Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011042.1 Corchorus capsularis cultivar CVL-1 contig11063, 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: 111769
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2545 original size:658 final size:652
Alignment explanation
Indices: 958--4707 Score: 4916
Period size: 658 Copynumber: 5.8 Consensus size: 652
948 TTTTCGCTAA
* * * * * *
958 AATTCAAAGT-AAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTTCATCTTATCCCGT
1 AATTCAACGTAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGA
* * * *
1022 ATTTATTTCTAATTAAATCTAAACAAGATTTAGATACTTGTAAAAACAAATCCTTATATCCAATG
66 ATTTATTTCTAATTAAATCGAAATAAGATTCAGATGCTTGTAAAAACAAATCCTTATATCCAATG
*
1087 TGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTC-TTGCGCCAAAAATCATGCAAA
131 TGGCTGAGATTTGGTTCGATGAATATAGAAATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAA
* * *
1151 ACTGAGCCAGGGCCCCGAAACGAGTTTTTAGCCCAAAACCGTGATGGATAGTACACGATTTCGGC
196 ACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCCAAAACCGTGATGGTTAGTACACGATTTCGGC
*
1216 TAAAAACTGACCCG-AAATTAATTTTTTCTAATTTTTATGCCATAATACTCAGAAAAAATATATA
261 TAAAAACTGACCCGAAAATT--TTTTTTCTAATTTTTATGCCACAATACTCAGAAAAAATATATA
* * * *
1280 ATTCAACGCTATAAAGATTGAAGGGTTTTTCACGCTTCTAATTTCGTTTTTCCATTTTTTCCAAA
324 ATTCAACGCTATAAAGATTGAAGGGGTTTTCACGATTCTAATATCGTTTTTCCATTTTTTCCGAA
* ** * * * *
1345 TTTATTTCTAATTAAATC-AAATTAAGATTCAGATGCTTGTGAAAACAAATCCTTATATCCGATG
389 TTAAAATCTAATTAAATCGAAA-CAAGATTCAGATGCTCGT-AAAAAAAATCCTTATATCCAATG
* * * * * * *
1409 TGGCTAAGATTTGGTACGATGAATATAGATATTTCAAGGAGTCTTTGCGCAAAAAATCATGCAAA
452 TGGCTGAGATTTGTTTCAATAAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATTATGCAAA
* * * * * * *
1474 ACTGAGCCGAGG-CTCTGAAACGTGGTTTTT-GCCCAAAAACCGTGTTGGGTTAGTACACGATTT
517 ATTGAGCCG-GGAATCCGGAACG-CGTTTTTCG-CCAAAAACCATGAT-GGTTAGTACACGATTT
* * * *
1537 CGGC--------T--AAAAACTTACACG-AAATTTTTT-TTCTAATTTTTATGCCACAATACTCA
578 TGGCTAAAATTTTGCAAAAACTGACCCGAAAATTTTTTCATC-AATTTTT-TGCCACAATACTCA
1590 GAAAAAATATAT
641 GAAAAAATATAT
* ** ** * *
1602 AATTCAACGCTATAATTATTGAAGGGGCTTTCACGTTTCTAATATCGTTTTTCCATTTTTTTCCA
1 AATTCAACG-TAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCG
* ** * * *
1667 AATTAAAATCTAATTAAATCGAAACAAGATTCTGATGCTCGTAAAAACAAATCCTTATATCCAAT
65 AATTTATTTCTAATTAAATCGAAATAAGATTCAGATGCTTGTAAAAACAAATCCTTATATCCAAT
*
1732 GTGGCTGAGATTTGGTTCCATGAATATAGATAA-TTCAAGGAGTCTTTGCGCCAAAAATCATTG-
130 GTGGCTGAGATTTGGTTCGATGAATATAGA-AATTTCAAGGAGTCTTTGCGCCAAAAATCA-TGC
* * * * * * *
1795 -AAACTTAGCCGGAGCCCCGAAACGTGTTTTTATCCAAAAATCGTGATGGTTAGTACACGATTTT
193 AAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCCAAAACCGTGATGGTTAGTACACGATTTC
* * * * *
1859 GGTTAAAAACTTACACGAAAATTTTTTTTTCTAATTTTTATACCACAATACTCAGAAAAAGTATA
258 GGCTAAAAACTGACCCGAAAA-TTTTTTTTCTAATTTTTATGCCACAATACTCAGAAAAAATATA
* * * *
1924 CAATTCAATGCTATAATGATTGAAGGGGTTTTAACGATTCTAATATC-TATTTTCCATTTTTTCC
322 TAATTCAACGCTATAAAGATTGAAGGGGTTTTCACGATTCTAATATCGT-TTTTCCATTTTTTCC
* * * *
1988 GAATTAAAATCAAATTAAATGGAAACAAGATTCTGATGCTCGT-AAAAAAATCCTTATATCAAAT
386 GAATTAAAATCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAATCCTTATATCCAAT
* * * *
2052 GCGGCTAAGATTTTTTTCAATAAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATTATGCAA
451 GTGGCTGAGATTTGTTTCAATAAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATTATGCAA
2117 AATTGAGCCGGGAATCCGGAACGCGTTTTTTCGCCAAAAACCATGATTTTGGTTAGTACACGATT
516 AATTGAGCCGGGAATCCGGAACGCG-TTTTTCGCCAAAAACCATGA---TGGTTAGTACACGATT
*
2182 TTGGCTAAAATTTTGCAAAAACTGACCCGAAAATTTTTTAATCAATGTTTTT-CCACAATACTCT
577 TTGGCTAAAATTTTGCAAAAACTGACCCGAAAATTTTTTCATCAAT-TTTTTGCCACAATACTC-
*
2246 AAAAAAATATATAT
640 AGAAAAA-ATATAT
* *
2260 AATTCAAAGTAAAAAAAATTGAAGGGTTTTTAACGCCTT-TAATATCGTTTTTCCATTTTTTTCC
1 AATTCAACGT-AAAAAAATTGAAGGGTTTTTCACG-CTTCTAATATCGTTTTTCCATTTTTTTCC
*
2324 GAATTTATTTCTAATTAAATCTAAATAAGATTCAGATGCTTGTAAAAACAAATCCTTATATCCAA
64 GAATTTATTTCTAATTAAATCGAAATAAGATTCAGATGCTTGTAAAAACAAATCCTTATATCCAA
* *
2389 TGTGGCTGAGATTTGCTTCGATGAATATAGAAATTTCAATGAGTCTTTGCGCCAAAAATCATGCA
129 TGTGGCTGAGATTTGGTTCGATGAATATAGAAATTTCAAGGAGTCTTTGCGCCAAAAATCATGCA
* * * * * *
2454 AAACTGAGTCGGGGCCCCGAATCGCGTTTTCAGCCCAAAATCGTGATGGTTAGTATACAATTTCG
