Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010689.1 Corchorus capsularis cultivar CVL-1 contig10710, 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: 19124
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Found at i:1249 original size:323 final size:324
Alignment explanation
Indices: 1--2752 Score: 3801
Period size: 323 Copynumber: 8.5 Consensus size: 324
* * * *
1 TCGTTTTTCTA-TTTTTTCCGATCAATTTCTAATTAAATCGTAACATGATTCAGATTCTCATAAA
1 TCGTTTTTCTATTTTTTTCCGATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCAAAAA
65 AACAAATCCATAAATCGAATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCT
66 AACAAATCCATAAATCGAATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCT
* * **
130 TTCTTCCAAAAATCATGCAAAACTGAGACAGGACCCCGAAACGCAATTTTAGC-CTATAAACTGT
131 TTCTGCCAAAAATCATGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCTC-ATAAACTGT
* ** * * * *
194 GATTGTTAGTACATTATTTTCGGCTAAAAATTTACCCGGAAA-TTTTTTCCTAAATTTTTTGGCG
195 GATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGGAAATTTTTTTTCTAAATTTTTTGGCA
* * *
258 CAATACTCAGAATGAATAATTAATTCAACCCCAAAAAGATTGAAAAACTTTTCATGCATCTAATA
260 CAATACTCAGAATGAATAAATAATTCAACGCCAAAAAGATTGAAAGACTTTTCATGCATCTAATA
* *
323 TCGTTTTTCTATTTTTTTCCCATTAATTTCTAATTAAGA--GAAACATGATTTAGATGCTC-AAA
1 TCGTTTTTCTATTTTTTTCCGATTAATTTCTAATTAA-ATCGAAACATGATTCAGATGCTCAAAA
385 AAACAAATCCATAAATCGAATGTGGCTGGGATTCT-CTTCGATGAATATAGATATTTCAAAGAGT
65 AAACAAATCCATAAATCGAATGTGGCTGGGATT-TGCTTCGATGAATATAGATATTTCAAAGAGT
*
449 CTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCCCATAAACTG
129 CTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCTCATAAACTG
514 T-A-----ACGTACACGATTTTCGGCTAAAAACTGACCC-GAAATTTTTTTTCCTAATATTTTTT
194 TGATGGTTA-GTACACGATTTTCGGCTAAAAACTGACCCGGAAATTTTTTTT-CTAA-ATTTTTT
* * * * * * *
572 GGCACAATACTAAGAATGAATAAATAATTCAACGTCGAGAAGTTTGAAATACTTTTAATGCATCT
256 GGCACAATACTCAGAATGAATAAATAATTCAACGCCAAAAAGATTGAAAGACTTTTCATGCATCT
637 AATA
321 AATA
* * * *
641 TCGTTTTTCTATTTTTTTCTGATTAATTTCTAA-TAAATCAAAACATGATTTAGATGCTTAAAAA
1 TCGTTTTTCTATTTTTTTCCGATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCAAAAA
* ** *
705 AATAAATATATAAATCGAATGTGGCTGGGATTTGCTTAGATGAATATAGATATTTCAAAGAGTCT
66 AACAAATCCATAAATCGAATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCT
* **
770 TTCTGCCAAAAATCATGCAAAACTGAGTCAGGAACTGGAAACGCGTTTTTAGC-CAATAAACTGT
131 TTCTGCCAAAAATCATGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCTC-ATAAACTGT
* * * * * *
834 GATGATTAGTACAAGATTCTCGGCTAAAAACTGACCTGGAAATTTTTTTACTAATTTTTTTGGCA
195 GATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGGAAATTTTTTTTCTAAATTTTTTGGCA
* * * * * *
899 CAATACTCAGAATGAATAAATAATTCAACACCAAAAAGATT-AACAGGCTTTTTACGCCTCGAAT
260 CAATACTCAGAATGAATAAATAATTCAACGCCAAAAAGATTGAA-AGACTTTTCATGCATCTAAT
963 A
324 A
* *
964 TCGTTTTTCTATTTTTTTCCGATTAATTTCTAATTAAATTGAAACATGATTCAGATGCTCATAAA
1 TCGTTTTTCTATTTTTTTCCGATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCAAAAA
* * *** * *
1029 AACAACTCCATGAATCGAATGTGGCTGGGATTTGCTTCCCGGAATATAGATATTTGAACGAGTCT
66 AACAAATCCATAAATCGAATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCT
* *
1094 TTCTACCAAAAATCAAGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCTCATAAACTGTG
131 TTCTGCCAAAAATCATGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCTCATAAACTGTG
* *
1159 ATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCAG-AATTTTTTTTCTTAATTTTTTGGCAC
196 ATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGGAAATTTTTTTTCTAAATTTTTTGGCAC
* * * * *
1223 AATACTCAGAATGAATAAATAATTCAACGCCCAAAAGATTGACAGACTTTTCAAGCATCTAGTG
261 AATACTCAGAATGAATAAATAATTCAACGCCAAAAAGATTGAAAGACTTTTCATGCATCTAATA
* * * * *
1287 TCCTTTTTCTATTTCTTTCCGATTAATTTCTAATTAAGTCGAAACATGATTTAGATACTCAAAAA
1 TCGTTTTTCTATTTTTTTCCGATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCAAAAA
* * * *
1352 AATAAATCCATAAATCGAATTTGGCTGGCATTTGCTTCGATGAATATAGATATTTGAAAGAGTCT
66 AACAAATCCATAAATCGAATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCT
*
1417 TTCTGCCAAAAATCAAGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCTCATAAACTGTG
131 TTCTGCCAAAAATCATGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCTCATAAACTGTG
* * *
1482 ATGGTTAGTACACGATTTTCAGCTAAAAACTGACCCAG-AATTTTTTTTCTTAATTTTTTGGCAC
196 ATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGGAAATTTTTTTTCTAAATTTTTTGGCAC
* * * *
1546 AATACTCAGAATGAATAAATAATTCAACGCAAAAAAGATTCACAGACTTTTCACGCATCTAATA
261 AATACTCAGAATGAATAAATAATTCAACGCCAAAAAGATTGAAAGACTTTTCATGCATCTAATA
* *
1610 TCGTTTTTCTATTTTTTTCCGATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTTATAAA
1 TCGTTTTTCTATTTTTTTCCGATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCAAAAA
*
1675 AACAAATCCATAAATCGAATTTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCT
66 AACAAATCCATAAATCGAATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCT
* * * * * * * *
1740 TTGTTCCAAAAATCATGCAAAAGTAAGACAGTATCTCGAAACGCGTTTTTAGCAT-ATAAACTGT
131 TTCTGCCAAAAATCATGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGC-TCATAAACTGT
