Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009647.1 Corchorus olitorius cultivar O-4 contig09679, 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: 2864
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Found at i:1742 original size:652 final size:652
Alignment explanation
Indices: 394--2864 Score: 2943
Period size: 652 Copynumber: 3.7 Consensus size: 652
384 AATCTAATGC
* *
394 GATGCTTAGTACACGATTCCGGTTCAAAATTTGCAAAAACTGACCCGAAAAAATTCTTCATCAAC
1 GATGCTTAGTACACGATTCCGGTTCAAATTTTGCAAAAACTGACCCGAAAAAATTCTTCATCAAT
**
459 TTTTGGCCACAATACTCATAAAAAATATATAATTCAACACCAAAAACATTGAAGGGAATTTCACG
66 TTTTGGCCACAATACTCATAAAAAATATATAATTCAACACCAAAAACATTGAAGGGCTTTTCACG
* *
524 CTTCTAATATCGTTTTTCCTATTTTTTCGAAATTAATTTTTGATTAAATCAAACAAGAGTCAGAT
131 CTTCTAATATCGTTTTTCCTATTTTTTCAAAACTAATTTTTGATTAAATCAAACAAGAGTCAGAT
*
589 ACTCGTAAAAACATATCCTTAAATCCAATGTAGCTGAGATTTGATTAGATGAATATAGATATTTC
196 ACTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTC
* * *
654 AAGGAGTCTTGGGTCCAAATATCATGCGAAACTGAGCCGGCGCCCCGGAACGCGTTTTTAGGCAA
261 AAGGAGTCTCGGGTCCAAAAATCATGCAAAACTGAGCCGGCGCCCCGGAACGCGTTTTTAGGCAA
* * * * * * * **
719 AAATCGTGATGGTTTGTACACTATTTCGGTTCAGAATTAGCACAAACTGACCCGAAAATTTTTTT
326 AAAACGTGATGATTTGAACACGATTTCGGTTCAGATTTTGCAAAAACTGACCCGAAAA--AATTT
* *
784 TTGTCAATTTTTGG-C-C---A--C-------A-ATATAATTCAACATTAAAAAGATTGAAGGTC
389 TCGTCAATTTTTGGCCACAATACTCATAAAAAATATATAATTCAACATTAAAAAGATTGAAGGGC
*
834 TTTTCACGCTTCTAATATCGTTTCTTTTTTTTCCAAATTAATTTTTGATTAAATTGAAACAAGAT
454 TTTTCACGCTTCTAATATCG-------TTTTTCCAAATTAATTTTT-ATTAAATCGAAACAAGAT
* * *
899 TCATATACTCGTAAAAACATATCCTTAAATCCAATGTGGCT-ATGATTTGATTAGATGAATATAG
511 TCAGATACTCGTAAAAACATATCCTGAAATCCAATGTGGCTGAT-ATTTGATTAGATGAATACAG
* * ** *
963 ATATTTCAAGGAGTATCGGCTCCAAAAATCATGCAAAACTCAGTTGGGGCCTCGGAACGCATTTT
575 ATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTCAGCCGGGGCC-CGGAACGCGTTTT
*
1028 TAGTAGAAAACTGT
639 TAGCAGAAAACTGT
* * * *
1042 GATGGTTAGTACACGATTTCGGTTCAAAATTTT-CAAAAACTGACCCGAAAAAAATT-TCCGTCA
1 GATGCTTAGTACACGATTCCGGTTC-AAATTTTGCAAAAACTGACCCG-AAAAAATTCTTCATCA
*
1105 ATTTTTGGCCACAATACTCATAAAAAATATATAATTCAACTCCAAAAACATTGAA-GGCTTTTCA
64 ATTTTTGGCCACAATACTCATAAAAAATATATAATTCAACACCAAAAACATTGAAGGGCTTTTCA
* * **
1169 CGCTTCTAATATCGTTTTTCCTATTTTTTCCAAACTAATTTTTGATTAAATTGAAACAAGA-TTT
129 CGCTTCTAATATCGTTTTTCCTATTTTTTCAAAACTAATTTTTGATTAAA-TCAAACAAGAGTCA
* * * *
1233 GAATGCTCGTAAAAATATATCCTTAAATCTAGTGTGGCTGAGATTTGATTAGATGAATATAGATA