194 AAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCCAAAACCGTGATGGTTAGTACACGATTTCG
* *
2519 GCTAAAAAATGACCCGAAAATTTTTTTTCTAATTCTTATGCCACAATACTCAGAAAAAATATATA
259 GCTAAAAACTGACCCGAAAATTTTTTTTCTAATTTTTATGCCACAATACTCAGAAAAAATATATA
* * *
2584 ATTTAACGCTATAAAGATTGAAGGGGTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTTCGA
324 ATTCAACGCTATAAAGATTGAAGGGGTTTTCACGATTCTAATATCGTTTTTCCA-TTTTTTCCGA
* * * *
2649 ATTAATATCTAATTAAATCGAAACAAGATTCTGATGCTTGTAAAAAAAATTCTTATATCCAATGT
388 ATTAAAATCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAATCCTTATATCCAATGT
*
2714 GGTTGAGATTTGTTTCAATAAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATTATGCAAAA
453 GGCTGAGATTTGTTTCAATAAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATTATGCAAAA
* * *
2779 TTGAGCCGGGTATCCAGAACGCGTTTTTAGCCCAAAAA-CAGTGATGGTTAGTACACGATTTTGG
518 TTGAGCCGGGAATCCGGAACGCGTTTTTCG-CCAAAAACCA-TGATGGTTAGTACACGATTTTGG
* ** * * *
2843 CTAAAATTTTGCAAAAAAAAATGAGTATCTAAAAGTTTTTCATCATTTTTTTGCCACAATACTCA
581 CTAAAATTTTGC---AAAAACTGA--CCCGAAAATTTTTTCATCAATTTTTTGCCACAATACTCA
2908 -AAAAAATATAT
641 GAAAAAATATAT
* *
2919 AA-TCTAACGTAAAAAAAATTGAAGGGTTTTTCACGCTTCTTATATTGTTTTTCCATTTTTTTCC
1 AATTC-AACGT-AAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCC
* *
2983 GAATTTATTTCTAATTAAATCGAAATAAGATTCAGATGCTTGTAAAAACATATTCTTATATCCAA
64 GAATTTATTTCTAATTAAATCGAAATAAGATTCAGATGCTTGTAAAAACAAATCCTTATATCCAA
* * * *
3048 TGTGGCTAAGATTTGGTTCGATGAATAAAGATATTTCAAAGAGTCTTTGCGCC-AAAATCATGCA
129 TGTGGCTGAGATTTGGTTCGATGAATATAGAAATTTCAAGGAGTCTTTGCGCCAAAAATCATGCA
** * * *
3112 AAACTGAGTTGGGGCCCCGAAACGCGTTTTTTGCTCAAAACCTGTGATGGTTAGTACAAGATTTC
194 AAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCCAAAACC-GTGATGGTTAGTACACGATTTC
* * * **
3177 GGTTAAAAACTGACCC-AAGATTTTTTTTCTAATTTTTATGCCACAATACTCAAAAAAAATATGC
258 GGCTAAAAACTGACCCGAAAATTTTTTTTCTAATTTTTATGCCACAATACTCAGAAAAAATATAT
** * * *
3241 AATTCAACGCTATAGCGATTGAAAGGGTTTTCACGATTCTAATATTGTTTTTCCATTTTTTTTCG
323 AATTCAACGCTATAAAGATTGAAGGGGTTTTCACGATTCTAATATCGTTTTTCCA-TTTTTTCCG
* * * * *
3306 AATTAAAATATAATTAAATCGAAACAAGATTCTGTTGCTCGTTATAAAAAAAACATTATA-CCAA
387 AATTAAAATCTAATTAAATCGAAACAAGATTCAGATGCTCG-TA-AAAAAAATCCTTATATCC-A
*
3370 ATGTGGCTGAGATTTGTTTCAATAAATATAGATATTTCAAGGAGTTTTTGCGCCAAAAATTATGC
449 ATGTGGCTGAGATTTGTTTCAATAAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATTATGC
* * * **
3435 AAAATTGAGCCGAGAATCCGAAACGCGTTTTTCGCCAAATA-TGTGATGGTTAGTACACGATTTT
514 AAAATTGAGCCGGGAATCCGGAACGCGTTTTTCGCCAAAAACCATGATGGTTAGTACACGATTTT
* * *
3499 GACTAAAATTTTGCAAAAACTGACTCGAAAATTTTTTTCATCAATTTTTTACCACAATACTCAG-
579 GGCTAAAATTTTGCAAAAACTGACCCGAAAA-TTTTTTCATCAATTTTTTGCCACAATACTCAGA
3563 AAAAATATAT
643 AAAAATATAT
* *** *
3573 AATTTCAACGTTAAAAAATTGAAGGG-AAATCACGCTTCTAATATCGTTTTT-CTTTTTTTTCCG
1 AA-TTCAACGTAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCG
* * *
3636 AATTTATTTCTAATTATATCTAAATAAGATTCAGATACTTGTAAAAACAAATCCTTATATCCAAT
65 AATTTATTTCTAATTAAATCGAAATAAGATTCAGATGCTTGTAAAAACAAATCCTTATATCCAAT
* *
3701 GTGGTTGAGATTTGGTTCGATGAATATAAAAATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAA
130 GTGGCTGAGATTTGGTTCGATGAATATAGAAATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAA
* * * *
3766 AACTGAGTCAGGGCCCCGAAACGCGTTTTTAGCCCAAAACTGTGATGGTTAGTATACGATTTCGG
195 AACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCCAAAACCGTGATGGTTAGTACACGATTTCGG
* * *
3831 CTAAAAACTTACCC-AAATTTTTTTTTTCTAATTCTTATGCCACAATACTCAGAAAAAATATATA
260 CTAAAAACTGACCCGAAA-ATTTTTTTTCTAATTTTTATGCCACAATACTCAGAAAAAATATATA
*
3895 ATTCAACGCTATAAAGATTGAAGGGGTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCGAA
324 ATTCAACGCTATAAAGATTGAAGGGGTTTTCACGATTCTAATATCGTTTTTCCATTTTTTCCGAA
3960 TTAAAATCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAGAAAATCCTTATATCCAATG
389 TTAAAATCTAATTAAATCGAAACAAGATTCAGATGCTCGT-AAAA-AAAATCCTTATATCCAATG
* *
4025 TGGTTGAGATTTGTTTCAATAAATATAGATATTTCAAGGCGTCTTTGCGCCAAAAATTATGCAAA
452 TGGCTGAGATTTGTTTCAATAAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATTATGCAAA
* ** * *
4090 ATTGAGCTGGGAATCCGGAATACGTTTTTCGCCAAAAACCGTGATGGTTAGTACACGAATTTGGC
517 ATTGAGCCGGGAATCCGGAACGCGTTTTTCGCCAAAAACCATGATGGTTAGTACACGATTTTGGC
* * *
4155 TAAAATTTTTCAAAAACTGACCCAAAAAGTTTTTCATCAATTTTTTGCCACAA-ACTCAGAAAAA
582 TAAAATTTTGCAAAAACTGACCCGAAAATTTTTTCATCAATTTTTTGCCACAATACTCAGAAAAA
