Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019425.1 Corchorus olitorius cultivar O-4 contig19458, 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: 13573
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Found at i:708 original size:329 final size:328
Alignment explanation
Indices: 31--1802 Score: 1457
Period size: 329 Copynumber: 5.4 Consensus size: 328
21 TGTGTCTTGG
* * * * * *
31 TGCCAAAAATCATGCAAAACTGAGCC-AGTCCTCGGAATGCATTTTTATCTC-AAAA-CGATGAT
1 TGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAA-CCGTTTTTAGC-CAAAAACCG-TGAT
* ** * * *
93 GGTTAGTAAACGATTTCGGTTTAAATTTTGCAAAAGTTG-ACCTGAATAATCTTT-CCTCGATTT
63 GGTTAGTACACGATTTCGGTTTAAATTTTGCAAAAAATGAACC-GAA-AGTTTTTCCCTCAATTT
* * * * * ** * *
156 TTTCCCACAATAGTCATAAGAAAATACATAATTTATCACCAAAAA-ATGGAAGGGCTTTTTACGC
126 TTTACCACAATACTCATAA-AAAGTATATAATTCA-CGTCAAAAAGATTGAAGGGCTTTTCACGC
* * * * **** *
220 ATT-TGATATCGTTTTTCCTATTTTTTCCGAATTATTTTTTAATTAAATTGAAACCGGTTTCTGA
189 -TTCT-ATATCGTTTTTCCTA-TTTTTCTGAATTAATTTCTAATTAAATCGAAACATAATTCAGA
* * * * * *
284 TGCTCGTAAAAACAAATCCTTAAATTCAATGTAGG-TTAGATCCT-GTTAGATTAATACAGATAT
251 TGCTCGTAAAAACAAATCCTCAAATCCAATGT-GGCTGAGAT-TTGGTTAGATGAATATAGATAT
* ** * * ***
347 GTCAATTACTGTCGG
314 TTCAAGAAGTCTTAC
* * *
362 TGCCAAAAATCATGCAAAAATGAGCTGGGGCCCCGGAACCTATTTTTAGCCAAAAACCGTGATGG
1 TGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACC-GTTTTTAGCCAAAAACCGTGATGG
* * * * ** *
427 TTTGTAAACGATTTCGGTTTAAGTTTTGCAAAAAAATGAATCGAAAGTTTTTCTTTTAATTTTTT
65 TTAGTACACGATTTCGGTTTAAATTTTGC-AAAAAATGAACCGAAAGTTTTTCCCTCAATTTTTT
* * * * * * *
492 ACCACAATACTCATAAATAGTATAGAATTCGACGCCAAAAACATTGAAAGCCTTTTCATGCTT-T
129 ACCACAATACTCATAAAAAGTATATAATTC-ACGTCAAAAAGATTGAAGGGCTTTTCACGCTTCT
* * * * ** *
556 -TATCGCTTTTCCTATTTTTTTTAATTAATTTCTAATTAAATCGAAGCA-AGATTCAGATTTTTG
193 ATATCGTTTTTCCTATTTTTCTGAATTAATTTCTAATTAAATCGAAACATA-ATTCAGATGCTCG
* * *
619 TAAAAACAAATCCTTAAACCCAATGTGGCTGATATTTGGTTAGATGAATATAGA-ATTTTCAAGA
257 TAAAAACAAATCCTCAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATA-TTTCAAGA
* *
683 ATTCTTGGC
321 AGTCTT-AC
*** * * * *
692 T-CCAAAAATCATGCAAAACTGATTTGGTGCCCCAGAATGCGTTTTTAGCC-AAAACTTGTGAAT
1 TGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAA-CCGTTTTTAGCCAAAAAC-CGTG-AT
* * *
755 -GTTAGTACACGATTTCGG-TTAAAATTTGCAAAAATTGACCCGAAAGATTTTT--CTCAA-TTT
63 GGTTAGTACACGATTTCGGTTTAAATTTTGCAAAAAATGAACCGAAAG-TTTTTCCCTCAATTTT
* * * * * *
815 TTAGCCACATTACTCATGAAAAAATAAATAATTCATCG-CAAGAAA-ATGGAATGAG-TTTGCAC
127 TTA-CCACAATACTCAT-AAAAAGTATATAATTCA-CGTCAA-AAAGATTGAA-GGGCTTTTCAC
* ** **** * *
877 GCTTCTATTATCGTTTTTCCCATTTTTCTGAATTAATTTCTAATTAAATTAAAACCGGTTTCTGG
187 GCTTCTA-TATCGTTTTTCCTATTTTTCTGAATTAATTTCTAATTAAATCGAAACATAATTCAGA
* * * *
942 TGCTCGTAAAAA-AAATCCAT-AAATCCAACGTGTCTGAGATTTGGTTCA-ATTAATATAGATAC
251 TGCTCGTAAAAACAAATCC-TCAAATCCAATGTGGCTGAGATTTGGTT-AGATGAATATAGATAT
