Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008078.1 Corchorus capsularis cultivar CVL-1 contig08099, 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: 12535
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:358 original size:16 final size:16
Alignment explanation
Indices: 337--379 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
327 CGGGTCGGGT
**
337 TCGGGTTCGGGTTGTC
1 TCGGGTTCGGGTAATC
*
353 TCGGGTTCGGGTAATT
1 TCGGGTTCGGGTAATC
369 TCGGGTTCGGG
1 TCGGGTTCGGG
380 CGGGTTCGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.05, C:0.16, G:0.44, T:0.35
Consensus pattern (16 bp):
TCGGGTTCGGGTAATC
Found at i:387 original size:16 final size:16
Alignment explanation
Indices: 320--389 Score: 52
Period size: 16 Copynumber: 4.3 Consensus size: 16
310 TATTTTGATC
*
320 TCGGGCTCGGGTCGGGT
1 TCGGGTTCGGG-CGGGT
**
337 TCGGGTTCGGG-TTGT
1 TCGGGTTCGGGCGGGT
****
352 CTCGGGTTCGGGTAATT
1 -TCGGGTTCGGGCGGGT
369 TCGGGTTCGGGCGGGT
1 TCGGGTTCGGGCGGGT
385 TCGGG
1 TCGGG
390 ATGTTGACTT
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
15 2 0.05
16 28 0.68
17 11 0.27
ACGTcount: A:0.03, C:0.19, G:0.49, T:0.30
Consensus pattern (16 bp):
TCGGGTTCGGGCGGGT
Found at i:1384 original size:335 final size:333
Alignment explanation
Indices: 610--1658 Score: 1315
Period size: 334 Copynumber: 3.1 Consensus size: 333
600 TCATCATAAC
* * *
610 AAATTTCACGTACATTGGATTTAAGGATTTATTTCTACAAGTTTCAGAAACTTGTTTCGATTTAA
1 AAATTTCACGCACATTGGATTTAAGGATTTGTTTCTACAAGTTTCAGAAACTGGTTTCGATTTAA
** * *
675 TTAGAAATTAATTTATTAATTAAAAAAAATGGAAAAATGATATTGAAAGCATGAAATCCACTTCA
66 TTAGAAATTAA--T-TT--GGAAAAAAAATGGAAAAATGATATTGAAAGCGTGAAATGCACTTCA
**
740 ATTTTTTT-GTGTTGAATTATATATTTTTAAAGAGTATTGTATCCAAAAATTGAGGAAAAGTTTT
126 ATTTTTTTGGTGTTGAATTATATATTTTTAAAGAGTATTGTGGCCAAAAATTGAGGAAAAGTTTT
* *** *
804 TCGGGTCAGTTTTTGTGAAATTTTAGCCAAAATCGTGAACTAACCATCAC-GGCTTTTTGATAAA
191 TCGGGTCAGTTTTTG-GAAATTTTAGCCGAAATCGTGAACTAACCATCACTTTTTTTTTGCTAAA
* * * * * *
868 AATGCGTTTCGGGACCACGACACAGTTTTGCATGATTTTTGACGGCAAGACTCATCGAAATATCT
255 AACGCGTTTCGGGGCCCCGACACAGTTTTACATGATTTTCGACGGCAAGACTTATCGAAATATCT
*
933 ATATTCATCTACAA
320 ATATTCATCTAAAA
* * * * * *
