
* *
42614 ACTAATATCTACAACAAAATTTTGTTCTCTTAAAGCTAATAATTTTGGTTAAGATGCCGAGTTAA
1 ACTGATATCTACAACAAAATTTTGTTCTCTTAAAGTTAATAATTTTGGTTAAGATGCCGAGTTAA
* *
42679 TCAAAGAAATTGCAAAATTACAAATTTGATGATGAAGAAAATGTTGACACATCTCAACATTTTCA
66 TCAAAGAAATTGCAAAATTACAAATTTGAAGATGAAGAAAATGTTGACACATCTCAACATTTTCG
42744 TGGAAAAGAGAAAGCTCAAGAAGAGGCAAAAGGTTGATGGAAGTAAAGATGGAAATGTAGATGCA
131 TGGAAAAGAGAAAGCTCAAGAAGAGGCAAAAGGTTGATGGAAGTAAAGATGGAAATGTAGATGCA
* * *
42809 GATTTAATTATACTCGATGGATGATTTGCCAAGACAAGCATATGAAAAACCAAAAAGAAAAAAAG
196 GACTTAATTATGCTCGATGGATGATTTGCCAAGACAAGCATATGAAAAACCAAAAAGAAAAAAGG
42874 AGTTGCAAGAAAA
261 AGTTGCAAGAAAA
42887 GCCAAGTTAG
Statistics
Matches: 522, Mismatches: 24, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
273 262 0.50
274 260 0.50
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (273 bp):
ACTGATATCTACAACAAAATTTTGTTCTCTTAAAGTTAATAATTTTGGTTAAGATGCCGAGTTAA
TCAAAGAAATTGCAAAATTACAAATTTGAAGATGAAGAAAATGTTGACACATCTCAACATTTTCG
TGGAAAAGAGAAAGCTCAAGAAGAGGCAAAAGGTTGATGGAAGTAAAGATGGAAATGTAGATGCA
GACTTAATTATGCTCGATGGATGATTTGCCAAGACAAGCATATGAAAAACCAAAAAGAAAAAAGG
AGTTGCAAGAAAA
Found at i:42843 original size:273 final size:273
Alignment explanation
Indices: 42071--42886 Score: 1452
Period size: 274 Copynumber: 3.0 Consensus size: 273
42061 ACTAGCACTG
*
42071 ATATCTACAACAAAATTTTGTTCTCTTAAATTTAATAATTTTGGTTAAGATGCCGAGTTAATCAA
1 ATATCTACAACAAAATTTTGTTCTCTTAAAGTTAATAATTTTGGTTAAGATGCCGAGTTAATCAA
42136 AGAAATTGCAAAATTACAAATTTGAAGATGAAGAAAATGTTGACACATCTCAACATTTTCGTGGA
66 AGAAATTGCAAAATTACAAATTTGAAGATGAAGAAAATGTTGACACATCTCAACATTTTCGTGGA
* * * *
42201 AAAGAGAAAACTCAAGAAGAGCCAAAAGGTTGATGGAAATAAAGATGGAAATGTAGATGCATACT
131 AAAGAGAAAGCTCAAGAAGAGGCAAAAGGTTGATGGAAGTAAAGATGGAAATGTAGATGCAGACT
* *
42266 TAATTATGCTCGATGGATGATTTGCCAAGATAAGCATATGAAAAACCAAAACGAAAAAAGGAGTT
196 TAATTATGCTCGATGGATGATTTGCCAAGACAAGCATATGAAAAACCAAAAAGAAAAAAGGAGTT
*
42331 GCAAGAAAAACTG
261 GCAAGAAAAACTA
* *
42344 ATATCTGCAACAAAATTTTGTTCTCTTAAAGTTAATAATTTTGGTTAAAATGCCGAGTTAATCAA
1 ATATCTACAACAAAATTTTGTTCTCTTAAAGTTAATAATTTTGGTTAAGATGCCGAGTTAATCAA
42409 AGAAATTGCAAAATTACAAATTTTGAAGATGAAGAAAATGTTGACACATCTCAACATTTTCGTGG
66 AGAAATTGCAAAATTACAAA-TTTGAAGATGAAGAAAATGTTGACACATCTCAACATTTTCGTGG
* *
42474 AAAAGAGAAAGCTCAAGAAGAGGCAAAAGGTTGATGTAAGTAAAGATGAAAATGTAGATGCAGAC
130 AAAAGAGAAAGCTCAAGAAGAGGCAAAAGGTTGATGGAAGTAAAGATGGAAATGTAGATGCAGAC
*
42539 TTAATTATGCTCGATGGATGATTTGCCAAGACAAGCATATGGAAAACCAAAAAGAAAAAAGGAGT
195 TTAATTATGCTCGATGGATGATTTGCCAAGACAAGCATATGAAAAACCAAAAAGAAAAAAGGAGT
42604 TGCAAGAAAAACTA
260 TGCAAGAAAAACTA
*
