Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022768.1 Corchorus olitorius cultivar O-4 contig22801, 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: 76727
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:9269 original size:178 final size:176
Alignment explanation
Indices: 8898--9281 Score: 432
Period size: 178 Copynumber: 2.2 Consensus size: 176
8888 TTTCCACCAT
* * * * *
8898 AAGCACAAATTATGTAATTATAAAGTAGATCGTCGATTCCCGCTAACCGAAACAACTAATTATTT
1 AAGCA-AAATTATATAA-TATTAAGTAGACCGTCGATTCCCACTAACCGAAACAACAAATTATTT
* *
8963 GAAGCATTTTTTATACCTTGAACATTAAATTTAGTTTTTGAGTCCTTCAAGAAAGTTGAAGATCA
64 GAAGCATTTTTTATACCTTGAACATTAAATGTAGTTTGTGAGTCCTTCAAGAAAGTTGAAGATCA
** * * *
9028 TGGGACAACCTTTCAAGAGACACTTGAATCACATCAATCAGACATCTG
129 TGAAACAACCTTTCAAGAGACACTTAAATCACATCAATCAGACAACCG
* * * *
9076 GAGCAAAAGTTATATAATATTAAGTGGACCGTCTATTCCCATTAACCGAAACAACAAATT-TTTC
1 AAGCAAAA-TTATATAATATTAAGTAGACCGTCGATTCCCACTAACCGAAACAACAAATTATTT-
* *
9140 GGAAGGATTTTTTATA-CTTGAAACATTAAATGTAGTTTGTGAGTCCTTC-AGAAAAGTTGTAGA
64 -GAAGCATTTTTTATACCTTG-AACATTAAATGTAGTTTGTGAGTCCTTCAAG-AAAGTTGAAGA
* * * * * * *
9203 TCATGAAACAATCTTTTAATAGACACTTAAATCACCTTAATCGGATAACCG
126 TCATGAAACAACCTTTCAAGAGACACTTAAATCACATCAATCAGACAACCG
* *
9254 AAGGGAAAATTATATAATATTAAATAGA
1 AA-GCAAAATTATATAATATTAAGTAGA
9282 TCGTTTAGCC
Statistics
Matches: 171, Mismatches: 29, Indels: 12
0.81 0.14 0.06
Matches are distributed among these distances:
176 3 0.02
177 45 0.26
178 118 0.69
179 5 0.03
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (176 bp):
AAGCAAAATTATATAATATTAAGTAGACCGTCGATTCCCACTAACCGAAACAACAAATTATTTGA
AGCATTTTTTATACCTTGAACATTAAATGTAGTTTGTGAGTCCTTCAAGAAAGTTGAAGATCATG
AAACAACCTTTCAAGAGACACTTAAATCACATCAATCAGACAACCG
Found at i:21394 original size:22 final size:22
Alignment explanation
Indices: 21366--21408 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
21356 TTTTCCGCAA
* *
21366 CAAGTCCTGGGCAGGAGTTGTC
1 CAAGTCCTGGACAGGACTTGTC
21388 CAAGTCCTGGACAGGACTTGT
1 CAAGTCCTGGACAGGACTTGT
21409 TCTGAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.23, G:0.33, T:0.23
Consensus pattern (22 bp):
CAAGTCCTGGACAGGACTTGTC
Found at i:21464 original size:21 final size:21
Alignment explanation
Indices: 21438--21479 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
21428 TTCAACAGAC
21438 CAAGTCCTGGGCAGGAGTTGT
1 CAAGTCCTGGGCAGGAGTTGT
21459 CAAGTCCTGGGCAGGAGTTGT
1 CAAGTCCTGGGCAGGAGTTGT
21480 TCTGAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.38, T:0.24
Consensus pattern (21 bp):
CAAGTCCTGGGCAGGAGTTGT
Found at i:21480 original size:71 final size:71
Alignment explanation
Indices: 21366--21550 Score: 316
Period size: 71 Copynumber: 2.6 Consensus size: 71
21356 TTTTCCGCAA
* * *
21366 CAAGTCCTGGGCAGGAGTTGTCCAAGTCCTGGACAGGACTTGTTCTGAATTTTCTTTCGTTTTTC
1 CAAGTCCTGGGCAGGAGTTGT-CAAGTCCTGGGCAGGACTTGTTCTGAATTTTCTTCCGTCTTTC
21431 AACAGAC
65 AACAGAC
*
21438 CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGAGTTGTTCTGAATTTTCTTCCGTCTTTCA
1 CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGTTCTGAATTTTCTTCCGTCTTTCA
21503 ACAGAC
66 ACAGAC
*
21509 CAGGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGT
1 CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGT
21551 CCTGTTTTTA
Statistics