947 AAATTTCAAGCACATTGGATTTAAGAATATGTTTTTACAAGTTTCAGAAACTAGTTTTCAATTTA
1 AAATTTCACGCACATTGGATTTAAGGATTTGTTTCTACAAGTTTCAGAAACT-GGTTTCGATTTA
* * * *
1012 TTTACAAATTAATTTGG-GAAAAAATAGAAAAATGATATTGAAAGCGTGAAATGCACTTCAATTT
65 ATTAGAAATTAATTTGGAAAAAAAATGGAAAAATGATATTGAAAGCGTGAAATGCACTTCAA-TT
* ** *
1076 TTTTTGGTGTTCAATTATATATTTTTACGGAGAATTGTGGCCAAAAATTGAGGAAAAGTTTTTCG
129 TTTTTGGTGTTGAATTATATATTTTTAAAGAGTATTGTGGCCAAAAATTGAGGAAAAGTTTTTCG
* **
1141 GGTCACTTTTTGCGAAATTTTAGCCGAAATCGTTTACTAACCATCACTTTTTTTTTGCTAAAAAC
194 GGTCAGTTTTTG-GAAATTTTAGCCGAAATCGTGAACTAACCATCACTTTTTTTTTGCTAAAAAC
*
1206 GCG-TTCTGGGGCCCCGACACATTTTTACA-GTATTTTCGACGGCAAGACTTATCGAAATATCTA
258 GCGTTTC-GGGGCCCCGACACAGTTTTACATG-ATTTTCGACGGCAAGACTTATCGAAATATCTA
1269 TATTCATCTAAAA
321 TATTCATCTAAAA
* * * *
1282 AAATTTCACGCACATTCGAATTAAGGATTTGTTTCTACGAGTTTCAGAAGCTGGTTTCGATTTAA
1 AAATTTCACGCACATTGGATTTAAGGATTTGTTTCTACAAGTTTCAGAAACTGGTTTCGATTTAA
1347 TTAGAAATTAATTTGGAAAAAAAATGGAAAAATGATATTGAAAGCGTGAAATGCACTTCAATTTT
66 TTAGAAATTAATTTGGAAAAAAAATGGAAAAATGATATTGAAAGCGTGAAATGCACTTCAATTTT
* * * * * * *
1412 TTTGGTGCTGAATTATATATTTTTATAGTGTATGGTGGCAAAAAATTGA-GTAATGTTTTTTCGG
131 TTTGGTGTTGAATTATATATTTTTAAAGAGTATTGTGGCCAAAAATTGAGGAAAAG-TTTTTCGG
* *
1476 GTCAGTTTTTAGGAAATTTTAGTCGAAATCGTGAACTAACTTATCACAGTTTTTTTTTTGGCTAA
195 GTCAGTTTTT-GGAAATTTTAGCCGAAATCGTGAACTAAC-CATCAC---TTTTTTTTT-GCTAA
* * * * * * *
1541 AAACGTGTTTCGGGGTCCCGGCACAGTTTTACATGATTTTCGGC-GCAAAGAATT-GCTAAAATA
254 AAACGCGTTTCGGGGCCCCGACACAGTTTTACATGATTTTCGACGGC-AAGACTTATC-GAAATA
1604 TCTATATTCATC-AAAA
317 TCTATATTCATCTAAAA
1620 CAAATTTCACGCACATTGGATTTAAGGATTTGTTTCTAC
1 -AAATTTCACGCACATTGGATTTAAGGATTTGTTTCTAC
1659 GAGTATTAAC
Statistics
Matches: 614, Mismatches: 79, Indels: 36
0.84 0.11 0.05
Matches are distributed among these distances:
332 40 0.07
333 11 0.02
334 211 0.34
335 169 0.28
336 1 0.00
337 46 0.07
338 35 0.06
339 97 0.16
340 4 0.01
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (333 bp):
AAATTTCACGCACATTGGATTTAAGGATTTGTTTCTACAAGTTTCAGAAACTGGTTTCGATTTAA
TTAGAAATTAATTTGGAAAAAAAATGGAAAAATGATATTGAAAGCGTGAAATGCACTTCAATTTT
TTTGGTGTTGAATTATATATTTTTAAAGAGTATTGTGGCCAAAAATTGAGGAAAAGTTTTTCGGG
TCAGTTTTTGGAAATTTTAGCCGAAATCGTGAACTAACCATCACTTTTTTTTTGCTAAAAACGCG
