Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015452.1 Corchorus olitorius cultivar O-4 contig15485, 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: 43290
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:203 original size:27 final size:27
Alignment explanation
Indices: 166--217 Score: 88
Period size: 27 Copynumber: 1.9 Consensus size: 27
156 AAAAGTAACT
166 AAGAAAAATAAAC-GAAAATAAAAGAAA
1 AAGAAAAAT-AACGGAAAATAAAAGAAA
193 AAGAAAAATAACGGAAAATAAAAGA
1 AAGAAAAATAACGGAAAATAAAAGA
218 TAAGGGTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 3 0.12
27 21 0.88
ACGTcount: A:0.75, C:0.04, G:0.13, T:0.08
Consensus pattern (27 bp):
AAGAAAAATAACGGAAAATAAAAGAAA
Found at i:3312 original size:336 final size:335
Alignment explanation
Indices: 2274--4483 Score: 3544
Period size: 336 Copynumber: 6.6 Consensus size: 335
2264 TGGTCTGATC
* * *
2274 AAAAGCTTTCGATTCAATTTTTGGAAAATTTAAGCCGAAATCGTGTACTAACCATCAGAGTTTTT
1 AAAAACTTTCGGTTCAATTTTTGGAAAATTTAAGCCGAAATCGTGTACTAACCATCACAGTTTTT
* * * *
2339 TAGCAAAAAACGCGCTCCG-GGACCCCGGCACGGTTTTGCATTATTTTTGACTCCAAGACTCCTT
66 TAGCAAAAAACGCGCTCCGAGG-CCCCGGCTCAGTTTTGCATTATTTTTGGCGCCAAGACTCCTT
* * *
2403 GTAATACCTATATTCATCAAACAAAAATCTCAGGCA-TATCAGATTTAAGGATTTGTTTTTACGA
130 GTAATATCTATATTCATCTAAC-CAAATCTCAGGCATTA-CAGATTTAAGGATTTGTTTTTACGA
*
2467 GCATCATAAACCGGTTTCAATTTAATTAGAAATTAATTCGGAAAAAAATCAGGAAAAACGATATT
193 GCATCAGAAACCGGTTTCAATTTAATTAGAAATTAATTCGGAAAAAAA-CAGGAAAAACGATATT
*
2532 AGAAGCGTGAAAAGCCCTTCAATCTTCTTTGACGATGAATTATATACTTTTTATGAGTATTGTGA
257 AGAAGCGTGAAAAGCCCTTCAATCTTCTTTGGCGATGAATTATATACTTTTTATGAGTATTGTGA
2597 CCAAAAATTGAGGG
322 CCAAAAATTGAGGG
***
2611 AAAAACTTTCGGTTCAATTTTTGGAAAATTTAAGCCGAAATCGTGTACTATTTATCACAGTTTTT
1 AAAAACTTTCGGTTCAATTTTTGGAAAATTTAAGCCGAAATCGTGTACTAACCATCACAGTTTTT
* * ** *
2676 TAGTAAAAAACGCGCTAC-ATGGCTTCGACTCAGTTTTGCATTATTTTTGGCGCCAAGACTCCTT
66 TAGCAAAAAACGCGCTCCGA-GGCCCCGGCTCAGTTTTGCATTATTTTTGGCGCCAAGACTCCTT
*
2740 GTAATATCTATATTCATCTAACCAAATCTCAGGCATGT-CAGATTTAAGGACTTGTTTTTACGAG
130 GTAATATCTATATTCATCTAACCAAATCTCAGGCAT-TACAGATTTAAGGATTTGTTTTTACGAG
* * *
2804 CACCAGAAACCGATTTCAATTTAATTATAAATTAATTCGG-AAAAAACAGGAAAAACGATATTAG
194 CATCAGAAACCGGTTTCAATTTAATTAGAAATTAATTCGGAAAAAAACAGGAAAAACGATATTAG
*
2868 AAGCGTGAAAAGCCCTTCAATCTTCTTCGGCGATGAATTATATACTTTTTATGAGTATTGTGACC
259 AAGCGTGAAAAGCCCTTCAATCTTCTTTGGCGATGAATTATATACTTTTTATGAGTATTGTGACC
2933 AAAAATTGAGGG
324 AAAAATTGAGGG
*
2945 AAAAACTTTCGGTTCAATTTTTGGAAAATTTAAGTCGAAATCGTGTACTAACCATCACAGTTTTT
1 AAAAACTTTCGGTTCAATTTTTGGAAAATTTAAGCCGAAATCGTGTACTAACCATCACAGTTTTT
*
3010 TAGCAAAAAACGCGCTCCGAGGCCCCGGCTCAGTTTTGCATTATTTTTGGCTCGCAAGACTCCTT
66 TAGCAAAAAACGCGCTCCGAGGCCCCGGCTCAGTTTTGCATTATTTTTGGCGC-CAAGACTCCTT
*
3075 CTAATATCTATATTCATCTAACCAAATCTCAGGCATTACAGATTTAAGGATTTGTTTTTACGAGC
130 GTAATATCTATATTCATCTAACCAAATCTCAGGCATTACAGATTTAAGGATTTGTTTTTACGAGC
* *
3140 ATCAGAAACCGGTTTCAATTTAATCAGAAATTAATTCGGAAAAAAACAGGAAAAATGATATTAGA
195 ATCAGAAACCGGTTTCAATTTAATTAGAAATTAATTCGGAAAAAAACAGGAAAAACGATATTAGA
* *
3205 AGCGTGAAAAGCCCTTCAATCTTCTTTGGCAATGAATTATATACTTTTTGTGAGTATTGTGACCA
260 AGCGTGAAAAGCCCTTCAATCTTCTTTGGCGATGAATTATATACTTTTTATGAGTATTGTGACCA