* *
1004 TACAAGGAGTCTTGAC
314 TTCAAGAAGTCTT-AC
* * ** * *
1020 -GCC-AAAATCATGCAAAACTTAGCCGGGACCCCGGAACGCGTTTTTAATCACAAACCGTGGTGG
1 TGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAAC-CGTTTTTAGCCAAAAACCGTGATGG
* *
1083 TTAGTACACGATTTC-CTCTTAAATTTTGCAAAAAATGAACCGAAAGTTTTTCCCTCAGTTTTTT
65 TTAGTACACGATTTCGGT-TTAAATTTTGCAAAAAATGAACCGAAAGTTTTTCCCTCAATTTTTT
**
1147 GTCACAATACTC--AAAAAGTATATAATTCAACGTCAAAAAGATTGAAGGGCTTTTCACGCTTCT
129 ACCACAATACTCATAAAAAGTATATAATTC-ACGTCAAAAAGATTGAAGGGCTTTTCACGCTTCT
* *
1210 AATATCGTTTTTCCTATTTTTTTCCGAATTAATTTATAATTAAATCGAAACATAATTCAGATGCT
193 -ATATCGTTTTTCCTA--TTTTTCTGAATTAATTTCTAATTAAATCGAAACATAATTCAGATGCT
* * * *
1275 CGTAAAATCAAATCCTCAAATCCAATGTTGTTGAGATTTTGTTAGATGAATATAGATATTTCAAT
255 CGTAAAAACAAATCCTCAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAA-
*
1340 G-AGTCTTAA
319 GAAGTCTTAC
* * *
1349 TGCCAAATATCATGAAAAACTGAGCCGGGG--CCGGAACACGTTTTTAGCCAAAAACCGTGGTGG
1 TGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAAC-CGTTTTTAGCCAAAAACCGTGATGG
* * * * * * *
1412 TTAGTACACGAATTTC-GCTTAAATTTTACAAAAACTGAACCAAAAGTTTCTCCCTCAGTTTTTG
65 TTAGTACACG-ATTTCGGTTTAAATTTTGCAAAAAATGAACCGAAAGTTTTTCCCTCAATTTTTT
** * * * *
1476 GTCTCAATACTCATAAAAAGTTTATAATTCTTA-GTTAAAAAGATTGAAGGGTTTTTCACGCTTC
129 ACCACAATACTCATAAAAAGTATATAATTC--ACGTCAAAAAGATTGAAGGGCTTTTCACGCTTC
* * * *
1540 TAATATCGTTTTTCCTATTTTCCCGAATTAA-TT-T-ATTAAATCGAAACATAATTCAAATACTC
192 T-ATATCGTTTTTCCTATTTTTCTGAATTAATTTCTAATTAAATCGAAACATAATTCAGATGCTC
* * *
1602 GTAAAATCATATCCTCAAATCCAATGTTGCTGAGATTTGGTTAGATGAATATAGATATTTCAA-A
256 GTAAAAACAAATCCTCAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGA
**
1666 GAGTCTTGT
321 -AGTCTTAC
* * * *
1675 TGGCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACATGTTTTTAGTCAAAAACCGTGATGG
1 TGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAAC-CGTTTTTAGCCAAAAACCGTGATGG
* * * *
1740 TTAGTACACGATTTCGGTTAAAATTTTGCAAAAATTGACCCGAATGATTTTT-CCTCAATTTTT
65 TTAGTACACGATTTCGGTTTAAATTTTGCAAAAAATGAACCGAAAG-TTTTTCCCTCAATTTTT
1803 GGCTAAAATA
Statistics
Matches: 1175, Mismatches: 204, Indels: 127
0.78 0.14 0.08
Matches are distributed among these distances:
325 6 0.01
326 174 0.15
327 131 0.11
328 179 0.15
329 367 0.31
330 80 0.07
331 109 0.09
332 79 0.07
333 48 0.04
334 2 0.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (328 bp):
TGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACCGTTTTTAGCCAAAAACCGTGATGGT
TAGTACACGATTTCGGTTTAAATTTTGCAAAAAATGAACCGAAAGTTTTTCCCTCAATTTTTTAC
CACAATACTCATAAAAAGTATATAATTCACGTCAAAAAGATTGAAGGGCTTTTCACGCTTCTATA
TCGTTTTTCCTATTTTTCTGAATTAATTTCTAATTAAATCGAAACATAATTCAGATGCTCGTAAA
AACAAATCCTCAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCT
TAC
Found at i:2890 original size:330 final size:328
Alignment explanation
Indices: 2147--4211 Score: 1530