TTTCGGGGCCCCGACACAGTTTTACATGATTTTCGACGGCAAGACTTATCGAAATATCTATATTC
ATCTAAAA
Found at i:4032 original size:336 final size:334
Alignment explanation
Indices: 1665--5757 Score: 5463
Period size: 334 Copynumber: 12.3 Consensus size: 334
1655 CTACGAGTAT
* * **
1665 TAACCATCACGGTGTTTTGCTAAAAACGCGTTCCGGGGCCCCGGCACAGTTTTGCATTATTTTTT
1 TAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGGGCCCCGGCACAGTTTTGCATGATTTTCG
* * * *
1730 ACGGCAAGACTCATCGAAATATCTATACTCATTTACAAAAATTTCAAACACAATGGATTTAATGA
66 ACGGCAAGACTCATCGAAATATCTATATTCATTTACAAAAATTTCAAGCACATTGGATTTAAGGA
* * *
1795 TTTGTTTTTACGAGTTTCAGAAACTTGTTTCAAGTTATTTAGAAATTAATTTGGAAAAAAAATGG
131 TTTGTTTCTACGAGTTTCAGAAACTTGTTTCAATTTAATTAGAAATTAATTTGG-AAAAAAATGG
* * * *
1860 AAAAATTATATTGAAAGTGTGAATTGCACTTCAATTTTTTTTTGGTGTTGGATTATATATTTTTA
195 AAAAATGATATTGAAAGCGTGAAATGCACTTCAATTTTTTTTTGGTGTTGAATTATATATTTTTA
* *
1925 TAGAGTGTTGGGGCCAAAAATTGAGGAAAATGTTTTTCGGGTCACTTTTTGCGAAATTTTAGCCG
260 TAGAGTATTGTGGCCAAAAATTGAGGAAAA-GTTTTTCGGGTCACTTTTTGCGAAATTTTAGCCG
1990 AAATCGTGTAC
324 AAATCGTGTAC
*
2001 TAACCATCACGGTTTTTTGCTAAAAACGCGTTCTGGGGCCCCGGCACAGTTTTGCATGATTTTCG
1 TAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGGGCCCCGGCACAGTTTTGCATGATTTTCG
* * * * * *
2066 GCGGCAAGACTCATCGAAATATCTATATTCATTTAAAAAAACTTCACGCACATTCGAATTAAGGA
66 ACGGCAAGACTCATCGAAATATCTATATTCATTTACAAAAATTTCAAGCACATTGGATTTAAGGA
* * * *
2131 TTTGTTTCTACGAGTTCCAGAAGCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAAATGGA
131 TTTGTTTCTACGAGTTTCAGAAACTTGTTTCAATTTAATTAGAAATTAATTTGGAAAAAAATGGA
* * *
2196 AAAATGACATTGAAAGCGTGAAATGCACTTCAA-TTTTTTTTGGCGTTGACTTATATATTTTTAT
196 AAAATGATATTGAAAGCGTGAAATGCACTTCAATTTTTTTTTGGTGTTGAATTATATATTTTTAT
* * * *
2260 AGAGTATTGTTGCCAAAAATTGAGGAAAATTTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAA
261 AGAGTATTGTGGCCAAAAATTGAGGAAAAGTTTTTCGGGTCACTTTTTGCGAAATTTTAGCCGAA
2325 ATCGTGTAC
326 ATCGTGTAC
* * **
2334 T-ACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGGTCCCCGGCACAGTTTTGCATTATTTTTT
1 TAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGGGCCCCGGCACAGTTTTGCATGATTTTCG
* * *
2398 ACGGCAAGACTCATTGAAATATCTATACTCATTTACAAAAATTTCAAGCACAATGGATTTAAGGA