* * * *
1804 GATTGTTAGGACATGATTTTCGGCTAAAAACTTACCCGGAAATTTTTTTTCCTAAATTTTTTGGC
195 GATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGGAAATTTTTTTT-CTAAATTTTTTGGC
* * * * *
1869 ACAATACTCAGAATGAATAAATAATTCAACGTCGAGAAGTTTGAAATACTTTTCATGCATCTAAT
259 ACAATACTCAGAATGAATAAATAATTCAACGCCAAAAAGATTGAAAGACTTTTCATGCATCTAAT
1934 A
324 A
* *
1935 TCGTTTTTCTATTTTTTCCCGATTAATTTCTAATTAAGTCGAAACATGATTCAGATGCTCAAAAA
1 TCGTTTTTCTATTTTTTTCCGATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCAAAAA
* * *
2000 AATAAATCCATAAATCGAATGTGCCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTTT
66 AACAAATCCATAAATCGAATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCT
* * *
2065 TTCTGCCAAAAATCATGCAAAACTGAGTCAGGACCCTGAAACGCGTTTATAGCTCATAAACTATG
131 TTCTGCCAAAAATCATGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCTCATAAACTGTG
* ** * *
2130 ATGGTTAGTACACGATTTTTGGCTAAAAACAAACCCAGAAATTTTTTTTCTTAATTTTTTTGGCA
196 ATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGGAAATTTTTTTTC-TAAATTTTTTGGCA
* * * *
2195 CAATACTCAGAATGAATGAATAATTCAATGCCAAGAAGATTGAAAGACTTTTCACGCATCTAATA
260 CAATACTCAGAATGAATAAATAATTCAACGCCAAAAAGATTGAAAGACTTTTCATGCATCTAATA
*
2260 TCGTTTATCTATTTTTTTCCGATTAATTTCTAA-TAAATCGAAACATGATTCAGATGCT-AATAA
1 TCGTTTTTCTATTTTTTTCCGATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCAA-AA
* * * * * * *
2323 ATACAAATCTATTATTCTAATGTGGCTGAGATTTGCTTCGATGAATATAGATATTACAAAGAGTC
65 AAACAAATCCATAAATCGAATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTC
* * * * * *
2388 TTTTTGCCAAAAATCATACAAAATTGAGTCAGGACCCCGAAACCCGTTTTTAGCCCAAAAACTGT
130 TTTCTGCCAAAAATCATGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCTCATAAACTGT
* * * * *
2453 GA-AGTAACGTACATGATTTTCGGTTAAAAACTGACCCGGAAA-TTTTTTTCTAAATTTTTTTGC
195 GATGGTTA-GTACACGATTTTCGGCTAAAAACTGACCCGGAAATTTTTTTTCTAAATTTTTTGGC
* * * *
2516 AAAATACTCATAATGAATAAATAATTCAATGCCAAAAAGATTGACATG-CTTTTCATGCATCTAA
259 ACAATACTCAGAATGAATAAATAATTCAACGCCAAAAAGATTGA-AAGACTTTTCATGCATCTAA
2580 TA
323 TA
* * *
2582 TCGTTTTTCTATTTTTTTCCGATTAATTTCTAATTAAGTCGAAACATGATTTAGATGCTTAAAAA
1 TCGTTTTTCTATTTTTTTCCGATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCAAAAA
* ** * *
2647 AATAAATATATAAATCGAATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAATTT
66 AACAAATCCATAAATCGAATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCT
*
2712 TTCTGCCAAAAAACATGCAAAACTGAGTCA-GACCCCGAAAC
131 TTCTGCCAAAAATCATGCAAAACTGAGTCAGGACCCCGAAAC
2753 ATGATTCAGA
Statistics
Matches: 2155, Mismatches: 241, Indels: 68
0.87 0.10 0.03
Matches are distributed among these distances:
315 5 0.00
316 32 0.01
317 7 0.00
318 117 0.05
319 122 0.06
320 2 0.00
321 124 0.06
322 143 0.07
323 817 0.38
324 385 0.18
325 401 0.19
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (324 bp):
TCGTTTTTCTATTTTTTTCCGATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCAAAAA
AACAAATCCATAAATCGAATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCT
TTCTGCCAAAAATCATGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCTCATAAACTGTG
ATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGGAAATTTTTTTTCTAAATTTTTTGGCAC
AATACTCAGAATGAATAAATAATTCAACGCCAAAAAGATTGAAAGACTTTTCATGCATCTAATA
Found at i:1440 original size:647 final size:648
Alignment explanation
Indices: 1--2752 Score: 3870
Period size: 647 Copynumber: 4.3 Consensus size: 648
* * * * * *
1 TCGTTTTTCTATTTTTTCCGATCAATTTCTAATTAAATCGTAACATGATTCAGATTCTCATAAAA
1 TCGTTTTTCTATTTTTTCCGATTAATTTCTAATTAAGTCGAAACATGATTTAGATGCTCAAAAAA
*
66 ACAAATCCATAAATCGAATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCTT
66 ATAAATCCATAAATCGAATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCTT
* * **
131 TCTTCCAAAAATCATGCAAAACTGAGACAGGACCCCGAAACGCAATTTTAGC-CTATAAACTGTG
131 TCTGCCAAAAATCATGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCTC-ATAAACTGTG
* ** * * * * * *
195 ATTGTTAGTACATTATTTTCGGCTAAAAATTTACCCGGAAA--TTTTTTCCTAAATTTTTTGGCG
195 ATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCAGAAATTTTTTTTCTTAATTTTTTTGGCA
* * * *
258 CAATACTCAGAATGAATAATTAATTCAACCCCAAAAAGATTGAAAAACTTTTCATGCATCTAATA
260 CAATACTCAGAATGAATAAATAATTCAACGCCAAAAAGATTGAAAGACTTTTCACGCATCTAATA
* *
323 TCGTTTTTCTATTTTTTTCCCATTAATTTCTAATTAAGA--GAAACATGATTTAGATGCTCA-AA
325 TCGTTTTTCTATTTTTTTCCGATTAATTTCTAATTAA-ATCGAAACATGATTCAGATGCTCATAA
385 AAACAAATCCATAAATCGAATGTGGCTGGGATTCT-CTTCGATGAATATAGATATTTCAAAGAGT
389 AAACAAATCCATAAATCGAATGTGGCTGGGATT-TGCTTCGATGAATATAGATATTTCAAAGAGT
*
449 CTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCCCATAAACTG
453 CTTTCTGCCAAAAATCAAGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCCCATAAACTG
514 T-A---ACGTACACGATTTTCGGCTAAAAACTGACCC-GAAATTTTTTTTCCTAATATTTTTTGG
518 TGAGTTACGTACACGATTTTCGGCTAAAAACTGACCCGGAAATTTTTTTTCCTAA-ATTTTTTGG
* * * * *
574 CACAATACTAAGAATGAATAAATAATTCAACGTCGAGAAGTTTGAAATACTTTT-AATGCATCTA
582 CACAATACTCAGAATGAATAAATAATTCAACGCCGAAAAGATTGAAAGACTTTTCAA-GCATCTA
638 ATA
646 ATA