3270 AAAATTGAGGG
325 AAAATTGAGGG
3281 AAAAACTTTCGGTTCAATTTTTGGAAAATTTAAGCCGAAATCGTGTACT-A-CATCACAGTTTTT
1 AAAAACTTTCGGTTCAATTTTTGGAAAATTTAAGCCGAAATCGTGTACTAACCATCACAGTTTTT
*
3344 TAGCAAAAAACGCGCTCCGAGGCCCCGGCTCAGTTTTGCATTA-TTTTGGCGCGCAAAACTCCTT
66 TAGCAAAAAACGCGCTCCGAGGCCCCGGCTCAGTTTTGCATTATTTTTGGCGC-CAAGACTCCTT
* *
3408 CTAATATCTATATTCATCTAACCAAATCTCAGGCATTACAGATTTAAGGATTTGTTTTTATGAGC
130 GTAATATCTATATTCATCTAACCAAATCTCAGGCATTACAGATTTAAGGATTTGTTTTTACGAGC
* *
3473 ATCAGAAACCGGTTTCAATTTAATCAGAAATTAATTCGGAAAAAAAAAACATGAAAAACGATATT
195 ATCAGAAACCGGTTTCAATTTAATTAGAAATTAATTCGG---AAAAAAACAGGAAAAACGATATT
*
3538 AGAAGCGTGAAAAGCCCTTCAATCTTCTTTGGCGATGAATTATATACTTTTTGTGAGTATTGTGA
257 AGAAGCGTGAAAAGCCCTTCAATCTTCTTTGGCGATGAATTATATACTTTTTATGAGTATTGTGA
*
3603 CCTAAAATTGAGGG
322 CCAAAAATTGAGGG
*
3617 AAAAACTTTCGGTTCAATTTTTGGAAAATTTAAGTCGAAATCGTGTACTAACCATCACAGTTTTT
1 AAAAACTTTCGGTTCAATTTTTGGAAAATTTAAGCCGAAATCGTGTACTAACCATCACAGTTTTT
* * *
3682 TAGCAAAAAACGCGCTCC-CGGACCCGACTCAGTTTTGCATTATTTTTTGG-GCGCAAGACTCCT
66 TAGCAAAAAACGCGCTCCGAGGCCCCGGCTCAGTTTTGCATTA-TTTTTGGCGC-CAAGACTCCT
*
3745 TGTAATATCTATATTCATCTAACCAAATCTCAGGCATGT-CAGATTTAAGGATTTGTTTTTATGA
129 TGTAATATCTATATTCATCTAACCAAATCTCAGGCAT-TACAGATTTAAGGATTTGTTTTTACGA
*
3809 GCATCAGAAACCGGTTTCAATTTAATTATAAATTAATTCGGAAAAAAACAGGAAAAACGATATTA
193 GCATCAGAAACCGGTTTCAATTTAATTAGAAATTAATTCGGAAAAAAACAGGAAAAACGATATTA
* * * *
3874 GAAGCGTGAAAATCCCTTCAATATTCTTTGGCTATGAATTATATACTTTTTATGAGTACTGTGAC
258 GAAGCGTGAAAAGCCCTTCAATCTTCTTTGGCGATGAATTATATACTTTTTATGAGTATTGTGAC
*
3939 CAAAAACTGAGGG
323 CAAAAATTGAGGG
*** *
3952 AAAAACTTTCGGTTCAATTTTTGGAAAATTTAAGCCGAAATCGTGTACTATTTATCACAATTTTT
1 AAAAACTTTCGGTTCAATTTTTGGAAAATTTAAGCCGAAATCGTGTACTAACCATCACAGTTTTT
* * * * *
4017 TAGCAAAAAACGCGCTCCGGGGCCCCGGCTCAGTTTTTCAATATTTTTGCCACCAAGACTCCTTG
66 TAGCAAAAAACGCGCTCCGAGGCCCCGGCTCAGTTTTGCATTATTTTTGGCGCCAAGACTCCTTG
*
4082 TAATATCTATATTCATCTAACCAAATCTCAGACATTACAGATTTAAGGATTTGTTTTTACGAGCA
131 TAATATCTATATTCATCTAACCAAATCTCAGGCATTACAGATTTAAGGATTTGTTTTTACGAGCA
* ** *
4147 TCAGAAACCGGATTCAATTTAATTTTAAATTAATTCCGAAAAAAAACAGGAAAAACGATATTAGA
196 TCAGAAACCGGTTTCAATTTAATTAGAAATTAATT-CGGAAAAAAACAGGAAAAACGATATTAGA
*
4212 AGCGTGACAAGCCCTTCAATCTTCTTTGGCGATGAATTATATACTTTTTATGAGTATTGTGACCA
260 AGCGTGAAAAGCCCTTCAATCTTCTTTGGCGATGAATTATATACTTTTTATGAGTATTGTGACCA
4277 AAAATTGAGGG
325 AAAATTGAGGG
* *
4288 AAAAACTTTCGGTTCAATTTTTGGAAAATTTAAGCTGAAATCGTGTAGTAACCATCACAGTTTTT
1 AAAAACTTTCGGTTCAATTTTTGGAAAATTTAAGCCGAAATCGTGTACTAACCATCACAGTTTTT
* * * *
4353 TAGCAAAAATCGCGCTCCTAAGCCCCGGCTCAGTTTTGCATTATTTTTTGCGCCAAGACTCCTTG
66 TAGCAAAAAACGCGCTCCGAGGCCCCGGCTCAGTTTTGCATTATTTTTGGCGCCAAGACTCCTTG
*
4418 TAATATCTATATTCATCTAACCAAATCTCAGGCATGT-CAGATTTAAGGATTTGTTTTTACGTGC
131 TAATATCTATATTCATCTAACCAAATCTCAGGCAT-TACAGATTTAAGGATTTGTTTTTACGAGC
4482 AT
195 AT
4484 GTTAGTTTTG
Statistics
Matches: 1743, Mismatches: 109, Indels: 43
0.92 0.06 0.02
Matches are distributed among these distances:
333 122 0.07
334 257 0.15
335 399 0.23
336 659 0.38
337 153 0.09
338 146 0.08
339 7 0.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (335 bp):