66 ACGGCAAGACTCATCGAAATATCTATATTCATTTACAAAAATTTCAAGCACATTGGATTTAAGGA
* * *
2463 TTTGTTTTTACGAGTTTCAGAAAC-TGATTTCAAGTTATTTAGAAATTAATTTGGAAAAAAATGG
131 TTTGTTTCTACGAGTTTCAGAAACTTG-TTTCAATTTAATTAGAAATTAATTTGGAAAAAAATGG
* * *
2527 AAAAATGATATTGAAAGTGTGAATTGCACTTCAATTTTTTTTTGGTGTTGGATTATATATTTTTA
195 AAAAATGATATTGAAAGCGTGAAATGCACTTCAATTTTTTTTTGGTGTTGAATTATATATTTTTA
* * *
2592 TAGAGTGTTGGGGCCAAAAATTGAGGAAATGTTTTTCGGGTCACTTTTTGCGAAATTTTAGCCGA
260 TAGAGTATTGTGGCCAAAAATTGAGGAAAAGTTTTTCGGGTCACTTTTTGCGAAATTTTAGCCGA
2657 AATCGTGTAC
325 AATCGTGTAC
* *
2667 TAACCATCACTGTTTTTTGCTAAAAACGCGTTCTGGGGCCCCGGCACAGTTTTGCATGATTTTCG
1 TAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGGGCCCCGGCACAGTTTTGCATGATTTTCG
* * * ** * * *
2732 GCGGCAAGACTCATCGAAATATCTATATTCATCTAAAAAAACGTCACGCACATTCGAATTAAGGA
66 ACGGCAAGACTCATCGAAATATCTATATTCATTTACAAAAATTTCAAGCACATTGGATTTAAGGA
* * * *
2797 TTTGTTTCTACGAGTTCCAGAAGCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAAATGGA
131 TTTGTTTCTACGAGTTTCAGAAACTTGTTTCAATTTAATTAGAAATTAATTTGGAAAAAAATGGA
* * * *
2862 AAAATGACATTGAAAGCGTGCAATGCACTTCAATTTTTTTTGGCGTTTGGCGTTGACTTATATAT
196 AAAATGATATTGAAAGCGTGAAATGCACTTCAA--TTTTTT----TTTGGTGTTGAATTATATAT
* * *
2927 TTTTATAGAGTATTGTTGCCAAAAATTGAGGAAAACTTTTTCGGGTCAATTTTTGCGAAATTTTA
255 TTTTATAGAGTATTGTGGCCAAAAATTGAGGAAAAGTTTTTCGGGTCACTTTTTGCGAAATTTTA
2992 GCCGAAATCGTGTAC
320 GCCGAAATCGTGTAC
* * *
3007 TAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGGGCCCCAGCACAGTTTTGCATTATTTTTG
1 TAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGGGCCCCGGCACAGTTTTGCATGATTTTCG
*
3072 ACGGCAAGACTCATCGAAATATCTATATTCATTTACAAAAATTTCAAGCACAATGGATTTAAGGA
66 ACGGCAAGACTCATCGAAATATCTATATTCATTTACAAAAATTTCAAGCACATTGGATTTAAGGA
* * * *
3137 TTTGTTTTTCCGAGTTTCAGAAACTTGTTTCAAGTTATTTAGAAATTAATTTGGAAAAAAAATGG
131 TTTGTTTCTACGAGTTTCAGAAACTTGTTTCAATTTAATTAGAAATTAATTTGG-AAAAAAATGG
* * * *
3202 AAAAATGATATTGAAAGTGTGAATTGCACTTCAATTTTTTTTTGGTGTTAAATTATATATTATTA
195 AAAAATGATATTGAAAGCGTGAAATGCACTTCAATTTTTTTTTGGTGTTGAATTATATATTTTTA
*
3267 TAGAGTATTGTGGCCAAAAATTGATGAAAAGTTTTTCGGGTCACTTTTTGCGAAATTTTAGCCGA
260 TAGAGTATTGTGGCCAAAAATTGAGGAAAAGTTTTTCGGGTCACTTTTTGCGAAATTTTAGCCGA
*
