Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019489.1 Corchorus olitorius cultivar O-4 contig19522, 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: 33741
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:1228 original size:322 final size:320
Alignment explanation
Indices: 160--1390 Score: 1339
Period size: 333 Copynumber: 3.8 Consensus size: 320
150 GGGGTTCCGG
* * * * *
160 CTCAGTTTTGCATGATTTTTGGC-GTAAAGAGTACTTGAAATATCTATATTCCTCGAACTAAATC
1 CTCAGTTTTGCATGATTTTTGGCAG-AAAGACTACTTGAAATATCTACATTCATCTAACCAAATC
* * * ** * * *
224 TCAGCTACATTGGATTTAATGATTTGTTTTTATGAATATCTGATTCTTG-TTTCGATTTAATTTG
65 TCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTTCAATTTAATTAG
* * * * *
288 AAATTAATTCGGAAAAAAAATGGAAAAATGATATTAGAGGCATGAAAAACCCTTCAATC-TTTTG
130 AAATAAATTCGAAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTG
* * * * * *
352 GCGTTGAATTATATATTTTTTTATGAGTATTGTGGCAAAAAATTGA-GAAAAATTTTTCGGGTCA
195 GTGTTGAATTATATA-TTTTTTCTGAATATTGTGGCAAAAAATTGAGGAAAAACTTTTCGGTTAA
* * * * * **
416 GTTTTTAGCCGAAATCATGTACCATCACAATTTTTTGCTAAAAACACGTTTCGGGGGCTTGA
259 GTTTTTAGCCGAAATCGTGTACTATCACAATTTTTCGCTAAAAACGCGTTTCGGGGCCCCGA
* * * * * * * *
478 CTCAGTTTTGCATGGTTTTTGTCATAAAGATTCCTTGAAATATATATC-TTCATCTAACCGAGTC
1 CTCAGTTTTGCATGATTTTTGGCAGAAAGACTACTTGAAATATCTA-CATTCATCTAACCAAATC
542 TCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTTCAATTTAATTAG
65 TCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTTCAATTTAATTAG
*
607 AAATAAATTCGAAAAAAAAATGGAAAAACGATATTAGAATCGTGAAAAACCCTTCAAT-TTTTTG
130 AAATAAATTCGAAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTG
* * *
671 GTGTTAAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTTGGGTCAA
195 GTGTTGAATTATATATTTTTTCTGAATATTGTGGCAAAAAATTGAGGAAAAAC-TTTTCGG----
** ** * *
736 TTTTTACAAAATTTTAATCGAAATTGTGTACTAACCATCACAATTTTTCGCTAAAAACGCGTTCC
255 ---TT--AAGTTTTTAGCCGAAATCGTGTACT----ATCACAATTTTTCGCTAAAAACGCGTTTC
*
801 GGGGCCCCGC
311 GGGGCCCCGA
* * * * *** * * * *
811 CTCAATTTTACATGACTTTTGACTCCAAGACTACTTGAAATATCTATACTCATCAAACAAAATCT
1 CTCAGTTTTGCATGATTTTTGGCAGAAAGACTACTTGAAATATCTACATTCATCTAACCAAATCT
* * * *
876 CAGCCACATTGGATATAAGGATTTGTTTTTATGAGCATCTAAATCTTATTTT-AATTTAATTAGA
66 CAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTTCAATTTAATTAGA
* * ** * *
940 AATTAATTCAGAAAAAAATTAATGGAAAAACAATATTAGAAGCGTGAAAAGGCCGTCAATCTTAT
131 AATAAATTC-GAAAAAAA--AATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATCTTTT
* * * *
1005 TGATGTTGAATTATATTTTTTTTTCTGAATATT-TTGCAAAAAATTGAGAAAAAACTTTTCGGTT
193 TGGTGTTGAATTATA-TATTTTTTCTGAATATTGTGGCAAAAAATTGAGGAAAAACTTTTCGGTT
*** **
1069 AAGTTTTTAGCCGAAATCGTGTACTATCATTGTTTTAGGCTAAAAACGCGTTTCGGGGCCCCGA
257 AAGTTTTTAGCCGAAATCGTGTACTATCACAATTTTTCGCTAAAAACGCGTTTCGGGGCCCCGA
