Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009904.1 Kokia drynarioides strain JFW-HI SEQ_124642, 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: 6514
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.27
Warning! 61 characters in sequence are not A, C, G, or T
Found at i:620 original size:216 final size:216
Alignment explanation
Indices: 1--2366 Score: 2635
Period size: 216 Copynumber: 10.9 Consensus size: 216
* * * * * ** *
1 GTTCATCCAAGAA-CAAGGGAGACACTATTCTCACGTAAATAAGTTTTAAATTCATAGATCAAAG
1 GTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAA
* * * * *
65 CTTGTTTTCAAAATGAAAAACTATTTCGACCAAATGATACGA-TTTCCCTCGCATGGAATGTTTG
66 CTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGACTTT-CCACGCATGGAATGTTCG
* * * * * * *
129 GAAAATTACTCGAAGGAATGGATCATCCTGAACACTTTAAGGAACAGGATTTAAAAAAGAACTCG
130 AAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGTTATAAAAGAACTCG
*
194 TAAAAGTTTGACTAGTTCGGAA
195 TAAAAGTTTGACAAGTTCGGAA
* * * * **
216 GTTCCTCAAACAA-TAGAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTC-AAGGATAAA
1 GTTCATCCAAGAACCA-AGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAA
* * * *
279 ACTTGTATACAAAATGAAAAACTATTTAGACCAAATGATACGA-TTTCCCTCGCATGAAATGTTC
65 ACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGACTTT-CCACGCATGGAATGTTC
* * * * * * * *
343 GAACAATTACTCGAAGGAATGGATCGTCTTTAACACTTTATGGAACAGGATTTAAAAAAGAACAC
129 GAAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGTTATAAAAGAACTC
408 GTAAAAGTTTGACAAGTTCGGAA
194 GTAAAAGTTTGACAAGTTCGGAA
* * * *
431 GTTCATCCAACAATCAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGGCCGAAA
1 GTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAA
* * * *
496 CTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACTATTCGAC-CATGTAATGTTCG
66 CTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGACT-TTCCACGCATGGAATGTTCG
* * * * * *
560 TAATATTACTCGAAGGATTGGATCGTCTTGAATACTTTAAGGAACCGAAGCTATAAAAGAAGTCG
130 AAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGTTATAAAAGAACTCG
* **
625 TAAAAGTTTGACAAGGTCAAAA
195 TAAAAGTTTGACAAGTTCGGAA
* *
647 GTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTTAAAGGCCAAAA
1 GTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAA
* * * * * * * *
712 CTTGTTTACAAAATTACAATCTTTTTAGACCAAATGACGCGACTTCCCGA-GCATGTAATGTTTG
66 CTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGACTTTCC-ACGCATGGAATGTTCG
* * * * *
776 AAAAATTGCTCGAAGGATTGGATCGACTTGAATACTTTAAGAAACCGAAGTTATAAAAGAACTCG
130 AAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGTTATAAAAGAACTCG
** *
841 TAAAAGTTCAACAAGTTCGGAT
195 TAAAAGTTTGACAAGTTCGGAA
* * * * **
863 GTTCATCCAAGACCCAAGAAAGACACAATTCTTACGTAAATAAGTTTTTAATTCAAAGATCAAAA
1 GTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAA
* *
928 CTTGTTTACAAAATGAAAAACTATTTACACCAAATGATGCGA-TTTCCCTCGCATGGAATGTTCG
66 CTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGACTTT-CCACGCATGGAATGTTCG
* * ** * *
992 AAAAATTACTCAAAGGAATGGATCGTCCTGAACACTTTAATAAACTGAAGCTATAAAAGAACTCG
130 AAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGTTATAAAAGAACTCG
* ** * **
1057 TAACAGTTTGTTAATTTTAGAA
195 TAAAAGTTTGACAAGTTCGGAA
* * * *
1079 TTTCGTCCAAGAACCAAGAGAGAAACAATTCTCAAGTAAATAAGTTTTTAATTCAATGGCCAAAA
1 GTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAA
* * * * * *
1144 CTTGTTTATAAAATGACAAACTTTTTAGACCAAATGATGTGACTTCCCGA-GCATGTAATGATT-
66 CTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGACTTTCC-ACGCATGGAATG-TTC
* * * * ** * *
1207 GAAAAATTGCTCGAAGGATTGGATCGACTTGAATACTACAAGAAACCAAAGTTATAAAAGAACTC
129 GAAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGTTATAAAAGAACTC
** *
1272 GTAAAAGTTAAACAAGTTCGGAT
194 GTAAAAGTTTGACAAGTTCGGAA
** * * **
1295 GTTCATCCAAGTCCCAAGAGAGACACAATTCTTACGTAAATAAGTTTTTAATTCAAAGATCAAAA
1 GTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAA
*
1360 CTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGA-TTTCCCTCGCATGGAATGTTCG
66 CTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGACTTT-CCACGCATGGAATGTTCG
* * * * *
1424 GAAAATTACTCGAAGGAATGGATCGTCCTGAACACTTTAATGAATCGAAGTTATAAAAGAAGTCG
130 AAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGTTATAAAAGAACTCG
* **
1489 TAAAACTTCAACAAGTTCGGAA
195 TAAAAGTTTGACAAGTTCGGAA
* * * * * *
1511 GTTCGTCCAAGAACAAAGAGAGACACAATTCTCACATAAATAAGTTTTTAATTGAAAGACCAAAA
1 GTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAA
* *
1576 CTTGTTTACAAAATGAAAAACTATTTAAACCAAATGATGCGA-TTTCCCTCGCATGGAATGCTT-
66 CTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGACTTT-CCACGCATGGAATG-TTC
* * * * * *
1639 GGAAAATTACTCGAAGGAATGGATCGTCTTGAAAATTTTAAGGAATCGGATTTA-AAAATGAACT
129 GAAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGTTATAAAA-GAACT
*
1703 CGTAAAAAGTTTGACAAGTTCGAAA
193 CGT-AAAAGTTTGACAAGTTCGGAA
* ** * * *
1728 GTTCATCCAACAATGAAGAGAGAAACAATTCTCATGTAAATATGTTTTTAATTCAAAGGCCGAAA
1 GTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAA
* * * *
1793 CTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACTATTCGAC-CATGTAATGTTCG
66 CTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGACT-TTCCACGCATGGAATGTTCG
* * * * * *
1857 TAATATTACTCGAAGGATTGGATCGTCTTGAATACTTTAAGGAACCGAAGCTATAAAAGAAGTCG
130 AAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGTTATAAAAGAACTCG
**
1922 TAAAAGTTTGACAAGTTCAAAA
195 TAAAAGTTTGACAAGTTCGGAA
* * *
1944 GTTCATCCAACAACCAAGAGAGAAACAATTCTAACGTAAATAAGTTTTTAATTCAAAGGCCGAAA
1 GTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAA
* * * * * *
2009 CTTGTTTACAAAATGACAAAA-TTTTTAGTCAAAAATGGTGCGACTTCCCGA-GCATGTAATGTT
66 CTTGTTTACAAAATGA-AAAACTATTTAGAC-CAAATGATGCGACTTTCC-ACGCATGGAATGTT
* * * * * * *
2072 TGAAAAATTGCTCGAAGGATTGGATCGACTTCAATACTTTAAGAAACCGAAGTTATAAAAGAACT
128 CGAAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGTTATAAAAGAACT
** *
2137 CGTAAAAGTTCAACAAGTTCGGAT
193 CGTAAAAGTTTGACAAGTTCGGAA
* * * * * ** **
2161 GTTCATCTAAGACCCAAGAGAGACACAATTCTTAAAGTTCGATAAGTTTTTAATTCAAAGATCAA
1 GTTCATCCAAGAACCAAGAGAGAAACAATTC-TCACG-TAAATAAGTTTTTAATTCAAAGGCCAA
* * * *
2226 AACTTGTTTATAAAATGGAAAACTATTTATACCAAATGATGCGAC-TTCCCCTGCATGGAATGTT
64 AACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGACTTTCCAC-GCATGGAATGTT
* * * *
2290 CAAAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAATGAACTGAAGCTATAAAAGAACT
128 CGAAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGTTATAAAAGAACT
2355 CGTAAAAGTTTG
193 CGTAAAAGTTTG
2367 TTATTTTAAG
Statistics
Matches: 1826, Mismatches: 294, Indels: 59
0.84 0.13 0.03
Matches are distributed among these distances:
215 214 0.12
216 1152 0.63
217 311 0.17
218 103 0.06
219 46 0.03
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (216 bp):
GTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAA
CTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGACTTTCCACGCATGGAATGTTCGA
AAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAAGTTATAAAAGAACTCGT
AAAAGTTTGACAAGTTCGGAA
Found at i:914 original size:432 final size:432
Alignment explanation
Indices: 1--2366 Score: 2950
Period size: 432 Copynumber: 5.5 Consensus size: 432
* * * * * *
1 GTTCATCCAAGA-ACAAGGGAGACACTATTCTCACGTAAATAAGTTTTAAATTCATAGATCAAAG
1 GTTCATCCAAGACCCAAGAGAGACACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAA
* * * * *
65 CTTGTTTTCAAAATGAAAAACTATTTCGACCAAATGATACGATTTCCCTCGCATGGAATGTTTGG
66 CTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTTCGA
* * * ** *
130 AAAATTACTCGAAGGAATGGATCATCCTGAACACTTTAAGGAACAGGATTTAAAAAAGAACTCGT
131 AAAATTACTCGAAGGAATGGATCGTCCTGAACACTTTAAGGAACCGAAGCTATAAAAGAACTCGT
* * * * *
195 AAAAGTTTGACTAGTTCGGAAGTTCCTCAAACAA-TAGAGAGAGAAACAATTCTCACGTAAATAA
196 AAAAGTTTGACAAGTTCAGAAGTTCATCCAACAACCA-AGAGAGAAACAATTCTCACGTAAATAA
** * * * * *
259 GTTTTTAATTC-AAGGATAAAACTTGTATACAAAATGAAAAACTATTTAGACCAAATGATACGAT
260 GTTTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGAC
** * * * * * * * * * *
323 TTCCCTCGCATGAAATGTTCGAACAATTACTCGAAGGAATGGATCGTCTTTAACACTTTATGGAA
325 TTCCCGAGCATGTAATGTTTGAAAAATTGCTCGAAGGATTGGATCGACTTGAATACTTTAAGAAA
* * * * * ** *
388 CAGGATTTAAAAAAGAACACGTAAAAGTTTGACAAGTTCGGAA
390 CCGAAGTTATAAAAGAACTCGTAAAAGTTCAACAAGTTCGGAT
* ** * * ** *
431 GTTCATCCAACAATCAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGGCCGAAA
1 GTTCATCCAAGACCCAAGAGAGACACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAA
* * ** *
496 CTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACTATT-CGAC-CATGTAATGTTC
66 CTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGA-T-TTCCCTCGCATGGAATGTTC
* * * * * *
559 GTAATATTACTCGAAGGATTGGATCGTCTTGAATACTTTAAGGAACCGAAGCTATAAAAGAAGTC
129 GAAAAATTACTCGAAGGAATGGATCGTCCTGAACACTTTAAGGAACCGAAGCTATAAAAGAACTC
* *
624 GTAAAAGTTTGACAAGGTCAAAAGTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAAATA
194 GTAAAAGTTTGACAAGTTCAGAAGTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAAATA
* * * *
689 AGTTTTTAATTTAAAGGCCAAAACTTGTTTACAAAATTACAATCTTTTTAGACCAAATGACGCGA
259 AGTTTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGA
754 CTTCCCGAGCATGTAATGTTTGAAAAATTGCTCGAAGGATTGGATCGACTTGAATACTTTAAGAA
324 CTTCCCGAGCATGTAATGTTTGAAAAATTGCTCGAAGGATTGGATCGACTTGAATACTTTAAGAA
819 ACCGAAGTTATAAAAGAACTCGTAAAAGTTCAACAAGTTCGGAT
389 ACCGAAGTTATAAAAGAACTCGTAAAAGTTCAACAAGTTCGGAT
* *
863 GTTCATCCAAGACCCAAGAAAGACACAATTCTTACGTAAATAAGTTTTTAATTCAAAGATCAAAA
1 GTTCATCCAAGACCCAAGAGAGACACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAA
*
928 CTTGTTTACAAAATGAAAAACTATTTACACCAAATGATGCGATTTCCCTCGCATGGAATGTTCGA
66 CTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTTCGA
* ** *
993 AAAATTACTCAAAGGAATGGATCGTCCTGAACACTTTAATAAACTGAAGCTATAAAAGAACTCGT
131 AAAATTACTCGAAGGAATGGATCGTCCTGAACACTTTAAGGAACCGAAGCTATAAAAGAACTCGT
* ** * * * * * *
1058 AACAGTTTGTTAATTTTAGAATTTCGTCCAAGAACCAAGAGAGAAACAATTCTCAAGTAAATAAG
196 AAAAGTTTGACAAGTTCAGAAGTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAG
* * *
1123 TTTTTAATTCAATGGCCAAAACTTGTTTATAAAATGACAAACTTTTTAGACCAAATGATGTGACT
261 TTTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACT
* **
1188 TCCCGAGCATGTAATGATTGAAAAATTGCTCGAAGGATTGGATCGACTTGAATACTACAAGAAAC
326 TCCCGAGCATGTAATGTTTGAAAAATTGCTCGAAGGATTGGATCGACTTGAATACTTTAAGAAAC
* *
1253 CAAAGTTATAAAAGAACTCGTAAAAGTTAAACAAGTTCGGAT
391 CGAAGTTATAAAAGAACTCGTAAAAGTTCAACAAGTTCGGAT
* *
1295 GTTCATCCAAGTCCCAAGAGAGACACAATTCTTACGTAAATAAGTTTTTAATTCAAAGATCAAAA
1 GTTCATCCAAGACCCAAGAGAGACACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAA
*
1360 CTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTTCGG
66 CTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTTCGA
* * * *
1425 AAAATTACTCGAAGGAATGGATCGTCCTGAACACTTTAATGAATCGAAGTTATAAAAGAAGTCGT
131 AAAATTACTCGAAGGAATGGATCGTCCTGAACACTTTAAGGAACCGAAGCTATAAAAGAACTCGT
* ** * * * * * *
1490 AAAACTTCAACAAGTTCGGAAGTTCGTCCAAGAACAAAGAGAGACACAATTCTCACATAAATAAG
196 AAAAGTTTGACAAGTTCAGAAGTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAG
* * * * * *
1555 TTTTTAATTGAAAGACCAAAACTTGTTTACAAAATGAAAAACTATTTAAACCAAATGATGCGATT
261 TTTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACT
** * * * * * * * * * *
1620 TCCCTCGCATGGAATGCTTGGAAAATTACTCGAAGGAATGGATCGTCTTGAAAATTTTAAGGAAT
326 TCCCGAGCATGTAATGTTTGAAAAATTGCTCGAAGGATTGGATCGACTTGAATACTTTAAGAAAC
* * ** * *
1685 CGGATTTA-AAAATGAACTCGTAAAAAGTTTGACAAGTTCGAAA
391 CGAAGTTATAAAA-GAACTCGT-AAAAGTTCAACAAGTTCGGAT
* *** * * * ** *
1728 GTTCATCCAACAATGAAGAGAGAAACAATTCTCATGTAAATATGTTTTTAATTCAAAGGCCGAAA
1 GTTCATCCAAGACCCAAGAGAGACACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAA
* * ** *
1793 CTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACTATT-CGAC-CATGTAATGTTC