3332 ATTCGTG---
325 AATCGTGTAC
*
3339 T-ACCATCACGGTTTTTTGCTAAAAACGCGTTCTGGGGCCCCGGCACAGTTTTGCATGATTTTCG
1 TAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGGGCCCCGGCACAGTTTTGCATGATTTTCG
* * * * * *
3403 GCGGCAAGACTCATCGAAATATCTATATTCATTTATAAAAACTTCACGCACATTCGAATTAAGGA
66 ACGGCAAGACTCATCGAAATATCTATATTCATTTACAAAAATTTCAAGCACATTGGATTTAAGGA
* * * *
3468 TTTCTTTCTACGAGTTCCAGAAGCTTGTTTCGATTTAATTAGAAATTAATTT--AAAAAAATGGA
131 TTTGTTTCTACGAGTTTCAGAAACTTGTTTCAATTTAATTAGAAATTAATTTGGAAAAAAATGGA
* * * *
3531 AAAATGACATTGAAAGCGTGAAATGCACTTCAA-TTTTTTTGGGCGTTGACTTATATATTTTTAT
196 AAAATGATATTGAAAGCGTGAAATGCACTTCAATTTTTTTTTGGTGTTGAATTATATATTTTTAT
* * * * *
3595 AGAGTATTGTTGCCAAAAATTGAGGAGAATTTTTTCGAGTCAGTTTTTGCGAAATTTTAGCCGAA
261 AGAGTATTGTGGCCAAAAATTGAGGAAAAGTTTTTCGGGTCACTTTTTGCGAAATTTTAGCCGAA
3660 ATCGTGTAC
326 ATCGTGTAC
* * *
3669 TAACCATCACGGTTTTTTACTAAAAACGCATTCCGGGGCCCCGGCACAGTTTTGCATTACTTTT-
1 TAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGGGCCCCGGCACAGTTTTGCATGA-TTTTC
*
3733 GACGGCAAGACTCATCGAAATATCTATATTCATTTACAAAAATTTCAAGCACAATGGATTTAAGG
65 GACGGCAAGACTCATCGAAATATCTATATTCATTTACAAAAATTTCAAGCACATTGGATTTAAGG
* * * * *
3798 ATTTGTTTTTACGAGTTTCAAAAACTGGTTTCAAGTTAGTTAGAAATTAATTTGGAAAAAAAAAT
130 ATTTGTTTCTACGAGTTTCAGAAACTTGTTTCAATTTAATTAGAAATTAATTTGG--AAAAAAAT
* * *
3863 GGAAAAATGAAATTGAAAGCGTGAATTGCACTTCAATTTTTTTTTGGTGTTGAATTATATATTAT
193 GGAAAAATGATATTGAAAGCGTGAAATGCACTTCAATTTTTTTTTGGTGTTGAATTATATATTTT
*
3928 TATAGAGTATTGTGGCCAAAAAGTGAGGAAAAGTTTTTCGGGTCACTTTTTGCGAAATTTTAGCC
258 TATAGAGTATTGTGGCCAAAAATTGAGGAAAAGTTTTTCGGGTCACTTTTTGCGAAATTTTAGCC
3993 GAAATCGTGTAC
323 GAAATCGTGTAC
* * * * *
4005 TAAGCATCACTGTTTTTTG-TCAAAAACGCGTTTCAGGGCCCCTGCACAGTTTTGCATGATTTTC
1 TAACCATCACGGTTTTTTGCT-AAAAACGCGTTCCGGGGCCCCGGCACAGTTTTGCATGATTTTC
** * * * * *
4069 GGTGCCAAGACTC-GCTGAAATATCTATATTCATCTA-AACAAATTTCACGCACATTGTATTTAA
65 GACGGCAAGACTCATC-GAAATATCTATATTCATTTACAA-AAATTTCAAGCACATTGGATTTAA
* ***
4132 GGATTTGTTTCTACGAGTTTCAGAAACTGGTTT-AGATTTAATTAGAAATTAATTTTTTAAAAAA
128 GGATTTGTTTCTACGAGTTTCAGAAACTTGTTTCA-ATTTAATTAGAAATTAATTTGGAAAAAAA
* * * *
4196 TGGAAAAATGATATTGAAAGCATGAAATGCACTTCAATTTTTTTTTGGCGTTGACTTTTATATTT