AAAAACTTTCGGTTCAATTTTTGGAAAATTTAAGCCGAAATCGTGTACTAACCATCACAGTTTTT
TAGCAAAAAACGCGCTCCGAGGCCCCGGCTCAGTTTTGCATTATTTTTGGCGCCAAGACTCCTTG
TAATATCTATATTCATCTAACCAAATCTCAGGCATTACAGATTTAAGGATTTGTTTTTACGAGCA
TCAGAAACCGGTTTCAATTTAATTAGAAATTAATTCGGAAAAAAACAGGAAAAACGATATTAGAA
GCGTGAAAAGCCCTTCAATCTTCTTTGGCGATGAATTATATACTTTTTATGAGTATTGTGACCAA
AAATTGAGGG
Found at i:3913 original size:671 final size:669
Alignment explanation
Indices: 2274--4483 Score: 3587
Period size: 671 Copynumber: 3.3 Consensus size: 669
2264 TGGTCTGATC
* * * *
2274 AAAAGCTTTCGATTCAATTTTTGGAAAATTTAAGCCGAAATCGTGTACTAACCATCAGAGTTTTT
1 AAAAACTTTCGGTTCAATTTTTGGAAAATTTAAGTCGAAATCGTGTACTAACCATCACAGTTTTT
* * * *
2339 TAGCAAAAAACGCGCTCCG-GGACCCCGGCACGGTTTTGCATTATTTTT-GACTCCAAGACTCCT
66 TAGCAAAAAACGCGCTCCGAGGA-CCCGGCTCAGTTTTGCATTATTTTTGGGC-GCAAGACTCCT
* * * *
2402 TGTAATACCTATATTCATCAAACAAAAATCTCAGGCATATCAGATTTAAGGATTTGTTTTTACGA
129 TGTAATATCTATATTCATCTAAC-CAAATCTCAGGCATGTCAGATTTAAGGATTTGTTTTTACGA
*
2467 GCATCATAAACCGGTTTCAATTTAATTAGAAATTAATTCGGAAAAAAATCAGGAAAAACGATATT
193 GCATCAGAAACCGGTTTCAATTTAATTAGAAATTAATTCGGAAAAAAA-CAGGAAAAACGATATT
* *
2532 AGAAGCGTGAAAAGCCCTTCAATCTTCTTTGACGATGAATTATATACTTTTTATGAGTATTGTGA
257 AGAAGCGTGAAAAGCCCTTCAATCTTCTTTGGCAATGAATTATATACTTTTTATGAGTATTGTGA
2597 CCAAAAATTGAGGGAAAAACTTTCGGTTCAATTTTTGGAAAATTTAAGCCGAAATCGTGTACTAT
322 CCAAAAATTGAGGGAAAAACTTTCGGTTCAATTTTTGGAAAATTTAAGCCGAAATCGTGTACTA-
* * ** *
2662 TTATCACAGTTTTTTAGTAAAAAACGCGCTAC-ATGGCTTCGACTCAGTTTTGCATTATTTTTGG
386 TTATCACAGTTTTTTAGCAAAAAACGCGCTCCGA-GGCCCCGGCTCAGTTTTGCATTA-TTTTGG
2726 CGCCAAGACTCCTTGTAATATCTATATTCATCTAACCAAATCTCAGGCATGT-CAGATTTAAGGA
449 CGCCAAGACTCCTTGTAATATCTATATTCATCTAACCAAATCTCAGGCAT-TACAGATTTAAGGA
* * *
2790 CTTGTTTTTACGAGCACCAGAAACCGATTTCAATTTAATTATAAATTAATTCGG--AAAAAACAG
513 TTTGTTTTTACGAGCATCAGAAACCGGTTTCAATTTAATTATAAATTAATTCGGAAAAAAAACAG
*
2853 GAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTCTTCGGCGATGAATTATATACTTTTT
578 GAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTCTTTGGCGATGAATTATATACTTTTT
2918 ATGAGTATTGTGACCAAAAATTGAGGG
643 ATGAGTATTGTGACCAAAAATTGAGGG
2945 AAAAACTTTCGGTTCAATTTTTGGAAAATTTAAGTCGAAATCGTGTACTAACCATCACAGTTTTT
1 AAAAACTTTCGGTTCAATTTTTGGAAAATTTAAGTCGAAATCGTGTACTAACCATCACAGTTTTT
* *
3010 TAGCAAAAAACGCGCTCCGAGGCCCCGGCTCAGTTTTGCATTATTTTTGGCTCGCAAGACTCCTT
66 TAGCAAAAAACGCGCTCCGAGGACCCGGCTCAGTTTTGCATTATTTTTGG-GCGCAAGACTCCTT
*
3075 CTAATATCTATATTCATCTAACCAAATCTCAGGCAT-TACAGATTTAAGGATTTGTTTTTACGAG
130 GTAATATCTATATTCATCTAACCAAATCTCAGGCATGT-CAGATTTAAGGATTTGTTTTTACGAG
* *
3139 CATCAGAAACCGGTTTCAATTTAATCAGAAATTAATTCGGAAAAAAACAGGAAAAATGATATTAG
194 CATCAGAAACCGGTTTCAATTTAATTAGAAATTAATTCGGAAAAAAACAGGAAAAACGATATTAG
*
3204 AAGCGTGAAAAGCCCTTCAATCTTCTTTGGCAATGAATTATATACTTTTTGTGAGTATTGTGACC
259 AAGCGTGAAAAGCCCTTCAATCTTCTTTGGCAATGAATTATATACTTTTTATGAGTATTGTGACC
*
3269 AAAAATTGAGGGAAAAACTTTCGGTTCAATTTTTGGAAAATTTAAGCCGAAATCGTGTACTA-CA
324 AAAAATTGAGGGAAAAACTTTCGGTTCAATTTTTGGAAAATTTAAGCCGAAATCGTGTACTATTA
3333 TCACAGTTTTTTAGCAAAAAACGCGCTCCGAGGCCCCGGCTCAGTTTTGCATTATTTTGGCGCGC
389 TCACAGTTTTTTAGCAAAAAACGCGCTCCGAGGCCCCGGCTCAGTTTTGCATTATTTTGGCGC-C
* *