66 CTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGA-T-TTCCCTCGCATGGAATGTTC
* * * * * *
1856 GTAATATTACTCGAAGGATTGGATCGTCTTGAATACTTTAAGGAACCGAAGCTATAAAAGAAGTC
129 GAAAAATTACTCGAAGGAATGGATCGTCCTGAACACTTTAAGGAACCGAAGCTATAAAAGAACTC
* *
1921 GTAAAAGTTTGACAAGTTCAAAAGTTCATCCAACAACCAAGAGAGAAACAATTCTAACGTAAATA
194 GTAAAAGTTTGACAAGTTCAGAAGTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAAATA
* * * * *
1986 AGTTTTTAATTCAAAGGCCGAAACTTGTTTACAAAATGACAAAATTTTTAGTCAAAAATGGTGCG
259 AGTTTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTTTTTAGAC-CAAATGATGCG
*
2051 ACTTCCCGAGCATGTAATGTTTGAAAAATTGCTCGAAGGATTGGATCGACTTCAATACTTTAAGA
323 ACTTCCCGAGCATGTAATGTTTGAAAAATTGCTCGAAGGATTGGATCGACTTGAATACTTTAAGA
2116 AACCGAAGTTATAAAAGAACTCGTAAAAGTTCAACAAGTTCGGAT
388 AACCGAAGTTATAAAAGAACTCGTAAAAGTTCAACAAGTTCGGAT
* * * **
2161 GTTCATCTAAGACCCAAGAGAGACACAATTCTTAAAGTTCGATAAGTTTTTAATTCAAAGATCAA
1 GTTCATCCAAGACCCAAGAGAGACACAATTC-TCACG-TAAATAAGTTTTTAATTCAAAGATCAA
* * * *
2226 AACTTGTTTATAAAATGGAAAACTATTTATACCAAATGATGCGACTTCCC-CTGCATGGAATGTT
64 AACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTC-GCATGGAATGTT
* * * *
2290 CAAAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAATGAACTGAAGCTATAAAAGAACT
128 CGAAAAATTACTCGAAGGAATGGATCGTCCTGAACACTTTAAGGAACCGAAGCTATAAAAGAACT
2355 CGTAAAAGTTTG
193 CGTAAAAGTTTG
2367 TTATTTTAAG
Statistics
Matches: 1648, Mismatches: 270, Indels: 31
0.85 0.14 0.02
Matches are distributed among these distances:
430 13 0.01
431 215 0.13
432 867 0.53
433 324 0.20
434 84 0.05
435 145 0.09
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (432 bp):
GTTCATCCAAGACCCAAGAGAGACACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAA
CTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTTCGA
AAAATTACTCGAAGGAATGGATCGTCCTGAACACTTTAAGGAACCGAAGCTATAAAAGAACTCGT
AAAAGTTTGACAAGTTCAGAAGTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAG
TTTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACT
TCCCGAGCATGTAATGTTTGAAAAATTGCTCGAAGGATTGGATCGACTTGAATACTTTAAGAAAC
CGAAGTTATAAAAGAACTCGTAAAAGTTCAACAAGTTCGGAT
Found at i:1265 original size:648 final size:648
Alignment explanation
Indices: 1--2366 Score: 3101
Period size: 648 Copynumber: 3.6 Consensus size: 648
* * * * * * * *
1 GTTCATCCAAGAA-CAAGGGAGACACTATTCTCACGTAAATAAGTTTTAAATTCATAGATCAAAG
1 GTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAA
* * * * ** *
65 CTTGTTTTCAAAATGAAAAACTATTTCGACCAAATGATACGATTTCCCTCGCATGGAATGTTTGG
66 CTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGACTTCCCGAGCATGGAATGTTTGA
* * * * *
130 AAAATTACTCGAAGGAATGGATC-ATCCTGAACACTTTAAGGAACAGGATTTAAAAAAGAACTCG
131 AAAATTACTCGAAGGAATGGATCGA-CCTGAACACTTTAAGAAACCGAAGTTATAAAAGAACTCG
** * * *
194 TAAAAGTTTGACTAGTTCGGAAGTTCCT-CAA-A-CAATAGAGAGAGAAACAATTCTCACGTAAA
195 TAAAAGTTCAACAAGTTCGGAAGTTCATCCAAGACCAA-AGA-A-AGACACAATTCTCACGTAAA
* * * *
256 TAAGTTTTTAATTCAAGGAT-AAAACTTGTATACAAAATGAAAAACTATTTAGACCAAATGATAC
257 TAAGTTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGAAAAACTATTTAAACCAAATGATGC
* * *
320 GATTTCCCTCGCATGAAATGTTCGAACAATTACTCGAAGGAATGGATCGTCTTTAACACTTT-AT
322 GATTTCCCTCGCATGGAATGTTCGAAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAT
* * ** * * * ** *
384 GGAACAGGATTTAAAAAAGAACACGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAACAATCAAG
387 -GAACTGAAGCTATAAAAGAACTCGTAAAAGTTTGACAATTTTAGAAGTTCATCCAACAACCAAG
449 AGAGAAACAATTCTCACA-TAAATAAGTTTTTAATTCAAAGGCCGAAACTTGTTTACAAAATGAC
451 AGAGAAACAATTCTCA-AGTAAATAAGTTTTTAATTCAAAGGCCGAAACTTGTTTACAAAATGAC
513 AAACTTTTTAGACCAAATGATGCGACTATTCGACCATGTAATGTTCGTAATATTACTCGAAGGAT
515 AAACTTTTTAGACCAAATGATGCGACTATTCGACCATGTAATGTTCGTAATATTACTCGAAGGAT
*
578 TGGATCGTCTTGAATACTTTAAGGAACCGAAGCTATAAAAGAAGTCGTAAAAGTTTGACAAGGTC
580 TGGATCGTCTTGAATACTTTAAGGAACCGAAGCTATAAAAGAAGTCGTAAAAGTTTGACAAGTTC
643 AAAA
645 AAAA
* *
647 GTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTTAAAGGCCAAAA
1 GTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAA
* * * * * *
712 CTTGTTTACAAAATTACAATCTTTTTAGACCAAATGACGCGACTTCCCGAGCATGTAATGTTTGA
66 CTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGACTTCCCGAGCATGGAATGTTTGA
* * * *
777 AAAATTGCTCGAAGGATTGGATCGACTTGAATACTTTAAGAAACCGAAGTTATAAAAGAACTCGT
131 AAAATTACTCGAAGGAATGGATCGACCTGAACACTTTAAGAAACCGAAGTTATAAAAGAACTCGT
* * *
842 AAAAGTTCAACAAGTTCGGATGTTCATCCAAGACCCAAGAAAGACACAATTCTTACGTAAATAAG
196 AAAAGTTCAACAAGTTCGGAAGTTCATCCAAGACCAAAGAAAGACACAATTCTCACGTAAATAAG
*
907 TTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGAAAAACTATTTACACCAAATGATGCGATT
261 TTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGAAAAACTATTTAAACCAAATGATGCGATT
* * *
972 TCCCTCGCATGGAATGTTCGAAAAATTACTCAAAGGAATGGATCGTCCTGAACACTTTAATAAAC
326 TCCCTCGCATGGAATGTTCGAAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAATGAAC
* ** * * *
1037 TGAAGCTATAAAAGAACTCGTAACAGTTTGTTAATTTTAGAATTTCGTCCAAGAACCAAGAGAGA
391 TGAAGCTATAAAAGAACTCGTAAAAGTTTGACAATTTTAGAAGTTCATCCAACAACCAAGAGAGA
* * *
1102 AACAATTCTCAAGTAAATAAGTTTTTAATTCAATGGCCAAAACTTGTTTATAAAATGACAAACTT
456 AACAATTCTCAAGTAAATAAGTTTTTAATTCAAAGGCCGAAACTTGTTTACAAAATGACAAACTT
* * * * * *
1167 TTTAGACCAAATGATGTGACT-TCCCGAGCATGTAATGATT-GAAAAATTGCTCGAAGGATTGGA
521 TTTAGACCAAATGATGCGACTAT-TCGACCATGTAATG-TTCGTAATATTACTCGAAGGATTGGA
* ** * * * * ** ** *
1230 TCGACTTGAATACTACAAGAAACCAAAGTTATAAAAGAACTCGTAAAAGTTAAACAAGTTCGGAT
584 TCGTCTTGAATACTTTAAGGAACCGAAGCTATAAAAGAAGTCGTAAAAGTTTGACAAGTTCAAAA
*** * * *
1295 GTTCATCCAAGTCCCAAGAGAGACACAATTCTTACGTAAATAAGTTTTTAATTCAAAGATCAAAA
1 GTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAA
* ** * *
1360 CTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTTCGG
66 CTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGACTTCCCGAGCATGGAATGTTTGA