192 TGGAAAAATGATATTGAAAGCGTGAAATGCACTTCAATTTTTTTTTGGTGTTGAATTATATATTT
** * * * * * *
4261 TTATAGTTTATTTTTGCCAAAAATTGAGGTAAATTTTTTCGAGTCAGTTTTTGCGAAATTTTAG-
257 TTATAGAGTATTGTGGCCAAAAATTGAGGAAAAGTTTTTCGGGTCACTTTTTGCGAAATTTTAGC
4325 C-----C---TA-
322 CGAAATCGTGTAC
* * * **
4329 T---CAT---GGTTTTTTGCTAAAAACGCGTTCCAGGGCCCTGACACAGTTTTGCATGATTTTTT
1 TAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGGGCCCCGGCACAGTTTTGCATGATTTTCG
* * *
4388 ACGGCAAGACTCATCGAAATATCTATATTTATGTACAAAAATTTCAAGCACATTGGTTTTAAGGA
66 ACGGCAAGACTCATCGAAATATCTATATTCATTTACAAAAATTTCAAGCACATTGGATTTAAGGA
* ** *
4453 TTTGTTTTTACTTGTTTCAGAAACTAGTTT-AGATTTAATTAGAAATTAATTTGG-AAAAAATGG
131 TTTGTTTCTACGAGTTTCAGAAACTTGTTTCA-ATTTAATTAGAAATTAATTTGGAAAAAAATGG
* * * *
4516 AAAAATGATATTGAAAGCGTGAAATGCACTTC-ACTTTTTTTTGGTGTTGGATTATATTTTTTTT
195 AAAAATGATATTGAAAGCGTGAAATGCACTTCAATTTTTTTTTGGTGTTGAATTATATATTTTTA
* * ** * *
4580 TATAGCATTGTGGCCAAAAATTGAGGAAAACCTTTTCGGGTCACTTTTTGCCAAATTTTAGCTGA
260 TAGAGTATTGTGGCCAAAAATTGAGGAAAAGTTTTTCGGGTCACTTTTTGCGAAATTTTAGCCGA
4645 AATCGTGTAC
325 AATCGTGTAC
* * * *
4655 TAACTATCAC-TTTTTTTGCTAAAAACGTGTTCC---ACCCCGGCACAGTTTTGCATGATTTTCG
1 TAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGGGCCCCGGCACAGTTTTGCATGATTTTCG
* * * * * * * *
4716 GCGACAAGACTC-GCTTAAATATCTATATTCATCTA-AACAAATTTCACGCACATTAGATTTAAA
66 ACGGCAAGACTCATC-GAAATATCTATATTCATTTACAA-AAATTTCAAGCACATTGGATTTAAG
* *
4779 GATTTGTTTCTACGAGTTTCAGAAACTGGTTTGAATTTAATTAGAAATTAATTTGGAAAAAAATG
129 GATTTGTTTCTACGAGTTTCAGAAACTTGTTTCAATTTAATTAGAAATTAATTTGGAAAAAAATG
* *
4844 GAAAAATGGAAAAAGATATTGAAAGCATGAAATGCACTTCAA-TTTTTTTTGGTGTTGACTTATA
194 GAAAAAT-------GATATTGAAAGCGTGAAATGCACTTCAATTTTTTTTTGGTGTTGAATTATA
* * * *
4908 TATTTTTATAGAGTATTGTTGCCAAAAATTGAGGAAAATTTTTTCGAGTCAGTTTTTGCGAAATT
252 TATTTTTATAGAGTATTGTGGCCAAAAATTGAGGAAAAGTTTTTCGGGTCACTTTTTGCGAAATT
*
4973 TTAGCCTAAATCGTGTAC
317 TTAGCCGAAATCGTGTAC
* * * *
4991 TAACCCATCACGGTTTTTTGCTAAAAATGCGTTCCGGGGCCCTGGCACAATTTTGCATGATTTTT
1 TAA-CCATCACGGTTTTTTGCTAAAAACGCGTTCCGGGGCCCCGGCACAGTTTTGCATGATTTTC
* * * * *
5056 TATGGCAAGACTCATCGATATATCTATATTCATGTACAAAAATTTGAAGCACATTGGATTTAAGG
65 GACGGCAAGACTCATCGAAATATCTATATTCATTTACAAAAATTTCAAGCACATTGGATTTAAGG