42618 ATATCTACAACAAAATTTTGTTCTCTTAAAGCTAATAATTTTGGTTAAGATGCCGAGTTAATCAA
1 ATATCTACAACAAAATTTTGTTCTCTTAAAGTTAATAATTTTGGTTAAGATGCCGAGTTAATCAA
* *
42683 AGAAATTGCAAAATTACAAATTTGATGATGAAGAAAATGTTGACACATCTCAACATTTTCATGGA
66 AGAAATTGCAAAATTACAAATTTGAAGATGAAGAAAATGTTGACACATCTCAACATTTTCGTGGA
*
42748 AAAGAGAAAGCTCAAGAAGAGGCAAAAGGTTGATGGAAGTAAAGATGGAAATGTAGATGCAGATT
131 AAAGAGAAAGCTCAAGAAGAGGCAAAAGGTTGATGGAAGTAAAGATGGAAATGTAGATGCAGACT
* *
42813 TAATTATACTCGATGGATGATTTGCCAAGACAAGCATATGAAAAACCAAAAAGAAAAAAAGAGTT
196 TAATTATGCTCGATGGATGATTTGCCAAGACAAGCATATGAAAAACCAAAAAGAAAAAAGGAGTT
42878 GCAAGAAAA
261 GCAAGAAAA
42887 GCCAAGTTAG
Statistics
Matches: 518, Mismatches: 24, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
273 258 0.50
274 260 0.50
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (273 bp):
ATATCTACAACAAAATTTTGTTCTCTTAAAGTTAATAATTTTGGTTAAGATGCCGAGTTAATCAA
AGAAATTGCAAAATTACAAATTTGAAGATGAAGAAAATGTTGACACATCTCAACATTTTCGTGGA
AAAGAGAAAGCTCAAGAAGAGGCAAAAGGTTGATGGAAGTAAAGATGGAAATGTAGATGCAGACT
TAATTATGCTCGATGGATGATTTGCCAAGACAAGCATATGAAAAACCAAAAAGAAAAAAGGAGTT
GCAAGAAAAACTA
Found at i:43802 original size:96 final size:96
Alignment explanation
Indices: 43638--43830 Score: 368
Period size: 96 Copynumber: 2.0 Consensus size: 96
43628 TGTCTTTACT
*
43638 AGTATATAATATAAGTTTAATCTCCTTTTAGGTGAAATGGGATTGGAAACGACAATTAATTTATT
1 AGTATATAATATAAGTTTAATCTCCTTTTAGGTGAAATGGGATTGGAAACGACAATTAATTTAAT
43703 TTTTTTTTCATTATTTACTATCCTATGCAGC
66 TTTTTTTTCATTATTTACTATCCTATGCAGC
*
43734 AGTATATAATATATGTTTAATCTCCTTTTAGGTGAAATGGGATTGGAAACGACAATTAATTTAAT
1 AGTATATAATATAAGTTTAATCTCCTTTTAGGTGAAATGGGATTGGAAACGACAATTAATTTAAT
43799 TTTTTTTTCATTATTTACTATCCTATGCAGC
66 TTTTTTTTCATTATTTACTATCCTATGCAGC
43830 A
1 A
43831 TCACTATATA
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 95 1.00
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (96 bp):
AGTATATAATATAAGTTTAATCTCCTTTTAGGTGAAATGGGATTGGAAACGACAATTAATTTAAT
TTTTTTTTCATTATTTACTATCCTATGCAGC
Found at i:52144 original size:15 final size:15
Alignment explanation
Indices: 52121--52150 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52111 GGGATTCGAC
*
52121 GTGATTCAATATTGG
1 GTGACTCAATATTGG
52136 GTGACTCAATATTGG
1 GTGACTCAATATTGG
52151 ATTAAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.10, G:0.27, T:0.37
Consensus pattern (15 bp):
GTGACTCAATATTGG
Found at i:54638 original size:33 final size:34
Alignment explanation
Indices: 54596--54665 Score: 124
Period size: 35 Copynumber: 2.1 Consensus size: 34
54586 ATCATCTAGC
54596 ACACCATTAAATGTAT-ATATCAGGTGCAATAAT
1 ACACCATTAAATGTATAATATCAGGTGCAATAAT