* * *
1425 AAAATTACTCGAAGGAATGGATCGTCCTGAACACTTTAATG-AATCGAAGTTATAAAAGAAGTCG
131 AAAATTACTCGAAGGAATGGATCGACCTGAACACTTTAA-GAAACCGAAGTTATAAAAGAACTCG
* * * * *
1489 TAAAACTTCAACAAGTTCGGAAGTTCGTCCAAGAACAAAGAGAGACACAATTCTCACATAAATAA
195 TAAAAGTTCAACAAGTTCGGAAGTTCATCCAAGACCAAAGAAAGACACAATTCTCACGTAAATAA
* *
1554 GTTTTTAATTGAAAGACCAAAACTTGTTTACAAAATGAAAAACTATTTAAACCAAATGATGCGAT
260 GTTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGAAAAACTATTTAAACCAAATGATGCGAT
* * * *
1619 TTCCCTCGCATGGAATGCTT-GGAAAATTACTCGAAGGAATGGATCGTCTTGAAAATTTTAAGGA
325 TTCCCTCGCATGGAATG-TTCGAAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAATGA
* ** * * **
1683 A-TCGGATTTA-AAAATGAACTCGTAAAAAGTTTGACAA-GTTCGAAAGTTCATCCAACAATGAA
389 ACT-GAAGCTATAAAA-GAACTCGT-AAAAGTTTGACAATTTTAG-AAGTTCATCCAACAACCAA
* *
1745 GAGAGAAACAATTCTCATGTAAATATGTTTTTAATTCAAAGGCCGAAACTTGTTTACAAAATGAC
450 GAGAGAAACAATTCTCAAGTAAATAAGTTTTTAATTCAAAGGCCGAAACTTGTTTACAAAATGAC
1810 AAACTTTTTAGACCAAATGATGCGACTATTCGACCATGTAATGTTCGTAATATTACTCGAAGGAT
515 AAACTTTTTAGACCAAATGATGCGACTATTCGACCATGTAATGTTCGTAATATTACTCGAAGGAT
1875 TGGATCGTCTTGAATACTTTAAGGAACCGAAGCTATAAAAGAAGTCGTAAAAGTTTGACAAGTTC
580 TGGATCGTCTTGAATACTTTAAGGAACCGAAGCTATAAAAGAAGTCGTAAAAGTTTGACAAGTTC
1940 AAAA
645 AAAA
* * *
1944 GTTCATCCAACAACCAAGAGAGAAACAATTCTAACGTAAATAAGTTTTTAATTCAAAGGCCGAAA
1 GTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAA
* * * * *
2009 CTTGTTTACAAAATGACAAAA-TTTTTAGTCAAAAATGGTGCGACTTCCCGAGCATGTAATGTTT
66 CTTGTTTACAAAATGA-AAAACTATTTAGAC-CAAATGATGCGACTTCCCGAGCATGGAATGTTT
* * * * *
2073 GAAAAATTGCTCGAAGGATTGGATCGACTTCAATACTTTAAGAAACCGAAGTTATAAAAGAACTC
129 GAAAAATTACTCGAAGGAATGGATCGACCTGAACACTTTAAGAAACCGAAGTTATAAAAGAACTC
* * * * * * **
2138 GTAAAAGTTCAACAAGTTCGGATGTTCATCTAAGACCCAAGAGAGACACAATTCTTAAAGTTCGA
194 GTAAAAGTTCAACAAGTTCGGAAGTTCATCCAAGACCAAAGAAAGACACAATTC-TCACG-TAAA
* * *
2203 TAAGTTTTTAATTCAAAGATCAAAACTTGTTTATAAAATGGAAAACTATTTATACCAAATGATGC
257 TAAGTTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGAAAAACTATTTAAACCAAATGATGC
* *
2268 GACTTCCC-CTGCATGGAATGTTCAAAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAA
322 GATTTCCCTC-GCATGGAATGTTCGAAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAA
2332 TGAACTGAAGCTATAAAAGAACTCGTAAAAGTTTG
386 TGAACTGAAGCTATAAAAGAACTCGTAAAAGTTTG
2367 TTATTTTAAG
Statistics
Matches: 1474, Mismatches: 219, Indels: 49
0.85 0.13 0.03
Matches are distributed among these distances:
646 12 0.01
647 214 0.15
648 676 0.46
649 287 0.19
650 135 0.09
651 14 0.01
652 131 0.09
653 5 0.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (648 bp):
GTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAA
CTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGACTTCCCGAGCATGGAATGTTTGA
AAAATTACTCGAAGGAATGGATCGACCTGAACACTTTAAGAAACCGAAGTTATAAAAGAACTCGT
AAAAGTTCAACAAGTTCGGAAGTTCATCCAAGACCAAAGAAAGACACAATTCTCACGTAAATAAG
TTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGAAAAACTATTTAAACCAAATGATGCGATT
TCCCTCGCATGGAATGTTCGAAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAATGAAC
TGAAGCTATAAAAGAACTCGTAAAAGTTTGACAATTTTAGAAGTTCATCCAACAACCAAGAGAGA
AACAATTCTCAAGTAAATAAGTTTTTAATTCAAAGGCCGAAACTTGTTTACAAAATGACAAACTT
TTTAGACCAAATGATGCGACTATTCGACCATGTAATGTTCGTAATATTACTCGAAGGATTGGATC
GTCTTGAATACTTTAAGGAACCGAAGCTATAAAAGAAGTCGTAAAAGTTTGACAAGTTCAAAA
Found at i:2702 original size:350 final size:351
Alignment explanation
Indices: 2050--2716 Score: 912
Period size: 350 Copynumber: 1.9 Consensus size: 351
2040 AAAATGGTGC
* * * *
2050 GACTTCCCGAGCATGTAATGTTTGAAAAATTGCTCGAAGGATTGGATCGACTTCAATACTTTAAG
1 GACTTCCCAAGCATGTAATGTTCGAAAAATAGCTCGAAGGATTGGATCGACTTCAATAATTTAAG
* * * *
2115 AAACCGAAGTTATAAAAGAACTCGTAAAAGTTCAACAAGTTCGGATGTTCATCTAAGACCCAAGA
66 AAACCGAAGATATAAAAGAACTCGTAAAAGTTCAACAAGTTCGAAAGTTCATCTAAGAACCAAGA
* * ** * *
2180 GAGACACAATTCTTAAAGTTCGATAAGTTTTTAATTCAAAGATCAAAACTTGTTTATAAAATGGA
131 GAGAAACAATTCTCAAAG-TAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGAA
* * *
2245 AAACTATTTATACCAAATGATGCGACTTCCCCTGCATGGAATGTTCAAAAAATTACTCGAAGGAA
195 AAACTATTTAGACCAAATGATACGACTTCCCCTGCATGAAATGTTCAAAAAATTACTCGAAGGAA
* * *
2310 TGGATCGTCTTGAACACTTTAATGAACTGAAGCTATAAAAGAACTCGTAAAAGTTTGTTATTTTA
260 TGGATCGTCTTGAACACTTTAATGAACAGAAGCTAAAAAAGAACACGTAAAAGTTTGTTATTTTA
2375 AGAATTTCGTCCAAGACCCAATGATGA
325 AGAATTTCGTCCAAGACCCAATGATGA
* * * * *
2402 GACTTCCCAAGCATGTAATGTTCGGAGAGTAGCTCGAAGGATTGGATCGTCTTGAATAATTTAAG
1 GACTTCCCAAGCATGTAATGTTCGAAAAATAGCTCGAAGGATTGGATCGACTTCAATAATTTAAG
* * ** *
2467 GAACTGAAGATATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCTAAGAACCAAGA
66 AAACCGAAGATATAAAAGAACTCGTAAAAGTTCAACAAGTTCGAAAGTTCATCTAAGAACCAAGA
* *
2532 GAGAAACAGTTCTCACA-TAAATAAG-TTTTAACTTCAAAGATCAAAA-TATGTTTACAAAATGA
131 GAGAAACAATTCTCAAAGTAAATAAGTTTTTAA-TTCAAAGATCAAAACT-TGTTTACAAAATGA
* * *
2594 AAAACTATTTAGACCAAATGATACGA-TTTCCCTCGCATGAAATGTTCGAACAATTACTCGAAGG
194 AAAACTATTTAGACCAAATGATACGACTTCCCCT-GCATGAAATGTTCAAAAAATTACTCGAAGG
* **
2658 AATGGATCGTCTTGAACACTTT-ATGGAACAGGATTTAAAAAAGAACACGTAAAAGTTTG
258 AATGGATCGTCTTGAACACTTTAAT-GAACAGAAGCTAAAAAAGAACACGTAAAAGTTTG
2717 ACAAGTTCGG
Statistics
Matches: 273, Mismatches: 38, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
349 15 0.05
350 133 0.49
352 125 0.46
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.28
Consensus pattern (351 bp):
GACTTCCCAAGCATGTAATGTTCGAAAAATAGCTCGAAGGATTGGATCGACTTCAATAATTTAAG
AAACCGAAGATATAAAAGAACTCGTAAAAGTTCAACAAGTTCGAAAGTTCATCTAAGAACCAAGA
GAGAAACAATTCTCAAAGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGAAA
AACTATTTAGACCAAATGATACGACTTCCCCTGCATGAAATGTTCAAAAAATTACTCGAAGGAAT
GGATCGTCTTGAACACTTTAATGAACAGAAGCTAAAAAAGAACACGTAAAAGTTTGTTATTTTAA
GAATTTCGTCCAAGACCCAATGATGA
Found at i:2802 original size:216 final size:214