Matches: 107, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
71 86 0.80
72 21 0.20
ACGTcount: A:0.19, C:0.22, G:0.28, T:0.30
Consensus pattern (71 bp):
CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGTTCTGAATTTTCTTCCGTCTTTCA
ACAGAC
Found at i:21538 original size:21 final size:21
Alignment explanation
Indices: 21512--21551 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
21502 AACAGACCAG
*
21512 GTCCTGGGCAGGAGTTGTCAA
1 GTCCTGGGCAGGACTTGTCAA
21533 GTCCTGGGCAGGACTTGTC
1 GTCCTGGGCAGGACTTGTC
21552 CTGTTTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.23, G:0.38, T:0.25
Consensus pattern (21 bp):
GTCCTGGGCAGGACTTGTCAA
Found at i:23134 original size:18 final size:19
Alignment explanation
Indices: 23102--23139 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
23092 CCCTCTTCTA
*
23102 AAACTAGAGAGAAAACTAG
1 AAACTAGAGAGAAAAATAG
23121 AAACTAGA-AGAAAAATAG
1 AAACTAGAGAGAAAAATAG
23139 A
1 A
23140 TGAAGAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.63, C:0.08, G:0.18, T:0.11
Consensus pattern (19 bp):
AAACTAGAGAGAAAAATAG
Found at i:25033 original size:60 final size:59
Alignment explanation
Indices: 24955--25259 Score: 244
Period size: 60 Copynumber: 5.1 Consensus size: 59
24945 CAAGATCAAG
* * *
24955 ATTAAGAGGTAAATAAAGGTAACAAGTAAAAAATTGGCTTAATTAAAGTTAATTAAGTTA
1 ATTAAGAGGAAAAGAAAGGTAAAAAGT-AAAAATTGGCTTAATTAAAGTTAATTAAGTTA
** *
25015 ATTCAA-AGGAAAAGAAAGGTAATTAGT-AAAATTGGCTTAATTAAAGTTAATTAAGTTG
1 ATT-AAGAGGAAAAGAAAGGTAAAAAGTAAAAATTGGCTTAATTAAAGTTAATTAAGTTA
* * * * * * ** *
25073 ATTAAGAGGTAAAGAAAAGTAAAAAGGTAATAATTGACTTAATTCAGGGCAATTAGGTTA
1 ATTAAGAGGAAAAGAAAGGTAAAAA-GTAAAAATTGGCTTAATTAAAGTTAATTAAGTTA
* * * * * * *
25133 AGTAAGAGGTAAAG-AAGAGTAAAAAGGTAATAATTGACTTAATTCATAG-CAATTAGGTTA
1 ATTAAGAGGAAAAGAAAG-GTAAAAA-GTAAAAATTGGCTTAATT-AAAGTTAATTAAGTTA
* * * *
25193 ACTAAGAGGTAAAG-AAGAGTAAAAAGGTAATAATTGGCTTAATTTAGAG-TAATTAAGTTA
1 ATTAAGAGGAAAAGAAAG-GTAAAAA-GTAAAAATTGGCTTAA-TTAAAGTTAATTAAGTTA
*
25253 ATCAAGA
1 ATTAAGA
25260 AGTAAAAAGG
Statistics
Matches: 209, Mismatches: 29, Indels: 14
0.83 0.12 0.06
Matches are distributed among these distances:
57 2 0.01
58 48 0.23
59 4 0.02
60 150 0.72
61 5 0.02
ACGTcount: A:0.48, C:0.04, G:0.20, T:0.28
Consensus pattern (59 bp):
ATTAAGAGGAAAAGAAAGGTAAAAAGTAAAAATTGGCTTAATTAAAGTTAATTAAGTTA
Found at i:25265 original size:60 final size:60
Alignment explanation
Indices: 24986--25381 Score: 366
Period size: 60 Copynumber: 6.7 Consensus size: 60
24976 ACAAGTAAAA
* * **
24986 AATTGGCTTAATT-AAAGTTAATTAAGTTAATTCAA-AGGAAAAGAA-AGGTAATTA-GTAA-
1 AATTGGCTTAATTCAGAG-TAATTAAGTTAA-TCAAGAGGTAAAGAAGA-GTAAAAAGGTAAT
* * * *
25044 AATTGGCTTAATT-AAAGTTAATTAAGTTGATTAAGAGGTAAAGAAAAGTAAAAAGGTAAT
1 AATTGGCTTAATTCAGAG-TAATTAAGTTAATCAAGAGGTAAAGAAGAGTAAAAAGGTAAT
* * * *
25104 AATTGACTTAATTCAGGGCAATTAGGTTAAGT-AAGAGGTAAAGAAGAGTAAAAAGGTAAT
1 AATTGGCTTAATTCAGAGTAATTAAGTTAA-TCAAGAGGTAAAGAAGAGTAAAAAGGTAAT
* * * *
25164 AATTGACTTAATTCATAGCAATTAGGTTAA-CTAAGAGGTAAAGAAGAGTAAAAAGGTAAT
1 AATTGGCTTAATTCAGAGTAATTAAGTTAATC-AAGAGGTAAAGAAGAGTAAAAAGGTAAT
* * * ** * *
25224 AATTGGCTTAATTTAGAGTAATTAAGTTAATCAAGAAGTAAA-AAGGGT-AATCGATAGT
1 AATTGGCTTAATTCAGAGTAATTAAGTTAATCAAGAGGTAAAGAAGAGTAAAAAGGTAAT
* * * **
25282 AATTAGCTTAATTCAGGGTAATTAAGTTAATCAAGAAGTAAA-AAGAAGTAACCA-GTAAT