193 G-ATACTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATA
** * * * * * *
1298 TTTCAAGGAGTCTCGGCACCAAAAATCATGTAAAACTGAGCTGGGGCACCGGAAAGCGTTTTT-T
257 TTTCAAGGAGTCTCGGGTCCAAAAATCATGCAAAACTGAGCCGGCGCCCCGGAACGCGTTTTTAG
* * *
1362 GCAAAAAAC-T-ATGATTAACGAACACGATTTCGATTCAGATTTTGTAAAAACTGACCCGAAAAA
322 GCAAAAAACGTGATGATT--TGAACACGATTTCGGTTCAGATTTTGCAAAAACTGACCCGAAAAA
* *
1425 ATTTTCGTCAATTTTTGGCCATAATACTTATAAAAAATATATAATTCAACATTAAAAAGATTGAA
385 ATTTTCGTCAATTTTTGGCCACAATACTCATAAAAAATATATAATTCAACATTAAAAAGATTGAA
*
1490 GGGCTTTTCACGCTTCTAGTATCGTTTTTCCAAATTAATTTTTATTAAATCGAAACAAGATTCAG
450 GGGCTTTTCACGCTTCTAATATCGTTTTTCCAAATTAATTTTTATTAAATCGAAACAAGATTCAG
*
1555 ATACTCGTAAAAACATATCCTGAAATCCAATGTGGCTGATATTTGATTGGATGAATACAGATATT
515 ATACTCGTAAAAACATATCCTGAAATCCAATGTGGCTGATATTTGATTAGATGAATACAGATATT
* * * * **
1620 CCAAGGAGTCTTGGCGCCAAAAATTATGCAAAACTGAG-CGGGGATCCCGGAACATGTTTTTAGC
580 TCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTCAGCCGGGG--CCCGGAACGCGTTTTTAGC
*
1684 AGAAAATTGT
643 AGAAAACTGT
* *
1694 GATGCTTATTACACGATTCCGGTTCAAGTTTTGCAAAAACTGACCCGAAAAAATTCTTCATCAAT
1 GATGCTTAGTACACGATTCCGGTTCAAATTTTGCAAAAACTGACCCGAAAAAATTCTTCATCAAT
* * *
1759 TTTTGACCATAATACTCATAAAAAATATATAATTCAACACCAAAAATATTGAAGGGCTTTTCACG
66 TTTTGGCCACAATACTCATAAAAAATATATAATTCAACACCAAAAACATTGAAGGGCTTTTCACG
* *
1824 CTTCTAATATCGTTTTTTCTATTGTTTTCAAAATTAATTTTTGATTAAATCAAACAAGAGTCAGA
131 CTTCTAATATCGTTTTTCCTATT-TTTTCAAAACTAATTTTTGATTAAATCAAACAAGAGTCAGA
* *
1889 TACTCGTAAAAACATATCCTTAAATACAATGTGGCTGAGATTTGATTAGATTAATATAGATATTT
195 TACTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTT
* *
1954 CAAGGAGTCTCGGGTCCAAAAATCATGCGAAACTGAGCCAGCGCCCCGGAACGCGTTTTTAGGC-
260 CAAGGAGTCTCGGGTCCAAAAATCATGCAAAACTGAGCCGGCGCCCCGGAACGCGTTTTTAGGCA
* * * * *
2018 AAAAACGTGAT-AGTTTGTACACTATTTCGGTTCAGATTTTGCAAAAATTTACCCGAAAAAGTTT
325 AAAAACGTGATGA-TTTGAACACGATTTCGGTTCAGATTTTGCAAAAACTGACCCGAAAAAATTT
* *
2082 TCCGTCAATTTTTGGCCACAATACTCATAAAAATTATATAATTAAACATTAAAAAGATTGAAGGG
389 T-CGTCAATTTTTGGCCACAATACTCATAAAAAATATATAATTCAACATTAAAAAGATTGAAGGG
* * **
2147 CTTTTCAAGCTTCTAGTATCATTTTTCCTATTTTTTTCCATGTTAATTTTTATTAAATCGAAACA
453 CTTTTCACGCTTCTA--AT-A----T-C---GTTTTTCCAAATTAATTTTTATTAAATCGAAACA
* * *
2212 AGATTCAGATGCTCGTAAAAACATATCCTGAAATCCGATGTGGCTGATATTGGATTAGATGAATA
507 AGATTCAGATACTCGTAAAAACATATCCTGAAATCCAATGTGGCTGATATTTGATTAGATGAATA
* * *
2277 CAGATATTTCAAGGAATCTCGGTGCCAAAAATCATGCAAAACTTAGCCGGGGCGCCGGAACGCGT
572 CAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTCAGCCGGGGC-CCGGAACGCGT