3398 AAAACTCCTTCTAATATCTATATTCATCTAACCAAATCTCAGGCATTACAGATTTAAGGATTTGT
453 AAGACTCCTTGTAATATCTATATTCATCTAACCAAATCTCAGGCATTACAGATTTAAGGATTTGT
* * * *
3463 TTTTATGAGCATCAGAAACCGGTTTCAATTTAATCAGAAATTAATTCGGAAAAAAAAAACATGAA
518 TTTTACGAGCATCAGAAACCGGTTTCAATTTAATTATAAATTAATTCGG--AAAAAAAACAGGAA
*
3528 AAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTCTTTGGCGATGAATTATATACTTTTTGTG
581 AAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTCTTTGGCGATGAATTATATACTTTTTATG
*
3593 AGTATTGTGACCTAAAATTGAGGG
646 AGTATTGTGACCAAAAATTGAGGG
3617 AAAAACTTTCGGTTCAATTTTTGGAAAATTTAAGTCGAAATCGTGTACTAACCATCACAGTTTTT
1 AAAAACTTTCGGTTCAATTTTTGGAAAATTTAAGTCGAAATCGTGTACTAACCATCACAGTTTTT
* *
3682 TAGCAAAAAACGCGCTCC-CGGACCCGACTCAGTTTTGCATTATTTTTTGGGCGCAAGACTCCTT
66 TAGCAAAAAACGCGCTCCGAGGACCCGGCTCAGTTTTGCATTA-TTTTTGGGCGCAAGACTCCTT
*
3746 GTAATATCTATATTCATCTAACCAAATCTCAGGCATGTCAGATTTAAGGATTTGTTTTTATGAGC
130 GTAATATCTATATTCATCTAACCAAATCTCAGGCATGTCAGATTTAAGGATTTGTTTTTACGAGC
*
3811 ATCAGAAACCGGTTTCAATTTAATTATAAATTAATTCGGAAAAAAACAGGAAAAACGATATTAGA
195 ATCAGAAACCGGTTTCAATTTAATTAGAAATTAATTCGGAAAAAAACAGGAAAAACGATATTAGA
* * * *
3876 AGCGTGAAAATCCCTTCAATATTCTTTGGCTATGAATTATATACTTTTTATGAGTACTGTGACCA
260 AGCGTGAAAAGCCCTTCAATCTTCTTTGGCAATGAATTATATACTTTTTATGAGTATTGTGACCA
*
3941 AAAACTGAGGGAAAAACTTTCGGTTCAATTTTTGGAAAATTTAAGCCGAAATCGTGTACTATTTA
325 AAAATTGAGGGAAAAACTTTCGGTTCAATTTTTGGAAAATTTAAGCCGAAATCGTGTACTA-TTA
* * * * * *
4006 TCACAATTTTTTAGCAAAAAACGCGCTCCGGGGCCCCGGCTCAGTTTTTCAATATTTTTGCCACC
389 TCACAGTTTTTTAGCAAAAAACGCGCTCCGAGGCCCCGGCTCAGTTTTGCATTA-TTTTGGCGCC
*
4071 AAGACTCCTTGTAATATCTATATTCATCTAACCAAATCTCAGACATTACAGATTTAAGGATTTGT
453 AAGACTCCTTGTAATATCTATATTCATCTAACCAAATCTCAGGCATTACAGATTTAAGGATTTGT
* * *
4136 TTTTACGAGCATCAGAAACCGGATTCAATTTAATTTTAAATTAATTCCGAAAAAAAACAGGAAAA
518 TTTTACGAGCATCAGAAACCGGTTTCAATTTAATTATAAATTAATTCGGAAAAAAAACAGGAAAA
*
4201 ACGATATTAGAAGCGTGACAAGCCCTTCAATCTTCTTTGGCGATGAATTATATACTTTTTATGAG
583 ACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTCTTTGGCGATGAATTATATACTTTTTATGAG
4266 TATTGTGACCAAAAATTGAGGG
648 TATTGTGACCAAAAATTGAGGG
*
4288 AAAAACTTTCGGTTCAATTTTTGGAAAATTTAAG-CTGAAATCGTGTAGTAACCATCACAGTTTT
1 AAAAACTTTCGGTTCAATTTTTGGAAAATTTAAGTC-GAAATCGTGTACTAACCATCACAGTTTT
* * * * *
4352 TTAGCAAAAATCGCGCTCCTAAGCCCCGGCTCAGTTTTGCATTATTTTT-TGCGCCAAGACTCCT
65 TTAGCAAAAAACGCGCTCCGAGGACCCGGCTCAGTTTTGCATTATTTTTGGGCG-CAAGACTCCT
*
4416 TGTAATATCTATATTCATCTAACCAAATCTCAGGCATGTCAGATTTAAGGATTTGTTTTTACGTG
129 TGTAATATCTATATTCATCTAACCAAATCTCAGGCATGTCAGATTTAAGGATTTGTTTTTACGAG
4481 CAT
194 CAT
4484 GTTAGTTTTG
Statistics
Matches: 1439, Mismatches: 81, Indels: 38
0.92 0.05 0.02
Matches are distributed among these distances:
667 10 0.01
668 153 0.11
669 1 0.00
670 146 0.10
671 723 0.50
672 241 0.17
673 158 0.11
674 7 0.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (669 bp):
AAAAACTTTCGGTTCAATTTTTGGAAAATTTAAGTCGAAATCGTGTACTAACCATCACAGTTTTT
TAGCAAAAAACGCGCTCCGAGGACCCGGCTCAGTTTTGCATTATTTTTGGGCGCAAGACTCCTTG
TAATATCTATATTCATCTAACCAAATCTCAGGCATGTCAGATTTAAGGATTTGTTTTTACGAGCA
TCAGAAACCGGTTTCAATTTAATTAGAAATTAATTCGGAAAAAAACAGGAAAAACGATATTAGAA