* * * *
641 TCGTTTTTCTATTTTTTTCTGATTAATTTCTAA-TAAATCAAAACATGATTTAGATGCTTAAAAA
1 TCGTTTTTCTA-TTTTTTCCGATTAATTTCTAATTAAGTCGAAACATGATTTAGATGCTCAAAAA
** *
705 AATAAATATATAAATCGAATGTGGCTGGGATTTGCTTAGATGAATATAGATATTTCAAAGAGTCT
65 AATAAATCCATAAATCGAATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCT
* **
770 TTCTGCCAAAAATCATGCAAAACTGAGTCAGGAACTGGAAACGCGTTTTTAGC-CAATAAACTGT
130 TTCTGCCAAAAATCATGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCTC-ATAAACTGT
* * * ** *
834 GATGATTAGTACAAGATTCTCGGCTAAAAACTGACCTGGAAATTTTTTTAC-TAATTTTTTTGGC
194 GATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCAGAAATTTTTTTTCTTAATTTTTTTGGC
* * * * *
898 ACAATACTCAGAATGAATAAATAATTCAACACCAAAAAGATT-AACAGGCTTTTTACGCCTCGAA
259 ACAATACTCAGAATGAATAAATAATTCAACGCCAAAAAGATTGAA-AGACTTTTCACGCATCTAA
*
962 TATCGTTTTTCTATTTTTTTCCGATTAATTTCTAATTAAATTGAAACATGATTCAGATGCTCATA
323 TATCGTTTTTCTATTTTTTTCCGATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCATA
* * *** * *
1027 AAAACAACTCCATGAATCGAATGTGGCTGGGATTTGCTTCCCGGAATATAGATATTTGAACGAGT
388 AAAACAAATCCATAAATCGAATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGT
* *
1092 CTTTCTACCAAAAATCAAGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCTCATAAACTG
453 CTTTCTGCCAAAAATCAAGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCCCATAAACTG
* *
1157 TGATGGTTA-GTACACGATTTTCGGCTAAAAACTGACCCAG-AATTTTTTTT-CTTAATTTTTTG
518 TGA--GTTACGTACACGATTTTCGGCTAAAAACTGACCCGGAAATTTTTTTTCCTAAATTTTTTG
* *
1219 GCACAATACTCAGAATGAATAAATAATTCAACGCCCAAAAGATTGACAGACTTTTCAAGCATCTA
581 GCACAATACTCAGAATGAATAAATAATTCAACGCCGAAAAGATTGAAAGACTTTTCAAGCATCTA
* *
1284 GTG
646 ATA
* *
1287 TCCTTTTTCTATTTCTTTCCGATTAATTTCTAATTAAGTCGAAACATGATTTAGATACTCAAAAA
1 TCGTTTTTCTATTT-TTTCCGATTAATTTCTAATTAAGTCGAAACATGATTTAGATGCTCAAAAA
* * *
1352 AATAAATCCATAAATCGAATTTGGCTGGCATTTGCTTCGATGAATATAGATATTTGAAAGAGTCT
65 AATAAATCCATAAATCGAATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCT
*
1417 TTCTGCCAAAAATCAAGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCTCATAAACTGTG
130 TTCTGCCAAAAATCATGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCTCATAAACTGTG
*
1482 ATGGTTAGTACACGATTTTCAGCTAAAAACTGACCCAG-AATTTTTTTTCTTAA-TTTTTTGGCA
195 ATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCAGAAATTTTTTTTCTTAATTTTTTTGGCA
* * *
1545 CAATACTCAGAATGAATAAATAATTCAACGCAAAAAAGATTCACAGACTTTTCACGCATCTAATA
260 CAATACTCAGAATGAATAAATAATTCAACGCCAAAAAGATTGAAAGACTTTTCACGCATCTAATA
*
1610 TCGTTTTTCTATTTTTTTCCGATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTTATAAA
325 TCGTTTTTCTATTTTTTTCCGATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCATAAA
*
1675 AACAAATCCATAAATCGAATTTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCT
390 AACAAATCCATAAATCGAATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCT
* * * * * * * * * **
1740 TTGTTCCAAAAATCATGCAAAAGTAAGACAGTATCTCGAAACGCGTTTTTAGCATATAAACTGTG
455 TTCTGCCAAAAATCAAGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCCCATAAACTGTG
* * *
1805 ATTGTTA-GGACATGATTTTCGGCTAAAAACTTACCCGGAAATTTTTTTTCCTAAATTTTTTGGC
520 A--GTTACGTACACGATTTTCGGCTAAAAACTGACCCGGAAATTTTTTTTCCTAAATTTTTTGGC
* * * * *
1869 ACAATACTCAGAATGAATAAATAATTCAACGTCGAGAAGTTTGAAATACTTTTCATGCATCTAAT
583 ACAATACTCAGAATGAATAAATAATTCAACGCCGAAAAGATTGAAAGACTTTTCAAGCATCTAAT
1934 A
648 A
*
1935 TCGTTTTTCTATTTTTTCCCGATTAATTTCTAATTAAGTCGAAACATGATTCAGATGCTCAAAAA
1 TCGTTTTTCTATTTTTT-CCGATTAATTTCTAATTAAGTCGAAACATGATTTAGATGCTCAAAAA
* *
2000 AATAAATCCATAAATCGAATGTGCCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTTT
65 AATAAATCCATAAATCGAATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCT
* * *
2065 TTCTGCCAAAAATCATGCAAAACTGAGTCAGGACCCTGAAACGCGTTTATAGCTCATAAACTATG
130 TTCTGCCAAAAATCATGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCTCATAAACTGTG
* **
2130 ATGGTTAGTACACGATTTTTGGCTAAAAACAAACCCAGAAATTTTTTTTCTTAATTTTTTTGGCA
195 ATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCAGAAATTTTTTTTCTTAATTTTTTTGGCA
* * *
2195 CAATACTCAGAATGAATGAATAATTCAATGCCAAGAAGATTGAAAGACTTTTCACGCATCTAATA
260 CAATACTCAGAATGAATAAATAATTCAACGCCAAAAAGATTGAAAGACTTTTCACGCATCTAATA
* *
2260 TCGTTTATCTATTTTTTTCCGATTAATTTCTAA-TAAATCGAAACATGATTCAGATGCTAATAAA
325 TCGTTTTTCTATTTTTTTCCGATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCATAAA
* * * * * * *
2324 TACAAATCTATTATTCTAATGTGGCTGAGATTTGCTTCGATGAATATAGATATTACAAAGAGTCT
390 AACAAATCCATAAATCGAATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCT
* * * *
2389 TTTTGCCAAAAATCATA-CAAAATTGAGTCAGGACCCCGAAACCCGTTTTTAGCCCAAAAACTGT
455 TTCTGCCAAAAATCA-AGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCCCATAAACTGT
* * * *
2453 GAAGTAACGTACATGATTTTCGGTTAAAAACTGACCCGGAAA-TTTTTTT-CTAAATTTTTTTGC
519 G-AGTTACGTACACGATTTTCGGCTAAAAACTGACCCGGAAATTTTTTTTCCTAAATTTTTTGGC
* * * * * *
2516 AAAATACTCATAATGAATAAATAATTCAATGCCAAAAAGATTGACATG-CTTTTCATGCATCTAA
583 ACAATACTCAGAATGAATAAATAATTCAACGCCGAAAAGATTGA-AAGACTTTTCAAGCATCTAA
2580 TA
647 TA
*
2582 TCGTTTTTCTATTTTTTTCCGATTAATTTCTAATTAAGTCGAAACATGATTTAGATGCTTAAAAA