* * *
1133 CTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTTAATTATCTACATTCATCTAACCAAATCT
1 CTCAGTTTTGCATGATTTTTGGCAGAAAGACTACTTGAAATATCTACATTCATCTAACCAAATCT
* * *
1198 CAGCCACAATGGATTTAAGGATTCGTTTTTACGAGCATCTGAATCTT-TGTTTCGATTTAATTAG
66 CAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT-TTTCAATTTAATTAG
* *
1262 AAATAAATTTGGAAAAAAAAA-GAAAGAAAAACGATATTAGAAGCGTGAAAAAACCCTTCAATTT
130 AAATAAA-TTCGAAAAAAAAATG---GAAAAACGATATTAGAAGCGTG-AAAAACCCTTCAATCT
* *
1326 TTTTGGTGTTGAATTATATATTTTTTCTGAATATTGTGGCAAAAAATTTAGGTAAAACTTTTCGG
190 TTTTGGTGTTGAATTATATATTTTTTCTGAATATTGTGGCAAAAAATTGAGGAAAAACTTTTCGG
1391 CTCAATTTTG
Statistics
Matches: 752, Mismatches: 128, Indels: 60
0.80 0.14 0.06
Matches are distributed among these distances:
318 122 0.16
319 89 0.12
320 7 0.01
321 3 0.00
322 128 0.17
323 61 0.08
324 55 0.07
326 20 0.03
327 1 0.00
328 2 0.00
329 17 0.02
332 20 0.03
333 135 0.18
335 41 0.05
336 36 0.05
337 15 0.02
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.37
Consensus pattern (320 bp):
CTCAGTTTTGCATGATTTTTGGCAGAAAGACTACTTGAAATATCTACATTCATCTAACCAAATCT
CAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTTCAATTTAATTAGA
AATAAATTCGAAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGG
TGTTGAATTATATATTTTTTCTGAATATTGTGGCAAAAAATTGAGGAAAAACTTTTCGGTTAAGT
TTTTAGCCGAAATCGTGTACTATCACAATTTTTCGCTAAAAACGCGTTTCGGGGCCCCGA
Found at i:1258 original size:655 final size:652
Alignment explanation
Indices: 8--1399 Score: 1760
Period size: 655 Copynumber: 2.1 Consensus size: 652
1 AACCCCG
* * *
8 TCAATTTTTTTGGCGTTGAATTATATATTTTTTCTAAGTATTATGG-AAAAGAATTGAGGAAAAA
1 TCAATTTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAA-AATTGAGG--AAA
* * * * * * * * *
72 AAATTTTCGGGACAGTTTTTGCAAAATTTTAGTCAAAATGGTTTACTCGTCACGATTTTTTGGCT
63 AACTTTTCGGGTCAATTTTTACAAAATTTTAATCAAAATGGTGTACTCATCACGAATTTTTCGCT
* * * ** * * * * * *
137 AAAAATGTGTTCTGGGGTTCCGGCTCAGTTTTGCATGATTTTTGGCGTAAAGAGTACTTGAAATA
128 AAAAACGCGTTCCGGGGCCCCGCCTCAATTTTACATGACTTTTGACGTAAAGACTACTTGAAATA
* * * * * * * * *
202 TCTATATTCCTCGAACTAAATCTCAGCTACATTGGATTTAATGATTTGTTTTTATGAATATCTGA
193 TCTATACTCATCAAACAAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTATGAACATCTAA
* * * * * ** *
267 TTCTTGTTTCGATTTAATTTGAAATTAATTCGGAAAAAAAATGGAAAAATGATATTAGAGGCATG
258 ATCTTATTTCAATTTAATTAGAAATTAATTCGAAAAAAAAATGGAAAAACAATATTAGAAGCATG
* * *
332 AAAAACCCTTCAATCTTTTGGCGTTGAATTATATATTTTTTTATGAGTATTGTGGCAAAAAATTG
323 AAAAACCCGTCAATCTTTTGACGTTGAATTATATATTTTTTTATGAATATTGTGGCAAAAAATTG
* * **
397 AGAAAAATTTTTCGGGTCAGTTTTTAGCCGAAATCATGTACCATCACAATTTTTTGCTAAAAACA
388 AGAAAAACTTTTCGGGTAAGTTTTTAGCCGAAATCATGTACCATCACAATTTTAGGCTAAAAACA
* ** * * * *