GCGTGAAAAGCCCTTCAATCTTCTTTGGCAATGAATTATATACTTTTTATGAGTATTGTGACCAA
AAATTGAGGGAAAAACTTTCGGTTCAATTTTTGGAAAATTTAAGCCGAAATCGTGTACTATTATC
ACAGTTTTTTAGCAAAAAACGCGCTCCGAGGCCCCGGCTCAGTTTTGCATTATTTTGGCGCCAAG
ACTCCTTGTAATATCTATATTCATCTAACCAAATCTCAGGCATTACAGATTTAAGGATTTGTTTT
TACGAGCATCAGAAACCGGTTTCAATTTAATTATAAATTAATTCGGAAAAAAAACAGGAAAAACG
ATATTAGAAGCGTGAAAAGCCCTTCAATCTTCTTTGGCGATGAATTATATACTTTTTATGAGTAT
TGTGACCAAAAATTGAGGG
Found at i:7472 original size:31 final size:31
Alignment explanation
Indices: 7434--7534 Score: 102
Period size: 31 Copynumber: 3.3 Consensus size: 31
7424 TTAATTTGTC
*
7434 CAAATAAGAGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
* * * **
7465 CAAATAAGGGCCCGATC-TT-T-TAATTTGGC-
1 CAAATAAGGG-CCTAACGTTATCGAAAAT-GCT
7494 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
7525 CAAATAAGGG
1 CAAATAAGGG
7535 TCTGGCGTCA
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
28 4 0.08
29 15 0.28
30 6 0.11
31 24 0.45
32 4 0.08
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.24
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCT
Found at i:7534 original size:60 final size:60
Alignment explanation
Indices: 7374--7534 Score: 243
Period size: 60 Copynumber: 2.7 Consensus size: 60
7364 GCTAATTGTT
* * ** * *
7374 CAAATAAGGGTCTAACGTT-TGCTAAAATATTCAAATAAGGACCCGATCTTTTAATTTGTC
1 CAAATAAGGGCCTAACGTTAT-CGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
*
7434 CAAATAAGAGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
7494 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGG
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGG
7535 TCTGGCGTCA
Statistics
Matches: 92, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
60 91 0.99
61 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
Found at i:7679 original size:61 final size:61
Alignment explanation
Indices: 7579--7740 Score: 247
Period size: 61 Copynumber: 2.7 Consensus size: 61
7569 TGATGCCAAG
* *
7579 CCCTTATTTGAGCA-TTTTGGCAAACATTAGGCCCTTATTTGGCCAAATTAAAAGATCGGA
1 CCCTTATTTGAGCATTTTTAGCAAACATTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
* * *
7639 TCCTTCTTTGAGCATTTTTAGCAAACATTAGGCCCTTATTTGGTCAAATTAAAAGATCAGA
1 CCCTTATTTGAGCATTTTTAGCAAACATTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
* *
7700 CCCTTATTTGAGTATTTTGA-CAAACATTAGGCCCTTATTTG
1 CCCTTATTTGAGCATTTTTAGCAAACATTAGGCCCTTATTTG
7741 AGCAACTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
60 33 0.36
61 59 0.64
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (61 bp):
CCCTTATTTGAGCATTTTTAGCAAACATTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
Found at i:21869 original size:5 final size:5
Alignment explanation
Indices: 21847--21905 Score: 66
Period size: 5 Copynumber: 11.6 Consensus size: 5
21837 TCAGCCATGG
* * *
21847 AAGAA AAGAA GAAG-A AAGCA AAGCAA AAGCA GAGAA AAGAA AAGAA AAGAA
1 AAGAA AAGAA -AAGAA AAGAA AAG-AA AAGAA AAGAA AAGAA AAGAA AAGAA
21898 AAGAA AAG
1 AAGAA AAG
21906 CTTTGGAAGA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
4 3 0.07
5 36 0.78
6 7 0.15
ACGTcount: A:0.71, C:0.05, G:0.24, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:37971 original size:325 final size:321