Period size: 326 Copynumber: 6.3 Consensus size: 328
2137 TATTTTTTTA
* * ** * * *
2147 ATGCTCGTAAAAATAAATCCTTAAATCCAATGTGTTTCA-ATTCGGTTAGATGAATATACATATT
1 ATGCTCGTAAAAACAAATCCTTAAATCAAATGTGGCTGAGATTTGGTTAGATGAATATAGATATT
* * ** * * * * * *
2211 TCAATGACTCTTAACGCCAAAAATCATGCAAAACGGAGCCAAGG-TCCCGAAACGCATTTTTAGA
66 ACAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGTC--GGACCCCGGAACGCAGTTTTAGC
* * * ** * * * *
2275 CAAACACCGTGAT-GTAGTACACAATTTCGACTCAAATTTTGCAAAAATTAAACAGAA--ATTTT
129 CAAAAACTGTGATGGTAGTACACGATTTCGGTTAAAATTTTGCAAAAATTGACCCGAATGA-TTT
* * * * * * * * * *
2337 TACCCTTAATTTTTTGCCACAATAATTATAAAAAGTATACAATTCAACACCAAAAAGATTGG-AT
193 T-CCCTCAATTTTTGGCCACAATACTCATAAAAAATATATAATT-ATCGCCAAAAA-AATGGAAC
* *** *
2401 GGATTTTCATAATTCTAATATCG-TTTT--T-TTTTTCTGAATTAATTTATAATTAAATCGAAAC
255 GGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTCTGAATTAATTTCTAATTAAATCGAAAC
*
2462 A-ATATTCAG
320 AGA-ATTCAT
* * * * * * *
2471 ATGCTCGCAAAACCAAATCCTTAATTCAAATGTGCCTGAGATTCGGTTGGATGAATATAGATAAT
1 ATGCTCGTAAAAACAAATCCTTAAATCAAATGTGGCTGAGATTTGGTTAGATGAATATAGATATT
* * * * * *
2536 AAAAGGAGTCTTGGCGCAAAAAATCATGCAAAACTGAGTTGAGACCCCGGAACGC-GTCTTAGTC
66 ACAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGTCG-GACCCCGGAACGCAGTTTTAGCC
* *
2600 AAAAACTGTGATGGTTAGTACACGATTTCAGTTAAAATTTTGCAAAAATCGACCCGAATGATTTT
130 AAAAACTGTGATGG-TAGTACACGATTTCGGTTAAAATTTTGCAAAAATTGACCCGAATGATTTT
* * * * * * *
2665 CCCTCAATCTTTGGCCATAATACTCATAAAAAATTTGTAACTTATCGCCAAACAAATGGGACGGA
194 CCCTCAATTTTTGGCCACAATACTCATAAAAAATATATAA-TTATCGCCAAAAAAATGGAACGGC
* * *
2730 TTTTCACGCTTCTAATATCGTTTTTCCTATTTTTCTGAATTAATTTCTGATTAAATCAAAACATA
258 TTTTCACGCTTCTAATATCGTTTTTCCTATTTTTCTGAATTAATTTCTAATTAAATCGAAACAGA
2795 ATTCAT
323 ATTCAT
** *
2801 ATGCTAATAAAAACAAATCCTTAAATGAAATGTGGCTGAGATTTGGTTAGATGAATATAGATATT
1 ATGCTCGTAAAAACAAATCCTTAAATCAAATGTGGCTGAGATTTGGTTAGATGAATATAGATATT
* * * * * *
2866 CCAATGAGTCTTGGTGCCAAAAATCGTGCAAAACTGAGTCGG-CCCCGAAATGCATTTTTAGCCA
66 ACAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGTCGGACCCCGGAACGCAGTTTTAGCCA
* * *
2930 AAAACCGTGAT-GTAGTACACGATTTCGGTTAAAATCTAGCAAAAATTGACCCGAATGATTTT-C
131 AAAACTGTGATGGTAGTACACGATTTCGGTTAAAATTTTGCAAAAATTGACCCGAATGATTTTCC
* * * * * * * *
2993 TTTAATTTTTGGTCAAAATACTCATAAAAAATATATATTTCATCCCCAAAAAAATGGAATGGCCT
196 CTCAATTTTTGGCCACAATACTCATAAAAAATATATAATT-ATCGCCAAAAAAATGGAACGGCTT
* * * ** * **
3058 TTCAAGCTTCTAATATAG-TTTTCCTATTTTTCTGAATTAATTTTTAATTAAATTAAAACCGGTT
260 TTCACGCTTCTAATATCGTTTTTCCTATTTTTCTGAATTAATTTCTAATTAAATCGAAACAGAAT
3122 TC-T
325 TCAT
* **
3125 AATGCTCGTAAAAA-AAATTCCTTAAATCCAATGT-GCTTGAGATTCAGTTAGATGAAATATAGA
1 -ATGCTCGTAAAAACAAA-TCCTTAAATCAAATGTGGC-TGAGATTTGGTTAGATG-AATATAGA
** * * * * * * *
3188 TATTTTAAT--TTCTGTATGCGCCAAAAATAATGCAAAACTGAGCCGGGA-TCCGGAACACATTT
62 TATTACAATGAGTCT-T-GGCGCCAAAAATCATGCAAAACTGAGTC-GGACCCCGGAACGCAGTT
