Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015352.1 Corchorus olitorius cultivar O-4 contig15385, 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: 37532
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:1038 original size:42 final size:43
Alignment explanation
Indices: 992--1081 Score: 128
Period size: 45 Copynumber: 2.1 Consensus size: 43
982 CATTATCTTA
*
992 ATTCTA-CTCCATCTCTAGGTAATTCATAAAAAAAAAGCTAAT
1 ATTCTACCTCCATCTCTAGATAATTCATAAAAAAAAAGCTAAT
* *
1034 ATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAGCTAAT
1 ATTCTA--CCTCCATCTCTAGATAATTCATAAAAAAAAAGCTAAT
1079 ATT
1 ATT
1082 AATTGTTGCT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
42 6 0.14
45 36 0.86
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.33
Consensus pattern (43 bp):
ATTCTACCTCCATCTCTAGATAATTCATAAAAAAAAAGCTAAT
Found at i:2235 original size:2 final size:2
Alignment explanation
Indices: 2228--2254 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2218 TCTTATGAGA
2228 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2255 ATTAATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4813 original size:17 final size:15
Alignment explanation
Indices: 4787--4833 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 15
4777 AACATTGATA
4787 TTTTTTTCTTATTCTT
1 TTTTTTTCTT-TTCTT
4803 TTTTCTTTCTTTTCTT
1 TTTT-TTTCTTTTCTT
4819 TTTGTTTTCGTTTTC
1 TTT-TTTTC-TTTTC
4834 CTTTCCTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 16 0.57
17 12 0.43
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.79
Consensus pattern (15 bp):
TTTTTTTCTTTTCTT
Found at i:6170 original size:2 final size:2
Alignment explanation
Indices: 6163--6200 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6153 TGCACCATAC
6163 AT AT AT AT AT AT 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 AT AT AT AT AT AT
6201 TTACCAGCAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20549 original size:36 final size:36
Alignment explanation
Indices: 20509--20592 Score: 123
Period size: 36 Copynumber: 2.3 Consensus size: 36
20499 AACCTCCAAC
*
20509 TCCAAGCCCTCCAAAAGTGGCACCACCTCATAATGT
1 TCCAAGCCCTCCAAAAGTGGCACCACCCCATAATGT
* *
20545 TCCAAGCCCTCCCAAAGTTGCACCACCCCATAATGT
1 TCCAAGCCCTCCAAAAGTGGCACCACCCCATAATGT
* *
20581 ACCAACCCCTCC
1 TCCAAGCCCTCC
20593 TAATGCACCA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.29, C:0.43, G:0.11, T:0.18
Consensus pattern (36 bp):
TCCAAGCCCTCCAAAAGTGGCACCACCCCATAATGT
Found at i:20686 original size:66 final size:66
Alignment explanation
Indices: 20616--20755 Score: 237
Period size: 66 Copynumber: 2.1 Consensus size: 66
20606 TTCCCCAAAG
* *
20616 CACCACCATCTCCCACCACCCCTTCCCCTCCAAAACTT-CCTCCACCGGCGCCACGTAATCCCAT
1 CACCACCATCTCCCACCACCCCTTCCCCTCCAAAA-TTACCTCCACCGGCACCACATAATCCCAT
20680 TA
65 TA
20682 CACCACCATCTCCCACCACCCCTTCCCCTCCAAAATTACCTCCACCGGCACCACATAATCCCATT
1 CACCACCATCTCCCACCACCCCTTCCCCTCCAAAATTACCTCCACCGGCACCACATAATCCCATT
*
20747 G
66 A
20748 CACCACCA
1 CACCACCA
20756 CAACCACATC
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
65 2 0.03
66 68 0.97
ACGTcount: A:0.25, C:0.53, G:0.05, T:0.17