Alignment explanation
Indices: 37084--38588 Score: 1488
Period size: 319 Copynumber: 4.6 Consensus size: 321
37074 GCACGATTTC
* * *
37084 GGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTT-CTCTCAATTTTTAGCCATAATACTCATA
1 GGCTAAAATTTTGCAAAAATT-AACCTAAAGATTTTGC-CTCAATTTTTAGCCACAATACTCATA
* * * * *
37148 AAAAATATATAATTAAATGCCAAATAGATTGAAGGACTTTACACTCTTCTAATATCGATTTTT-T
64 AAAAATATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCG-TTTTTCT
* * * * * *
37212 C-ATATTTTTTCGAATTAATTTCTAATTAAATCTAAAC-CGATTTTAATGGTCGTAAAAACAAA-
128 CTTTATTTTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTATGATGCTCGTAAAAACAAAT
* * * * *
37274 CTCTTAAAACTAATGTGGCTGAGATTTGGTT--AT--ATA-A-ATATTTCAATGAGTCTTCGGGG
193 C-CTTAAATCCAATGTGCCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTT-GGCG
* * **
37333 TCAAAAATCATTCAAAACTGAGTCGGGG-CCATGGAACGCGTTTTTAGCCAAAAATCGTGATGGA
256 CCAAAAATCATGCAAAACTGAGTCGGGGCCCA--GAACGCGTTTTTAGCCAAAAA-C-CCAT-G-
* *
37397 ACATACACGATTTC
315 --AT----G-GTTA
* * *
37411 GGCTAAAATTTTGCAAAAATTGACCTGAAAGATTTTTCCTCAATTTTTAGCCAAAATACTCATAA
1 GGCTAAAATTTTGCAAAAATTAACCT-AAAGATTTTGCCTCAATTTTTAGCCACAATACTCATAA
* *** * ** *
37476 AAAATATATCATTCAATAATAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTAAT-A
65 AAAATATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCTCT
* * * * *
37540 TT-TCTTTCCGAATTATTTTC-ATCTTAAATCGAAACAAGATTAAGATGCTCGTAAAAACAAATC
130 TTATTTTTTCGAATTAATTTCTA-ATTAAATCGAAACAAGATTATGATGCTCGTAAAAACAAATC
*
37603 CTTAAATCCAATGTGCCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCA
194 CTTAAATCCAATGTGCCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCA
* *
37668 AGAATCATGCAAATA-TGAGTCGGGGTCCCAGAATGCGTTTTTAGCC-AAAACCCATGATGGTTA
259 AAAATCATGCAAA-ACTGAGTCGGGG-CCCAGAACGCGTTTTTAGCCAAAAACCCATGATGGTTA
* * **
37731 GGCTAAAATTTTGCAAAAATTAACCTAAATATTTTGCCTCAATGTTTAATCACAATACTCATAAA
1 GGCTAAAATTTTGCAAAAATTAACCTAAAGATTTTGCCTCAATTTTTAGCCACAATACTCATAAA
* *
37796 AAATATACAATTCAATGCCAAAAAAATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCTTTC
66 AAATATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTC--TC
* * * * *
37861 TTTCTTTTTTTCGAAATTAATTTCTAACTAAATCGAAACAAGATTATGATCCTTGTAAAAGCAAA
129 TTT-ATTTTTTCG-AATTAATTTCTAATTAAATCGAAACAAGATTATGATGCTCGTAAAAACAAA
* * *
37926 TCCTTAAATCTAATGTGCCTGAGATTTGGTTAGATGAATATAGATATTTTAAGGAGTTTTGGCGC
192 TCCTTAAATCCAATGTGCCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGC
* * * * * *
37991 CAAAATTCATGCAAAATTGAGTTGGGGCCCTGAAACGCGTTTTTAGCCAAAAATCCGTGATGGTT
257 CAAAAATCATGCAAAACTGAGTCGGGGCCCAG-AACGCGTTTTTAGCCAAAAACCCATGATGGTT
38056 A
321 A
* * * * * *
38057 GTACACGATTTCCACCAAAATTTTGCAAAGATTGACCATAAAGATTTTTCCTTAATTTCTAGCCA
1 G-----G-------CTAAAATTTTGCAAAAATTAACC-TAAAGATTTTGCCTCAATTTTTAGCCA
* * * * * *
38122 CAATACTCATAAAAAATTTATAATTCAATTCCAAAAATATTGAAGGGATTTTCACGTTTCTAGTA
53 CAATACTCATAAAAAATATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATA
* * * *
38187 TCGTTTTTC-C--TATTTTTTCGGAATTAATTTCTTATTAAACCGAAATAAGATTATGATGTTCG
118 TCGTTTTTCTCTTTATTTTTTC-GAATTAATTTCTAATTAAATCGAAACAAGATTATGATGCTCG
* *