** * * * * *
3250 TTAG-TGAAAAGTCGTGATGGTTAGTATACGATTTCGGCT-CAATTTTG-----A---A-CCAAA
124 TTAGCCAAAAACT-GTGATGG-TAGTACACGATTTCGGTTAAAATTTTGCAAAAATTGACCCGAA
* * * * *
3304 AGTTTTTCCCTCAATTTTTGGCCACAATATTCATAAAAAATATATAATTCA-C-CACAAGAAGAT
187 TGATTTTCCCTCAATTTTTGGCCACAATACTCATAAAAAATATATAATT-ATCGC-CAAAAAAAT
* * * * *
3367 TGAAAGGTTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATTTTTAATTAAAT
250 GGAACGGCTTTTCACGCTTCTAATATCGTTTTTCCTA-TTTTTCTGAATTAATTTCTAATTAAAT
* * **
3432 TGAAACCGGTTTC-T
314 CGAAACAGAATTCAT
* * ** ** * * *
3446 GATGATCGTAAAAACAAATCTTTAAATCCGACATGCCTGAGATTTGGTTAAATGAATGTAGATAT
1 -ATGCTCGTAAAAACAAATCCTTAAATCAAATGTGGCTGAGATTTGGTTAGATGAATATAGATAT
* * * * * *
3511 TACAAGGAGTCTTGGCACCAAAAATAATGCAAAACTGAGCACGGCCCCCGGAGCGC-GTTTTTAG
65 TACAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAG-TCGGACCCCGGAACGCAG-TTTTAG
* * * * * *
3575 CCAAAAAAGTGTGATGGTAGTACACGATTTCCGCTT-AAATTTTTCAAAAATTGAACTG-ATGTT
128 CC-AAAAACTGTGATGGTAGTACACGATTT-CGGTTAAAATTTTGCAAAAATTGACCCGAATGAT
** * * * * * * *
3638 TTTCCCTCAATTTTTGGTAACAATACTCATGAAAAGTATATAATTGATAGCCAACAAGATTGAAG
191 TTTCCCTCAATTTTTGGCCACAATACTCATAAAAAATATATAATT-ATCGCCAAAAAAATGGAAC
* * * *
3703 GGCTTTTGACGCTGCTAATATCGTTTTTCCTTTTTTTTCCGAATTAATTTCCTAATTAAATCGAA
255 GGCTTTTCACGCTTCTAATATCGTTTTTCC-TATTTTTCTGAATTAATTT-CTAATTAAATCGAA
* *
3768 ACATAATTCAG
318 ACAGAATTCAT
* * * *
3779 ATGCTCGTAAAAACAAAT-CTTTAATCCAATATGGATGAGATTTGGTTAGATGAATATAGATATC
1 ATGCTCGTAAAAACAAATCCTTAAATCAAATGTGGCTGAGATTTGGTTAGATGAATATAGATAT-
* * * ** * * * *
3843 T-CAATGAGTC-TGGTGCCAAAAATCATGCAAAACTGAATCGGGCCTTGAAATGCA-ATTTACCC
65 TACAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGTCGGACCCCGGAACGCAGTTTTAGCC
* * * * *
3905 AAAAACTGTGA-CG-A--ACACGATTTCGGTTAAAATTTTACAAAAGTTGACCCAAATGATTTTT
130 AAAAACTGTGATGGTAGTACACGATTTCGGTTAAAATTTTGCAAAAATTGACCCGAATGATTTTC
* * *
3966 CCTCAATTTTTGACCACAATACTCATAAAAAATATATAATCGATTGCCAAAAAAAATGGAACGGC
195 CCTCAATTTTTGGCCACAATACTCATAAAAAATATATAAT-TATCGCC-AAAAAAATGGAACGGC
* * * * ** *
4031 TTTTCATGCTTCCAATATTGATTTTCCTATTTTTTCTGAAAAAAAATTTCTAATTAAATTGAAAC
258 TTTTCACGCTTCTAATATCGTTTTTCCTA-TTTTTCTG--AATTAATTTCTAATTAAATCGAAAC
* **
4096 TAG-TTTCGG
320 -AGAATTCAT
* ** * * * *
4105 ATGCTCGTAAAAACAATTTTTTAAATTC-AATGT-GCTTGAGATTCGGCTATATGAATATAGTTA
1 ATGCTCGTAAAAACAAATCCTTAAA-TCAAATGTGGC-TGAGATTTGGTTAGATGAATATAGATA
** * * * * * *
4168 TTTTAATTATTATTGGTGTCAAAAATTATGCAAAACTGAGTCGG
64 TTACAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGTCGG
4212 GATGGCTAAA
Statistics
Matches: 1389, Mismatches: 282, Indels: 136
0.77 0.16 0.08
Matches are distributed among these distances:
318 1 0.00
319 39 0.03
320 85 0.06
321 104 0.07
322 27 0.02
323 34 0.02
324 105 0.08
325 191 0.14
326 239 0.17
327 133 0.10
328 53 0.04
329 44 0.03
330 194 0.14
331 103 0.07
332 37 0.03
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (328 bp):