1 AATTGGCTTAATTCAGAGTAATTAAGTTAATCAAGAGGTAAAGAAG-AGTAAAAAGGTAAT
* * *
25341 AATTAGCTTAATTCAGGGTAATTAAGTTAATCAAGAAGTAA
1 AATTGGCTTAATTCAGAGTAATTAAGTTAATCAAGAGGTAA
25382 GAAAAGGTAA
Statistics
Matches: 293, Mismatches: 34, Indels: 21
0.84 0.10 0.06
Matches are distributed among these distances:
57 3 0.01
58 91 0.31
59 56 0.19
60 139 0.47
61 4 0.01
ACGTcount: A:0.46, C:0.05, G:0.20, T:0.29
Consensus pattern (60 bp):
AATTGGCTTAATTCAGAGTAATTAAGTTAATCAAGAGGTAAAGAAGAGTAAAAAGGTAAT
Found at i:25265 original size:120 final size:120
Alignment explanation
Indices: 24986--25402 Score: 362
Period size: 118 Copynumber: 3.5 Consensus size: 120
24976 ACAAGTAAAA
* * * * *
24986 AATTGGCTTAATT-AAAGTTAATTAAGTTAATTCAA-AGGAAAAGAA-AGGTAATTA-GTAA-AA
1 AATTGGCTTAATTCAGAG-TAATTAAGTTAAGTCAAGAAGTAAAGAAGA-GTAAATAGGTAATAA
* * *
25046 TTGGCTTAATT-AAAGTTAATTAAGTTGATTAAGAGGTAAAGAAAAGTAAAAAGGTAAT
64 TTGACTTAATTCAAAG-TAATTAAGTT-AATAAGAGGTAAAGAAGAGTAAAAAGGTAAT
* * * * * *
25104 AATTGACTTAATTCAGGGCAATTAGGTTAAGT-AAGAGGTAAAGAAGAGTAAAAAGGTAATAATT
1 AATTGGCTTAATTCAGAGTAATTAAGTTAAGTCAAGAAGTAAAGAAGAGTAAATAGGTAATAATT
* * *
25168 GACTTAATTCATAGCAATTAGGTTAACTAAGAGGTAAAGAAGAGTAAAAAGGTAAT
66 GACTTAATTCAAAGTAATTAAGTTAA-TAAGAGGTAAAGAAGAGTAAAAAGGTAAT
* * * * *
25224 AATTGGCTTAATTTAGAGTAATTAAGTTAA-TCAAGAAGTAAA-AAGGGT-AATCGATAGTAATT
1 AATTGGCTTAATTCAGAGTAATTAAGTTAAGTCAAGAAGTAAAGAAGAGTAAATAGGTAATAATT
** * **
25286 -AGCTTAATTCAGGGTAATTAAGTTAATCAAGAAGTAAA-AAGAAGTAACCA-GTAAT
66 GA-CTTAATTCAAAGTAATTAAGTTAAT-AAGAGGTAAAGAAG-AGTAAAAAGGTAAT
* * *
25341 AATTAGCTTAATTCAGGGTAATTAAGTTAA-TCAAGAAGT-AAGAAAAGGTAAATCA-GTAATAA
1 AATTGGCTTAATTCAGAGTAATTAAGTTAAGTCAAGAAGTAAAGAAGA-GTAAAT-AGGTAATAA
25403 GTAGCCCAAT
Statistics
Matches: 243, Mismatches: 41, Indels: 29
0.78 0.13 0.09
Matches are distributed among these distances:
116 2 0.01
117 50 0.21
118 84 0.35
119 22 0.09
120 82 0.34
121 3 0.01
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.28
Consensus pattern (120 bp):
AATTGGCTTAATTCAGAGTAATTAAGTTAAGTCAAGAAGTAAAGAAGAGTAAATAGGTAATAATT
GACTTAATTCAAAGTAATTAAGTTAATAAGAGGTAAAGAAGAGTAAAAAGGTAAT
Found at i:25303 original size:58 final size:58
Alignment explanation
Indices: 24986--25542 Score: 308
Period size: 60 Copynumber: 9.4 Consensus size: 58
24976 ACAAGTAAAA
* * * * * * * *
24986 AATTGGCTTAATTAAAGTTAATTAAGTTAATTCAA-AGGAAAAGAAAGGTAATTAGTAA-
1 AATTAGCTTAATTCAGGGTAATTAAGTTAA-TCAAGAAGTAAA-AAGGGTAATCAGTAAT
* * * * * * * ** **
25044 AATTGGCTTAATTAAAGTTAATTAAGTTGATTAAGAGGTAAAGAAAAGTAAAAAGGTAAT
1 AATTAGCTTAATTCAGGGTAATTAAGTTAATCAAGAAGTAAA-AAGGGTAATCA-GTAAT
* * * * **
25104 AATT-GACTTAATTCAGGGCAATTAGGTTAAGT-AAGAGGTAAAGAAGAGTAAAAAGGTAAT
1 AATTAG-CTTAATTCAGGGTAATTAAGTTAA-TCAAGAAGTAAA-AAGGGTAATCA-GTAAT
** * * * * **
25164 AATT-GACTTAATTCATAGCAATTAGGTTAA-CTAAGAGGTAAAGAAGAGTAAAAAGGTAAT
1 AATTAG-CTTAATTCAGGGTAATTAAGTTAATC-AAGAAGTAAA-AAGGGTAATCA-GTAAT
* * * *
25224 AATTGGCTTAATTTAGAGTAATTAAGTTAATCAAGAAGTAAAAAGGGTAATC-GATAGT
1 AATTAGCTTAATTCAGGGTAATTAAGTTAATCAAGAAGTAAAAAGGGTAATCAG-TAAT
* *
25282 AATTAGCTTAATTCAGGGTAATTAAGTTAATCAAGAAGTAAAAAGAAGTAACCAGTAAT
1 AATTAGCTTAATTCAGGGTAATTAAGTTAATCAAGAAGTAAAAAG-GGTAATCAGTAAT
*
25341 AATTAGCTTAATTCAGGGTAATTAAGTTAATCAAGAAGTAAGAAAAGGTAAATCAGTAAT