462 CGTTTCGGGGGCTTGACTCAGTTTTGCATGGTTTTTGTCATAAAGATTCCTTGAAATATATATCT
453 CGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATATATCT
* * * *
527 TCATCTAACCGAGTCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
518 TCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATTCGTTTTTACGAGCATCTGAATCTTGT
*
592 TTTCAATTTAATTAGAAATAAA-TTCGAAAAAAAAATG-GAAAAACGATATTAGAATCGTG-AAA
583 TTTCAATTTAATTAGAAATAAATTTCGAAAAAAAAA-GAGAAAAACGATATTAGAAGCGTGAAAA
654 AACCCT
647 AACCCT
*
660 TCAA-TTTTTTGGTGTTAAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAAC
1 TCAATTTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAAC
* * *
724 TTTTTGGGTCAATTTTTACAAAATTTTAATCGAAATTGTGTACTAACCATCAC-AATTTTTCGCT
66 TTTTCGGGTCAATTTTTACAAAATTTTAATCAAAATGGTGTACT---CATCACGAATTTTTCGCT
*
788 AAAAACGCGTTCCGGGGCCCCGCCTCAATTTTACATGACTTTTGAC-TCCAAGACTACTTGAAAT
128 AAAAACGCGTTCCGGGGCCCCGCCTCAATTTTACATGACTTTTGACGT-AAAGACTACTTGAAAT
*
852 ATCTATACTCATCAAACAAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTATGAGCATCTA
192 ATCTATACTCATCAAACAAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTATGAACATCTA
*
917 AATCTTATTTTAATTTAATTAGAAATTAATTCAGAAAAAAATTAATGGAAAAACAATATTAGAAG
257 AATCTTATTTCAATTTAATTAGAAATTAATTC-GAAAAAAA--AATGGAAAAACAATATTAGAAG
* ** * * * *
982 CGTGAAAAGGCCGTCAATCTTATTGATGTTGAATTATATTTTTTTTTCTGAATATT-TTGCAAAA
319 CATGAAAAACCCGTCAATCTT-TTGACGTTGAATTATATATTTTTTTATGAATATTGTGGCAAAA
* * * ***
1046 AATTGAGAAAAAACTTTTCGGTTAAGTTTTTAGCCGAAATCGTGTACTATCATTGTTTTAGGCTA
383 AATTGAG-AAAAACTTTTCGGGTAAGTTTTTAGCCGAAATCATGTACCATCACAATTTTAGGCTA
* * *
1111 AAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTTAATTAT
447 AAAACACGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATAT
*
1176 CTA-CATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATTCGTTTTTACGAGCATCTGA
512 ATATC-TTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATTCGTTTTTACGAGCATCTGA
* *
1240 ATCTT-TGTTTCGATTTAATTAGAAATAAATTTGGAAAAAAAAAGAAAGAAAAACGATATTAGAA
576 ATCTTGT-TTTCAATTTAATTAGAAATAAATTTCGAAAAAAAAAG--AGAAAAACGATATTAGAA
1304 GCGTGAAAAAACCCT
638 GCGTGAAAAAACCCT
* * *
1319 TCAATTTTTTTGGTGTTGAATTATATATTTTTTCTGAATATTGTGGCAAAAAATTTAGGTAAAAC
1 TCAATTTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAAC
*
1384 TTTTCGGCTCAATTTT
66 TTTTCGGGTCAATTTT
1400 GGAAAATTTT
Statistics
Matches: 631, Mismatches: 91, Indels: 28
0.84 0.12 0.04
Matches are distributed among these distances:
649 41 0.06
650 1 0.00
651 186 0.29
652 20 0.03
654 52 0.08
655 215 0.34
656 12 0.02
658 21 0.03
659 13 0.02
660 70 0.11
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.37
Consensus pattern (652 bp):
TCAATTTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAAC
TTTTCGGGTCAATTTTTACAAAATTTTAATCAAAATGGTGTACTCATCACGAATTTTTCGCTAAA