ATGCTCGTAAAAACAAATCCTTAAATCAAATGTGGCTGAGATTTGGTTAGATGAATATAGATATT
ACAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGTCGGACCCCGGAACGCAGTTTTAGCCA
AAAACTGTGATGGTAGTACACGATTTCGGTTAAAATTTTGCAAAAATTGACCCGAATGATTTTCC
CTCAATTTTTGGCCACAATACTCATAAAAAATATATAATTATCGCCAAAAAAATGGAACGGCTTT
TCACGCTTCTAATATCGTTTTTCCTATTTTTCTGAATTAATTTCTAATTAAATCGAAACAGAATT
CAT
Found at i:6159 original size:21 final size:21
Alignment explanation
Indices: 6125--6200 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
6115 TTCCCAATTG
* *
6125 ACATTGAACTTTCCTTGATTC
1 ACATTCAACATTCCTTGATTC
** *
6146 ACATTCAACATTCC-CAATTA
1 ACATTCAACATTCCTTGATTC
*
6166 ACATTGAAC-TTGCCTTGATTC
1 ACATTCAACATT-CCTTGATTC
*
6187 ACTTTCAACATTCC
1 ACATTCAACATTCC
6201 CAATTGACAT
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
19 2 0.05
20 13 0.32
21 24 0.59
22 2 0.05
ACGTcount: A:0.29, C:0.28, G:0.07, T:0.37
Consensus pattern (21 bp):
ACATTCAACATTCCTTGATTC
Found at i:6164 original size:41 final size:40
Alignment explanation
Indices: 6102--6266 Score: 226
Period size: 41 Copynumber: 4.1 Consensus size: 40
6092 TACGCGGCGC
* * *
6102 ATTCACATTGAATTTCCCAATTGACATTGAACTTTCCTTG
1 ATTCACATTCAAATTCCCAATTGACATTGAACTTGCCTTG
*
6142 ATTCACATTCAACATTCCCAATTAACATTGAACTTGCCTTG
1 ATTCACATTCAA-ATTCCCAATTGACATTGAACTTGCCTTG
*
6183 ATTCACTTTCAACATTCCCAATTGACATTGAACTTGCCTT-
1 ATTCACATTCAA-ATTCCCAATTGACATTGAACTTGCCTTG
* *
6223 ATCTCACA-TCCAATTCCCAATTGACATTGAACTTGCCTTA
1 AT-TCACATTCAAATTCCCAATTGACATTGAACTTGCCTTG
6263 ATTC
1 ATTC
6267 TCACATCCAA
Statistics
Matches: 114, Mismatches: 8, Indels: 7
0.88 0.06 0.05
Matches are distributed among these distances:
39 29 0.25
40 18 0.16
41 67 0.59
ACGTcount: A:0.29, C:0.27, G:0.08, T:0.36
Consensus pattern (40 bp):
ATTCACATTCAAATTCCCAATTGACATTGAACTTGCCTTG
Found at i:6210 original size:82 final size:80
Alignment explanation
Indices: 6115--6266 Score: 234
Period size: 80 Copynumber: 1.9 Consensus size: 80
6105 CACATTGAAT
*
6115 TTCCCAATTGACATTGAACTTTCCTTGAT-TCACATTCAACATTCCCAATTAACATTGAACTTGC
1 TTCCCAATTGACATTGAACTTGCCTT-ATCTCACA-TCAA-ATTCCCAATTAACATTGAACTTGC
*
6179 CTTGATTCACTTTCAACA
63 CTTAATTCACTTTCAACA
* *
6197 TTCCCAATTGACATTGAACTTGCCTTATCTCACATCCAATTCCCAATTGACATTGAACTTGCCTT
1 TTCCCAATTGACATTGAACTTGCCTTATCTCACATCAAATTCCCAATTAACATTGAACTTGCCTT
6262 AATTC
66 AATTC
6267 TCACATCCAA
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
80 30 0.46
81 5 0.08
82 30 0.46
ACGTcount: A:0.28, C:0.28, G:0.08, T:0.36
Consensus pattern (80 bp):
TTCCCAATTGACATTGAACTTGCCTTATCTCACATCAAATTCCCAATTAACATTGAACTTGCCTT
AATTCACTTTCAACA
Found at i:6288 original size:33 final size:33
Alignment explanation
Indices: 6246--6461 Score: 396
Period size: 33 Copynumber: 6.5 Consensus size: 33
6236 TTCCCAATTG
6246 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