4219 ATATAT
647 ATATAT
* * *
4225 AATTCAACGTAAAAAAAAATGAAGGATTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTTCG
1 AATTCAACGT-AAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCG
*
4290 AATTTATTTCTAATTAAATCGAAATAAGATTTAGATGCTTGTAAAAA-AAATCCTTATATCCAAT
65 AATTTATTTCTAATTAAATCGAAATAAGATTCAGATGCTTGTAAAAACAAATCCTTATATCCAAT
* * * *
4354 GTGGCTGAGATTTGGTTTGATTAATATAGATATTTCAAGGAGTATTTGCGCCAAAAATCATGCAA
130 GTGGCTGAGATTTGGTTCGATGAATATAGAAATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAA
* *
4419 AACTGAGCCGGGGCCCCGAAACGCGTTTTTTGCCCAAAAACCGT-A-----ACGTACACGGTTTC
195 AACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCC-AAAACCGTGATGGTTA-GTACACGATTTC
* * * * *
4478 GGTTAAAAACTGCCCCG-AAATTTTTTTTCTAA-TTTTATACCATAATACTCTGAAAAAATATAT
258 GGCTAAAAACTGACCCGAAAATTTTTTTTCTAATTTTTATGCCACAATACTCAGAAAAAATATAT
*
4541 AATTCAACGCTATAAAGATTGAAGGGGTTTTCACAATTCTAATATCGTTTTTCCATTTTTTCCGA
323 AATTCAACGCTATAAAGATTGAAGGGGTTTTCACGATTCTAATATCGTTTTTCCATTTTTTCCGA
* * * *
4606 ATTAAAATCTAATTAAATCGAAACAAGATTCACATACTCGTAAAAAATATGCTTATATCCAATGT
388 ATTAAAATCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAATCCTTATATCCAATGT
***
4671 AATTGAGATTTGTTTC---AAATATAGATATTTCAAGGAG
453 GGCTGAGATTTGTTTCAATAAATATAGATATTTCAAGGAG
4708 ATAAGTATTC
Statistics
Matches: 2734, Mismatches: 303, Indels: 140
0.86 0.10 0.04
Matches are distributed among these distances:
642 20 0.01
643 3 0.00
644 114 0.04
645 35 0.01
646 353 0.13
647 152 0.06
648 17 0.01
649 25 0.01
651 18 0.01
652 355 0.13
653 345 0.13
654 115 0.04
655 13 0.00
656 24 0.01
657 56 0.02
658 488 0.18
659 339 0.12
660 230 0.08
661 6 0.00
662 26 0.01
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (652 bp):
AATTCAACGTAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGA
ATTTATTTCTAATTAAATCGAAATAAGATTCAGATGCTTGTAAAAACAAATCCTTATATCCAATG
TGGCTGAGATTTGGTTCGATGAATATAGAAATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAA
ACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCCAAAACCGTGATGGTTAGTACACGATTTCGGC
TAAAAACTGACCCGAAAATTTTTTTTCTAATTTTTATGCCACAATACTCAGAAAAAATATATAAT
TCAACGCTATAAAGATTGAAGGGGTTTTCACGATTCTAATATCGTTTTTCCATTTTTTCCGAATT
AAAATCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAATCCTTATATCCAATGTGGC
TGAGATTTGTTTCAATAAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATTATGCAAAATTG
AGCCGGGAATCCGGAACGCGTTTTTCGCCAAAAACCATGATGGTTAGTACACGATTTTGGCTAAA
ATTTTGCAAAAACTGACCCGAAAATTTTTTCATCAATTTTTTGCCACAATACTCAGAAAAAATAT
AT
Found at i:2804 original size:322 final size:322
Alignment explanation
Indices: 973--4707 Score: 3998
Period size: 323 Copynumber: 11.5 Consensus size: 322
963 AAAGTAAAAA
* * * * * * * *
973 ATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTTCATCTTATCCCGTATTTATTTCTAATTAA
1 ATTGAAGGGGTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATATCTAATTAA
* * * *
1038 ATCTAAACAAGATTTAGATACTTGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTT
66 ATCGAAACAAGATTCAGATGCTTGTAAAAA-AAATCCTTATATCCAATGTGGCTGAGATTTGTTT
1103 CGATGAATATAGATATTTCAAGGAGTC-TTGCGCCAAAAATCATGCAAAACTGAGCCAGGG-CCC
130 CGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACTGAGCC-GGGACCC
* *
1166 CGAAACGAGTTTTTAGCCCAAAACCGTGATGGATAGTACACGATTTCGGCTAAAAACTGACCCG-
194 CGAAACGCGTTTTTAGCCCAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGA
*
1230 AAATTAATTTTTTCTAATTTTTATGCCATAATACTCAGAAAAAATATATAATTCAACGCTATAAA
259 AAATT--TTTTTTCTAATTTTTATGCCACAATACTCAGAAAAAATATATAATTCAACGCTATAAA
1295 G
322 G
* * * * *
1296 ATTGAAGGGTTTTTCACGCTTCTAATTTCGTTTTTCCA-TTTTTTCCAAATTTATTTCTAATTAA
1 ATTGAAGGGGTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATATCTAATTAA
* * * * *
1360 ATC-AAATTAAGATTCAGATGCTTGTGAAAACAAATCCTTATATCCGATGTGGCTAAGATTTGGT
66 ATCGAAA-CAAGATTCAGATGCTTGT-AAAAAAAATCCTTATATCCAATGTGGCTGAGATTTGTT
* * *
1424 ACGATGAATATAGATATTTCAAGGAGTCTTTGCGCAAAAAATCATGCAAAACTGAGCCGAGG-CT
129 TCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACTGAGCCG-GGACC
* * * *
1488 CTGAAACGTGGTTTTT-GCCCAAAAACCGTGTTGGGTTAGTACACGATTTCGGCTAAAAACTTAC
193 CCGAAACG-CGTTTTTAGCCC-AAAACCGTGAT-GGTTAGTACACGATTTCGGCTAAAAACTGAC
*
1552 ACG-AAATTTTTTTTCTAATTTTTATGCCACAATACTCAGAAAAAATATATAATTCAACGCTATA
255 CCGAAAATTTTTTTTCTAATTTTTATGCCACAATACTCAGAAAAAATATATAATTCAACGCTATA