1 AATTAGCTTAATTCAGGGTAATTAAGTTAATCAAGAAGTAA-AAAGGGT-AATCAGTAAT
* ** * * *
25401 AAGTAGCCCAATTCAGGGTAATTAAGTCAAAT-AAGAAGCTGAGAATA-GGTAA-AAGGTAAT
1 AATTAGCTTAATTCAGGGTAATTAAGT-TAATCAAGAAG-T-A-AAAAGGGTAATCA-GTAAT
* * ** * * * * *
25461 AATCAGCTTAATTTAGGACAATTAACTTAATTAAGAGGTTGAGAAA-GATAATCAGTAAT
1 AATTAGCTTAATTCAGGGTAATTAAGTTAATCAAGAAG-T-AAAAAGGGTAATCAGTAAT
* * *
25520 AAGTGGATTAATTCAGGGTAATT
1 AATTAGCTTAATTCAGGGTAATT
25543 GAGCCAACTA
Statistics
Matches: 417, Mismatches: 61, Indels: 41
0.80 0.12 0.08
Matches are distributed among these distances:
57 4 0.01
58 89 0.21
59 94 0.23
60 216 0.52
61 10 0.02
62 3 0.01
63 1 0.00
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.28
Consensus pattern (58 bp):
AATTAGCTTAATTCAGGGTAATTAAGTTAATCAAGAAGTAAAAAGGGTAATCAGTAAT
Found at i:25460 original size:60 final size:59
Alignment explanation
Indices: 25241--25462 Score: 211
Period size: 59 Copynumber: 3.7 Consensus size: 59
25231 TTAATTTAGA
* * * * * **
25241 GTAATTAAGTTAATCAAGAAGTAA-AAAGGGTAATC-GATAGTAATTAGCTTAATTCAGG
1 GTAATTAAGTAAATCAAGAAGTAAGAAAAGGTAAACAG-TAATAAGTAGCCCAATTCAGG
* * * * **
25299 GTAATTAAGTTAATCAAGAAGTAA-AAAGAAGTAACCAGTAATAATTAGCTTAATTCAGG
1 GTAATTAAGTAAATCAAGAAGTAAGAAA-AGGTAAACAGTAATAAGTAGCCCAATTCAGG
*
25358 GTAATTAAGTTAATCAAGAAGTAAGAAAAGGTAAATCAGTAATAAGTAGCCCAATTCAGG
1 GTAATTAAGTAAATCAAGAAGTAAGAAAAGGTAAA-CAGTAATAAGTAGCCCAATTCAGG
* *
25418 GTAATTAAGTCAAAT-AAGAAGCTGAGAATAGGTAAA-AGGTAATAA
1 GTAATTAAGT-AAATCAAGAAG-TAAGAAAAGGTAAACA-GTAATAA
25463 TCAGCTTAAT
Statistics
Matches: 145, Mismatches: 12, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
58 27 0.19
59 55 0.38
60 48 0.33
61 15 0.10
ACGTcount: A:0.47, C:0.08, G:0.20, T:0.26
Consensus pattern (59 bp):
GTAATTAAGTAAATCAAGAAGTAAGAAAAGGTAAACAGTAATAAGTAGCCCAATTCAGG
Found at i:25559 original size:119 final size:120
Alignment explanation
Indices: 25336--25559 Score: 272
Period size: 119 Copynumber: 1.9 Consensus size: 120
25326 GAAGTAACCA
* ** * *
25336 GTAATAATTAGCTTAATTCAGGGTAATTAAGTTAATCAAGAAGTAAGAAAAGGTAAATCAGTAAT
1 GTAATAATCAGCTTAATTCAGGACAATTAACTTAATCAAGAAGTAAGAAAAGATAAATCAGTAAT
* * *
25401 AAGTAGCCCAATTCAGGGTAATTAAGTCAAATAAGAAGCTGAGAATAGGTAAAAG
66 AAGTAGACCAATTCAGGGTAATTAAGCCAAATAAAAAGCTGAGAATAGGTAAAAG
* * * *
25456 GTAATAATCAGCTTAATTTAGGACAATTAACTTAATTAAGAGGT-TGAGAAAGAT-AATCAGTAA
1 GTAATAATCAGCTTAATTCAGGACAATTAACTTAATCAAGAAGTAAGA-AAAGATAAATCAGTAA
* ** * *
25519 TAAGTGGATTAATTCAGGGTAATTGAGCCAACTAAAAAGCT
65 TAAGTAGACCAATTCAGGGTAATTAAGCCAAATAAAAAGCT
25560 AAGTAAGGTG
Statistics
Matches: 86, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
119 44 0.51
120 42 0.49
ACGTcount: A:0.44, C:0.09, G:0.20, T:0.27
Consensus pattern (120 bp):
GTAATAATCAGCTTAATTCAGGACAATTAACTTAATCAAGAAGTAAGAAAAGATAAATCAGTAAT
AAGTAGACCAATTCAGGGTAATTAAGCCAAATAAAAAGCTGAGAATAGGTAAAAG
Found at i:31852 original size:328 final size:328
Alignment explanation
Indices: 31254--31909 Score: 1068
Period size: 328 Copynumber: 2.0 Consensus size: 328
31244 CTAAACCTGT
* * * *
31254 CTTGACTTTAGCGTTTTTCATCTCTTTTCTTTTCTATTTTGCTAGGAAAACCAATCTGAGAGGAC
1 CTTGACTGTAGCGCTTTTCATCTATTTTCTTTTCTATTTTGCTAGGAAAACCAAGCTGAGAGGAC
* *
31319 TGATAACAGAGAATCAAATCCTTGCAACTCAGTCATCAATAGAGTTGGTGCAAACTCATCCAAAG
66 TGATAACAGAGAATCAAATCCTTGCAACTCAATCATCAATAGAGTTGGTGCAAACTCAACCAAAG