1 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
6279 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
1 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
*
6312 ACATTGAACTTGCCTTATTTCTCACATCCAAAAA
1 ACATTGAACTTGCCTTAATTCTCACATCC-AAAA
6346 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
1 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
6379 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
1 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
*
6412 ACATTGAACTTGCCTTATTTCTCACATCCAAAAA
1 ACATTGAACTTGCCTTAATTCTCACATCC-AAAA
6446 ACATTGAACTTGCCTT
1 ACATTGAACTTGCCTT
6462 CACTCACATT
Statistics
Matches: 178, Mismatches: 3, Indels: 3
0.97 0.02 0.02
Matches are distributed among these distances:
33 126 0.71
34 52 0.29
ACGTcount: A:0.35, C:0.27, G:0.06, T:0.31
Consensus pattern (33 bp):
ACATTGAACTTGCCTTAATTCTCACATCCAAAA
Found at i:6374 original size:67 final size:66
Alignment explanation
Indices: 6246--6461 Score: 396
Period size: 67 Copynumber: 3.2 Consensus size: 66
6236 TTCCCAATTG
6246 ACATTGAACTTGCCTTAATTCTCACATCCAAAAACATTGAACTTGCCTTAATTCTCACATCCAAA
1 ACATTGAACTTGCCTTAATTCTCACATCCAAAAACATTGAACTTGCCTTAATTCTCACATCCAAA
6311 A
66 A
*
6312 ACATTGAACTTGCCTTATTTCTCACATCCAAAAAACATTGAACTTGCCTTAATTCTCACATCCAA
1 ACATTGAACTTGCCTTAATTCTCACATCC-AAAAACATTGAACTTGCCTTAATTCTCACATCCAA
6377 AA
65 AA
*
6379 ACATTGAACTTGCCTTAATTCTCACATCCAAAAACATTGAACTTGCCTTATTTCTCACATCCAAA
1 ACATTGAACTTGCCTTAATTCTCACATCCAAAAACATTGAACTTGCCTTAATTCTCACATCC-AA
6444 AA
65 AA
6446 ACATTGAACTTGCCTT
1 ACATTGAACTTGCCTT
6462 CACTCACATT
Statistics
Matches: 145, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
66 60 0.41
67 85 0.59
ACGTcount: A:0.35, C:0.27, G:0.06, T:0.31
Consensus pattern (66 bp):
ACATTGAACTTGCCTTAATTCTCACATCCAAAAACATTGAACTTGCCTTAATTCTCACATCCAAA
A
Found at i:6385 original size:100 final size:100
Alignment explanation
Indices: 6246--6461 Score: 432
Period size: 100 Copynumber: 2.2 Consensus size: 100
6236 TTCCCAATTG
6246 ACATTGAACTTGCCTTAATTCTCACATCCAAAAACATTGAACTTGCCTTAATTCTCACATCCAAA
1 ACATTGAACTTGCCTTAATTCTCACATCCAAAAACATTGAACTTGCCTTAATTCTCACATCCAAA
6311 AACATTGAACTTGCCTTATTTCTCACATCCAAAAA
66 AACATTGAACTTGCCTTATTTCTCACATCCAAAAA
6346 ACATTGAACTTGCCTTAATTCTCACATCCAAAAACATTGAACTTGCCTTAATTCTCACATCCAAA
1 ACATTGAACTTGCCTTAATTCTCACATCCAAAAACATTGAACTTGCCTTAATTCTCACATCCAAA
6411 AACATTGAACTTGCCTTATTTCTCACATCCAAAAA
66 AACATTGAACTTGCCTTATTTCTCACATCCAAAAA
6446 ACATTGAACTTGCCTT
1 ACATTGAACTTGCCTT
6462 CACTCACATT
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 116 1.00
ACGTcount: A:0.35, C:0.27, G:0.06, T:0.31
Consensus pattern (100 bp):
ACATTGAACTTGCCTTAATTCTCACATCCAAAAACATTGAACTTGCCTTAATTCTCACATCCAAA
AACATTGAACTTGCCTTATTTCTCACATCCAAAAA
Found at i:13106 original size:333 final size:325
Alignment explanation
Indices: 12375--13462 Score: 1079
Period size: 326 Copynumber: 3.3 Consensus size: 325