**
1616 ATT
320 AAG
* * * *
1619 ATTGAAGGGGCTTTCACGTTTCTAATATCGTTTTTCCATTTTTTTCCAAATTAAAATCTAATTAA
1 ATTGAAGGGGTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATATCTAATTAA
* * *
1684 ATCGAAACAAGATTCTGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTT
66 ATCGAAACAAGATTCAGATGCTTGTAAAAA-AAATCCTTATATCCAATGTGGCTGAGATTTGTTT
* * *
1749 CCATGAATATAGATAATTCAAGGAGTCTTTGCGCCAAAAATCATTG--AAACTTAGCC-GGAGCC
130 CGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCA-TGCAAAACTGAGCCGGGA-CC
* * * * * * * *
1811 CCGAAACGTGTTTTTATCCAAAAATCGTGATGGTTAGTACACGATTTTGGTTAAAAACTTACACG
193 CCGAAACGCGTTTTTAGCCCAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCG
* * * * *
1876 AAAATTTTTTTTTCTAATTTTTATACCACAATACTCAGAAAAAGTATACAATTCAATGCTATAAT
258 AAAA-TTTTTTTTCTAATTTTTATGCCACAATACTCAGAAAAAATATATAATTCAACGCTATAAA
1941 G
322 G
* * * *
1942 ATTGAAGGGGTTTTAACGATTCTAATATC-TATTTTCCA-TTTTTTCCGAATTAAAATCAAATTA
1 ATTGAAGGGGTTTTCACGCTTCTAATATCGT-TTTTCCATTTTTTTCCGAATTAATATCTAATTA
* * * * * * *
2005 AATGGAAACAAGATTCTGATGCTCGT-AAAAAAATCCTTATATCAAATGCGGCTAAGATTTTTTT
65 AATCGAAACAAGATTCAGATGCTTGTAAAAAAAATCCTTATATCCAATGTGGCTGAGATTTGTTT
* * * * * **
2069 CAATAAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATTATGCAAAATTGAGCCGGGAATCC
130 CGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACTGAGCCGGGACCCC
* * * * *
2134 GGAACGCGTTTTTTCGCCAAAAACCATGATTTTGGTTAGTACACGATTTTGGCTAAAATTTTGCA
195 GAAACGCG-TTTTTAGCCCAAAACCGTGA---TGGTTAGTACACGATTTCGGC--------T--A
* *
2199 AAAACTGACCCGAAAATTTTTTAATC-AATGTTTT-T-CCACAATACTCTAAAAAAATATATATA
246 AAAACTGACCCGAAAATTTTTT-TTCTAAT-TTTTATGCCACAATACTC-AGAAAAA-ATATATA
* * *
2261 ATTCAAAG-TAAAAAAA
307 ATTCAACGCT-ATAAAG
* * * *
2277 ATTGAAGGGTTTTTAACGCCTT-TAATATCGTTTTTCCATTTTTTTCCGAATTTATTTCTAATTA
1 ATTGAAGGGGTTTTCACG-CTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATATCTAATTA
* * *
2341 AATCTAAATAAGATTCAGATGCTTGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGCT
65 AATCGAAACAAGATTCAGATGCTTGTAAAAA-AAATCCTTATATCCAATGTGGCTGAGATTTGTT
* * * *
2406 TCGATGAATATAGAAATTTCAATGAGTCTTTGCGCCAAAAATCATGCAAAACTGAGTCGGGGCCC
129 TCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACTGAGCCGGGACCC
* * * * * *
2471 CGAATCGCGTTTTCAGCCCAAAATCGTGATGGTTAGTATACAATTTCGGCTAAAAAATGACCCGA
194 CGAAACGCGTTTTTAGCCCAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGA
* *
2536 AAATTTTTTTTCTAATTCTTATGCCACAATACTCAGAAAAAATATATAATTTAACGCTATAAAG
259 AAATTTTTTTTCTAATTTTTATGCCACAATACTCAGAAAAAATATATAATTCAACGCTATAAAG
*
2600 ATTGAAGGGGTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTTCGAATTAATATCTAATTAA
1 ATTGAAGGGGTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATATCTAATTAA
* * *
2665 ATCGAAACAAGATTCTGATGCTTGTAAAAAAAATTCTTATATCCAATGTGGTTGAGATTTGTTTC
66 ATCGAAACAAGATTCAGATGCTTGTAAAAAAAATCCTTATATCCAATGTGGCTGAGATTTGTTTC
* * * * * *
2730 AATAAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATTATGCAAAATTGAGCCGGGTATCCA
131 GATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACTGAGCCGGG-ACCCC
* * ** **
2795 G-AACGCGTTTTTAGCCCAAAAACAGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAA
195 GAAACGCGTTTTTAGCCC-AAAACCGTGATGGTTAGTACACGATTTCGGCTAAAA-ACTG--ACC
** * *
2859 AAAAATGAGTATCTAAAAGTTTTTCATCATTTTTTTGCCACAATACTCA-AAAAAATATATAA-T
256 CGAAA--A-T-T-T-----TTTTTC-TAATTTTTATGCCACAATACTCAGAAAAAATATATAATT
* *
2922 CTAACG-TAAAAAAA
310 C-AACGCT-ATAAAG
* * * * *
2936 ATTGAAGGGTTTTTCACGCTTCTTATATTGTTTTTCCATTTTTTTCCGAATTTATTTCTAATTAA
1 ATTGAAGGGGTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATATCTAATTAA
* * * * *
3001 ATCGAAATAAGATTCAGATGCTTGTAAAAACATATTCTTATATCCAATGTGGCTAAGATTTGGTT
66 ATCGAAACAAGATTCAGATGCTTGTAAAAA-AAATCCTTATATCCAATGTGGCTGAGATTTGTTT
* * ** *
3066 CGATGAATAAAGATATTTCAAAGAGTCTTTGCGCC-AAAATCATGCAAAACTGAGTTGGGGCCCC
130 CGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACTGAGCCGGGACCCC
* * * *
3130 GAAACGCGTTTTTTGCTCAAAACCTGTGATGGTTAGTACAAGATTTCGGTTAAAAACTGACCC-A
195 GAAACGCGTTTTTAGCCCAAAACC-GTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGA
* * ** **
3194 AGATTTTTTTTCTAATTTTTATGCCACAATACTCAAAAAAAATATGCAATTCAACGCTATAGCG
259 AAATTTTTTTTCTAATTTTTATGCCACAATACTCAGAAAAAATATATAATTCAACGCTATAAAG
* * * * * *
3258 ATTGAAAGGGTTTTCACGATTCTAATATTGTTTTTCCATTTTTTTTCGAATTAAAATATAATTAA