* *
31384 GGAGAGGAAAAGGAGCCATATCAGACTGTCATCAAGCTACAACAGCTGCTGGTGGTGAATCTACA
131 GGAGAGGAAAAGGAGCCATATCAGACTATCATCAAGCTACAACAACTGCTGGTGGTGAATCTACA
31449 AAAGCAAATGCTTCTGGATCATTTGTTGTTGGTGGCTATCAACCTCAAGCACCAATTGTTTAAGC
196 AAAGCAAATGCTTCTGGATCATTTGTTGTTGGTGGCTATCAACCTCAAGCACCAATTGTTTAAGC
31514 ACATTTCAATGTGTCTTTGCTTCAGCTAGGGTTCCCACTTTCAACACAGGTGCCTGCAAATGCCA
261 ACATTTCAATGTGTCTTTGCTTCAGCTAGGGTTCCCA-TTTCAACACAGGTGCCTGCAAATGCCA
31579 TTGC
325 TTGC
* *
31583 CTTGACTGTAGTGCTTTTCATCTATTTTCTTTTCTATTTTGCTAGGAAAACCAAGCTGTGAGGAC
1 CTTGACTGTAGCGCTTTTCATCTATTTTCTTTTCTATTTTGCTAGGAAAACCAAGCTGAGAGGAC
*
31648 TGATAACAGAGAATCAAATCCCTT-CAGCTCAATCA-CAATAGA-TCTGGTGCAAACTCAACCAA
66 TGATAACAGAGAATCAAAT-CCTTGCAACTCAATCATCAATAGAGT-TGGTGCAAACTCAACCAA
* *
31710 AGGGAGAGGAAAATGG-GCCATGTCAGACTATCATCAAGCTACAACAATTGCTGGTGGTGAATCT
129 AGGGAGAGGAAAA-GGAGCCATATCAGACTATCATCAAGCTACAACAACTGCTGGTGGTGAATCT
* * * *
31774 GCAGAAGCAAATGCTTCTGGATCGTTTGTTGTTGGTGGCTATCAACCTCAAGCACCAATTGTTTT
193 ACAAAAGCAAATGCTTCTGGATCATTTGTTGTTGGTGGCTATCAACCTCAAGCACCAATTGTTTA
* * *
31839 AGCACATTTCAATGTGTCTTTGCTTTAGCTAGGGTTCCCATTTCAGCACAGGTGTCTGCAAATGC
258 AGCACATTTCAATGTGTCTTTGCTTCAGCTAGGGTTCCCATTTCAACACAGGTGCCTGCAAATGC
31904 CATTGC
323 CATTGC
31910 TATAGTGTCT
Statistics
Matches: 304, Mismatches: 20, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
327 30 0.10
328 181 0.60
329 89 0.29
330 4 0.01
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.30
Consensus pattern (328 bp):
CTTGACTGTAGCGCTTTTCATCTATTTTCTTTTCTATTTTGCTAGGAAAACCAAGCTGAGAGGAC
TGATAACAGAGAATCAAATCCTTGCAACTCAATCATCAATAGAGTTGGTGCAAACTCAACCAAAG
GGAGAGGAAAAGGAGCCATATCAGACTATCATCAAGCTACAACAACTGCTGGTGGTGAATCTACA
AAAGCAAATGCTTCTGGATCATTTGTTGTTGGTGGCTATCAACCTCAAGCACCAATTGTTTAAGC
ACATTTCAATGTGTCTTTGCTTCAGCTAGGGTTCCCATTTCAACACAGGTGCCTGCAAATGCCAT
TGC
Found at i:36045 original size:131 final size:132
Alignment explanation
Indices: 35810--36067 Score: 500
Period size: 131 Copynumber: 2.0 Consensus size: 132
35800 TTTGGATTAG
35810 GATGAGAGAGAGGGTGGCTTTTAATGCGAAAAAAAGTTAATTTATTTTTTTTCTAAATTTTACAA
1 GATGAGAGAGAGGGTGGCTTTTAATGCGAAAAAAAGTTAATTTATTTTTTTTCTAAATTTTACAA
35875 AATTCTATTTTCCAAGTTGTTAGACATGTCACCTTGTCTGAGGTCGTGTTCAACAAGCACACTAG
66 AATTCTATTTTCCAAGTTGTTAGACATGTCACCTTGTCTGAGGTCGTGTTCAACAAGCACACTAG
35940 TC
131 TC
*
35942 GATGAGAGAGAGGGTGGCTTTTAATGCGGAAAAAAGTTAATTTA-TTTTTTTCTAAATTTTACAA
1 GATGAGAGAGAGGGTGGCTTTTAATGCGAAAAAAAGTTAATTTATTTTTTTTCTAAATTTTACAA
36006 AATTCTATTTTCCAAGTTGTTAGACATGTCACCTTGTCTGAGGTCGTGTTCAACAAGCACAC
66 AATTCTATTTTCCAAGTTGTTAGACATGTCACCTTGTCTGAGGTCGTGTTCAACAAGCACAC
36068 CAGCCGATTC
Statistics
Matches: 125, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
131 82 0.66
132 43 0.34
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.36
Consensus pattern (132 bp):
GATGAGAGAGAGGGTGGCTTTTAATGCGAAAAAAAGTTAATTTATTTTTTTTCTAAATTTTACAA
AATTCTATTTTCCAAGTTGTTAGACATGTCACCTTGTCTGAGGTCGTGTTCAACAAGCACACTAG
TC
Found at i:36183 original size:56 final size:56
Alignment explanation
Indices: 36097--36209 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
36087 CGGCCAGGCA
36097 AACATTATATCATGAATTGAGTCTTTAGCTCCTTAGGTATCTTCTTTGGGTCGCGC
1 AACATTATATCATGAATTGAGTCTTTAGCTCCTTAGGTATCTTCTTTGGGTCGCGC
*