54629 ACACCATTAAATGTATACATATCAGGTGCAATAAT
1 ACACCATTAAATGTATA-ATATCAGGTGCAATAAT
54664 AC
1 AC
54666 GCTCAGCAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 16 0.46
35 19 0.54
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (34 bp):
ACACCATTAAATGTATAATATCAGGTGCAATAAT
Found at i:57992 original size:31 final size:31
Alignment explanation
Indices: 57957--58018 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
57947 AAAGTTATTA
* * *
57957 ATGAATATTGTGATTATTCATGAATGAAGAG
1 ATGAATATTGTAAATATTCATGAATCAAGAG
*
57988 ATGAATATTGTAAATATTTATGAATCAAGAG
1 ATGAATATTGTAAATATTCATGAATCAAGAG
58019 TTCTCTTGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.35
Consensus pattern (31 bp):
ATGAATATTGTAAATATTCATGAATCAAGAG
Found at i:58848 original size:111 final size:112
Alignment explanation
Indices: 58654--58875 Score: 401
Period size: 111 Copynumber: 2.0 Consensus size: 112
58644 ATTTTTCCAA
*
58654 GTTCTTCGAAGAGAAGGAAACAATGCTGATGACATGGCTGGCGAAGGGTGGATATTTAAACTGCT
1 GTTCTTCAAAGAGAAGGAAACAATGCTGATGACATGGCTGGCGAAGGGTGGATATTTAAACTGCT
*
58719 TGGTTAGCTTGAAATAAGTTTCTCAATAGGGCCAGAAA-TTCGCTTC
66 TGGTTAGCTTGAAATAAGTTTCTCAATAAGGCCAGAAATTTCGCTTC
* *
58765 GTTCTTCAAAGAGAAGGAAACAATGCTGATGACATGGCTGGCGAAGGGTGGATATTTAGACTGGT
1 GTTCTTCAAAGAGAAGGAAACAATGCTGATGACATGGCTGGCGAAGGGTGGATATTTAAACTGCT
58830 TGGTTAGCTTGAAATAAGTTTCTCAATAAGGCCAGAAATTTCGCTT
66 TGGTTAGCTTGAAATAAGTTTCTCAATAAGGCCAGAAATTTCGCTT
58876 TGTTGAATGA
Statistics
Matches: 106, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
111 99 0.93
112 7 0.07
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.28
Consensus pattern (112 bp):
GTTCTTCAAAGAGAAGGAAACAATGCTGATGACATGGCTGGCGAAGGGTGGATATTTAAACTGCT
TGGTTAGCTTGAAATAAGTTTCTCAATAAGGCCAGAAATTTCGCTTC
Found at i:58936 original size:1 final size:1
Alignment explanation
Indices: 58930--58954 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
58920 GCTTCTGTGG
58930 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
58955 GCTCTGCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:67108 original size:32 final size:31
Alignment explanation
Indices: 67072--67164 Score: 105
Period size: 32 Copynumber: 2.9 Consensus size: 31
67062 ATTTCAAGTT
* **
67072 ATTAAATGCAAATAAAGCCAAAATTGCAATGC
1 ATTAAATGCAAA-AAAGCCAAAATTACAACCC
*
67104 ATTAAATGCAAAACAAGACAAAATTACAACCC
1 ATTAAATGCAAAA-AAGCCAAAATTACAACCC
* * *
67136 ATTAATTGCAAAAATGCCAAATTTACAAC
1 ATTAAATGCAAAAAAGCCAAAATTACAAC
67165 GATTGATGGG
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
31 14 0.27
32 38 0.73
ACGTcount: A:0.52, C:0.18, G:0.09, T:0.22
Consensus pattern (31 bp):