* *
5121 ATTTGTTTTTACGAGTTTCAGAAACTAGTTT-AGATTTAATTAGAAATTAATTTGGAAAAAAATG
130 ATTTGTTTCTACGAGTTTCAGAAACTTGTTTCA-ATTTAATTAGAAATTAATTTGGAAAAAAATG
* *
5185 GAAAAATGATATTGAAAGCGTGAAATGCACTTCAATTTTTTTTTTGTATTGAATTATATATTTTT
194 GAAAAATGATATTGAAAGCGTGAAATGCACTTCAATTTTTTTTTGGTGTTGAATTATATATTTTT
* *
5250 ATAGAGTATTGTGGCCGAAAATTGAGGAAAAGTTTTTCAGGTCACTTTTTGCGAAATTTTAGCCG
259 ATAGAGTATTGTGGCCAAAAATTGAGGAAAAGTTTTTCGGGTCACTTTTTGCGAAATTTTAGCCG
5315 AAATCGTGTAC
324 AAATCGTGTAC
* * * *
5326 TAACCATCATGGTTTTTTGCTAAAAACGCGTTCAGGAGCCCCGGCACAATTTTGCATGATTTTCG
1 TAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGGGCCCCGGCACAGTTTTGCATGATTTTCG
* ** * * * * *
5391 GCTACAAGACTC-GCTGAAATATCTATATTCATCTAAAAAAATTTCACGCACATTGGATTTAAAG
66 ACGGCAAGACTCATC-GAAATATCTATATTCATTTACAAAAATTTCAAGCACATTGGATTTAAGG
* * *
5455 ATTTGTTTCTACGAGTTTCAGAAACTAGTTTCGATTTAATTAAAAATTAATTTGGAAAAAAATGG
130 ATTTGTTTCTACGAGTTTCAGAAACTTGTTTCAATTTAATTAGAAATTAATTTGGAAAAAAATGG
*
5520 AAAAAATGATATTGAAAGCGTGATATGCACTTCAA--TTTTTTTGGTGTTGAATTATATATTTTT
195 -AAAAATGATATTGAAAGCGTGAAATGCACTTCAATTTTTTTTTGGTGTTGAATTATATATTTTT
* **
5583 ATAGAGTATTGTGGCCAAAAATTGAGGAAAAGCTTTTCATGTCACTTTTT-CGAAATTTTAGCCG
259 ATAGAGTATTGTGGCCAAAAATTGAGGAAAAGTTTTTCGGGTCACTTTTTGCGAAATTTTAGCCG
*
5647 AAATCATGTAC
324 AAATCGTGTAC
* * * * *
5658 TAATCATCACTGTTTTTTGGTAAAAACGCGTTCCGAGGCCCCGGCACAGTTTTGCATGGTTTTCG
1 TAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGGGCCCCGGCACAGTTTTGCATGATTTTCG
* * *
5723 ATGACAAGACTC-GCTGAAATATCTATATTCGATTT
66 ACGGCAAGACTCATC-GAAATATCTATATTC-ATTT
5758 GACAGAATGA
Statistics
Matches: 3287, Mismatches: 400, Indels: 143
0.86 0.10 0.04
Matches are distributed among these distances:
316 74 0.02
317 40 0.01
318 145 0.04
319 4 0.00
321 3 0.00
322 1 0.00
324 1 0.00
325 4 0.00
326 1 0.00
327 93 0.03
328 163 0.05
329 18 0.01
330 1 0.00
331 339 0.10
332 311 0.09
333 217 0.07
334 562 0.17
335 312 0.09
336 530 0.16
337 7 0.00
338 20 0.01
339 6 0.00
340 254 0.08
341 178 0.05
342 3 0.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (334 bp):
TAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGGGCCCCGGCACAGTTTTGCATGATTTTCG
ACGGCAAGACTCATCGAAATATCTATATTCATTTACAAAAATTTCAAGCACATTGGATTTAAGGA