1 TCGTTTTTCTA-TTTTTTCCGATTAATTTCTAATTAAGTCGAAACATGATTTAGATGCTCAAAAA
** * *
2647 AATAAATATATAAATCGAATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAATTT
65 AATAAATCCATAAATCGAATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCT
*
2712 TTCTGCCAAAAAACATGCAAAACTGAGTCA-GACCCCGAAAC
130 TTCTGCCAAAAATCATGCAAAACTGAGTCAGGACCCCGAAAC
2753 ATGATTCAGA
Statistics
Matches: 1887, Mismatches: 194, Indels: 56
0.88 0.09 0.03
Matches are distributed among these distances:
640 190 0.10
641 121 0.06
642 27 0.01
643 120 0.06
644 1 0.00
645 3 0.00
646 384 0.20
647 413 0.22
648 340 0.18
649 186 0.10
650 102 0.05
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (648 bp):
TCGTTTTTCTATTTTTTCCGATTAATTTCTAATTAAGTCGAAACATGATTTAGATGCTCAAAAAA
ATAAATCCATAAATCGAATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCTT
TCTGCCAAAAATCATGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCTCATAAACTGTGA
TGGTTAGTACACGATTTTCGGCTAAAAACTGACCCAGAAATTTTTTTTCTTAATTTTTTTGGCAC
AATACTCAGAATGAATAAATAATTCAACGCCAAAAAGATTGAAAGACTTTTCACGCATCTAATAT
CGTTTTTCTATTTTTTTCCGATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCATAAAA
ACAAATCCATAAATCGAATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCTT
TCTGCCAAAAATCAAGCAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCCCATAAACTGTGA
GTTACGTACACGATTTTCGGCTAAAAACTGACCCGGAAATTTTTTTTCCTAAATTTTTTGGCACA
ATACTCAGAATGAATAAATAATTCAACGCCGAAAAGATTGAAAGACTTTTCAAGCATCTAATA
Found at i:2949 original size:232 final size:233
Alignment explanation
Indices: 2535--2985 Score: 753
Period size: 232 Copynumber: 1.9 Consensus size: 233
2525 ATAATGAATA
* *
2535 AATAATTCAATGCCAAAAAGATTGACATGCTTTTCATGCATCTAATATCGTTTTTCTATTTTTTT
1 AATAATTCAACGCCAAAAAGATTGACATGCTTTTCACGCATCTAATATCGTTTTTCTATTTTTTT
* * * *
2600 CCGATTAATTTCTAATTAAGTCGAAACATGATTTAGATGCTTAAAAAAATAAATATATAAATCGA
66 CCGATTAATTTCTAATTAAATCGAAACATGATTCAAATGCTTAAAAAAATAAATACATAAATCGA
*
2665 ATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAATTTTTCTGCCAAAAAA-CATG
131 ATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAATCTTTCTG-CAAAAAATCATG
2729 CAAAACTGAGTCA-GACCCCGAAACATGATTCAGATGCT
195 CAAAACTGAGTCAGGACCCCGAAACATGATTCAGATGCT
2767 AATAATTCAACGCCAAAAAGATTGACATGCTTTTCACGCATCTAATATCGTTTTTCTATTTTTTT
1 AATAATTCAACGCCAAAAAGATTGACATGCTTTTCACGCATCTAATATCGTTTTTCTATTTTTTT
* * * *
2832 CCGATTAATTTCTAATTAAATTGAAACATGATTCAAATGTTTATAAAAATAAATCCATAAATCGA
66 CCGATTAATTTCTAATTAAATCGAAACATGATTCAAATGCTTAAAAAAATAAATACATAAATCGA
* *
2897 ATGTGGCTGGGATTTGTTTCGATGAATATAGATATTTCAAAGAGTCTTTCTGCAAAAAATCATGC
131 ATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAATCTTTCTGCAAAAAATCATGC
*
2962 AAAACTGAGTTAGGACCCCGAAAC
196 AAAACTGAGTCAGGACCCCGAAAC
2986 GCGTTTTTAA
Statistics
Matches: 203, Mismatches: 14, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
231 7 0.03
232 185 0.91
233 11 0.05
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (233 bp):
AATAATTCAACGCCAAAAAGATTGACATGCTTTTCACGCATCTAATATCGTTTTTCTATTTTTTT
CCGATTAATTTCTAATTAAATCGAAACATGATTCAAATGCTTAAAAAAATAAATACATAAATCGA
ATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAATCTTTCTGCAAAAAATCATGC
AAAACTGAGTCAGGACCCCGAAACATGATTCAGATGCT
Found at i:3357 original size:324 final size:323
Alignment explanation
Indices: 2767--4381 Score: 2329
Period size: 324 Copynumber: 5.0 Consensus size: 323
2757 TTCAGATGCT
2767 AATAATTCAACGCCAAAAAGATTGACATG-CTTTTCACGCATCTAATATCGTTTTTCTATTTTTT
1 AATAATTCAACGCCAAAAAGATTGACA-GACTTTTCACGCATCTAATATCGTTTTTCTATTTTTT
* * * * *
2831 TCCGATTAATTTCTAATTAAATTGAAACATGATTCAAATGTTTATAAAAATAAATCCATAAATCG
65 TCCGATTAATTTCTAA-TAAATCGAAACATGATTCAGATGCTAATAAAAACAAATCCATAAATCG
* *
2896 AATGTGGCTGGGATTTGTTTCGATGAATATAGATATTTCAAAGAGTCTTTCTGCAAAAAATCATG
129 AATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCTTTCTGCCAAAAATCATG
* *
2961 CAAAACTGAGTTAGGACCCCGAAACGCGTTTTTAACCCATAAACTGTGATGGTTAGTACACGATT
194 CAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCCCATAAACTGTGATGGTTAGTACACGATT
* **
3026 TTCGGCTAAAAACTGACCTGGAAATTTTTTTTCCTAAATTTTTTGGCACAATACTCATAATTTAT
259 TTCGGCTAAAAACTGACCTGGAAA-TTTTTTTCCTAAATTTTTTGGCACAATACTCAGAATGAAT
3091 A
323 A
* * * *
3092 AATAATTCAACACCGAAAAGATTGACAGACTTTTCAAGCATCTAATACCGTTTTTCTATTTTTTT
1 AATAATTCAACGCCAAAAAGATTGACAGACTTTTCACGCATCTAATATCGTTTTTCTATTTTTTT
* * * * *
3157 CTGATTAATTTCTAATAAATCGAAACATGATTCAGATGCTAATAAATACAAATCCATTATTCTAA
66 CCGATTAATTTCTAATAAATCGAAACATGATTCAGATGCTAATAAAAACAAATCCATAAATCGAA
* * * *
3222 TGTGGTTGAGATTTGTTTCGATGAATATAGATATTTCAAAGAGTCTTTCTGCTAAAAATCATGCA
131 TGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCTTTCTGCCAAAAATCATGCA
3287 AAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCCCATAAACTGTGATGGTTAGTACACGATTTT
196 AAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCCCATAAACTGTGATGGTTAGTACACGATTTT
*
3352 CGGCTAAAAACTGACCTGGAAATTTTTTTCCTAAATTTTTTGGCACAATACTCATAATGAATA
261 CGGCTAAAAACTGACCTGGAAATTTTTTTCCTAAATTTTTTGGCACAATACTCAGAATGAATA