ATTAAATGCAAAAAAGCCAAAATTACAACCC
Found at i:67702 original size:32 final size:32
Alignment explanation
Indices: 67660--67800 Score: 146
Period size: 32 Copynumber: 4.4 Consensus size: 32
67650 TGGGCTTGAG
*
67660 TCAGG-TCGGGTT-CATTTCAGGTCAAGTTAAT
1 TCAGGTTCGGGTTGAATTT-AGGTCAAGTTAAT
* * *
67691 TTAGGTTCGGGTTGAATTTGGGTCAGGTTAAT
1 TCAGGTTCGGGTTGAATTTAGGTCAAGTTAAT
* *
67723 TCAGGTTCGGGTTGAATTTGGGTCAGGTTAAT
1 TCAGGTTCGGGTTGAATTTAGGTCAAGTTAAT
* *
67755 TCGGGTTTCGGGTTGAATTT-GAGT-TAGATTAAT
1 TCAGG-TTCGGGTTGAATTTAG-GTCAAG-TTAAT
67788 TCAGGTTCGGGTT
1 TCAGGTTCGGGTT
67801 CTATTTGGGT
Statistics
Matches: 96, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
31 4 0.04
32 63 0.66
33 29 0.30
ACGTcount: A:0.19, C:0.10, G:0.32, T:0.39
Consensus pattern (32 bp):
TCAGGTTCGGGTTGAATTTAGGTCAAGTTAAT
Found at i:67765 original size:65 final size:64
Alignment explanation
Indices: 67660--67810 Score: 189
Period size: 65 Copynumber: 2.4 Consensus size: 64
67650 TGGGCTTGAG
* * * *
67660 TCAGG-TCGGGTTC-ATTTCAGGTCAAGTTAATTTAGGTTCGGGTTGAATTTGGGTCAGGTTAAT
1 TCAGGTTCGGGTTCAATTT-GGGTCAAGTTAATTCAGGTTCGGGTTGAATTTGAGTCAGATTAAT
* * * *
67723 TCAGGTTCGGGTTGAATTTGGGTCAGGTTAATTCGGGTTTCGGGTTGAATTTGAGTTAGATTAAT
1 TCAGGTTCGGGTTCAATTTGGGTCAAGTTAATTCAGG-TTCGGGTTGAATTTGAGTCAGATTAAT
*
67788 TCAGGTTCGGGTTCTATTTGGGT
1 TCAGGTTCGGGTTCAATTTGGGT
67811 TTTGGCCAGA
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
63 5 0.07
64 21 0.28
65 49 0.65
ACGTcount: A:0.19, C:0.10, G:0.32, T:0.40
Consensus pattern (64 bp):
TCAGGTTCGGGTTCAATTTGGGTCAAGTTAATTCAGGTTCGGGTTGAATTTGAGTCAGATTAAT
Found at i:67807 original size:32 final size:32
Alignment explanation
Indices: 67679--67810 Score: 183
Period size: 32 Copynumber: 4.1 Consensus size: 32
67669 GTTCATTTCA
* *
67679 GGTCAAGTTAATTTAGGTTCGGGTTGAATTTG
1 GGTCAGGTTAATTCAGGTTCGGGTTGAATTTG
67711 GGTCAGGTTAATTCAGGTTCGGGTTGAATTTG
1 GGTCAGGTTAATTCAGGTTCGGGTTGAATTTG
*
67743 GGTCAGGTTAATTCGGGTTTCGGGTTGAATTTG
1 GGTCAGGTTAATTCAGG-TTCGGGTTGAATTTG
* * * **
67776 AGTTAGATTAATTCAGGTTCGGGTTCTATTTG
1 GGTCAGGTTAATTCAGGTTCGGGTTGAATTTG
67808 GGT
1 GGT
67811 TTTGGCCAGA
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
32 61 0.69
33 28 0.31
ACGTcount: A:0.19, C:0.08, G:0.33, T:0.40
Consensus pattern (32 bp):
GGTCAGGTTAATTCAGGTTCGGGTTGAATTTG
Found at i:67977 original size:16 final size:16
Alignment explanation
Indices: 67956--67995 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
67946 CATTTTCAGA
*
67956 TTCGGGTTCAGGTTAT
1 TTCGGGTTCAAGTTAT
*
67972 TTCGGGTTCAAGTTGT
1 TTCGGGTTCAAGTTAT
67988 TTCGGGTT
1 TTCGGGTT