Alignment explanation
Indices: 2434--3147 Score: 885
Period size: 216 Copynumber: 3.3 Consensus size: 214
2424 CGGAGAGTAG
* * * *
2434 CTCGAAGGATTGGATCGTCTTGAATAATTTAAGGAACTGAAGATATAAAAGAACTCGTAAAAGTT
1 CTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTT
* * * *
2499 TGACAAGTTCGAAAGTTCGTCTAAGAACCAAGAGAGAAACAGTTCTCACATAAATAAGTTTTAAC
66 TGACAAGTTCGGAAGTTCATCCAA-AACCAAGAGAGAAACAATTCTCACATAAATAAGTTTTAA-
*
2564 TTCAAAGATCAAAA-TATGTTTACAAAATGAAAAACTATTTAGACCAAATGATACGATTTCCCTC
129 TTCAAAGATCAAAACT-TGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTC
*
2628 GCATGAAATGTTCGAACAATTA
193 GCATGAAATGTTCGAAAAATTA
* * * * * *
2650 CTCGAAGGAATGGATCGTCTTGAACACTTTATGGAACAGGATTTAAAAAAGAACACGTAAAAGTT
1 CTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTT
* *
2715 TGACAAGTTCGGAAGTTCATCCAACAATCAAGAGAGAGACAATTCTCACATAAATAAGTTTTTAA
66 TGACAAGTTCGGAAGTTCATCCAA-AACCAAGAGAGAAACAATTCTCACATAAATAAG-TTTTAA
** * * * * **
2780 TTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTTTTTAGACAAAATGATGCGACTTCCCGAG
129 TTCAAAGATCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCG
* * *
2845 CATGTAATGTTTGAAAAATTT
194 CATGAAATGTTCGAAAAATTA
* ** * * * *
2866 CTCGAAGGATTGGATCGAGTTGAATACTTTAAGAAACCGAAGTTATAAAAGAACTCATAAAA-TT
1 CTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTT
* * ** * * * *
2930 TCAACAAGTTCTGTTGTTCATCCAAGACCGAAGAGAGACACAATTCTTACGTAAATAAGGTTTTA
66 T-GACAAGTTCGGAAGTTCATCCAAAACC-AAGAGAGAAACAATTCTCACATAAATAA-GTTTTA
*
2995 ATTCAAAGATCAAAACTTGTTTACAAAATGGAAAACTATTTAGACCAAATGATGCGATTTCCCTC
128 ATTCAAAGATCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTC
*
3060 GCATGGAATGTTC-AAAAATTA
193 GCATGAAATGTTCGAAAAATTA
* * **
3081 CTCAAAGGAATGGATCGTCTTGAACACTTTAATGAACTGAAACTATAAAAGAACTCGTAAAAGTT
1 CTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTT
3146 TG
66 TG
3148 TTATTTAAGA
Statistics
Matches: 417, Mismatches: 75, Indels: 13
0.83 0.15 0.03
Matches are distributed among these distances:
215 63 0.15
216 346 0.83
217 8 0.02
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (214 bp):
CTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTT
TGACAAGTTCGGAAGTTCATCCAAAACCAAGAGAGAAACAATTCTCACATAAATAAGTTTTAATT
CAAAGATCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCA
TGAAATGTTCGAAAAATTA
Found at i:2814 original size:20 final size:20
Alignment explanation
Indices: 2791--2830 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
2781 TCAAAGGCCA
2791 AAACTTGTTT-ACAAAATGAC
1 AAACTT-TTTAACAAAATGAC
2811 AAACTTTTTAGACAAAATGA
1 AAACTTTTTA-ACAAAATGA
2831 TGCGACTTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.17
20 6 0.33
21 9 0.50
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.30
Consensus pattern (20 bp):
AAACTTTTTAACAAAATGAC
Found at i:3733 original size:216 final size:214
Alignment explanation
Indices: 3359--6032 Score: 2453
Period size: 216 Copynumber: 12.4 Consensus size: 214
3349 GATCAAAATA
* * * * * *
3359 TTCGAAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTATGGAACAGGATTTAAAAAAGAA
1 TTCG-AAAATTACTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAA
* *
3424 CTCGTAAAAGTTTGACAAGTTCGGATGTTCATCCAACAACCAAGAGGGAAACAATTCTCACGTAA
65 CTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAA
* * *
3489 ATAAGTTTTTAATTCAAAGGCCGAAACTTGCTTACAAAATGACAAACTTTTTAGACCAAATGATG
130 ATAAGTTTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATG
* *
3554 CGACTTTTCGACCATGTAATG
195 CGA-TTTCCGACCATGGAATG
* * * *
3575 TTCGAAATATTGCTTGAAGGATTGGATCGTCTTGAATACTTTAAGGAACCGAAGCTATAAAAGAA
1 TTCGAAA-ATTACTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAA
* * * * ** * *
3640 GTCGTAAAAGTCTGACAAGTTCGAAAGTTTATCCAACAAATAAGAGAGATATAATTCTCACGTAA
65 CTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAA
** * * * *
3705 ATAAGTTTTTAATTCAAAGGCTGAAACTTGTTTGCAAAATGACAAACTTTTTAGCCCAAATGGTG
130 ATAAGTTTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATG
* * *
3770 CGACTTCCCGAGCATGTAATG
195 CGA-TTTCCGACCATGGAATG
* * * * * ** * *
3791 TTTGAAAAATTGCTCGAATGATTGGATCGACTTGAATACTACAAGAAACCAAAGTTATAAAAGAA
1 TTCG-AAAATTACTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAA
** * * * * *
3856 CTCGTAAAAGTTCAACAAGTTCGGATGTTCATCCAAGACCCAAGAGAGACACAATTCTTACGTAA
65 CTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAA
** *
3921 ATAAGTTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATG
130 ATAAGTTTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATG
**
3986 CGATTTCCCTCGCATGGAATG
195 CGATTTCCGAC-CATGGAATG
* * * * * * *
4007 TTCGGAAAATTACTCGAAGGAATGGATCATCCTGAACACTTTCATGAACTGAAGCTATAAAAGAA
1 TTC-GAAAATTACTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAA
** * * * * *
4072 CTCGTAAAAGTTTGTTAATTTCAGAATTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAA
65 CTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAA
* *** * * *
4137 ATAAGTTTCTAATTCAAAAATCAAAACTTGTTCACAAAATGAAAAACTATTTAAACCAAATGATG
130 ATAAGTTTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATG
** *
4202 CGATTTCCCTCTTATGGAATG
195 CGATTTCCGAC-CATGGAATG
* * * * * *
4223 CTCGAAAATTTACTCGAAGGAATGGATTGTCTTGAAAATTTTAAGGAACCGGATTTA-AAAATGA
1 TTCGAAAA-TTACTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAA-GA
** *
4287 ACTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAACAATGAAGAGAGAAACAATTCTCATGTA
64 ACTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTA
* * *
4352 AATAAGTTTTTAATTCAAAGGCCGAAACTTGTTTACAAAATGACAAACTTTTTAGGCCAAATGAT
129 AATAAGTTTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGAT
* *
4417 GCGACTTCCCGACCATGTAATG
194 GCGA-TTTCCGACCATGGAATG
* * * * * * *
4439 CTCGAAATATTGCTTGAAGGATTGGATCATCTTGAATACTTTAAGGAACTGAAGCTATAAAAGAA
1 TTCGAAA-ATTACTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAA
* * * * *