*** * * * *
3415 AATAATTCAACATAAAAAATATTGATACACTTTTCACACATCTAATATCGTTTTTCTAATTTTTT
1 AATAATTCAACGCCAAAAAGATTGACAGACTTTTCACGCATCTAATATCGTTTTTCT-A-TTTTT
** * *
3480 TTATGATGAATTTCTAATAAATCGAAACATGATTCAGATGCTAATAAAAACAAATCAATAAATCG
64 TTCCGATTAATTTCTAATAAATCGAAACATGATTCAGATGCTAATAAAAACAAATCCATAAATCG
* * * * **
3545 AATTTCGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGACTTCCAACCAAAAATCATG
129 AATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCTTTCTGCCAAAAATCATG
* *
3610 CAAAATTGAGTCAGGACCCCGAAACGCGTTTTTAGCCCATAAACTGTGATGATTAGTACACGATT
194 CAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCCCATAAACTGTGATGGTTAGTACACGATT
* * * * * *
3675 TTCGGCCAAAAACTTACCTGGAAATTTTTTCCCGAATTTTTTTGCCACAATACTCAGAATGAATA
259 TTCGGCTAAAAACTGACCTGGAAATTTTTTTCCTAAATTTTTTGGCACAATACTCAGAATGAATA
* * *
3740 AATAATTCAATGCCAAAAAGATTGACAGACTTTTCACGCATCTAATATAGTTTGTCTATTTTTTT
1 AATAATTCAACGCCAAAAAGATTGACAGACTTTTCACGCATCTAATATCGTTTTTCTATTTTTTT
*
3805 CCGATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCATAAAAACAAATCCATAAATCGA
66 CCGATTAATTTCTAA-TAAATCGAAACATGATTCAGATGCTAATAAAAACAAATCCATAAATCGA
* *
3870 ATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAACGAGTCTTTCTGCCATAAATCATGC
130 ATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCTTTCTGCCAAAAATCATGC
* * * *
3935 AAAACTGAGACAGGACCCTGAAACGCGTTTTTAGCCTATAAACTGTGAT-GTAACGTACACGATT
195 AAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCCCATAAACTGTGATGGTTA-GTACACGATT
* * * *
3999 TTCGAG-TAAAAACTGACCCGAAAATTTTTTTTCTAAATTTTTTGGCACAATACACAGAATGAAT
259 TTCG-GCTAAAAACTGACCTGGAAATTTTTTTCCTAAATTTTTTGGCACAATACTCAGAATGAAT
4063 A
323 A
* * * * *
4064 AATAATTTAACGCAAAAAATATTGACAGACTTTTCACGCATCTAATATCATTTTTCTATTATTTT
1 AATAATTCAACGCCAAAAAGATTGACAGACTTTTCACGCATCTAATATCGTTTTTCTATTTTTTT
*
4129 CCGATTAATTTCTAATAAATCGAAACATGATTCAGATGCTTATAAAAACAAATCCATAAAATCGA
66 CCGATTAATTTCTAATAAATCGAAACATGATTCAGATGCTAATAAAAACAAATCCAT-AAATCGA
* * * *
4194 ATGTGGTTGGGATTTGCTTC----------GATATTTGAAAGACTCTTTTTGCCAAAAATCATGC
130 ATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCTTTCTGCCAAAAATCATGC
*
4249 AAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCCCATAAACTGTGATGGTTAGTACACGATTG
195 AAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCCCATAAACTGTGATGGTTAGTACACGATTT
* * * *
4314 TCGGCTAAAAACTGACCCAGAAAATTTTTTTCTTAAATTTTTTGGCACAATACTCAGAATAAATA
260 TCGGCTAAAAACTGA-CCTGGAAATTTTTTTCCTAAATTTTTTGGCACAATACTCAGAATGAATA
4379 AAT
1 AAT
4382 CGAATGTGGT
Statistics
Matches: 1160, Mismatches: 120, Indels: 30
0.89 0.09 0.02
Matches are distributed among these distances:
313 1 0.00
314 99 0.09
315 50 0.04
323 149 0.13
324 501 0.43
325 360 0.31
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Consensus pattern (323 bp):
AATAATTCAACGCCAAAAAGATTGACAGACTTTTCACGCATCTAATATCGTTTTTCTATTTTTTT
CCGATTAATTTCTAATAAATCGAAACATGATTCAGATGCTAATAAAAACAAATCCATAAATCGAA
TGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCTTTCTGCCAAAAATCATGCA
AAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCCCATAAACTGTGATGGTTAGTACACGATTTT
CGGCTAAAAACTGACCTGGAAATTTTTTTCCTAAATTTTTTGGCACAATACTCAGAATGAATA
Found at i:4011 original size:649 final size:646
Alignment explanation
Indices: 2767--4381 Score: 2345
Period size: 649 Copynumber: 2.5 Consensus size: 646
2757 TTCAGATGCT
* * * **
2767 AATAATTCAACGCCAAAAAGATTGACATGCTTTTCACGCATCTAATATCGTTTTTCTATTTTTTT
1 AATAATTCAACACAAAAAATATTGACACACTTTTCACGCATCTAATATCGTTTTTCTATTTTTTT
* * * *
2832 CCGATTAATTTCTAATTAAATTGAAACATGATTCAAATGTTTATAAAAATAAATCCATAAATCGA
66 CCGATTAATTTCTAA-TAAATCGAAACATGATTCAGATGCTTATAAAAACAAATCCATAAATCGA
* *
2897 ATGTGGCTGGGATTTGTTTCGATGAATATAGATATTTCAAAGAGTCTTTCTGCAAAAAATCATGC
130 ATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCTTTCTGCCAAAAATCATGC
* *
2962 AAAACTGAGTTAGGACCCCGAAACGCGTTTTTAACCCATAAACTGTGATGGTTAGTACACGATTT
195 AAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCCCATAAACTGTGATGGTTAGTACACGATTT
* **
3027 TCGGCTAAAAACTGACCTGGAAATTTTTTTTCCTAAATTTTTTGGCACAATACTCATAATTTATA
260 TCGGCTAAAAACTGACCTGGAAA-TTTTTTTCCTAAATTTTTTGGCACAATACTCAGAATAAATA
* * *
3092 AATAATTCAACACCGAAAAGATTGACAGACTTTTCAAGCATCTAATACCGTTTTTCTATTTTTTT
324 AATAATTCAACACCAAAAAGATTGACAGACTTTTCAAGCATCTAATACAGTTTGTCTATTTTTTT
* * * * *
3157 CTGATTAATTTCTAATAAATCGAAACATGATTCAGATGCTAATAAATACAAATCCATTATTCTAA
389 CCGATTAATTTCTAATAAATCGAAACATGATTCAGATGCTAATAAAAACAAATCCATAAATCGAA
* * *
3222 TGTGGTTGAGATTTGTTTCGATGAATATAGATATTTCAAAGAGTCTTTCTGCTAAAAATCATGCA
454 TGTGGCTGAGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCTTTCTGCCAAAAATCATGCA
* *
3287 AAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCCCATAAACTGTGATGGTTAGTACACGATTTT
519 AAACTGAGACAGGACCCCGAAACGCGTTTTTAGCCCATAAACTGTGATGGTAAGTACACGATTTT
* * * *
3352 CGGCTAAAAACTGACCTGGAAATTTTTTTCCTAAATTTTTTGGCACAATACTCATAATGAATA
584 CGGCTAAAAACTGACCCGAAAATTTTTTTCCTAAATTTTTTGGCACAATACACAGAATGAATA
* * *
3415 AATAATTCAACATAAAAAATATTGATACACTTTTCACACATCTAATATCGTTTTTCTAATTTTTT
1 AATAATTCAACACAAAAAATATTGACACACTTTTCACGCATCTAATATCGTTTTTCT-A-TTTTT