67996 TGAGATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.10, C:0.12, G:0.33, T:0.45
Consensus pattern (16 bp):
TTCGGGTTCAAGTTAT
Found at i:68006 original size:16 final size:16
Alignment explanation
Indices: 67987--68024 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
67977 GTTCAAGTTG
67987 TTTCGGGTTTGAGATT
1 TTTCGGGTTTGAGATT
*
68003 TTTCGGGTTTGAGCTT
1 TTTCGGGTTTGAGATT
68019 TTTCGG
1 TTTCGG
68025 ATTCGGGTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.08, C:0.11, G:0.32, T:0.50
Consensus pattern (16 bp):
TTTCGGGTTTGAGATT
Found at i:68620 original size:30 final size:30
Alignment explanation
Indices: 68579--68670 Score: 87
Period size: 34 Copynumber: 2.9 Consensus size: 30
68569 CCATTTTATG
68579 GAGGGACTAAATCGATTTTTTTTAATAATA
1 GAGGGACTAAATCGATTTTTTTTAATAATA
*
68609 GAGGTACTAAATTGACAGATTTTATTTT-ATAATA
1 GAGGGACTAAA-T--C-GATTTT-TTTTAATAATA
* * *
68643 GAGGGATTAAATTGATCTTTTTCTAATA
1 GAGGGACTAAATCGAT-TTTTTTTAATA
68671 GCACAAGGAC
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
30 16 0.32
31 7 0.14
33 2 0.04
34 21 0.42
35 4 0.08
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (30 bp):
GAGGGACTAAATCGATTTTTTTTAATAATA
Found at i:68641 original size:34 final size:34
Alignment explanation
Indices: 68592--68657 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
68582 GGACTAAATC
*
68592 GATTTTTTTTAATAATAGAGGTACTAAATTGACA
1 GATTTTTTTTAATAATAGAGGGACTAAATTGACA
*
68626 GATTTTATTTT-ATAATAGAGGGATTAAATTGA
1 GATTTT-TTTTAATAATAGAGGGACTAAATTGA
68658 TCTTTTTCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 25 0.86
35 4 0.14
ACGTcount: A:0.38, C:0.03, G:0.17, T:0.42
Consensus pattern (34 bp):
GATTTTTTTTAATAATAGAGGGACTAAATTGACA
Found at i:69537 original size:17 final size:17
Alignment explanation
Indices: 69515--69564 Score: 75
Period size: 17 Copynumber: 2.9 Consensus size: 17
69505 AAGATTTGAG
69515 AAACATTACTAGTCATA
1 AAACATTACTAGTCATA
*
69532 AAACATGACTAGTTC-TA
1 AAACATTACTAG-TCATA
69549 AAACATTACTAGTCAT
1 AAACATTACTAGTCAT
69565 GTGGTATGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 2 0.07
17 25 0.86
18 2 0.07
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.30
Consensus pattern (17 bp):
AAACATTACTAGTCATA
Found at i:72139 original size:14 final size:14
Alignment explanation
Indices: 72120--72146 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
72110 TGTGTGTGTG
72120 TGTGAGAGAGAGAT
1 TGTGAGAGAGAGAT
72134 TGTGAGAGAGAGA
1 TGTGAGAGAGAGA
72147 AAAAGTTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.44, T:0.19
Consensus pattern (14 bp):
TGTGAGAGAGAGAT
Done.