*
2342 TTTTAGCAGGAAACTGT
636 TTTTAGCAGAAAACTGT
* * * * *
2359 GATGGTTAGTACATGATTTCGGTTCAAATTTTGCAAAAACTAATCCGAAAAAAAAATTCTTCATC
1 GATGCTTAGTACACGATTCCGGTTCAAATTTTGCAAAAACTGACCCG---AAAAAATTCTTCATC
*
2424 AATTTTTAGCCACAATACTCATAAAAAATATATAATTCAACACCAAAAACATTGAAGGGCTTTTC
63 AATTTTTGGCCACAATACTCATAAAAAATATATAATTCAACACCAAAAACATTGAAGGGCTTTTC
* * * *
2489 ACGCTTCGAATATCGTTTTTCATGTTTTTTTCAAAATTAGTTTTTATTAAATCGAATTATTAAAT
128 ACGCTTCTAATATCGTTTTTC----------C-----TA-TTTTT-TCAAAACTAATT-TT---T
* **
2554 CGAATTATTAAATCAAAACAAGATTCAGATGTTCGTAAAAACATATCCTTAAATCCAATGTGGCT
172 -G----ATTAAATC-AAACAAGAGTCAGATACTCGTAAAAACATATCCTTAAATCCAATGTGGCT
* * * * * *
2619 GATATTTGATTAGATGAATATAGGTATTCCAAGGAGTCTCGGGGT-TAAAAATTATGCAAAACGG
231 GAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTC-GGGTCCAAAAATCATGCAAAACTG
* * **
2683 AG-CTGCGGCCTCGGAACGCGTTTTTAGGCAAAAATTGTGATGATTAAT-AA-ACGATTTCGGTT
295 AGCCGGC-GCCCCGGAACGCGTTTTTAGGCAAAAAACGTGATGATT--TGAACACGATTTCGGTT
* * * * *
2745 CAAATTTTTCAAAAACTAACCCGAAAAATATTTTCGTCAATTTTCGACCACAATACTCATAAAAA
357 CAGATTTTGCAAAAACTGACCCGAAAAA-ATTTTCGTCAATTTTTGGCCACAATACTCATAAAAA
* * * *
2810 ATATATAATTGAAC-TCCAAAAACATTGAAGGGCTTTTCACGCTGCTAATATCGTT
421 ATATATAATTCAACAT-TAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTT
Statistics
Matches: 1562, Mismatches: 176, Indels: 134
0.83 0.09 0.07
Matches are distributed among these distances:
645 21 0.01
646 2 0.00
647 101 0.06
648 215 0.14
649 14 0.01
650 1 0.00
651 18 0.01
652 225 0.14
653 224 0.14
654 102 0.07
655 4 0.00
656 1 0.00
657 1 0.00
659 1 0.00
660 49 0.03
661 1 0.00
662 1 0.00
664 1 0.00
665 196 0.13
666 5 0.00
668 95 0.06
678 1 0.00
683 5 0.00
684 12 0.01
685 2 0.00
687 1 0.00
688 2 0.00
689 1 0.00
692 1 0.00
693 13 0.01
694 121 0.08
695 118 0.08
696 6 0.00
697 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (652 bp):
GATGCTTAGTACACGATTCCGGTTCAAATTTTGCAAAAACTGACCCGAAAAAATTCTTCATCAAT
TTTTGGCCACAATACTCATAAAAAATATATAATTCAACACCAAAAACATTGAAGGGCTTTTCACG
CTTCTAATATCGTTTTTCCTATTTTTTCAAAACTAATTTTTGATTAAATCAAACAAGAGTCAGAT
ACTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTC
AAGGAGTCTCGGGTCCAAAAATCATGCAAAACTGAGCCGGCGCCCCGGAACGCGTTTTTAGGCAA
AAAACGTGATGATTTGAACACGATTTCGGTTCAGATTTTGCAAAAACTGACCCGAAAAAATTTTC
GTCAATTTTTGGCCACAATACTCATAAAAAATATATAATTCAACATTAAAAAGATTGAAGGGCTT
TTCACGCTTCTAATATCGTTTTTCCAAATTAATTTTTATTAAATCGAAACAAGATTCAGATACTC
GTAAAAACATATCCTGAAATCCAATGTGGCTGATATTTGATTAGATGAATACAGATATTTCAAGG