AACGCGTTCCGGGGCCCCGCCTCAATTTTACATGACTTTTGACGTAAAGACTACTTGAAATATCT
ATACTCATCAAACAAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTATGAACATCTAAATC
TTATTTCAATTTAATTAGAAATTAATTCGAAAAAAAAATGGAAAAACAATATTAGAAGCATGAAA
AACCCGTCAATCTTTTGACGTTGAATTATATATTTTTTTATGAATATTGTGGCAAAAAATTGAGA
AAAACTTTTCGGGTAAGTTTTTAGCCGAAATCATGTACCATCACAATTTTAGGCTAAAAACACGT
TTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATATATCTTCA
TCTAACCAAATCTCAGCCACAATGGATTTAAGGATTCGTTTTTACGAGCATCTGAATCTTGTTTT
CAATTTAATTAGAAATAAATTTCGAAAAAAAAAGAGAAAAACGATATTAGAAGCGTGAAAAAACC
CT
Found at i:1459 original size:26 final size:26
Alignment explanation
Indices: 1430--1506 Score: 145
Period size: 26 Copynumber: 3.0 Consensus size: 26
1420 GCATACTTTA
1430 TTTTTTGCCAACGAAATCGTGTACTT
1 TTTTTTGCCAACGAAATCGTGTACTT
*
1456 TTTTTTGCCAACGAAATCGTATACTT
1 TTTTTTGCCAACGAAATCGTGTACTT
1482 TTTTTTGCCAACGAAATCGTGTACT
1 TTTTTTGCCAACGAAATCGTGTACT
1507 AACCATCACG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (26 bp):
TTTTTTGCCAACGAAATCGTGTACTT
Found at i:2169 original size:323 final size:322
Alignment explanation
Indices: 1555--2141 Score: 734
Period size: 323 Copynumber: 1.8 Consensus size: 322
1545 CTCGGTTCAA
* * * * *
1555 TTTTGCATGATTTTTGACACAACGACTCTTTGAAATATCTATATTTTATCGAACCAAATCTCAGC
1 TTTTGAATGATTTTTGACACAAAGACTCCTTAAAATATCTATATTTCATCGAACCAAATCTCAGC
* * * * *
1620 CACATTATATATAAAAATTTGTTTTTACGAGAATCTGAATGTTGTTTCGATTTAATTAGAAATTA
66 CACAATAGATATAAAAATTTGTTTTTACAAGAATCTGAATGTTATTTCGATTTAATTAGAAATAA
* * * * ** *
1685 ATTCGGAAAAAATGGAAAAACGATATTAGAAGCGTGAGAAGGCGTCAATCTTTTTGACGTTGAAT
131 ATTCAGAAAAAAAGGAAAAACGATATTAGAAGCGTAAAAAACCGTCAATCTTTTTGACGTTAAAT
* * * * *
1750 TATATGTTTTTTCTGCATATTTTGCAAAAAATTGAGAAAAAACTTTTCGGGTTAGCTTTTAGCCA
196 TATATATTTTTTCTGCATATTTGGCAAAAAATTGAGAAAAAACTTTTCAGGTCAGATTTTAGCCA
* *
1815 AAATCGTGTACTAACCATCACGTTTTTTTTTTGCTAAATACGCATTTCATGGCCCCGGCTCAG
261 AAATC-TGTACTAACAATCACGTCTTTTTTTTGCTAAATACGCATTTCATGGCCCCGGCTCAG
* * * *
1878 TTTTGAATGATTTTTGGCAGAAAGACTCCTTAAAATATCTATA-TTCATCTAAGCAAATCTCAGC
1 TTTTGAATGATTTTTGACACAAAGACTCCTTAAAATATCTATATTTCATCGAACCAAATCTCAGC
* * ** * *
1942 CACAATGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTTATTTCGATTTAATTAGAAATA
66 CACAATAGATATAAAAATTTGTTTTTACAAGAATCTGAAT-GTTATTTCGATTTAATTAGAAATA
* * *
2007 AATTCAGAAAAAAAGGAAAAACGATATTAGAAGCGTAAAAAACCATTCAATTTTTTTTG-TGTTA
130 AATTCAGAAAAAAAGGAAAAACGATATTAGAAGCGTAAAAAACC-GTCAA-TCTTTTTGACGTTA
*
2071 AATTATATATTTTTTCTG-ATTATTGTGGCAAAAAATTGAGGAAAAACTTTTCAGGTCA-ATTTT
193 AATTATATATTTTTTCTGCA-TATT-TGGCAAAAAATTGAGAAAAAACTTTTCAGGTCAGATTTT
*
2134 TG-CAAAAT
256 AGCCAAAAT
2142 TTTAGCTGAA
Statistics
Matches: 222, Mismatches: 37, Indels: 10
0.83 0.14 0.04
Matches are distributed among these distances:
322 50 0.23
323 103 0.46
324 33 0.15
325 36 0.16
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (322 bp):
TTTTGAATGATTTTTGACACAAAGACTCCTTAAAATATCTATATTTCATCGAACCAAATCTCAGC
CACAATAGATATAAAAATTTGTTTTTACAAGAATCTGAATGTTATTTCGATTTAATTAGAAATAA
ATTCAGAAAAAAAGGAAAAACGATATTAGAAGCGTAAAAAACCGTCAATCTTTTTGACGTTAAAT
TATATATTTTTTCTGCATATTTGGCAAAAAATTGAGAAAAAACTTTTCAGGTCAGATTTTAGCCA
AAATCTGTACTAACAATCACGTCTTTTTTTTGCTAAATACGCATTTCATGGCCCCGGCTCAG
Found at i:3200 original size:321 final size:316
Alignment explanation
Indices: 2194--3329 Score: 1217
Period size: 321 Copynumber: 3.6 Consensus size: 316
2184 TGTACTAACT
* * * * **
2194 GTCACGGTTTTTTGCTAAAAACGCGTTCCGGAGTCCCGACTCAATTTTGTATGATTTTTTG-CAT
1 GTCAC-GTTTTTGGCTAAAAACGCGTTCC-GAGCCCCGACTCAATTTTGCATGATTTTTGGCCGC
** * *
2258 AAAGACTTTTTGAAAATATCTATATTTATCGAACCAAATTTTAGCCACATTGTATATAAGGATTT
64 AAAGACTCCTTG-AAATATCTATATTCATCGAACCAAA-TTTAGCCACATTGGATATAAGGATTT
*
2323 GTTTTTACGAGCATCCGAATCTTGTTTCGATTTAATTAGAAATTAATTCGG-AAAAAAATGGAAA
127 GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGGAAA
* *
2387 AACGGTATTAGAAGCGTGAAAAACCCATCAATCTCTTTGGCATTGAATTATATATTTTTTCTGAA
192 AACGATATTAGAAGCGTGAAAAACCCATCAATCT-TTTGGCATTGAATTATATATTTTTTCTGAG
* * *
2452 TATT-TTGCAAAAAATTGAGAAAAAAATTTTTGGGTTAGTTTTTAGCCGAAA-TCGTG-T--AC
256 TATTGTGGCAAAAAATTGAG--AAAAA-TTTTGGGTCAGTTTTTAGCCGAAATTTGTGCTAAAC
* ** * * * * * *
2511 GTTACGATTTTTGGCTAAAAATACGTTTCGGGTCCCGGCTCATTTTTGCATGATTTTTGGCAG-A
1 GTCACG-TTTTTGGCTAAAAACGCGTTCCGAGCCCCGACTCAATTTTGCATGATTTTTGGCCGCA
* * * *
2575 AAGACTCCTTGAAATATCTATATTCATCTAACAAAATTTCAGCCACAATGGATTTAAGGATTTGT
65 AAGACTCCTTGAAATATCTATATTCATCGAACCAAATTT-AGCCACATTGGATATAAGGATTTGT
* * **
2640 TTTTACGAGCATCTCAATCTTTGTTTCGATTTAATTAGAAATAAATTCGGTAAAAAAAAAAAGAA
129 TTTTACGAGCATCTGAATC-TTGTTTCGATTTAATTAGAAATTAATTCGG--AAAAAAAATGGAA
* * * * *
2705 AAACGATATTAGAAGGGTGAAAAACCCTTCAATCTTTGTGGCGTTAAATTATATATTTTTTCTAA
191 AAACGATATTAGAAGCGTGAAAAACCCATCAATCTTT-TGGCATTGAATTATATATTTTTTCTGA
* * ** *
2770 GTATTGTGGCAAAAAATTGAGGAAATACTTGTTGGGTCA-TTTTTTG-AAAAATTT-TAGCCGAA
255 GTATTGTGGCAAAAAATTGA-GAAA-AATT-TTGGGTCAGTTTTTAGCCGAAATTTGT-G-CTAA
2832 ATC
315 A-C
* *
2835 GTGC-GGTTTTTGGCTAAAAACGCGTTCCGAAGCCCCGGCTCAATTTTGCATGATTTTT-GCCGC
1 GT-CACGTTTTTGGCTAAAAACGCGTTCCG-AGCCCCGACTCAATTTTGCATGATTTTTGGCCGC
*
2898 AAAGACTCCTTGAAATAT-TCATATTCATCGAACCAAATGTTAGCCACATTGGATATGAGGATTT
64 AAAGACTCCTTGAAATATCT-ATATTCATCGAACCAAAT-TTAGCCACATTGGATATAAGGATTT
* *
2962 GTTTTTACTAGTATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGGAAA
127 GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGGAAA
* * *
3027 AACGATATTAGAAGCGTGAAAAGCCCATCAATCTATTTTGCATTGAATTATAT-TTTTTTTTGAG
192 AACGATATTAGAAGCGTGAAAAACCCATCAATCT-TTTGGCATTGAATTATATATTTTTTCTGAG