** * * *
3480 TTATGATGAATTTCTAATAAATCGAAACATGATTCAGATGCTAATAAAAACAAATCAATAAATCG
64 TTCCGATTAATTTCTAATAAATCGAAACATGATTCAGATGCTTATAAAAACAAATCCATAAATCG
* * * * **
3545 AATTTCGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGACTTCCAACCAAAAATCATG
129 AATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCTTTCTGCCAAAAATCATG
* *
3610 CAAAATTGAGTCAGGACCCCGAAACGCGTTTTTAGCCCATAAACTGTGATGATTAGTACACGATT
194 CAAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCCCATAAACTGTGATGGTTAGTACACGATT
* * * * * * *
3675 TTCGGCCAAAAACTTACCTGGAAATTTTTTCCCGAATTTTTTTGCCACAATACTCAGAATGAATA
259 TTCGGCTAAAAACTGACCTGGAAATTTTTTTCCTAAATTTTTTGGCACAATACTCAGAATAAATA
** * *
3740 AATAATTCAATGCCAAAAAGATTGACAGACTTTTCACGCATCTAATATAGTTTGTCTATTTTTTT
324 AATAATTCAACACCAAAAAGATTGACAGACTTTTCAAGCATCTAATACAGTTTGTCTATTTTTTT
*
3805 CCGATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCATAAAAACAAATCCATAAATCGA
389 CCGATTAATTTCTAA-TAAATCGAAACATGATTCAGATGCTAATAAAAACAAATCCATAAATCGA
* * *
3870 ATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAACGAGTCTTTCTGCCATAAATCATGC
453 ATGTGGCTGAGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCTTTCTGCCAAAAATCATGC
* *
3935 AAAACTGAGACAGGACCCTGAAACGCGTTTTTAGCCTATAAACTGTGAT-GTAACGTACACGATT
518 AAAACTGAGACAGGACCCCGAAACGCGTTTTTAGCCCATAAACTGTGATGGTAA-GTACACGATT
*
3999 TTCGAG-TAAAAACTGACCCGAAAATTTTTTTTCTAAATTTTTTGGCACAATACACAGAATGAAT
582 TTCG-GCTAAAAACTGACCCGAAAATTTTTTTCCTAAATTTTTTGGCACAATACACAGAATGAAT
4063 A
646 A
* * * * *
4064 AATAATTTAACGCAAAAAATATTGACAGACTTTTCACGCATCTAATATCATTTTTCTATTATTTT
1 AATAATTCAACACAAAAAATATTGACACACTTTTCACGCATCTAATATCGTTTTTCTATTTTTTT
4129 CCGATTAATTTCTAATAAATCGAAACATGATTCAGATGCTTATAAAAACAAATCCATAAAATCGA
66 CCGATTAATTTCTAATAAATCGAAACATGATTCAGATGCTTATAAAAACAAATCCAT-AAATCGA
* * * *
4194 ATGTGGTTGGGATTTGCTTC----------GATATTTGAAAGACTCTTTTTGCCAAAAATCATGC
130 ATGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCTTTCTGCCAAAAATCATGC
*
4249 AAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCCCATAAACTGTGATGGTTAGTACACGATTG
195 AAAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCCCATAAACTGTGATGGTTAGTACACGATTT
* * *
4314 TCGGCTAAAAACTGACCCAGAAAATTTTTTTCTTAAATTTTTTGGCACAATACTCAGAATAAATA
260 TCGGCTAAAAACTGA-CCTGGAAATTTTTTTCCTAAATTTTTTGGCACAATACTCAGAATAAATA
4379 AAT
324 AAT
4382 CGAATGTGGT
Statistics
Matches: 858, Mismatches: 102, Indels: 23
0.87 0.10 0.02
Matches are distributed among these distances:
638 103 0.12
639 44 0.05
647 58 0.07
648 183 0.21
649 450 0.52
650 20 0.02
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Consensus pattern (646 bp):
AATAATTCAACACAAAAAATATTGACACACTTTTCACGCATCTAATATCGTTTTTCTATTTTTTT
CCGATTAATTTCTAATAAATCGAAACATGATTCAGATGCTTATAAAAACAAATCCATAAATCGAA
TGTGGCTGGGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCTTTCTGCCAAAAATCATGCA
AAACTGAGTCAGGACCCCGAAACGCGTTTTTAGCCCATAAACTGTGATGGTTAGTACACGATTTT
CGGCTAAAAACTGACCTGGAAATTTTTTTCCTAAATTTTTTGGCACAATACTCAGAATAAATAAA
TAATTCAACACCAAAAAGATTGACAGACTTTTCAAGCATCTAATACAGTTTGTCTATTTTTTTCC
GATTAATTTCTAATAAATCGAAACATGATTCAGATGCTAATAAAAACAAATCCATAAATCGAATG
TGGCTGAGATTTGCTTCGATGAATATAGATATTTCAAAGAGTCTTTCTGCCAAAAATCATGCAAA
ACTGAGACAGGACCCCGAAACGCGTTTTTAGCCCATAAACTGTGATGGTAAGTACACGATTTTCG
GCTAAAAACTGACCCGAAAATTTTTTTCCTAAATTTTTTGGCACAATACACAGAATGAATA
Found at i:5040 original size:320 final size:319
Alignment explanation
Indices: 4376--6019 Score: 1523
Period size: 320 Copynumber: 5.2 Consensus size: 319
4366 CTCAGAATAA
* * * * *
4376 ATAAATCGAATGTGGTTGGGATTTGGTTCCATTAATATAGATAATTCAAAGAGTCTTTCTGCCAA
1 ATAAATCGAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAAGAGTCTTTCTGCCAA
* * * * * * *
4441 AAATCATGCACAACTGAGCCAGGACTC-CGAAACCCCTTTTTAACCAAAAAAACAGTGATGGTTA
66 AAATCATGCAAAACTGAGCCAGAAC-CACGAAACGCGTTTTTAGCC-CAAAAACCGTGA----TA
* ** * * * * *
4505 GAACGAGATTTCGGCTAAAAACTGATCCG-AAATTTTTTTC-C-A---------A-AATATTCAG
125 GTACTCGATTTCGACTAAAAACCGACCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACTCAT
* *
4557 AAAAAATAAATAATTCAACG-CAGAAAAGGTTGAAGGATTTTTCACGCTTCTAATATCG---TT-
190 AAAAAATAAATAATTCAATGCCA-AAAAGATTGAAGG-TTTTTCACGCTTCTAATATCGTTTTTC
* * * * * * * *
4617 T-TTTTTTTCCCAAATGAATTTTTATTTAAGTCGAAACAAGATTTAGATGCTCATAAAACCAAAT
253 TATTTTTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAAT
4681 CC
318 CC
* * * * * * * *
4683 ATAAATCAAATATGACTG-GAATTTGGTTTGATGAATATATATATTTAAAAGAGTCTTTCTACCT
1 ATAAATCGAATGTGGCTGAG-ATTTGGTTCGATGAATATAGATATTTCAAAGAGTCTTTCTGCCA
* *
4747 AAAATCATGCAAAATTGAGCCAGAACCACAAAACGCGTTTTTAG-CCAAAAACCGTGAT-GTACT
65 AAAATCATGCAAAACTGAGCCAGAACCACGAAACGCGTTTTTAGCCCAAAAACCGTGATAGTACT
* *
4810 CGATTTCGACAAAAAAACCGACCC-AAAATTTTTTTCTCAATTTTTTGCCACAACACTCATAAAA
130 CGATTTCGAC-TAAAAACCGACCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACTCATAAAA
*
4874 AATAAATAATTCAATGCCAAAAAGATTCAAGAGTTTTTCACGCTTCTAATATCGTTTTTCTAATT
194 AATAAATAATTCAATGCCAAAAAGATTGAAG-GTTTTTCACGCTTCTAATATCGTTTTTCT-A-T