4504 GTCATAAAAGTTTGACAAGTTCGAAACTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAT
65 CTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAA
* *
4569 ATAAGTTTTTAATTCAAAGGCCGAAACTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATG
130 ATAAGTTTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATG
* * *
4634 CGACTTCCCGAGCATGTAATG
195 CGA-TTTCCGACCATGGAATG
* * * * *
4655 TTTGAAAAATTACTCGGAGGATTGGATCGACTTGAATACTTTAAGAAACCGAAGTTATAAAAGAA
1 TTCG-AAAATTACTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAA
** * * * * * * *
4720 CTCGTAAAAGTTCAACAAGTTCGGATGTTCATCCAAGACCCAAGAAAGACACAATTCTTATGTAA
65 CTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAA
** *
4785 ATAAGTTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATG
130 ATAAGTTTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATG
* ** * *
4850 CGATTTCCCTAGGAAGAAATG
195 CGATTT-CCGACCATGGAATG
* * * *
4871 TTCGGAAAATTACTCGAAGGAATGGATCGTCCTGAACACTTTAATGAATCGAAGTTATAAAAGAA
1 TTC-GAAAATTACTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAA
* * ** ******************************************
4936 GTCGTAAAACTTCAACAAGTTCGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
65 CTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAA
********************* *
5001 NNNNNNNNNNNNNNNNNNNATCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATG
130 ATAAGTTTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATG
* ** *
5066 CGATTTCCCTAGGAAGGAATG
195 CGATTT-CCGACCATGGAATG
* * * *
5087 TTCGGAAAATTACTCGAAGGAATGGATCGTCCTGAACACTTTAATGAATCGAAGTTATAAAAGAA
1 TTC-GAAAATTACTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAA
* * ** * * * * *
5152 GTCGTAAAACTTCAACAAGTTCGGAAGTTCGTCCAAAAACAAAGAGAGACACAATTCTCACATAA
65 CTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAA
* * * *
5217 ATAAGTTTTTAATTGAAAGACCAAAACTTGTTTACAAAATGAAAAACTATTTAAACCAAATGATG
130 ATAAGTTTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATG
* *
5282 CGATTTCCCGAGCACGGAATG
195 CGATTT-CCGACCATGGAATG
* * * * * * *
5303 CTCGGGAAATTACTCGAAGGAATGGATCGTCTTGAAAATTTTAAGGAATCGGATTTA-AAAATGA
1 TTC-GAAAATTACTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAA-GA
* ** *
5367 ACTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCCAACAATGAAGAGAGAAACAATTCTCATGTA
64 ACTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTA
* *
5432 AATAAGTTTTTAATTCAAAGGCCGAAACTTGTTTACAAAATGACAAACTTTTTAGACCAAATGAT
129 AATAAGTTTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGAT
*
5497 GCGACTATT-CGACCATGTAATG
194 GCGA-T-TTCCGACCATGGAATG
* * * * *
5519 TTCGTAATATTGCTCGAAGGATTGGGTCGTCTTGAATACTTTAAGGAACCGAAGCTATAAAAGAA
1 TTCG-AAAATTACTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAA
* ** *
5584 GTCGTAAAAGTTTGACAAGTTCAAAAGTTCATCCAACAACCAAGAGAGAAACAATTCTAACGTAA
65 CTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAA
* * * * *
5649 ATAAGTTTTTAATTCAAAGGCCGAAACTTGTTTACAAAATGACAAACTTTTTAGTCAAAAATGGT
130 ATAAGTTTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTATTTAGAC-CAAATGAT
* ** *
5714 GCGACTTCCCGAGAATGCAATG
194 GCGA-TTTCCGACCATGGAATG
* ** * * *
5736 TTTGAAAAATTGTTCGAAGGATTGGATTGACTTGAATACTTTAA-GAACCCGAAGTTATAAAAGA
1 TTCG-AAAATTACTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA-CCGAAGTTATAAAAGA
** * * * * * *
5800 ACTCGTAAAAGTTCAACAAGTTCGGATGTTCATCCAAGACCCAAGAGAGACACAATTCTTAAAGT
64 ACTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAACAACCAAGAGAGAAACAATTC-TCACG-
** ** *
5865 TCGATAAGTTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGGA-AATCTATTTAGACCAAAT
127 TAAATAAGTTTTTAATTCAAAGGCCAAAACTTGTTTACAAAAT-GACAAACTATTTAGACCAAAT
*
5929 GATGCGATTTCC-CCTGCATGGAATG
191 GATGCGATTTCCGAC--CATGGAATG
* * * *
5954 TTCGAAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAATGAACTGAAGCTATAAAAGAA
1 TTCG-AAAATTACTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAA
6019 CTCGTAAAAGTTTG
65 CTCGTAAAAGTTTG
6033 TTATTTTAAG
Statistics
Matches: 2004, Mismatches: 428, Indels: 50
0.81 0.17 0.02
Matches are distributed among these distances:
215 23 0.01
216 1691 0.84
217 150 0.07
218 87 0.04
219 51 0.03
220 2 0.00
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.27
Consensus pattern (214 bp):
TTCGAAAATTACTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAAC
TCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAAA
TAAGTTTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGC
GATTTCCGACCATGGAATG
Found at i:5028 original size:864 final size:860
Alignment explanation
Indices: 3364--6032 Score: 3129
Period size: 864 Copynumber: 3.1 Consensus size: 860
3354 AAATATTCGA
* *
3364 AAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTATGGAACAGGATTTAAAAAAGAACTCGT
1 AAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGGATTT-AAAAAGAACTCGT
* * *
3429 AAAAGTTTGACAAGTTCGGATGTTCATCCAACAACCAAGAGGGAAACAATTCTCACGTAAATAAG
65 AAAAGTTTGACAAGTTCGGAAGTTCATCCAACAACAAAGAGAGAAACAATTCTCACGTAAATAAG
*
3494 TTTTTAATTCAAAGGCCGAAACTTGCTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACT
130 TTTTTAATTCAAAGGCCGAAACTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACT
** *
3559 TTTCGACCATGTAATGTTCGAAATATTGCTTGAAGGATTGGATCGTCTTGAATACTTTAAGGAAC
195 TCCCGACCATGTAATGCTCGAAATATTGCTTGAAGGATTGGATCGTCTTGAATACTTTAAGGAAC
* * * *
3624 CGAAGCTATAAAAGAAGTCGTAAAAGTCTGACAAGTTCGAAAGTTTATCCAACAAATAAGAGAGA
260 TGAAGCTATAAAAGAAGTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCCAACAAACAAGAGAGA
* * * *
3689 TATAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCTGAAACTTGTTTGCAAAATGACAAACTT
325 AACAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCGAAACTTGTTTACAAAATGACAAACTT
* * *
3754 TTTAGCCCAAATGGTGCGACTTCCCGAGCATGTAATGTTTGAAAAATTGCTCGAATGATTGGATC
390 TTTAGACCAAATGATGCGACTTCCCGAGCATGTAATGTTTGAAAAATTGCTCGAAGGATTGGATC