AGTCTCGGCGCCAAAAATCATGCAAAACTCAGCCGGGGCCCGGAACGCGTTTTTAGCAGAAAACT
GT
Found at i:2229 original size:332 final size:330
Alignment explanation
Indices: 394--2864 Score: 2709
Period size: 332 Copynumber: 7.4 Consensus size: 330
384 AATCTAATGC
* * * *
394 GATGCTTAGTACACGATTCCGGTTCAAAATTTGCAAAAACTGACCCGAAAAAATTCTTCATCAAC
1 GATG-TTAGTACACGATTTCGGTTCAAATTTTGCAAAAACTGACCCGAAAAAATT-TTCGTCAAT
* **
459 TTTTGGCCACAATACTCATAAAAAATATATAATTCAACACCAAAAACATTGAAGGGAATTTCACG
64 TTTTGGCCACAATACTCATAAAAAATATATAATTCAACATCAAAAACATTGAAGGGCTTTTCACG
* *
524 CTTCTAATATCGTTTTTCCTA-TTTTTTCGAAATTAATTTTTGATTAAATC-AAACAAGAGTCAG
129 CTTCTAATATCGTTTTTCCTATTTTTTTCCAAATTAATTTTTGATTAAATCGAAACAAGATTCAG
*
587 ATACTCGTAAAAACATATCCTTAAATCCAATGTAGCTGAGATTTGATTAGATGAATATAGATATT
194 ATACTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATT
* * * *
652 TCAAGGAGTCTTGGGTCCAAATATCATGCGAAACTGAGCCGGCGCCCCGGAACGCGTTTTTAGGC
259 TCAAGGAGTCTCGGGTCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTA-GC
717 AAAAATCGT
323 AAAAA-CGT
* * * * ** *
726 GATGGTTTGTACACTATTTCGGTTCAGAA-TTAGCACAAACTGACCCGAAAATTTTTTTTTGTCA
1 GAT-GTTAGTACACGATTTCGGTTCA-AATTTTGCAAAAACTGACCCGAAAA--AATTTTCGTCA
* * *
790 ATTTTTGG-C-C---A--C-------A-ATATAATTCAACATTAAAAAGATTGAAGGTCTTTTCA
62 ATTTTTGGCCACAATACTCATAAAAAATATATAATTCAACATCAAAAACATTGAAGGGCTTTTCA
*
840 CGCTTCTAATATCG--TTT-CT-TTTTTTTCCAAATTAATTTTTGATTAAATTGAAACAAGATTC
127 CGCTTCTAATATCGTTTTTCCTATTTTTTTCCAAATTAATTTTTGATTAAATCGAAACAAGATTC
*
901 ATATACTCGTAAAAACATATCCTTAAATCCAATGTGGCT-ATGATTTGATTAGATGAATATAGAT
192 AGATACTCGTAAAAACATATCCTTAAATCCAATGTGGCTGA-GATTTGATTAGATGAATATAGAT
* * * ** * *
965 ATTTCAAGGAGTATCGGCTCCAAAAATCATGCAAAACTCAGTTGGGGCCTCGGAACGCATTTTTA
256 ATTTCAAGGAGTCTCGGGTCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTA
*
1030 GTAGAAAACTGT
321 GCA-AAAAC-GT
*
1042 GATGGTTAGTACACGATTTCGGTTCAAAATTTT-CAAAAACTGACCCGAAAAAAATTTCCGTCAA
1 GAT-GTTAGTACACGATTTCGGTTC-AAATTTTGCAAAAACTGACCCG-AAAAAATTTTCGTCAA
1106 TTTTTGGCCACAATACTCATAAAAAATATATAATTCAAC-TCCAAAAACATTGAA-GGCTTTTCA
63 TTTTTGGCCACAATACTCATAAAAAATATATAATTCAACAT-CAAAAACATTGAAGGGCTTTTCA
* *
1169 CGCTTCTAATATCGTTTTTCCTA-TTTTTTCCAAACTAATTTTTGATTAAATTGAAACAAGATT-
127 CGCTTCTAATATCGTTTTTCCTATTTTTTTCCAAATTAATTTTTGATTAAATCGAAACAAGATTC
* * * * *
1232 TGAATGCTCGTAAAAATATATCCTTAAATCTAGTGTGGCTGAGATTTGATTAGATGAATATAGAT
192 AG-ATACTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGAT
** * * * * *
1297 ATTTCAAGGAGTCTCGGCACCAAAAATCATGTAAAACTGAGCTGGGGCACCGGAAAGCGTTTTTT