TTTGTTTCTACGAGTTTCAGAAACTTGTTTCAATTTAATTAGAAATTAATTTGGAAAAAAATGGA
AAAATGATATTGAAAGCGTGAAATGCACTTCAATTTTTTTTTGGTGTTGAATTATATATTTTTAT
AGAGTATTGTGGCCAAAAATTGAGGAAAAGTTTTTCGGGTCACTTTTTGCGAAATTTTAGCCGAA
ATCGTGTAC
Found at i:6356 original size:69 final size:71
Alignment explanation
Indices: 6246--6394 Score: 275
Period size: 69 Copynumber: 2.1 Consensus size: 71
6236 AAAAGAGAAC
6246 TTGAGTGAATTGGAATTATATATATAGTTTAAGAGAGTAACCTTTATTTTGTTTAATAATTATTC
1 TTGAGTGAATTGGAATTATATATATAGTTTAAGAGAGTAACCTTTATTTTGTTTAATAATTATTC
6311 AAATTT
66 AAATTT
6317 TTGAGTGAATTGGAA-T-TATATATAGTTTAAGAGAGTAACCTTTATTTTGTTTAATAATTATTC
1 TTGAGTGAATTGGAATTATATATATAGTTTAAGAGAGTAACCTTTATTTTGTTTAATAATTATTC
6380 AAATTT
66 AAATTT
*
6386 TTGATTGAA
1 TTGAGTGAA
6395 CTAACTTTCA
Statistics
Matches: 77, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
69 61 0.79
70 1 0.01
71 15 0.19
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.46
Consensus pattern (71 bp):
TTGAGTGAATTGGAATTATATATATAGTTTAAGAGAGTAACCTTTATTTTGTTTAATAATTATTC
AAATTT
Found at i:11119 original size:29 final size:29
Alignment explanation
Indices: 11055--11127 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
11045 GGTTGAGTGG
* * *
11055 GTAAAACGTCACAAAATTGAAGTTTAGGGG
1 GTAAAACGTC-CAAAATTGAAATTTAGAGA
* * *
11085 GCAAAATGTCCAATATTGAAATTTAGAGA
1 GTAAAACGTCCAAAATTGAAATTTAGAGA
11114 GTAAAACGTCCAAA
1 GTAAAACGTCCAAA
11128 CGCTACAAGT
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
29 26 0.76
30 8 0.24
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.23
Consensus pattern (29 bp):
GTAAAACGTCCAAAATTGAAATTTAGAGA
Found at i:12456 original size:30 final size:30
Alignment explanation
Indices: 12412--12488 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
12402 CGTTTGAACG
*
12412 TTTTG-CCTCCTGAACCTCAATCTTTGGAC-
1 TTTTGCCCCCCTGAACCTCAAT-TTTGGACA
*
12441 TTTTGCCCCCCTGAACTTCAATTTTGGACA
1 TTTTGCCCCCCTGAACCTCAATTTTGGACA
* *
12471 TCTTGCCCCCCTCAACCT
1 TTTTGCCCCCCTGAACCT
12489 AACAGCTCCA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 12 0.29
30 29 0.71
ACGTcount: A:0.17, C:0.36, G:0.12, T:0.35
Consensus pattern (30 bp):
TTTTGCCCCCCTGAACCTCAATTTTGGACA
Done.