** *
3819 GACTTGAATACTACAAGAAACCAAAGTTATAAAAGAACTCGTAAAAGTTCAACAAGTTCGGATGT
455 GACTTGAATACTTTAAGAAACCGAAGTTATAAAAGAACTCGTAAAAGTTCAACAAGTTCGGATGT
3884 TCATCCAAGACCCAAGAGAGACACAATTCTTACGTAAATAAGTTTTTAATTCAAAGATCAAAACT
520 TCATCCAAGACCCAAGAGAGACACAATTCTTACGTAAATAAGTTTTTAATTCAAAGATCAAAACT
* * * *
3949 TGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGCATGGAATGTTCGGAA
585 TGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTAGGAAGAAATGTTCGGAA
* * *
4014 AATTACTCGAAGGAATGGATCATCCTGAACACTTTCATGAACTGAAGCTATAAAAGAACTCGTAA
650 AATTACTCGAAGGAATGGATCGTCCTGAACACTTTAATGAAC-GAAGTTATAAAAGAACTCGTAA
**** *
4079 AAGTTTGTTAATTTCAGAATTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
714 AAGTTCAACAAGTTC-GAATTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
4144 TCTAATTCAAAAATCAAAACTTGTTCACAAAATGAAAAACTATTTAAACCAAATGATGCGATTTC
778 TCTAATTCAAAAATCAAAACTTGTTCACAAAATGAAAAACTATTTAAACCAAATGATGCGATTTC
*** *
4209 CCTCTTATGGAATGCTCG
843 CCTAGGAAGGAATGCTCG
* * *
4227 AAAATTTACTCGAAGGAATGGATTGTCTTGAAAATTTTAAGGAACCGGATTTAAAAATGAACTCG
1 AAAA-TTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGGATTTAAAAA-GAACTCG
** *
4292 TAAAAGTTTGACAAGTTCGGAAGTTCATCCAACAATGAAGAGAGAAACAATTCTCATGTAAATAA
64 TAAAAGTTTGACAAGTTCGGAAGTTCATCCAACAACAAAGAGAGAAACAATTCTCACGTAAATAA
*
4357 GTTTTTAATTCAAAGGCCGAAACTTGTTTACAAAATGACAAACTTTTTAGGCCAAATGATGCGAC
129 GTTTTTAATTCAAAGGCCGAAACTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGAC
*
4422 TTCCCGACCATGTAATGCTCGAAATATTGCTTGAAGGATTGGATCATCTTGAATACTTTAAGGAA
194 TTCCCGACCATGTAATGCTCGAAATATTGCTTGAAGGATTGGATCGTCTTGAATACTTTAAGGAA
* * *
4487 CTGAAGCTATAAAAGAAGTCATAAAAGTTTGACAAGTTCGAAACTTCATCCAACAACCAAGAGAG
259 CTGAAGCTATAAAAGAAGTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCCAACAAACAAGAGAG
*
4552 AAACAATTCTCACGTATATAAGTTTTTAATTCAAAGGCCGAAACTTGTTTACAAAATGACAAACT
324 AAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCGAAACTTGTTTACAAAATGACAAACT
* *
4617 TTTTAGACCAAATGATGCGACTTCCCGAGCATGTAATGTTTGAAAAATTACTCGGAGGATTGGAT
389 TTTTAGACCAAATGATGCGACTTCCCGAGCATGTAATGTTTGAAAAATTGCTCGAAGGATTGGAT
4682 CGACTTGAATACTTTAAGAAACCGAAGTTATAAAAGAACTCGTAAAAGTTCAACAAGTTCGGATG
454 CGACTTGAATACTTTAAGAAACCGAAGTTATAAAAGAACTCGTAAAAGTTCAACAAGTTCGGATG
* *
4747 TTCATCCAAGACCCAAGAAAGACACAATTCTTATGTAAATAAGTTTTTAATTCAAAGATCAAAAC
519 TTCATCCAAGACCCAAGAGAGACACAATTCTTACGTAAATAAGTTTTTAATTCAAAGATCAAAAC
4812 TTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTAGGAAGAAATGTTCGGA
584 TTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTAGGAAGAAATGTTCGGA
*
4877 AAATTACTCGAAGGAATGGATCGTCCTGAACACTTTAATGAATCGAAGTTATAAAAGAAGTCGTA
649 AAATTACTCGAAGGAATGGATCGTCCTGAACACTTTAATGAA-CGAAGTTATAAAAGAACTCGTA
* ***********************************************
4942 AAACTTCAACAAGTTCGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
713 AAAGTTCAACAAGTTCG-AATTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGT
************* * *
5007 NNNNNNNNNNNNNATCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTT
777 TTCTAATTCAAAAATCAAAACTTGTTCACAAAATGAAAAACTATTTAAACCAAATGATGCGATTT
*
5072 CCCTAGGAAGGAATGTTCGG
842 CCCTAGGAAGGAATGCTC-G
* * * * * *
5092 AAAATTACTCGAAGGAATGGATCGTCCTGAACACTTTAATGAATCGAAGTTATAAAAGAAGTCGT
1 AAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGGATTTA-AAAAGAACTCGT
* ** * * * *
5157 AAAACTTCAACAAGTTCGGAAGTTCGTCCAAAAACAAAGAGAGACACAATTCTCACATAAATAAG
65 AAAAGTTTGACAAGTTCGGAAGTTCATCCAACAACAAAGAGAGAAACAATTCTCACGTAAATAAG
* * * * * * *
5222 TTTTTAATTGAAAGACCAAAACTTGTTTACAAAATGAAAAACTATTTAAACCAAATGATGCGATT
130 TTTTTAATTCAAAGGCCGAAACTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACT
* * * * * * * * *
5287 TCCCGAGCACGGAATGCTCGGGAA-ATTACTCGAAGGAATGGATCGTCTTGAAAATTTTAAGGAA
195 TCCCGACCATGTAATGCTC-GAAATATTGCTTGAAGGATTGGATCGTCTTGAATACTTTAAGGAA
* ** * **
5351 -TCGGATTTA-AAAATGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCCAACAATGAAGAG
259 CT-GAAGCTATAAAA-GAAGTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCCAACAAACAAGAG
*
5414 AGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAAGGCCGAAACTTGTTTACAAAATGACAAA
322 AGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCGAAACTTGTTTACAAAATGACAAA
* * * * *
5479 CTTTTTAGACCAAATGATGCGACTAT-TCGACCATGTAATGTTCGTAATATTGCTCGAAGGATTG
387 CTTTTTAGACCAAATGATGCGACT-TCCCGAGCATGTAATGTTTGAAAAATTGCTCGAAGGATTG
* * * * * ** **
5543 GGTCGTCTTGAATACTTTAAGGAACCGAAGCTATAAAAGAAGTCGTAAAAGTTTGACAAGTTCAA
451 GATCGACTTGAATACTTTAAGAAACCGAAGTTATAAAAGAACTCGTAAAAGTTCAACAAGTTCGG
* * * * * ** *
5608 AAGTTCATCCAACAACCAAGAGAGAAACAATTCTAACGTAAATAAGTTTTTAATTCAAAGGCCGA
516 ATGTTCATCCAAGACCCAAGAGAGACACAATTCTTACGTAAATAAGTTTTTAATTCAAAGATCAA
* * * * * * * *
5673 AACTTGTTTACAAAATGACAAACTTTTTAGTCAAAAATGGTGCGACTTCCCGA-GAATGCAATGT
581 AACTTGTTTACAAAATGAAAAACTATTTAGAC-CAAATGATGCGATTTCCCTAGGAA-GAAATGT
* * ** * * * * *
5737 TTGAAAAATTGTTCGAAGGATTGGATTGACTTGAATACTTTAA-GAACCCGAAGTTATAAAAGAA
644 TCGGAAAATTACTCGAAGGAATGGATCGTCCTGAACACTTTAATGAA--CGAAGTTATAAAAGAA
* * * * * *
5801 CTCGTAAAAGTTCAACAAGTTCGGATGTTCATCCAAGACCCAAGAGAGACACAATTCTTAAAGTT
707 CTCGTAAAAGTTCAACAAGTTCGAAT-TTCGTCCAAGAACCAAGAGAGAAACAATTC-TCACG-T
** * * * * * *
5866 CGATAAGTTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGGAAATCTATTTAGACCAAATGA
769 AAATAAGTTTCTAATTCAAAAATCAAAACTTGTTCACAAAATGAAAAACTATTTAAACCAAATGA
* * *
5931 TGCGATTTCCCCT-GCATGGAATGTTCG
834 TGCGATTT-CCCTAGGAAGGAATGCTCG
* * * **
5958 AAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAATGAACTGAAGCTATAAAAGAACTCG
1 -AAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGGATTTA-AAAAGAACTCG
6023 TAAAAGTTTG
64 TAAAAGTTTG
6033 TTATTTTAAG
Statistics
Matches: 1504, Mismatches: 284, Indels: 32
0.83 0.16 0.02
Matches are distributed among these distances:
863 15 0.01
864 1250 0.83
865 107 0.07
866 1 0.00
867 127 0.08
868 4 0.00