36153 AACATTATATCCTGAATTGAGTCTTTAGCTCCTTAGGTATCTTCTTTGGGTCGCGC
1 AACATTATATCATGAATTGAGTCTTTAGCTCCTTAGGTATCTTCTTTGGGTCGCGC
36209 A
1 A
36210 GCTAGGTTTA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.39
Consensus pattern (56 bp):
AACATTATATCATGAATTGAGTCTTTAGCTCCTTAGGTATCTTCTTTGGGTCGCGC
Found at i:36247 original size:56 final size:56
Alignment explanation
Indices: 36187--36300 Score: 219
Period size: 56 Copynumber: 2.0 Consensus size: 56
36177 TTAGCTCCTT
*
36187 AGGTATCTTCTTTGGGTCGCGCAGCTAGGTTTATTGGGTAAGTCTATCAACAAGGC
1 AGGTATCTTCATTGGGTCGCGCAGCTAGGTTTATTGGGTAAGTCTATCAACAAGGC
36243 AGGTATCTTCATTGGGTCGCGCAGCTAGGTTTATTGGGTAAGTCTATCAACAAGGC
1 AGGTATCTTCATTGGGTCGCGCAGCTAGGTTTATTGGGTAAGTCTATCAACAAGGC
36299 AG
1 AG
36301 ATGCGTTTGT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.31
Consensus pattern (56 bp):
AGGTATCTTCATTGGGTCGCGCAGCTAGGTTTATTGGGTAAGTCTATCAACAAGGC
Found at i:38243 original size:12 final size:12
Alignment explanation
Indices: 38226--38265 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
38216 AAATATTAGG
38226 TTTTTATTTTAT
1 TTTTTATTTTAT
38238 TTTTTATTTTAT
1 TTTTTATTTTAT
38250 TATTTT-TATTTAT
1 T-TTTTAT-TTTAT
38263 TTT
1 TTT
38266 ATTTTTTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTATTTTAT
Found at i:38254 original size:15 final size:16
Alignment explanation
Indices: 38228--38272 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
38218 ATATTAGGTT
*
38228 TTTATTTTATTTTTTA
1 TTTATATTATTTTTTA
38244 TTT-TATTA-TTTTTA
1 TTTATATTATTTTTTA
*
38258 TTTATTTTATTTTTT
1 TTTATATTATTTTTT
38273 TGGTGAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 9 0.36
15 8 0.32
16 8 0.32
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTATATTATTTTTTA
Found at i:38261 original size:18 final size:16
Alignment explanation
Indices: 38227--38273 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 16
38217 AATATTAGGT
38227 TTTTATTTTATTTTTTA
1 TTTTATTTT-TTTTTTA
38244 TTTTATTATTTTTATTTA
1 TTTTATT-TTTTT-TTTA
38262 TTTTATTTTTTT
1 TTTTATTTTTTT
38274 GGTGAGAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 15 0.54
18 13 0.46
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTATTTTTTTTTTA
Found at i:38685 original size:38 final size:38
Alignment explanation
Indices: 38642--38752 Score: 124
Period size: 38 Copynumber: 3.0 Consensus size: 38
38632 TTCCTTCTCT
38642 ATATTAGCTAAGGGGTTTTATAGGCTACATCTTCTTTG
1 ATATTAGCTAAGGGGTTTTATAGGCTACATCTTCTTTG
** * * * *
38680 ATATTAGCTCGGGGGTATTGATA--TTTC--CTTCTCT-
1 ATATTAGCTAAGGGGT-TTTATAGGCTACATCTTCTTTG
38714 ATATTAGCTAAGGGGTTTTATAGGCTACATCTTCTTTG
1 ATATTAGCTAAGGGGTTTTATAGGCTACATCTTCTTTG
38752 A
1 A
38753 GGTTCTCTAG
Statistics
Matches: 55, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
33 5 0.09
34 14 0.25
35 8 0.15
37 8 0.15
38 15 0.27
39 5 0.09
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.42
Consensus pattern (38 bp):
ATATTAGCTAAGGGGTTTTATAGGCTACATCTTCTTTG
Found at i:38729 original size:34 final size:34
Alignment explanation
Indices: 38624--38729 Score: 106
Period size: 34 Copynumber: 3.0 Consensus size: 34
38614 TAGTATTTGC
38624 ATTGATATTTCCTTCTCTATATTAGCTAAGGGGT
1 ATTGATATTTCCTTCTCTATATTAGCTAAGGGGT
* * * * **
38658 -TTTATAGGCTACATCTTCTTTGATATTAGCTCGGGGGT
1 ATTGATA--TTTC--CTTCTCT-ATATTAGCTAAGGGGT