** * * *
4939 TTTTTTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCATAAAAGCAAATCC
256 TTTTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCC
* * * * * * *
5003 TTAAATCCAATGTGGCTGAGATTTGATTTGATGAATATGGATATTTCAAGGAGTCTTTATGCCAA
1 ATAAATCGAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAAGAGTCTTTCTGCC--
* * * *
5068 AAAAAACCATGCAAAATTGAGTCCAG-ACCACGAAACGCGTTTTT-GTCCAAAAACCGTTTTGGT
64 -AAAAATCATGCAAAACTGAG-CCAGAACCACGAAACGCGTTTTTAGCCCAAAAACCG---T-GA
* * ** *
5131 TAGTACTCGATTTCGAC-AGAAACTGACCCGAATTTTTTTTTCTCAA-TTTTTGCCACAATACTG
123 TAGTACTCGATTTCGACTAAAAACCGACCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACTC
* * *
5194 ATAAAAAATAAATAATTCAATACCAAAAATATTAAAGGGTTTTTTCACGCTTCTAATATCGTTTT
188 ATAAAAAATAAATAATTCAATGCCAAAAAGATTGAA-GG-TTTTTCACGCTTCTAATATCGTTTT
* * * * * * *
5259 TCGA-TTTTTTCCCGAATTAGTTTCTAATTAAATCGAAACATGATCCAAATGATTGTAAAAACAA
251 TCTATTTTTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
5323 ATCC
316 ATCC
* * * *
5327 GTAAATCGAATGTGGCTGGGATTTGGTTCGATGAATATAGGTATTTCAAATAGTCTTTCTGCCAA
1 ATAAATCGAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAAGAGTCTTTCTGCCAA
** * * *
5392 AAATCATGCAAAACAAAGCCAGGATCC-TGAAACGCGTTTTTAGCCCAAAAACCAT-A-ACGTAC
66 AAATCATGCAAAACTGAGCCA-GAACCACGAAACGCGTTTTTAGCCCAAAAACCGTGATA-GTAC
* * * ** * *
5454 ACGATTTCGGCTAAAAACTGACCCGGAATTTTTTTTTCCCAAATTTTATTGCCACAATACTCAGA
129 TCGATTTCGACTAAAAACCGACCC-GAAAATTTTTTTCTC-AATTTT-TTGCCACAATACTCATA
* * * * *
5519 GAAAATAAATAATTCAACGCCAAAAAGATTGACGAATTTTTCACGCATCTAATATCGTTTTTCTA
191 AAAAATAAATAATTCAATGCCAAAAAGATTGAAG-GTTTTTCACGCTTCTAATATCGTTTTTCTA
* *
5584 -TTTTTT-CCGAATTAATTTCAAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATCC
255 TTTTTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCC
* ** * * * * *
5647 TTATGTCCAATGTGGCTGAGATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTATATGCCAA
1 ATAAATCGAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAAGAGTCTTTCTGCCAA
* * * *
5712 AAACCATGCAAAACTGAATCCAG-ACCACGAAACGTGTTTTTAG-CCAAAAACTGTGATGGTTAG
66 AAATCATGCAAAACTG-AGCCAGAACCACGAAACGCGTTTTTAGCCCAAAAACCGTGA----TAG
* * *
5775 TACTCAATTTCGACT-AAAACCGATCCGAAAATTTTTTTTTTCTCAATTTTTTGCCACAATACTT
126 TACTCGATTTCGACTAAAAACCGACCCGAAAA---TTTTTTTCTCAATTTTTTGCCACAATACTC
* * * **
5839 ATAAAAATTAAATAATTCAACGTCAAAAAGATTGAAGGCTTTTTCACGCTTCTAATATCGGATTT
188 ATAAAAAATAAATAATTCAATGCCAAAAAGATTGAAGG-TTTTTCACGCTTCTAATATCGTTTTT
* * * * * *
5904 CGATTTTTTTCCCGAATTAATTTTTAAGTAAAT-GAAATCATGA-TCTAAATGCTCGTAAAAATA
252 CTATTTTTTTCCCGAATTAATTTCTAATTAAATCGAAA-CAAGATTC-AGATGCTCGTAAAAACA
5967 AATCC
315 AATCC
*
5972 ATAAATCGAATGTGGCTG-GAATTTGGTTCGATGAATATAAATATTTCA
1 ATAAATCGAATGTGGCTGAG-ATTTGGTTCGATGAATATAGATATTTCA
6020 TGCAAAATTA
Statistics
Matches: 1099, Mismatches: 172, Indels: 114
0.79 0.12 0.08
Matches are distributed among these distances:
300 11 0.01
301 22 0.02
302 1 0.00
303 1 0.00
305 10 0.01
306 3 0.00
307 85 0.08
312 1 0.00
313 56 0.05
314 3 0.00
316 3 0.00
317 14 0.01
318 11 0.01
319 26 0.02
320 242 0.22
321 72 0.07
322 58 0.05
323 124 0.11
324 144 0.13
325 92 0.08
326 61 0.06
327 44 0.04
328 15 0.01
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.33
Consensus pattern (319 bp):
ATAAATCGAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAAGAGTCTTTCTGCCAA
AAATCATGCAAAACTGAGCCAGAACCACGAAACGCGTTTTTAGCCCAAAAACCGTGATAGTACTC
GATTTCGACTAAAAACCGACCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACTCATAAAAAA
TAAATAATTCAATGCCAAAAAGATTGAAGGTTTTTCACGCTTCTAATATCGTTTTTCTATTTTTT
TCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCC
Found at i:6487 original size:321 final size:320
Alignment explanation
Indices: 6039--7819 Score: 1818
Period size: 321 Copynumber: 5.6 Consensus size: 320
6029 AAGGTTGAAG
* *
6039 CACGAAACACGTTTTTAGCCAAAAACCGTAATGGTTAGTACTCGATTTCGAC-AAAAGACCGACC
1 CACGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACTCGATTTCGACTAAAA-ACCGACC
* * * * * * *
6103 CGAATTTTTTTTTCTCAATTTTCTGTCAAAATACTCATAAAAAATAAATAATTCAATGCCAAAAA
65 CGAA-ATTTTTTTCTAAATTTTTTGCCACAATACTCAGAAAAAATAAATAATTCAACGCCAAAAA
* * *
6168 GATTGAAGGGTTTTTAACGTTTCTAATATCGTTTTTCAATTTTTCCCGAATTAATTTCTAATTAA
129 GATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCATTTTTTCCCGAATTAATTTCTAATTAA
* * *
6233 ATCGTAACAAGATCCAGATGCTCGTAAAAACAAATCTATAAATCGAATGTGCCTGAGATTTGGTT
194 ATCGAAACAAGATCCAGATGCTCGTAAAAACAAATCCATAAATCGAATGTGGCTGAGATTTGGTT
6298 CGATGAATATAGATATTTCAAAGAGTCTTTCT-CTCAAAAATCATGCAAAACTGAGCCAGGAC
259 CGATGAATATAGATATTTCAAAGAGTCTTTCTGC-CAAAAATCATGCAAAACTGAGCCAGGAC
* * * * * **
6360 CCCGAAACGCGTTTTTGGCCCAAAAACCGTCATGTTTAGTACACGATTTCG-CTAAAAACTTACC
1 CACGAAACGCGTTTTTAG-CCAAAAACCGTGATGGTTAGTACTCGATTTCGACTAAAAACCGACC
* ** * *
6424 TAGAAATTTTTTAATAAATTTTTTTCCACAATACTCAGAAAAAATAACTAATTCAACGCCAAAAA
65 -CGAAATTTTTTTCTAAATTTTTTGCCACAATACTCAGAAAAAATAAATAATTCAACGCCAAAAA
* * * *
6489 AATTGAATGGTTTTTCACGCTTCTAATATCGTTTTTTGA-TTTTTCCCGAATTTATTTCTAATTA
129 GATTGAAGGGTTTTTCACGCTTCTAATATCG-TTTTTCATTTTTTCCCGAATTAATTTCTAATTA
* * * *