1 ATTGAAGGGGTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATATCTAATTAA
* * * * *
3323 ATCGAAACAAGATTCTGTTGCTCGTTATAAAAAAAACATTATA-CCAAATGTGGCTGAGATTTGT
66 ATCGAAACAAGATTCAGATGCTTG-TA-AAAAAAATCCTTATATCC-AATGTGGCTGAGATTTGT
* * * * * * **
3387 TTCAATAAATATAGATATTTCAAGGAGTTTTTGCGCCAAAAATTATGCAAAATTGAGCCGAGAAT
128 TTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACTGAGCCGGGACC
* * * *
3452 CCGAAACGCGTTTTTCG-CCAAATA-TGTGATGGTTAGTACACGATTTTGACTAAAATTTTGCAA
193 CCGAAACGCGTTTTTAGCCCAAA-ACCGTGATGGTTAGTACACGATTTCGGC--------T--AA
* *
3515 AAACTGACTCGAAAA-TTTTTTTCATCAATTTTT-TACCACAATACTCAG-AAAAATATATAATT
247 AAACTGACCCGAAAATTTTTTTTC-T-AATTTTTATGCCACAATACTCAGAAAAAATATATAA-T
* *
3577 TCAACGTTA-AAAA
309 TCAACGCTATAAAG
*** * * * *
3590 ATTGAA-GGGAAATCACGCTTCTAATATCGTTTTT-CTTTTTTTTCCGAATTTATTTCTAATTAT
1 ATTGAAGGGGTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATATCTAATTAA
* * * * *
3653 ATCTAAATAAGATTCAGATACTTGTAAAAACAAATCCTTATATCCAATGTGGTTGAGATTTGGTT
66 ATCGAAACAAGATTCAGATGCTTGTAAAAA-AAATCCTTATATCCAATGTGGCTGAGATTTGTTT
* * *
3718 CGATGAATATAAAAATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACTGAGTCAGGG-CCC
130 CGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACTGAG-CCGGGACCC
* * *
3782 CGAAACGCGTTTTTAGCCCAAAACTGTGATGGTTAGTATACGATTTCGGCTAAAAACTTACCC-A
194 CGAAACGCGTTTTTAGCCCAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGA
* *
3846 AATTTTTTTTTTCTAATTCTTATGCCACAATACTCAGAAAAAATATATAATTCAACGCTATAAAG
259 AA-ATTTTTTTTCTAATTTTTATGCCACAATACTCAGAAAAAATATATAATTCAACGCTATAAAG
*
3911 ATTGAAGGGGTTTTCACGCTTCTAATATCGTTTTTCCA-TTTTTTCCGAATTAAAATCTAATTAA
1 ATTGAAGGGGTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATATCTAATTAA
* *
3975 ATCGAAACAAGATTCAGATGCTCGTAAAAAGAAAATCCTTATATCCAATGTGGTTGAGATTTGTT
66 ATCGAAACAAGATTCAGATGCTTGT-AAAA-AAAATCCTTATATCCAATGTGGCTGAGATTTGTT
* * * * * * **
4040 TCAATAAATATAGATATTTCAAGGCGTCTTTGCGCCAAAAATTATGCAAAATTGAGCTGGGAATC
129 TCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACTGAGCCGGGACCC
* ** * *
4105 CGGAATACGTTTTTCGCCAAAAACCGTGATGGTTAGTACACGAATTT-GGCTAAAATTTTTCAAA
194 CGAAACGCGTTTTTAGCCCAAAACCGTGATGGTTAGTACACG-ATTTCGGC---------T-AAA
* **
4169 AACTGACCCAAAAAGTTTTTCATC-AATTTTT-TGCCACAA-ACTCAGAAAAAATATATAATTCA
248 AACTGACCCGAAAA-TTTTTTTTCTAATTTTTATGCCACAATACTCAGAAAAAATATATAATTCA
* *
4231 ACG-TAAAAAAA
312 ACGCT-ATAAAG
* ** * * *
4242 AATGAAGGATTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTTCGAATTTATTTCTAATTAA
1 ATTGAAGGGGTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATATCTAATTAA
* *
4307 ATCGAAATAAGATTTAGATGCTTGTAAAAAAAATCCTTATATCCAATGTGGCTGAGATTTGGTTT
66 ATCGAAACAAGATTCAGATGCTTGTAAAAAAAATCCTTATATCCAATGTGGCTGAGATTT-GTTT
* * *
4372 -GATTAATATAGATATTTCAAGGAGTATTTGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCC
130 CGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACTGAGCCGGGACCCC
* * * *
4436 GAAACGCGTTTTTTGCCCAAAAACCGT-A-----ACGTACACGGTTTCGGTTAAAAACTGCCCCG
195 GAAACGCGTTTTTAGCCC-AAAACCGTGATGGTTA-GTACACGATTTCGGCTAAAAACTGACCCG
* * *
4495 -AAATTTTTTTTCTAA-TTTTATACCATAATACTCTGAAAAAATATATAATTCAACGCTATAAAG
258 AAAATTTTTTTTCTAATTTTTATGCCACAATACTCAGAAAAAATATATAATTCAACGCTATAAAG
** *
4558 ATTGAAGGGGTTTTCACAATTCTAATATCGTTTTTCCA-TTTTTTCCGAATTAAAATCTAATTAA
1 ATTGAAGGGGTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATATCTAATTAA
* * * * * ***
4622 ATCGAAACAAGATTCACATACTCGTAAAAAATATGCTTATATCCAATGTAATTGAGATTTGTTTC
66 ATCGAAACAAGATTCAGATGCTTGTAAAAAAAATCCTTATATCCAATGTGGCTGAGATTTGTTTC
4687 -A--AATATAGATATTTCAAGGAG
131 GATGAATATAGATATTTCAAGGAG
4708 ATAAGTATTC
Statistics
Matches: 2873, Mismatches: 408, Indels: 273
0.81 0.11 0.08
Matches are distributed among these distances:
312 20 0.01
314 16 0.01
315 83 0.03
316 73 0.03
317 2 0.00
319 11 0.00
320 101 0.04
321 107 0.04
322 480 0.17
323 612 0.21
324 208 0.07
325 76 0.03
326 14 0.00
327 1 0.00
328 6 0.00
329 96 0.03
330 175 0.06
331 105 0.04
332 91 0.03
333 56 0.02
334 52 0.02
335 79 0.03
336 220 0.08
337 100 0.03
338 89 0.03
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Consensus pattern (322 bp):
ATTGAAGGGGTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATATCTAATTAA
ATCGAAACAAGATTCAGATGCTTGTAAAAAAAATCCTTATATCCAATGTGGCTGAGATTTGTTTC
GATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACTGAGCCGGGACCCCG
AAACGCGTTTTTAGCCCAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAA
ATTTTTTTTCTAATTTTTATGCCACAATACTCAGAAAAAATATATAATTCAACGCTATAAAG
Found at i:6216 original size:7 final size:7
Alignment explanation
Indices: 6201--6245 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
6191 TCTTCTTCTG
6201 TCAGCCA
1 TCAGCCA
*
6208 TCGGCCA
1 TCAGCCA
6215 TCAGCCA
1 TCAGCCA
6222 TCAGCCA
1 TCAGCCA
*
6229 TCCGCCA
1 TCAGCCA
*
6236 TCAGCAA
1 TCAGCCA
6243 TCA
1 TCA
6246 CATGAGACTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (7 bp):
TCAGCCA
Found at i:6227 original size:21 final size:21
Alignment explanation
Indices: 6201--6245 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
6191 TCTTCTTCTG
* *
6201 TCAGCCATCGGCCATCAGCCA
1 TCAGCCATCCGCCATCAGCAA
6222 TCAGCCATCCGCCATCAGCAA
1 TCAGCCATCCGCCATCAGCAA
6243 TCA
1 TCA
6246 CATGAGACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (21 bp):
TCAGCCATCCGCCATCAGCAA
Found at i:15948 original size:2 final size:2
Alignment explanation
Indices: 15941--15971 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
15931 GAAAGGAAGT
15941 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
15972 CTGAAAGCGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:16609 original size:3 final size:3
Alignment explanation
Indices: 16601--16646 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
16591 GTGTTTTCTC
16601 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
16647 TTAAGCTGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:17422 original size:22 final size:22
Alignment explanation
Indices: 17389--17464 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 22
17379 TAAGTAGTTG
*
17389 CCAAAATCTCATAGGAAGGTTA
1 CCAAAATTTCATAGGAAGGTTA
* * *
17411 CTAAAATTTCATAGTATGGTTA
1 CCAAAATTTCATAGGAAGGTTA
* *
17433 CCAAAATTTTATACGAAGGTTA
1 CCAAAATTTCATAGGAAGGTTA
*
17455 TCGAAAATTT
1 -CCAAAATTT
17465 AAAGTATGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
22 35 0.81
23 8 0.19
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.33
Consensus pattern (22 bp):
CCAAAATTTCATAGGAAGGTTA
Found at i:17451 original size:44 final size:44
Alignment explanation
Indices: 17389--17476 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 44
17379 TAAGTAGTTG
* * *
17389 CCAAAATCTCATAGGAAGGTTA-CTAAAATTTCATAGTATGGTTA
1 CCAAAATCTCATACGAAGGTTATCGAAAATTT-AAAGTATGGTTA
* *
17433 CCAAAATTTTATACGAAGGTTATCGAAAATTTAAAGTATGGTTA
1 CCAAAATCTCATACGAAGGTTATCGAAAATTTAAAGTATGGTTA
17477 AAAAACTTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
44 30 0.79
45 8 0.21
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (44 bp):
CCAAAATCTCATACGAAGGTTATCGAAAATTTAAAGTATGGTTA
Found at i:17549 original size:22 final size:22
Alignment explanation
Indices: 17524--18152 Score: 145
Period size: 22 Copynumber: 28.4 Consensus size: 22
17514 GAAACCATCC
17524 AAATTTCATAGTATGGTTATCA
1 AAATTTCATAGTATGGTTATCA
** *
17546 AAATTTCATA-TGAAAGTTATTA
1 AAATTTCATAGT-ATGGTTATCA
** *
17568 GTATTTCATAGTAAGGTTATCA
1 AAATTTCATAGTATGGTTATCA
* * *
17590 AGATTTTATAGTCTGGTTA-CA
1 AAATTTCATAGTATGGTTATCA
* * * *
17611 AAACTTTCATAATATTGATGTCA
1 AAA-TTTCATAGTATGGTTATCA
* * * **** *
17634 AATTTTCACAAGGA-AACCATCT
1 AAATTTCA-TAGTATGGTTATCA
* *
17656 AAATTTCATAGTCTGATTATCA
1 AAATTTCATAGTATGGTTATCA
* ** *
17678 AAATTTTATA-TGAAAGTTATTA
1 AAATTTCATAGT-ATGGTTATCA
** *
17700 GTATTTCATAGTAAGGTTATCA
1 AAATTTCATAGTATGGTTATCA
* *
17722 AGATTTCATAGTGTGGTTATCA
1 AAATTTCATAGTATGGTTATCA
* * * * *
17744 ATATTTTATAAGGAGGTGTTACCA
1 AAATTTCAT-AGTATG-GTTATCA
* **
17768 AAATTTCATAGTGT-AATATCA
1 AAATTTCATAGTATGGTTATCA
* * * *
17789 AAATTTCATTGAAAGGTTACCA
1 AAATTTCATAGTATGGTTATCA
**
17811 AAATTTCATAG--TGCAATATCA
1 AAATTTCATAGTATG-GTTATCA
*** *
17832 AAATTTCATAACGTGCTTATCA
1 AAATTTCATAGTATGGTTATCA
* *
17854 AAA-TTCAATTGGGA-GGTTATCA
1 AAATTTC-A-TAGTATGGTTATCA
** **
17876 ACTTTTCATAGTGA-GGTTAAGA
1 AAATTTCATAGT-ATGGTTATCA
* * * * **
17898 AAATTTTAATGGGA-GATTATTG
1 AAA-TTTCATAGTATGGTTATCA
** * *
17920 AAATTTCATAGGCTAGTTATTA
1 AAATTTCATAGTATGGTTATCA
** * * *
17942 GGATTCCATTGTACGGTTATCA
1 AAATTTCATAGTATGGTTATCA
*
17964 AAATTTCATAAGGAT-GTTATCA
1 AAATTTCAT-AGTATGGTTATCA
* * *