38696 ATTGATATTTCCTTCTCTATATTAGCTAAGGGGT
1 ATTGATATTTCCTTCTCTATATTAGCTAAGGGGT
38730 TTTATAGGCT
Statistics
Matches: 54, Mismatches: 12, Indels: 12
0.69 0.15 0.15
Matches are distributed among these distances:
33 5 0.09
34 14 0.26
35 8 0.15
37 8 0.15
38 14 0.26
39 5 0.09
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.43
Consensus pattern (34 bp):
ATTGATATTTCCTTCTCTATATTAGCTAAGGGGT
Found at i:42779 original size:47 final size:47
Alignment explanation
Indices: 42710--42890 Score: 335
Period size: 47 Copynumber: 3.9 Consensus size: 47
42700 CTAACAGTCT
* *
42710 AACACTTTACCAACAGACTATATTCGACTGCAGGCTGCATGTATTTC
1 AACACTTTACCAACAGACTATATTCGACCGCAGGCTGCATGTACTTC
*
42757 AACACTTTACCAACAGACTATATTCAACCGCAGGCTGCATGTACTTC
1 AACACTTTACCAACAGACTATATTCGACCGCAGGCTGCATGTACTTC
42804 AACACTTTACCAACAGACTATATTCGACCGCAGGCTGCATGTACTTC
1 AACACTTTACCAACAGACTATATTCGACCGCAGGCTGCATGTACTTC
42851 AACACTTTACCAACAGACTATATTCGACCGCAGGCTGCAT
1 AACACTTTACCAACAGACTATATTCGACCGCAGGCTGCAT
42891 ATTCAAGTTA
Statistics
Matches: 130, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 130 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (47 bp):
AACACTTTACCAACAGACTATATTCGACCGCAGGCTGCATGTACTTC
Found at i:44405 original size:11 final size:11
Alignment explanation
Indices: 44362--44399 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
44352 TTCCTATATA
*
44362 AAATAAATTAT
1 AAATTAATTAT
44373 CAAA-TAATTAT
1 -AAATTAATTAT
44384 AAATTAATTAT
1 AAATTAATTAT
44395 AAATT
1 AAATT
44400 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:46974 original size:13 final size:13
Alignment explanation
Indices: 46956--46980 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46946 TTCATTCAAA
46956 ATAATAATAATAT
1 ATAATAATAATAT
46969 ATAATAATAATA
1 ATAATAATAATA
46981 AGAGTAAGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATAATAATAATAT
Found at i:52056 original size:6 final size:6
Alignment explanation
Indices: 52047--52091 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
52037 TGTATATGTA
52047 TGTGGG TGTGGG TGTGGG TGTGGG TGTGGG TGTGGG TGTGGG TGT
1 TGTGGG TGTGGG TGTGGG TGTGGG TGTGGG TGTGGG TGTGGG TGT
52092 TATATGAGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.64, T:0.36
Consensus pattern (6 bp):
TGTGGG
Found at i:53712 original size:21 final size:21
Alignment explanation
Indices: 53688--53732 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
53678 TTGACACTGT
*
53688 TTAGCAACTGTACAGATTAGA
1 TTAGCAACTGTACAGATGAGA
**
53709 TTAGGTACTGTACAGATGAGA
1 TTAGCAACTGTACAGATGAGA
53730 TTA
1 TTA
53733 TTAGAGCAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (21 bp):
TTAGCAACTGTACAGATGAGA
Found at i:55682 original size:60 final size:60
Alignment explanation
Indices: 55551--55683 Score: 142
Period size: 60 Copynumber: 2.2 Consensus size: 60
55541 TGTGACACCA
* * * * *
55551 AACCCTTATTTGAATATTTTTGCATTCATTCAGGTCATATTCAACCAAATTAAAAGTATG
1 AACCCTAAATTGAACATTTTTACATACATTCAGGTCATATTCAACCAAATTAAAAGTATG
*** * * * *
55611 GGTCCTCAATTGAACATTTTTACATACATT-AGGATCTTATTTAACCAAATTACAAGTATG
1 AACCCTAAATTGAACATTTTTACATACATTCAGG-TCATATTCAACCAAATTAAAAGTATG
55671 AACCCTAAATTGA
1 AACCCTAAATTGA
55684 GTAATCTCGC
Statistics
Matches: 57, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
59 3 0.05
60 54 0.95