256 ATTTCAAGGAGTCTCGGGTCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTA
1362 GCAAAAAAC-T
321 GC-AAAAACGT
* * * *
1372 -ATGATTAACGAACACGATTTCGATTCAGATTTTGTAAAAACTGACCCGAAAAAATTTTCGTCAA
1 GATG-TT-A-GTACACGATTTCGGTTCAAATTTTGCAAAAACTGACCCGAAAAAATTTTCGTCAA
* * * *
1436 TTTTTGGCCATAATACTTATAAAAAATATATAATTCAACATTAAAAAGATTGAAGGGCTTTTCAC
63 TTTTTGGCCACAATACTCATAAAAAATATATAATTCAACATCAAAAACATTGAAGGGCTTTTCAC
*
1501 GCTTCTAGTATCG-----------TTTTTCCAAATTAATTTTT-ATTAAATCGAAACAAGATTCA
128 GCTTCTAATATCGTTTTTCCTATTTTTTTCCAAATTAATTTTTGATTAAATCGAAACAAGATTCA
* * * *
1554 GATACTCGTAAAAACATATCCTGAAATCCAATGTGGCTGATATTTGATTGGATGAATACAGATAT
193 GATACTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATAT
* * * * **
1619 TCCAAGGAGTCTTGGCG-CCAAAAATTATGCAAAACTGAG-CGGGGATCCCGGAACATGTTTTTA
258 TTCAAGGAGTCTCGG-GTCCAAAAATCATGCAAAACTGAGCCGGGG-CCCCGGAACGCGTTTTTA
*
1682 GCAGAAAATTGT
321 GCA-AAAA-CGT
* * * *
1694 GATGCTTATTACACGATTCCGGTTCAAGTTTTGCAAAAACTGACCCGAAAAAATTCTTCATCAAT
1 GATG-TTAGTACACGATTTCGGTTCAAATTTTGCAAAAACTGACCCGAAAAAATT-TTCGTCAAT
* * * *
1759 TTTTGACCATAATACTCATAAAAAATATATAATTCAACACCAAAAATATTGAAGGGCTTTTCACG
64 TTTTGGCCACAATACTCATAAAAAATATATAATTCAACATCAAAAACATTGAAGGGCTTTTCACG
* * * *
1824 CTTCTAATATCGTTTTTTCTATTGTTTTCAAAATTAATTTTTGATTAAATC-AAACAAGAGTCAG
129 CTTCTAATATCGTTTTTCCTATTTTTTTCCAAATTAATTTTTGATTAAATCGAAACAAGATTCAG
* *
1888 ATACTCGTAAAAACATATCCTTAAATACAATGTGGCTGAGATTTGATTAGATTAATATAGATATT
194 ATACTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATT
* * *
1953 TCAAGGAGTCTCGGGTCCAAAAATCATGCGAAACTGAGCCAGCGCCCCGGAACGCGTTTTTAGGC
259 TCAAGGAGTCTCGGGTCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTA-GC
2018 AAAAACGT
323 AAAAACGT
* * * * * *
2026 GATAGTTTGTACACTATTTCGGTTCAGATTTTGCAAAAATTTACCCGAAAAAGTTTTCCGTCAAT
1 GAT-GTTAGTACACGATTTCGGTTCAAATTTTGCAAAAACTGACCCGAAAAAATTTT-CGTCAAT
* * * * *
2091 TTTTGGCCACAATACTCATAAAAATTATATAATTAAACATTAAAAAGATTGAAGGGCTTTTCAAG
64 TTTTGGCCACAATACTCATAAAAAATATATAATTCAACATCAAAAACATTGAAGGGCTTTTCACG
* * **
2156 CTTCTAGTATCATTTTTCCTATTTTTTTCCATGTTAATTTTT-ATTAAATCGAAACAAGATTCAG
129 CTTCTAATATCGTTTTTCCTATTTTTTTCCAAATTAATTTTTGATTAAATCGAAACAAGATTCAG
* * * * * *
2220 ATGCTCGTAAAAACATATCCTGAAATCCGATGTGGCTGATATTGGATTAGATGAATACAGATATT
194 ATACTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATT
* * *
2285 TCAAGGAATCTC-GGTGCCAAAAATCATGCAAAACTTAGCCGGGGCGCCGGAACGCGTTTTTAGC
259 TCAAGGAGTCTCGGGT-CCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGC
*
2349 AGGAAACTGT