12365 TAGGGTTAGG
* * * * * **
12375 ATGTGGCTGAGATTTTATTAGATGAATATAGATATTTCAAGGATTGTCGGAACCAAAAATCATGC
1 ATGTGGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTTGGCGCCAAAAATCATGC
** * * *
12440 AAAACTGAGCTGGTACCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTACTACACGATTTT
66 AAAACTGAGC-GGGGCCCCGAAACGCTTTTTTAGCCAAAAACCGTGATGGTTATTACACGATTTC
* * * * *
12505 GGTTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCCTCAATTTTTGGATAAAATACTCAT-A
130 GGCTAAAATTTTG-AAAAATTGACCC-AAAAATATTTCCTCAAATTTTGGCTAAAATACTCATAA
* ** * * *
12569 AAATATATATAATTCAACGGTAAAAAGATTGGAGGAGTTTTCATGTTTTTAATATCGTTTTT-CA
193 AAAAATATATAA-TCAACGCCAAAAAGATTGAAGG-GTTTTCACGTTTCTAATATCGTTTTTCCA
** * * *
12633 TATTTTTCTGAATTAAAATCTAATTAGATC-AAAACAAGATTTAGTTGCTTA-TAAAAACAAATT
256 T-TTTTTC-GAATTAATTTCTAATTAAATCGAAAA-AAGATTTAGATGC-TAGTAAAAACAAATC
*
12696 ATTAAATCTA
317 CTTAAATC-A
* * * * * * *
12706 ATGTGGGTGAGATTTGTTTAAATAAATATAGAAATCTTAAGGAGTCTTGGCGCCAAGAATCATGC
1 ATGTGGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTTGGCGCCAAAAATCATGC
* *
12771 AAAACTGAGTCGGGGCCCC-AGAACGCTTTTTTATCCAAAAACTGTGATGGTTATTACACGATTT
66 AAAACTGAG-CGGGGCCCCGA-AACGCTTTTTTAGCCAAAAACCGTGATGGTTATTACACGATTT
** * * *
12835 CAACTATACTTTTGTAAAAATTGACCCAAAACATATTTCCCCAAATTTTGGCTAAAATACTCATA
129 CGGCTAAAATTTTG-AAAAATTGACCCAAAA-ATATTTCCTCAAATTTTGGCTAAAATACTCATA
* *
12900 AAAAAATATATAACTCATCGCCAAAAAGATTGAAGGGCTTTTGACGTTTCTAATATCGTTTTTCC
192 AAAAAATATATAA-TCAACGCCAAAAAGATTGAAGGG-TTTTCACGTTTCTAATATCGTTTTT-C
* * * *
12965 CATTTTTTACAAATTAATTTCTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCC
254 CATTTTTT-CGAATTAATTTCTAATTAAATCGAAAAAAGATTTAGATGCTAGTAAAAACAAATCC
13030 TTAAATGCA
318 TTAAAT-CA
* *
13039 ATGTGGCTGAGATTTGATTAGATGAATATAGATATCTCAAGTAGTCTTAGCGCCAAAAATCATGC
1 ATGTGGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTTGGCGCCAAAAATCATGC
* * * * * *
13104 AAAACTGACCCGAGGCCCTGAAAC-TTATTTTTAGCCAAAAACCGTGATGATTATTATACGA-TT
66 AAAACTGA-GCGGGGCCCCGAAACGCT-TTTTTAGCCAAAAACCGTGATGGTTATTACACGATTT
* ** *
13167 CGGCTAAAATTTTG-CAAATTGA-CCATAAAGATATTTCCTCAAATTTTTACTAAATTA-TCATT
129 CGGCTAAAATTTTGAAAAATTGACCCA-AAA-ATATTTCCTCAAATTTTGGCTAAAATACTCA-T
* * * * *
13229 AAAAAAATA-AT--TCAACACCAAAAATATCGAAGGGTTTTTTACGTTTCTAATATAGTTTTTTC
191 AAAAAAATATATAATCAACGCCAAAAAGATTGAAGGG-TTTTCACGTTTCTAATATCG-TTTTTC
* * * * *
13291 AACTTTTTCCGAATTAATTTCAAATTAAATCGAAAAAAGATTTAAATGTTAGTAAAAACAAATCC
254 CA-TTTTTTCGAATTAATTTCTAATTAAATCGAAAAAAGATTTAGATGCTAGTAAAAACAAATCC
13356 TTAAATCCA
318 TTAAAT-CA
* ** * *
13365 ATTTGGCTGAGATTTGATTAGATGAATATAGATAGT-TCACTGAGACTTGGTGCCAAAAATCATG
1 ATGTGGCTGAGATTTGATTAGATGAATATAGATA-TCTCAAGGAGTCTTGGCGCCAAAAATCATG
* * * * *
13429 CAATACTGACCCGAGGTCCCGAAGCGCTTTTTTA
65 CAAAACTGA-GCGGGGCCCCGAAACGCTTTTTTA
13463 CTTAAAAAAA
Statistics
Matches: 630, Mismatches: 107, Indels: 45
0.81 0.14 0.06