38249 TAAAAAAAAATCTTTAAATCCAATGTGCCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGA
182 TAAAAACAAATCCTTAAATCCAATGTGCCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGA
* * * * * * *
38314 GTCTTGACTCCAAAAATCATGTAAAACTGAGTCGGGTCTCGGAACGCGTTTTTAGCCAAAAA-CT
247 GTCTTGGCGCCAAAAATCATGCAAAACTGAGTCGGGGCCCAGAACGCGTTTTTAGCCAAAAACCC
*
38378 GTGATGGTTA
312 ATGATGGTTA
* * **
38388 GGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTGCCTCAAACTTTAGCCACAATACTCATAA
1 GGCTAAAATTTTGCAAAAATT-AACCTAAAGATTTTGCCTCAATTTTTAGCCACAATACTCATAA
* * * * * *
38453 AAAATATATAATTGAATTCCAAAGAGATTGAAGGGTTTTTCACCCTTATAATATCGTTTTTC-CT
65 AAAATATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCTCT
* * * * * * *
38517 ATTTTTTTTTCCAAATTAATCTCTATTTAAAACGAAACAAGATTATGATACTCGTAAAAATAAAT
130 -TTATTTTTT-CGAATTAATTTCTAATTAAATCGAAACAAGATTATGATGCTCGTAAAAACAAAT
*
38582 CTTTAAA
193 CCTTAAA
38589 ACCGAACTGA
Statistics
Matches: 988, Mismatches: 145, Indels: 95
0.80 0.12 0.08
Matches are distributed among these distances:
319 189 0.19
320 29 0.03
321 2 0.00
322 60 0.06
323 1 0.00
324 11 0.01
325 142 0.14
326 50 0.05
327 151 0.15
328 3 0.00
329 4 0.00
330 1 0.00
331 20 0.02
332 62 0.06
333 150 0.15
334 5 0.01
336 1 0.00
338 20 0.02
339 87 0.09
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (321 bp):
GGCTAAAATTTTGCAAAAATTAACCTAAAGATTTTGCCTCAATTTTTAGCCACAATACTCATAAA
AAATATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCTCTT
TATTTTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTATGATGCTCGTAAAAACAAATCCT
TAAATCCAATGTGCCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAA
AATCATGCAAAACTGAGTCGGGGCCCAGAACGCGTTTTTAGCCAAAAACCCATGATGGTTA
Found at i:41709 original size:31 final size:31
Alignment explanation
Indices: 41638--41898 Score: 338
Period size: 31 Copynumber: 8.9 Consensus size: 31
41628 AAAAATAGAC
*
41638 ATGAGCCCTACTGAATATGCAACTACATGGT
1 ATGAGCCCTACTGAATATGCAACTATATGGT
*
41669 AT--GCCCTACTGAATATGCAACTATACGGT
1 ATGAGCCCTACTGAATATGCAACTATATGGT
41698 ATGAGCCCTACTGAATATGCAAC--TA---T
1 ATGAGCCCTACTGAATATGCAACTATATGGT
41724 ATGAGCCCTACTGAATATGCAACTATATGGT
1 ATGAGCCCTACTGAATATGCAACTATATGGT
* *
41755 ATGGGCCCTACTGAATATGAAACTATAT-G-
1 ATGAGCCCTACTGAATATGCAACTATATGGT
*
41784 A-G-TCCCTACTGAATATGCAACTATAT-G-
1 ATGAGCCCTACTGAATATGCAACTATATGGT
* *
41811 --G-CCCCTACTGAATATGCGACTATATGGT
1 ATGAGCCCTACTGAATATGCAACTATATGGT
*
41839 ATGAGCCCTACTGAATATGCAACTATATGAT
1 ATGAGCCCTACTGAATATGCAACTATATGGT
41870 ATGAGCCCTACTGAATATGCAACTATATG
1 ATGAGCCCTACTGAATATGCAACTATATG
41899 CCCTACTGAA
Statistics
Matches: 207, Mismatches: 11, Indels: 24
0.86 0.05 0.10
Matches are distributed among these distances:
26 47 0.23
27 24 0.12
28 3 0.01
29 30 0.14
30 2 0.01
31 101 0.49
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (31 bp):
ATGAGCCCTACTGAATATGCAACTATATGGT
Found at i:41756 original size:57 final size:57
Alignment explanation
Indices: 41638--41922 Score: 368
Period size: 57 Copynumber: 5.0 Consensus size: 57
41628 AAAAATAGAC
* *
41638 ATGAGCCCTACTGAATATGCAACTACATGGTATGCCCTACTGAATATGCAACTATACGGT
1 ATGAGCCCTACTGAATATGCAACTATAT-G-A-GCCCTACTGAATATGCAACTATATGGT