323 A-AAAAC-GT
* * * *
2359 GATGGTTAGTACATGATTTCGGTTCAAATTTTGCAAAAACTAATCCGAAAAAAAAATTCTTCATC
1 GAT-GTTAGTACACGATTTCGGTTCAAATTTTGCAAAAACTGACCCG---AAAAAATT-TTCGTC
* *
2424 AATTTTTAGCCACAATACTCATAAAAAATATATAATTCAACACCAAAAACATTGAAGGGCTTTTC
61 AATTTTTGGCCACAATACTCATAAAAAATATATAATTCAACATCAAAAACATTGAAGGGCTTTTC
* * * *
2489 ACGCTTCGAATATCGTTTTTCATGTTTTTTTCAAAATTAGTTTTTATTAAATCGAATTATTAAAT
126 ACGCTTCTAATATCGTTTTTCCTATTTTTTTC--CA--A------A-T---T--AATT-TT---T
* **
2554 CGAATTATTAAATCAAAACAAGATTCAGATGTTCGTAAAAACATATCCTTAAATCCAATGTGGCT
171 -G----ATTAAATCGAAACAAGATTCAGATACTCGTAAAAACATATCCTTAAATCCAATGTGGCT
* * * * * *
2619 GATATTTGATTAGATGAATATAGGTATTCCAAGGAGTCTCGGGGT-TAAAAATTATGCAAAACGG
231 GAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTC-GGGTCCAAAAATCATGCAAAACTG
* * * *
2683 AGCTGCGGCCTCGGAACGCGTTTTTAGGCAAAAATTGT
295 AGCCGGGGCCCCGGAACGCGTTTTTA-GCAAAAA-CGT
* * * *
2721 GATGATTAATAAACGATTTCGGTTCAAATTTTTCAAAAACTAACCCGAAAAATATTTTCGTCAAT
1 GATG-TTAGTACACGATTTCGGTTCAAATTTTGCAAAAACTGACCCGAAAAA-ATTTTCGTCAAT
* * *
2786 TTTCGACCACAATACTCATAAAAAATATATAATTGAAC-TCCAAAAACATTGAAGGGCTTTTCAC
64 TTTTGGCCACAATACTCATAAAAAATATATAATTCAACAT-CAAAAACATTGAAGGGCTTTTCAC
*
2850 GCTGCTAATATCGTT
128 GCTTCTAATATCGTT
Statistics
Matches: 1804, Mismatches: 228, Indels: 187
0.81 0.10 0.08
Matches are distributed among these distances:
315 48 0.03
316 172 0.10
317 8 0.00
318 45 0.02
319 6 0.00
320 126 0.07
321 59 0.03
322 82 0.05
323 5 0.00
326 1 0.00
328 2 0.00
329 28 0.02
330 94 0.05
331 71 0.04
332 470 0.26
333 198 0.11
334 16 0.01
336 95 0.05
337 2 0.00
338 1 0.00
347 1 0.00
350 1 0.00
352 4 0.00
353 2 0.00
356 1 0.00
359 84 0.05
360 3 0.00
361 1 0.00
362 172 0.10
363 3 0.00
364 3 0.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (330 bp):
GATGTTAGTACACGATTTCGGTTCAAATTTTGCAAAAACTGACCCGAAAAAATTTTCGTCAATTT
TTGGCCACAATACTCATAAAAAATATATAATTCAACATCAAAAACATTGAAGGGCTTTTCACGCT
TCTAATATCGTTTTTCCTATTTTTTTCCAAATTAATTTTTGATTAAATCGAAACAAGATTCAGAT
ACTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTC
AAGGAGTCTCGGGTCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCAAA
AACGT
Found at i:2548 original size:13 final size:13
Alignment explanation
Indices: 2532--2567 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
2522 AAATTAGTTT
2532 TTATTAAATCGAA
1 TTATTAAATCGAA
2545 TTATTAAATCGAA
1 TTATTAAATCGAA
2558 TTATTAAATC
1 TTATTAAATC
2568 AAAACAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (13 bp):
TTATTAAATCGAA
Done.