Matches are distributed among these distances:
326 178 0.28
327 12 0.02
329 8 0.01
330 48 0.08
331 153 0.24
332 67 0.11
333 155 0.25
334 9 0.01
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (325 bp):
ATGTGGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTTGGCGCCAAAAATCATGC
AAAACTGAGCGGGGCCCCGAAACGCTTTTTTAGCCAAAAACCGTGATGGTTATTACACGATTTCG
GCTAAAATTTTGAAAAATTGACCCAAAAATATTTCCTCAAATTTTGGCTAAAATACTCATAAAAA
AATATATAATCAACGCCAAAAAGATTGAAGGGTTTTCACGTTTCTAATATCGTTTTTCCATTTTT
TCGAATTAATTTCTAATTAAATCGAAAAAAGATTTAGATGCTAGTAAAAACAAATCCTTAAATCA
Found at i:13563 original size:326 final size:324
Alignment explanation
Indices: 12920--13543 Score: 724
Period size: 326 Copynumber: 1.9 Consensus size: 324
12910 TAACTCATCG
* * * *
12920 CCAAAAAGATTGAAGGGCTTTTGACGTTTCTAATATCGTTTTTCCCATTTTTTACAAATTAATTT
1 CCAAAAAGATCGAAGGGCTTTTGACGTTTCTAATATAGTTTTTCCAACTTTTTACAAATTAATTT
* * * * *
12985 CTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTGAG
66 CAAATTAAATCGAAAAAAGATTCAAATGCTAGTAAAAACAAATCCTTAAATCCAATGTGGCTGAG
*
13050 ATTTGATTAGATGAATATAGATATCTCAAGTAGTCTTAGCGCCAAAAATCATGCAAAACTGACCC
131 ATTTGATTAGATGAATATAGATATCTCAAGTAGACTTAGCGCCAAAAATCATGCAAAACTGACCC
** **
13115 GAGGCCCTGAAACTTATTTTTAGCCAAAAACCGTGATGATTATTATACGATTCGGCTAAAATTTT
196 GAGGCCCTGAAACTTATTTTTAGAAAAAAACCGTGATGATTAGCATAC-ATTCGGCTAAAATTTT
* * * * *
13180 GCAAATTGACCATAAAGATATTTCCTCAAATTTTTACTAAATTATCATTAAAAAAATAATTCAAC
260 CCAAAATGACCAGAAAGATATTTCCTCAAATTTTCACCAAA-TATCATTAAAAAAATAATTCAAC
13245 A
324 A
* * * * * *
13246 CCAAAAATATCGAAGGGTTTTTTACGTTTCTAATATAGTTTTTTCAACTTTTTCCGAATTAATTT
1 CCAAAAAGATCGAAGGGCTTTTGACGTTTCTAATATAGTTTTTCCAACTTTTTACAAATTAATTT
* * *
13311 CAAATTAAATCGAAAAAAGATTTAAATGTTAGTAAAAACAAATCCTTAAATCCAATTTGGCTGAG
66 CAAATTAAATCGAAAAAAGATTCAAATGCTAGTAAAAACAAATCCTTAAATCCAATGTGGCTGAG
* * * *
13376 ATTTGATTAGATGAATATAGATAGT-TC-ACTGAGACTTGGTGCCAAAAATCATGCAATACTGAC
131 ATTTGATTAGATGAATATAGATA-TCTCAAGT-AGACTTAGCGCCAAAAATCATGCAAAACTGAC
* * *
13439 CCGAGGTCCC-GAAGCGCTTTTTTACTTA-AAAAAAACCGTGATG-TTACGCA-A-TTTCGGCTA
194 CCGAGG-CCCTGAA--ACTTATTT--TTAGAAAAAAACCGTGATGATTA-GCATACATTCGGCTA
* * * *
13499 ATATTTTCCAAAAAAATGACCCGAAATATTTTTCCTC-AATTTTCA
253 AAATTTTCC---AAAATGACCAGAAAGATATTTCCTCAAATTTTCA
13544 GCCACAACTC
Statistics
Matches: 249, Mismatches: 38, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
325 2 0.01
326 189 0.76
327 4 0.02
328 17 0.07
329 34 0.14
330 3 0.01
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.33
Consensus pattern (324 bp):
CCAAAAAGATCGAAGGGCTTTTGACGTTTCTAATATAGTTTTTCCAACTTTTTACAAATTAATTT
CAAATTAAATCGAAAAAAGATTCAAATGCTAGTAAAAACAAATCCTTAAATCCAATGTGGCTGAG
ATTTGATTAGATGAATATAGATATCTCAAGTAGACTTAGCGCCAAAAATCATGCAAAACTGACCC
GAGGCCCTGAAACTTATTTTTAGAAAAAAACCGTGATGATTAGCATACATTCGGCTAAAATTTTC
CAAAATGACCAGAAAGATATTTCCTCAAATTTTCACCAAATATCATTAAAAAAATAATTCAACA
Done.