*
3091 TATTGCGGCAAAAAATTGAGAACAAATGTTTCGGGTCAGTTTTTAGCCGAAATTGTGTGCTAAAC
256 TATTGTGGCAAAAAATTGAGAA-AAAT-TTT-GGGTCAGTTTTTAGCCGAAATT-TGTGCTAAAC
* * * * *
3156 ATCACGTTTTTGACTAAAAACGTGTTCCAGAGCCCCGACTCAATTTTGCATGATTTTTGGCCTCG
1 GTCACGTTTTTGGCTAAAAACGCGTTCC-GAGCCCCGACTCAATTTTGCATGATTTTTGGCCGCA
* ** * * * * * *
3221 AA-ATTCCTTGAAATATCTATATT-ATTTAATCAAATCTCAGGCATATTGGATTTGAGGATTTGT
65 AAGACTCCTTGAAATATCTATATTCATCGAACCAAAT-TTAGCCACATTGGATATAAGGATTTGT
* * * * * * *
3284 TTTTACAAGTATTTAAATGTTATTTCGATTTAATTAAAAATTAATT
129 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATT
3330 TAAAATATAT
Statistics
Matches: 687, Mismatches: 96, Indels: 69
0.81 0.11 0.08
Matches are distributed among these distances:
314 3 0.00
315 61 0.09
316 66 0.10
317 22 0.03
318 6 0.01
319 90 0.13
320 129 0.19
321 131 0.19
322 19 0.03
323 56 0.08
324 102 0.15
325 2 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (316 bp):
GTCACGTTTTTGGCTAAAAACGCGTTCCGAGCCCCGACTCAATTTTGCATGATTTTTGGCCGCAA
AGACTCCTTGAAATATCTATATTCATCGAACCAAATTTAGCCACATTGGATATAAGGATTTGTTT
TTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGGAAAAACG
ATATTAGAAGCGTGAAAAACCCATCAATCTTTTGGCATTGAATTATATATTTTTTCTGAGTATTG
TGGCAAAAAATTGAGAAAAATTTTGGGTCAGTTTTTAGCCGAAATTTGTGCTAAAC
Found at i:4351 original size:11 final size:12
Alignment explanation
Indices: 4322--4374 Score: 56
Period size: 11 Copynumber: 4.3 Consensus size: 12
4312 TCATGCACCC
4322 AAAACAATTTAATT
1 AAAAC-ATTTAA-T
4336 AAAACATTT-AT
1 AAAACATTTAAT
4347 AAAACAATTTAAT
1 AAAAC-ATTTAAT
*
4360 AAAACA-GTAAT
1 AAAACATTTAAT
4371 AAAA
1 AAAA
4375 TAGTTCCTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
11 14 0.39
12 6 0.17
13 11 0.31
14 5 0.14
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.28
Consensus pattern (12 bp):
AAAACATTTAAT
Found at i:4361 original size:13 final size:13
Alignment explanation
Indices: 4322--4365 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
4312 TCATGCACCC
4322 AAAACAATTTAATT
1 AAAACAATTTAA-T
4336 AAAAC-ATTT-AT
1 AAAACAATTTAAT
4347 AAAACAATTTAAT
1 AAAACAATTTAAT
4360 AAAACA
1 AAAACA
4366 GTAATAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 6 0.21
12 5 0.18
13 12 0.43
14 5 0.18
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAACAATTTAAT
Found at i:4372 original size:24 final size:25
Alignment explanation
Indices: 4322--4374 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 25
4312 TCATGCACCC
* *
4322 AAAACAATTTAATTAAAACATTTAT
1 AAAACAATTTAATTAAAACAGTAAT
4347 AAAACAATTTAA-TAAAACAGTAAT
1 AAAACAATTTAATTAAAACAGTAAT
4371 AAAA
1 AAAA
4375 TAGTTCCTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 14 0.54
25 12 0.46
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.28