41698 ATGAGCCCTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGGT
1 ATGAGCCCTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGGT
* *
41755 ATGGGCCCTACTGAATATGAAACTATATGAGTCCCTACTGAATATGCAACTATAT-G-
1 ATGAGCCCTACTGAATATGCAACTATATGAG-CCCTACTGAATATGCAACTATATGGT
* * *
41811 --G-CCCCTACTGAATATGCGACTATATGGTATGAGCCCTACTGAATATGCAACTATATGAT
1 ATGAGCCCTACTGAATATGCAAC--TA---TATGAGCCCTACTGAATATGCAACTATATGGT
*
41870 ATGAGCCCTACTGAATATGCAACTATAT--GCCCTACTGAAGATGCAACTATATG
1 ATGAGCCCTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATG
41923 CCCCCTACTG
Statistics
Matches: 203, Mismatches: 11, Indels: 27
0.84 0.05 0.11
Matches are distributed among these distances:
53 16 0.08
54 1 0.00
55 26 0.13
57 82 0.40
58 30 0.15
59 1 0.00
60 29 0.14
61 1 0.00
62 17 0.08
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.28
Consensus pattern (57 bp):
ATGAGCCCTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGGT
Found at i:41846 original size:115 final size:109
Alignment explanation
Indices: 41638--41935 Score: 377
Period size: 115 Copynumber: 2.6 Consensus size: 109
41628 AAAAATAGAC
*
41638 ATGAGCCCTACTGAATATGCAACTACATGGTATGCCCTACTGAATATGCAACTATACGGTATGAG
1 ATGAGCCCTACTGAATATGCAACTATATGG--T-CCCTACTGAATATGCAAC--TA---TATG-G
*
41703 -CCCTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGGT
57 CCCCTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAT
* *
41755 ATGGGCCCTACTGAATATGAAACTATATGAGTCCCTACTGAATATGCAACTATATGGCCCCTACT
1 ATGAGCCCTACTGAATATGCAACTATATG-GTCCCTACTGAATATGCAACTATATGGCCCCTACT
*
41820 GAATATGCGACTATATGGTATGAGCCCTACTGAATATGCAACTATATGAT
65 GAATATGCAAC--TA---TATGAGCCCTACTGAATATGCAACTATATGAT
* *
41870 ATGAGCCCTACTGAATATGCAACTATAT-G-CCCTACTGAAGATGCAACTATATGCCCCCTACTG
1 ATGAGCCCTACTGAATATGCAACTATATGGTCCCTACTGAATATGCAACTATATGGCCCCTACTG
41933 AAT
66 AAT
41936 GATCTATATG
Statistics
Matches: 165, Mismatches: 9, Indels: 19
0.85 0.05 0.10
Matches are distributed among these distances:
109 1 0.01
110 21 0.13
112 37 0.22
113 3 0.02
115 75 0.45
116 1 0.01
117 26 0.16
118 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (109 bp):
ATGAGCCCTACTGAATATGCAACTATATGGTCCCTACTGAATATGCAACTATATGGCCCCTACTG
AATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAT
Found at i:41902 original size:24 final size:24
Alignment explanation
Indices: 41874--41935 Score: 97
Period size: 24 Copynumber: 2.5 Consensus size: 24
41864 TATGATATGA
41874 GCCCTACTGAATATGCAACTATAT
1 GCCCTACTGAATATGCAACTATAT
*
41898 GCCCTACTGAAGATGCAACTATAT
1 GCCCTACTGAATATGCAACTATAT
41922 GCCCCCTACTGAAT
1 G--CCCTACTGAAT
41936 GATCTATATG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 24 0.71
26 10 0.29
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.26
Consensus pattern (24 bp):
GCCCTACTGAATATGCAACTATAT
Found at i:42222 original size:17 final size:17
Alignment explanation
Indices: 42202--42236 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
42192 CTGTGTATAA
42202 TAAGTAAGCTAGTATTC
1 TAAGTAAGCTAGTATTC
42219 TAAGTAAGCTAGTATTC
1 TAAGTAAGCTAGTATTC
42236 T
1 T
42237 GCTTATACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.37
Consensus pattern (17 bp):
TAAGTAAGCTAGTATTC
Done.