17986 AAATTTTATAGTAAGTTTATCA
1 AAATTTCATAGTATGGTTATCA
* * *
18008 AAATTTCATAGTGTGTTTATTA
1 AAATTTCATAGTATGGTTATCA
* * * *
18030 AGATTTCAAAAGGAT-GTTAACA
1 AAATTTC-ATAGTATGGTTATCA
*
18052 AAATTTCATAATATATATGGTTATCA
1 AAATTTC---ATA-GTATGGTTATCA
* * *
18078 CAATTTCATAAGGA-GATTATCA
1 AAATTTCAT-AGTATGGTTATCA
* * *
18100 AAATTTCATAGTGTAGTTATAA
1 AAATTTCATAGTATGGTTATCA
* * * *
18122 AAAATTAATA-TGGTGATTATCA
1 AAATTTCATAGT-ATGGTTATCA
18144 AAATTTCAT
1 AAATTTCAT
18153 TGCAAATAGT
Statistics
Matches: 418, Mismatches: 159, Indels: 60
0.66 0.25 0.09
Matches are distributed among these distances:
20 1 0.00
21 54 0.13
22 298 0.71
23 34 0.08
24 17 0.04
25 2 0.00
26 12 0.03
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (22 bp):
AAATTTCATAGTATGGTTATCA
Found at i:17725 original size:132 final size:132
Alignment explanation
Indices: 17448--17740 Score: 480
Period size: 132 Copynumber: 2.2 Consensus size: 132
17438 ATTTTATACG
* *
17448 AAGGTTATCGAA-AATTTAAAGTATGGTTAAAAAACTTTCATAATATTGATGTCAAATTTTCACA
1 AAGGTTATC-AAGATTTTATAGTATGGTTAAAAAACTTTCATAATATTGATGTCAAATTTTCACA
*
17512 AGGAAACCATCCAAATTTCATAGTATGGTTATCAAAATTTCATATGAAAGTTATTAGTATTTCAT
65 AGGAAACCATCCAAATTTCATAGTATGATTATCAAAATTTCATATGAAAGTTATTAGTATTTCAT
17577 AGT
130 AGT
* *
17580 AAGGTTATCAAGATTTTATAGTCTGGTTACAAAACTTTCATAATATTGATGTCAAATTTTCACAA
1 AAGGTTATCAAGATTTTATAGTATGGTTAAAAAACTTTCATAATATTGATGTCAAATTTTCACAA
* * *
17645 GGAAACCATCTAAATTTCATAGTCTGATTATCAAAATTTTATATGAAAGTTATTAGTATTTCATA
66 GGAAACCATCCAAATTTCATAGTATGATTATCAAAATTTCATATGAAAGTTATTAGTATTTCATA
17710 GT
131 GT
* *
17712 AAGGTTATCAAGATTTCATAGTGTGGTTA
1 AAGGTTATCAAGATTTTATAGTATGGTTA
17741 TCAATATTTT
Statistics
Matches: 150, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
131 2 0.01
132 148 0.99
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (132 bp):
AAGGTTATCAAGATTTTATAGTATGGTTAAAAAACTTTCATAATATTGATGTCAAATTTTCACAA
GGAAACCATCCAAATTTCATAGTATGATTATCAAAATTTCATATGAAAGTTATTAGTATTTCATA
GT
Found at i:17790 original size:21 final size:21
Alignment explanation
Indices: 17766--17841 Score: 84
Period size: 21 Copynumber: 3.6 Consensus size: 21
17756 GAGGTGTTAC
*
17766 CAAAATTTCATAGTGTAATAT
1 CAAAATTTCATAGTGAAATAT
*
17787 CAAAATTTCAT--TGAAAGGTTAC
1 CAAAATTTCATAGTGAAA---TAT
*
17809 CAAAATTTCATAGTGCAATAT
1 CAAAATTTCATAGTGAAATAT
17830 CAAAATTTCATA
1 CAAAATTTCATA
17842 ACGTGCTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
19 4 0.09
21 25 0.54
22 13 0.28
24 4 0.09
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.34
Consensus pattern (21 bp):
CAAAATTTCATAGTGAAATAT
Found at i:18261 original size:22 final size:22
Alignment explanation
Indices: 18213--18269 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
18203 TTATTGTGTT
* *
18213 ATTATCAAAATCTCATATAGAG
1 ATTATCAAAATTTCATATAGAA
*
18235 GTTATCAAAATTTCATACT-GAA
1 ATTATCAAAATTTCATA-TAGAA
18257 ATTATCAAAATTT
1 ATTATCAAAATTT
18270 AATGAAGTGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 29 0.97
23 1 0.03
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (22 bp):
ATTATCAAAATTTCATATAGAA
Found at i:18283 original size:22 final size:22
Alignment explanation
Indices: 18258--18313 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
18248 CATACTGAAA
18258 TTATCAAAATTTAAT-G-AAGTGG
1 TTATCAAAATTTAATAGCAA--GG
* *
18280 TTATCAATATTTAGTAGCAAGG
1 TTATCAAAATTTAATAGCAAGG
18302 TTATCAAAATTT
1 TTATCAAAATTT
18314 TATATTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 26 0.90
23 1 0.03
24 2 0.07
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTAATAGCAAGG
Found at i:33481 original size:13 final size:13
Alignment explanation
Indices: 33463--33488 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33453 TAAAAATTAC
33463 TATATATATATAT
1 TATATATATATAT
33476 TATATATATATAT
1 TATATATATATAT
33489 AATAGTAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATATATAT
Found at i:37601 original size:16 final size:16
Alignment explanation
Indices: 37580--37610 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
37570 AAATAAAAGT
*
37580 TTTGTTGGTCCTTGTA
1 TTTGTTCGTCCTTGTA
37596 TTTGTTCGTCCTTGT
1 TTTGTTCGTCCTTGT
37611 TGGTACTCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.03, C:0.16, G:0.23, T:0.58
Consensus pattern (16 bp):
TTTGTTCGTCCTTGTA