6553 AATCGAAACAAGATCCAGATGTTCGTAAAAACAAATCCATAAATCGAATGTTGCTGGGATTTGAT
193 AATCGAAACAAGATCCAGATGCTCGTAAAAACAAATCCATAAATCGAATGTGGCTGAGATTTGGT
* * *
6618 TCGATGAATATAGATATTTCAAAGAG--TTTCTGCCAAAAATCATGCAAAACTAAGTCAAGAC
258 TCGATGAATATAGATATTTCAAAGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCAGGAC
* * * *
6679 CTCGAAACGTGTTTTTAGCCCCAAAACCATGAT-G---GT--T--A----G--T----A-C-A--
1 CACGAAACGCGTTTTTAG-CCAAAAACCGTGATGGTTAGTACTCGATTTCGACTAAAAACCGACC
* *
6722 C--AATTTTTTTCCTAAATCTTTTGCCACAATACTCAGAAAAGATAAATAATTCAA---C-----
65 CGAAATTTTTTT-CTAAATTTTTTGCCACAATACTCAGAAAAAATAAATAATTCAACGCCAAAAA
* * ***
6777 -----------TTTTCACGCTTCTAATATAGTTTTTTCTTCTTTTTTTTTGAATTAATTTCTAAT
129 GATTGAAGGGTTTTTCACGCTTCTAATATCG-TTTTTC--ATTTTTTCCCGAATTAATTTCTAAT
* * * * * *
6831 TAAATCTAAACAAGATTCAGATGCTCGTTAAAACAAATCCTTAAATCCAATGTGGCTGAAATTTG
191 TAAATCGAAACAAGATCCAGATGCTCGTAAAAACAAATCCATAAATCGAATGTGGCTGAGATTTG
** * * * * * *
6896 GTTAAATGAATACAGATATTTCAAGGAGTCTTTATGCCAAAAACCATGCAAAATTGAGCCCA-AA
256 GTTCGATGAATATAGATATTTCAAAGAGTCTTTCTGCCAAAAATCATGCAAAACTGAG-CCAGGA
6960 C
320 C
* * * **
6961 CACGAATCGCGTTTTTAGCCAAAAACAGTGATGGTTAGTACTCGGTTTTAACTAAAAACCGACCC
1 CACGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACTCGATTTCGACTAAAAACCGACCC
* * * * *
7026 GAATTTTTTTTTCTCAATTTCTTGCCACAATACTCTTA-AAAAAATGAATAATTCAATGCCAAAA
66 GAA-ATTTTTTTCTAAATTTTTTGCCACAATACTC--AGAAAAAATAAATAATTCAACGCCAAAA
* * * *
7090 AGATTGAA-GGTTTTTCACGCTTCTAATAT-GGTTTTCTTTTTTTTCCCGAATGAATTTCTATTT
128 AGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTC-ATTTTTTCCCGAATTAATTTCTAATT
** * * * *
7153 AAATCGAAACAAGATTTAGATGCTCATAAAAATAAATCCCTAAATCGAATGTGGCTGGGATTTGG
192 AAATCGAAACAAGATCCAGATGCTCGTAAAAACAAATCCATAAATCGAATGTGGCTGAGATTTGG
* * ** * * *
7218 TTTGATGAATATAAATATTGAAAAGAGTCTTTCCGTCAAAAATCATGCAAAACTAAGCCAGGAC
257 TTCGATGAATATAGATATTTCAAAGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCAGGAC
* *
7282 CACGAAACGC-ATTTTAGCCAAAAACCGTGATGGTTAGTACTCGATTTCGACAAAAAAAACCGAC
1 CACGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACTCGATTTCGAC--TAAAAACCGAC
* * * * *
7346 CTGAAAATTTTTTTCTTAATTTTTTGCCACAATACTCATAAAAAATAAATAATTCAATGCAAAAA
64 CCG-AAATTTTTTTCTAAATTTTTTGCCACAATACTCAGAAAAAATAAATAATTCAACGC--CAA
* * * *
7411 AAAAATTGAAGGGTTTTTTACGCTTCTAGTATCGTTTTTTGATTTTTTTTCCCGAATTAATTTCT
126 AAAGATTGAAGGGTTTTTCACGCTTCTAATATCG-TTTTTCA--TTTTTTCCCGAATTAATTTCT
* * * *
7476 AATTAAATCGAAATAAGATCCAGATGCTCGTAAAAATAAATTCATAAATCGATTGTGGCT-AGGA
188 AATTAAATCGAAACAAGATCCAGATGCTCGTAAAAACAAATCCATAAATCGAATGTGGCTGA-GA
* * *
7540 TTTAGTTCGATGAATATAGATATTTCAAAGAGTATTTCTGCCAAAAATCATGCAAAACTGAGTCA
252 TTTGGTTCGATGAATATAGATATTTCAAAGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCA
7605 GGAC
317 GGAC
* * * * * *
7609 CTCGAAACGCGTTTTTAGTCCAAAAACCATGATGGTTAGTACACGATTTTCGGCTATAAACTGAC
1 CACGAAACGCGTTTTTAG-CCAAAAACCGTGATGGTTAGTACTCGA-TTTCGACTAAAAACCGAC
7674 CCGAAAATTTTTTTACTAAATTTTTTGCCACAATACTCAGAAAAAATAAATAATTCAACGCCAAA
64 CCG-AAATTTTTTT-CTAAATTTTTTGCCACAATACTCAGAAAAAATAAATAATTCAACGCCAAA
* ** * * * *
7739 AAGATTGACGGACTTTTCGCGCATCTAATATCGTTTTTCTATTTTTTTCTGAATTAATTTCTAAT
127 AAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTC-ATTTTTTCCCGAATTAATTTCTAAT
7804 TAAATCGAAACAAGAT
191 TAAATCGAAACAAGAT
7820 TTTATATAGT
Statistics
Matches: 1198, Mismatches: 187, Indels: 146
0.78 0.12 0.10
Matches are distributed among these distances:
277 25 0.02
280 98 0.08
281 11 0.01
282 42 0.04
283 2 0.00
285 2 0.00
287 1 0.00
293 1 0.00
295 9 0.01
296 38 0.03
299 1 0.00
300 2 0.00
301 1 0.00
302 1 0.00
303 1 0.00
305 21 0.02
306 24 0.02
307 2 0.00
309 1 0.00
311 1 0.00
315 2 0.00
319 57 0.05
320 41 0.03
321 357 0.30
322 87 0.07
323 14 0.01
324 37 0.03
325 38 0.03
326 9 0.01
327 171 0.14
328 27 0.02
329 68 0.06
330 6 0.01
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.33
Consensus pattern (320 bp):
CACGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACTCGATTTCGACTAAAAACCGACCC
GAAATTTTTTTCTAAATTTTTTGCCACAATACTCAGAAAAAATAAATAATTCAACGCCAAAAAGA
TTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCATTTTTTCCCGAATTAATTTCTAATTAAAT
CGAAACAAGATCCAGATGCTCGTAAAAACAAATCCATAAATCGAATGTGGCTGAGATTTGGTTCG
ATGAATATAGATATTTCAAAGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCAGGAC
Found at i:7842 original size:5 final size:5
Alignment explanation
Indices: 7832--7860 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
7822 TATATAGTGG
7832 TAAGA TAAGA TAAGA TAAGA TAAGA TAAG
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAG
7861 GTTAGGATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.21, T:0.21
Consensus pattern (5 bp):
TAAGA
Found at i:16806 original size:11 final size:11
Alignment explanation
Indices: 16792--16829 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
16782 ATTCATAACA
16792 AATTTATAATT
1 AATTTATAATT
16803 AATTTATAATT
1 AATTTATAATT
16814 -ATTTGATAATT
1 AATTT-ATAATT
*
16825 TATTT
1 AATTT
16830 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Done.