Consensus pattern (25 bp):
AAAACAATTTAATTAAAACAGTAAT
Found at i:5660 original size:40 final size:40
Alignment explanation
Indices: 5598--5678 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
5588 ACTTGACCCT
* * *
5598 CCTAATAATTAATAAAATAAATTAAATACGGGTTTAGCCC
1 CCTAATAATTAAGAAAAGAAATTAAATACAGGTTTAGCCC
** *
5638 CCTAATAATTAAGGTAAGAAATTAAATCCAGGTTTAGCCC
1 CCTAATAATTAAGAAAAGAAATTAAATACAGGTTTAGCCC
5678 C
1 C
5679 TAGTTATAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.28
Consensus pattern (40 bp):
CCTAATAATTAAGAAAAGAAATTAAATACAGGTTTAGCCC
Found at i:8160 original size:4 final size:4
Alignment explanation
Indices: 8151--8179 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
8141 AAATCATGTA
8151 TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
8180 AAGAAGGCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:18721 original size:4 final size:4
Alignment explanation
Indices: 18676--18716 Score: 55
Period size: 4 Copynumber: 10.0 Consensus size: 4
18666 CAAACAGCCC
* *
18676 CTTT CTCT CTTTT TTTT CTTT CTTT CTTT CTTT CTTT CTTT
1 CTTT CTTT C-TTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
18717 TTTTTCCTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
4 30 0.94
5 2 0.06
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
CTTT
Found at i:20756 original size:2 final size:2
Alignment explanation
Indices: 20749--20801 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
20739 ATACTTCTTC
*
20749 TG TG TG TG TG TG TG TG TG TA TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
20791 TG TG TG TG TG T
1 TG TG TG TG TG T
20802 TGGAGACAGT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.02, C:0.00, G:0.47, T:0.51
Consensus pattern (2 bp):
TG
Found at i:26854 original size:37 final size:35
Alignment explanation
Indices: 26774--26866 Score: 107
Period size: 37 Copynumber: 2.5 Consensus size: 35
26764 TGCTTGGGCC
*
26774 TGGCCCGGCGCTTGGGCCAAGCTCTGGCCCGCGCG
1 TGGCCTGGCGCTTGGGCCAAGCTCTGGCCCGCGCG
* *
26809 TGAAGCCTGGCGCCTGGGCCAAG-TGCTGGCCCGCTCGCT
1 TG--GCCTGGCGCTTGGGCCAAGCT-CTGGCCCG--CGCG
26848 TGGCCTGGCGCTTGGGCCA
1 TGGCCTGGCGCTTGGGCCA
26867 GCAAGGCCTG
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
35 2 0.04
36 1 0.02
37 41 0.84
39 5 0.10
ACGTcount: A:0.08, C:0.37, G:0.39, T:0.17
Consensus pattern (35 bp):
TGGCCTGGCGCTTGGGCCAAGCTCTGGCCCGCGCG
Found at i:30491 original size:19 final size:19
Alignment explanation
Indices: 30467--30504 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
30457 GTTTATCATG
*
30467 TTGAATTGAATAAACTAAT
1 TTGAATTGAAAAAACTAAT
30486 TTGAATTGAAAAAACTAAT
1 TTGAATTGAAAAAACTAAT
30505 CATTAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (19 bp):
TTGAATTGAAAAAACTAAT
Done.