Found at i:41830 original size:29 final size:30
Alignment explanation
Indices: 41794--41874 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 30
41784 TCTCGTTTTT
41794 AAAAGTTAAGGGGCCAATTTGTCCCAAAA-
1 AAAAGTTAAGGGGCCAATTTGTCCCAAAAG
* *
41823 AAAAGTTAAGGAGCCAAATTGTCCCAAAATG
1 AAAAGTTAAGGGGCCAATTTGTCCCAAAA-G
* * *
41854 GATAGTTAAGGGGCTAATTTG
1 AAAAGTTAAGGGGCCAATTTG
41875 AGTATTAAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 27 0.63
31 16 0.37
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.23
Consensus pattern (30 bp):
AAAAGTTAAGGGGCCAATTTGTCCCAAAAG
Found at i:43886 original size:342 final size:342
Alignment explanation
Indices: 43260--43943 Score: 1323
Period size: 342 Copynumber: 2.0 Consensus size: 342
43250 GACAATTTGA
* *
43260 TCATTAATTGTGTATAATATAATAATAAGATAATAGTAACTCTCTGTATGTCAAAGACACTAAAT
1 TCATTAATTGTGTATAATATAATAATAAGACAATAGTAACTCTATGTATGTCAAAGACACTAAAT
43325 ATCCAATAAGAGAATCATTAAACTAACAATACTAATATTAGACCATATTGAAGAGGATAATACTA
66 ATCCAATAAGAGAATCATTAAACTAACAATACTAATATTAGACCATATTGAAGAGGATAATACTA
43390 ACCGCATAAAATGAGAGAGTCCAACGGTCAACAACAACACAATTAAGCGAGACAGATCATGGGAA
131 ACCGCATAAAATGAGAGAGTCCAACGGTCAACAACAACACAATTAAGCGAGACAGATCATGGGAA
*
43455 GTTAATGTCTTTCATAAACTCATCAACTAATTAGAAAGAGACGCATGTTACATGGAGAGAAACCA
196 GTTAATGTCTTTCATAAACTCATCAACTAATTAGAAAGAGACACATGTTACATGGAGAGAAACCA
*
43520 AATAAGTTGGAGAGAAGCTTTAAGGACTTGATGATAACGTATGATAACGTATCCGGGATGTAAAT
261 AATAAGTTGGAGAGAAGCTTTAAGGACTTGATGATAACGTATGATAACGTATCCAGGATGTAAAT
43585 GATATGATACCACTCGC
326 GATATGATACCACTCGC
43602 TCATTAATTGTGTATAATATAATAATAAGACAATAGTAACTCTATGTATGTCAAAGACACTAAAT
1 TCATTAATTGTGTATAATATAATAATAAGACAATAGTAACTCTATGTATGTCAAAGACACTAAAT
43667 ATCCAATAAGAGAATCATTAAACTAACAATACTAATATTAGACCATATTGAAGAGGATAATACTA
66 ATCCAATAAGAGAATCATTAAACTAACAATACTAATATTAGACCATATTGAAGAGGATAATACTA
43732 ACCGCATAAAATGAGAGAGTCCAACGGTCAACAACAACACAATTAAGCGAGACAGATCATGGGAA
131 ACCGCATAAAATGAGAGAGTCCAACGGTCAACAACAACACAATTAAGCGAGACAGATCATGGGAA
43797 GTTAATGTCTTTCATAAACTCATCAACTAATTAGAAAGAGACACATGTTACATGGAGAGAAACCA
196 GTTAATGTCTTTCATAAACTCATCAACTAATTAGAAAGAGACACATGTTACATGGAGAGAAACCA
*
43862 AATAAGTTGGAGAGAAGTTTTAAGGACTTGATGATAACGTATGATAACGTATCCAGGATGTAAAT
261 AATAAGTTGGAGAGAAGCTTTAAGGACTTGATGATAACGTATGATAACGTATCCAGGATGTAAAT
43927 GATATGATACCACTCGC
326 GATATGATACCACTCGC
43944 AGATTATCCC
Statistics
Matches: 337, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
342 337 1.00
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (342 bp):
TCATTAATTGTGTATAATATAATAATAAGACAATAGTAACTCTATGTATGTCAAAGACACTAAAT
ATCCAATAAGAGAATCATTAAACTAACAATACTAATATTAGACCATATTGAAGAGGATAATACTA
ACCGCATAAAATGAGAGAGTCCAACGGTCAACAACAACACAATTAAGCGAGACAGATCATGGGAA
GTTAATGTCTTTCATAAACTCATCAACTAATTAGAAAGAGACACATGTTACATGGAGAGAAACCA
AATAAGTTGGAGAGAAGCTTTAAGGACTTGATGATAACGTATGATAACGTATCCAGGATGTAAAT
GATATGATACCACTCGC
Found at i:59316 original size:12 final size:11
Alignment explanation
Indices: 59289--59314 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
59279 TACTTTCCAT
59289 AAAAGAAAAAA
1 AAAAGAAAAAA
59300 AAAAGAAAAAA
1 AAAAGAAAAAA
59311 AAAA
1 AAAA
59315 AGGAGATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:72008 original size:3 final size:3
Alignment explanation
Indices: 71960--72000 Score: 55
Period size: 3 Copynumber: 13.0 Consensus size: 3
71950 TACAGCTAGC
*
71960 AAT ATAT AATT AAT AAT AAT AAT AAT AAT AAT AAG AAT AAT
1 AAT A-AT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
72001 TTAATAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 28 0.82
4 6 0.18
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:72672 original size:2 final size:2
Alignment explanation
Indices: 72665--72690 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
72655 TTTACGCAAG
72665 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
72691 TCTCTCGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:88385 original size:20 final size:21
Alignment explanation
Indices: 88346--88385 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
88336 ATTTTATAAT
* *
88346 TATGATTCATATAAATATATA
1 TATGATTCATAAAAAAATATA
88367 TATG-TTCATAAAAAAATAT
1 TATGATTCATAAAAAAATAT
88386 TCTCAATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (21 bp):
TATGATTCATAAAAAAATATA
Done.