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.27
Consensus pattern (860 bp):
AAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGGATTTAAAAAGAACTCGTA
AAAGTTTGACAAGTTCGGAAGTTCATCCAACAACAAAGAGAGAAACAATTCTCACGTAAATAAGT
TTTTAATTCAAAGGCCGAAACTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACTT
CCCGACCATGTAATGCTCGAAATATTGCTTGAAGGATTGGATCGTCTTGAATACTTTAAGGAACT
GAAGCTATAAAAGAAGTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCCAACAAACAAGAGAGAA
ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCGAAACTTGTTTACAAAATGACAAACTTT
TTAGACCAAATGATGCGACTTCCCGAGCATGTAATGTTTGAAAAATTGCTCGAAGGATTGGATCG
ACTTGAATACTTTAAGAAACCGAAGTTATAAAAGAACTCGTAAAAGTTCAACAAGTTCGGATGTT
CATCCAAGACCCAAGAGAGACACAATTCTTACGTAAATAAGTTTTTAATTCAAAGATCAAAACTT
GTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCTAGGAAGAAATGTTCGGAAA
ATTACTCGAAGGAATGGATCGTCCTGAACACTTTAATGAACGAAGTTATAAAAGAACTCGTAAAA
GTTCAACAAGTTCGAATTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTCT
AATTCAAAAATCAAAACTTGTTCACAAAATGAAAAACTATTTAAACCAAATGATGCGATTTCCCT
AGGAAGGAATGCTCG
Found at i:6160 original size:134 final size:134
Alignment explanation
Indices: 5920--6166 Score: 343
Period size: 134 Copynumber: 1.8 Consensus size: 134
5910 AAATCTATTT
* * ** * *
5920 AGACCAAATGATGCGATTTCCCCTGCATGGAATGTTCGAAAAATTACTCGAAGGAATGGATCGTC
1 AGACCAAATGATGAGACTTCCCAAGCATGGAATGTTCGAAAAAGTACTCGAAGGAATGAATCGTC
* * * *
5985 TTGAACACTTTAATGAACTGAAGCTATAAAAGAACTCGTAAAAGTTTGTTATTTTAAGAATTTCG
66 TTGAACAATTTAAGGAACCGAAGATATAAAAGAACTCGTAAAAGTTTGTTATTTTAAGAATTTCG
6050 TCCA
131 TCCA
* * * *
6054 AGACCCAATGATGAGACTTCCCAAGCATGTAATGTTCG-AAGAGTAGCTCGAAGGATTGAATCGT
1 AGACCAAATGATGAGACTTCCCAAGCATGGAATGTTCGAAAAAGTA-CTCGAAGGAATGAATCGT
*
6118 CTTGAATAATTTAAGGAACCGAAGATATAAAAGAACTCGTAAAAGTTTG
65 CTTGAACAATTTAAGGAACCGAAGATATAAAAGAACTCGTAAAAGTTTG
6167 ACAAGTTCGA
Statistics
Matches: 97, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
133 5 0.05
134 92 0.95
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (134 bp):
AGACCAAATGATGAGACTTCCCAAGCATGGAATGTTCGAAAAAGTACTCGAAGGAATGAATCGTC
TTGAACAATTTAAGGAACCGAAGATATAAAAGAACTCGTAAAAGTTTGTTATTTTAAGAATTTCG
TCCA
Found at i:6184 original size:134 final size:134
Alignment explanation
Indices: 5920--6195 Score: 313
Period size: 134 Copynumber: 2.1 Consensus size: 134
5910 AAATCTATTT
* * * ** * *
5920 AGACCAAATGATGCGATTTCCCCTGCATGGAATGTTCGAAAAATTACTCGAAGGAATGGATCGTC
1 AGACCCAATGATGAGACTTCCCAAGCATGGAATGTTCGAAAAAGTACTCGAAGGAATGAATCGTC
* * * * ** * * *
5985 TTGAACACTTTAATGAACTGAAGCTATAAAAGAACTCGTAAAAGTTTGTTATTTTAAGAATTTCG
66 TTGAACAATTTAAGGAACCGAAGATATAAAAGAACTCGTAAAAGTTTGCAAGTTCAAGAAGTTCG
6050 TCCA
131 TCCA
* * *
6054 AGACCCAATGATGAGACTTCCCAAGCATGTAATGTTCG-AAGAGTAGCTCGAAGGATTGAATCGT
1 AGACCCAATGATGAGACTTCCCAAGCATGGAATGTTCGAAAAAGTA-CTCGAAGGAATGAATCGT
* *
6118 CTTGAATAATTTAAGGAACCGAAGATATAAAAGAACTCGTAAAAGTTTGACAAGTTCGA-AAGTT
65 CTTGAACAATTTAAGGAACCGAAGATATAAAAGAACTCGTAAAAGTTTG-CAAGTTCAAGAAGTT
*
6182 CGTCTA
129 CGTCCA
*
6188 AGAACCAA
1 AGACCCAA
6196 GAGAGAAACA
Statistics
Matches: 117, Mismatches: 23, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
133 5 0.04
134 108 0.92
135 4 0.03
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (134 bp):
AGACCCAATGATGAGACTTCCCAAGCATGGAATGTTCGAAAAAGTACTCGAAGGAATGAATCGTC
TTGAACAATTTAAGGAACCGAAGATATAAAAGAACTCGTAAAAGTTTGCAAGTTCAAGAAGTTCG
TCCA
Found at i:6368 original size:350 final size:351
Alignment explanation
Indices: 5749--6382 Score: 902
Period size: 350 Copynumber: 1.8 Consensus size: 351
5739 GAAAAATTGT
* * * *
5749 TCGAAGGATTGGATTGACTTGAATACTTTAAGAACCCGAAGTTATAAAAGAACTCGTAAAAGTTC
1 TCGAAGGATTGAATCGACTTGAATAATTTAAGAACCCGAAGATATAAAAGAACTCGTAAAAGTTC
* * * * * **
5814 AACAAGTTCGGATGTTCATCCAAGACCCAAGAGAGACACAATTCTTAAAGTTCGATAAGTTTTTA
66 AACAAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCAAAG-TAAATAAGTTTTTA
* *
5879 ATTCAAAGATCAAAACTTGTTTACAAAATGGAAATCTATTTAGACCAAATGATGCGATTTCCCCT
130 ATTCAAAGATCAAAACTTGTTTACAAAATGAAAATCTATTTAGACCAAATGATACGATTTCCCCT
* *
5944 GCATGGAATGTTCGAAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAATGAACTGAAGC
195 GCATGAAATGTTCGAAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAATGAACAGAAGC
* *
6009 TATAAAAGAACTCGTAAAAGTTTGTTATTTTAAGAATTTCGTCCAAGACCCAATGATGAGACTTC
260 TAAAAAAGAACACGTAAAAGTTTGTTATTTTAAGAATTTCGTCCAAGACCCAATGATGAGACTTC
6074 CCAAGCATGTAATGTTCGAAGAGTAGC
325 CCAAGCATGTAATGTTCGAAGAGTAGC
*
6101 TCGAAGGATTGAATCGTCTTGAATAATTTAAGGAA-CCGAAGATATAAAAGAACTCGTAAAAGTT
1 TCGAAGGATTGAATCGACTTGAATAATTTAA-GAACCCGAAGATATAAAAGAACTCGTAAAAGTT
** * * * *
6165 TGACAAGTTCGAAAGTTCGTCTAAGAACCAAGAGAGAAACAGTTCTCACA-TAAATAAG-TTTTA
65 CAACAAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCAAAGTAAATAAGTTTTTA
*
6228 ACTTCAAAGATCAAAATTTGTTTACAAAATGAAAAAT-TATTTAGACCAAATGATACGATTT-CC
130 A-TTCAAAGATCAAAACTTGTTTACAAAATG-AAAATCTATTTAGACCAAATGATACGATTTCCC
* *
6291 CTCGCATGAAATGTTCGAACAATTACTCGAAGGAATGGATCGTCTTTAACACTTT-ATGGAACAG
193 CT-GCATGAAATGTTCGAAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAT-GAACAG
* **
6355 GATTTAAAAAAGAACACGTAAAAGTTTG
256 AAGCTAAAAAAGAACACGTAAAAGTTTG
6383 ACAAGTTCGG
Statistics
Matches: 247, Mismatches: 30, Indels: 12
0.85 0.10 0.04
Matches are distributed among these distances:
349 12 0.05
350 134 0.54
351 4 0.02
352 94 0.38
353 3 0.01
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (351 bp):
TCGAAGGATTGAATCGACTTGAATAATTTAAGAACCCGAAGATATAAAAGAACTCGTAAAAGTTC
AACAAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCAAAGTAAATAAGTTTTTAA
TTCAAAGATCAAAACTTGTTTACAAAATGAAAATCTATTTAGACCAAATGATACGATTTCCCCTG
CATGAAATGTTCGAAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAATGAACAGAAGCT
AAAAAAGAACACGTAAAAGTTTGTTATTTTAAGAATTTCGTCCAAGACCCAATGATGAGACTTCC
CAAGCATGTAATGTTCGAAGAGTAGC
Done.