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (60 bp):
AACCCTAAATTGAACATTTTTACATACATTCAGGTCATATTCAACCAAATTAAAAGTATG
Found at i:56646 original size:29 final size:28
Alignment explanation
Indices: 56590--56647 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
56580 TTCTTGTCTC
*
56590 TGTTGCGCCAAAAATCTCTTCGGGAGTT
1 TGTTGCGCCAAAAATCTCTTCGAGAGTT
*
56618 TGTTGCGCCAAAAATCTCTTGCTAGAGTT
1 TGTTGCGCCAAAAATCTCTT-CGAGAGTT
56647 T
1 T
56648 TCGCGAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 20 0.74
29 7 0.26
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.34
Consensus pattern (28 bp):
TGTTGCGCCAAAAATCTCTTCGAGAGTT
Found at i:59701 original size:33 final size:34
Alignment explanation
Indices: 59663--59728 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
59653 TTTATTTAAC
* *
59663 ATGCATGATCTCCTTCTTCTACCTTT-TTTTATT
1 ATGCATAATCTCCTCCTTCTACCTTTCTTTTATT
*
59696 ATGCATAATCTTCTCCTTCTACCTTTCTTTTAT
1 ATGCATAATCTCCTCCTTCTACCTTTCTTTTAT
59729 CATTAAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 23 0.79
34 6 0.21
ACGTcount: A:0.17, C:0.26, G:0.05, T:0.53
Consensus pattern (34 bp):
ATGCATAATCTCCTCCTTCTACCTTTCTTTTATT
Found at i:66085 original size:39 final size:39
Alignment explanation
Indices: 66036--66114 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
66026 GAAAAAAATA
66036 AGTATTCTCATCTCATGTATAACTAATTCAAGACTAAGT
1 AGTATTCTCATCTCATGTATAACTAATTCAAGACTAAGT
66075 AGTATTCTCATCTCATGTATAACTAATTCAAGACTAAGT
1 AGTATTCTCATCTCATGTATAACTAATTCAAGACTAAGT
66114 A
1 A
66115 CTCTTTCAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (39 bp):
AGTATTCTCATCTCATGTATAACTAATTCAAGACTAAGT
Found at i:66611 original size:27 final size:28
Alignment explanation
Indices: 66580--66641 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
66570 GAATTTTGAA
* *
66580 AGTTTAGGGGCAAATTGTCTTTAAT-AT
1 AGTTTAGGGGCAAAATGTCCTTAATCAT
*
66607 AGTTTAGGGGTAAAATGTCCTTAATCCAT
1 AGTTTAGGGGCAAAATGTCCTTAAT-CAT
66636 AGTTTA
1 AGTTTA
66642 ACGGACAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 22 0.73
29 8 0.27
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.39
Consensus pattern (28 bp):
AGTTTAGGGGCAAAATGTCCTTAATCAT
Found at i:71685 original size:28 final size:27
Alignment explanation
Indices: 71628--71698 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
71618 TATATATATT
* *
71628 TTTTATAATAATAT-TATTATTTCTGAA
1 TTTT-TAATAATATATATTATATCTAAA
*
71655 TTTTTAATAATATATATTATATGTAATA
1 TTTTTAATAATATATATTATATCTAA-A
*
71683 TTTTTAAAAATGATAT
1 TTTTTAATAAT-ATAT
71699 TAATTTAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 9 0.24
27 13 0.35
28 11 0.30
29 4 0.11
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (27 bp):
TTTTTAATAATATATATTATATCTAAA
Found at i:73886 original size:21 final size:21
Alignment explanation
Indices: 73860--73922 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
73850 GATTTTAATA
73860 AACCTTCCTATGAAATTTTGT
1 AACCTTCCTATGAAATTTTGT
* *
73881 AACCTTTCTATG-ATTTTTGAT
1 AACCTTCCTATGAAATTTTG-T
* * *
73902 AACCTCCCTGTGAGATTTTGT
1 AACCTTCCTATGAAATTTTGT
73923 TAATCTCCAT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
20 6 0.18
21 22 0.67
22 5 0.15
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (21 bp):
AACCTTCCTATGAAATTTTGT
Done.