Consensus pattern (66 bp):
CACCACCATCTCCCACCACCCCTTCCCCTCCAAAATTACCTCCACCGGCACCACATAATCCCATT
A
Found at i:28054 original size:332 final size:330
Alignment explanation
Indices: 25698--31034 Score: 4163
Period size: 332 Copynumber: 16.3 Consensus size: 330
25688 CGAATTTTTG
* * * *
25698 TTTCATATTTTTTTGAATTAATTTCTAATTAAATCGAAACAAAATTTAAATACTCGTAAAAACAA
1 TTTCATATTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
* * * **
25763 ATTCTTAAATACAATGTGGCTGATATTTGATTAGATGAATAAAGATATTTCAAGGAGTCTCGGTC
66 ATTCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTAG-C
** * * * ** **
25828 -CCAAAAATCATGCAAAACAAAGCAGTGGCCCCCGAAACGCGTTCTTAGTAAAAAAAAAGTGATG
130 GCCAAAAATCATGCAAAACTGAGCCG-GGGCCCCGAAACGCGTTTTTAG-CCAAAAACCGTGATG
* * * * *
25892 ATTAGTACACAATTTCGGC--------T--AAAAACTGACCCGAAAAGTTTTT-CTCAATTTTTT
193 GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTG
* ** * * * * * *
25946 ACCACTATACTGA-GAAAAATATATAATTCAACGCCAAAAAGATTGGCAGGCTTTTCAAGCTTAT
258 GCCAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATT-GAAGGTTTTTCACGCTTTT
26010 AATATCGTT
322 AATATCGTT
*** * ** **
26019 TTTCCAT-TTTTCCCGAATTAATTTCTAATAAAATATAAACAAGATTCATCTGC-CTGTAAAAAC
1 TTT-CATATTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTC-GTAAAAAC
* * * * * * * *
26082 AAATCCTTATATCCAATGTGCCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTTTTTG
64 AAATTCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTAG
* * * ** *
26147 CACCAAAAATCATGCAAAATTGAGTCGGGGTTCCG-AACACGTTTTTAGCCAAAAACCGTGAT-G
129 CGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGG
* * * **
26210 --AGTACATGATTTCGGCTAAAATTTTGCAAAAATTAACCCGAAAAGTTTTTCCTCAATTTTTTT
194 TTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGG
* * * * *
26273 CCATAATACTCA-AAAAAA-ATATAATTTAACGCCATAAAAG-TTAAAGCATTTTTCACGCTTCT
259 CCAAAATACTCATAAAAAATATATAATTCAACGCCA-AAAAGATTGAAG-GTTTTTCACGCTTTT
*
26335 ACTATCGTT
322 AATATCGTT
* * *
26344 TTTCATATTTTTTTTCCCGAATTTATTTCTAATTAAATAGAAACAAGATTTAGATGCTCGTAAAA
1 TTTCATA-TTTTTTT---GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
* *
26409 ACAAATCCTTAAATTCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTT
62 ACAAATTCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTC-T
* * * * * *
26474 TA-TGTCAAAAACCATGCAAAACTGAGTCGAGGCCCTGAAACGCGTTTTTAGCCAAAAACCGTGA
126 TAGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGA
* * * *
26538 TGGTTAGTATACGATTTCGGC--------T--AAAAATTGATCCTAAAAATTTTTTCTCAATTTT
191 TGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTT
* * * *
26593 TTGCCAAAATACTCATAAAAAATATATAATTCAATGTCAAAAAGATTGAAGAATTTTTCACG---
256 TGGCCAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAG-GTTTTTCACGCTT
26655 -----ATCGTT
320 TTAATATCGTT
* * *
26661 TTTCCAT-TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAAATTCAGATGCATGCTTGGAA
1 TTT-CATATTTTTT-TGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGC-T-C---GTA
* * * * * * *
26725 AAAACAAA-TCATTATA-TCGAATGTGACTGGGATTTGATTCGATAAATATTGGTATTTCAAGGA
59 AAAACAAATTC-TTAAATTC-AATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGA
* * * ** *
26788 GTCTTTA-CGCCAAAAATCATGCAAAACTGAACAGGGTCATCGGAACGCGTTTTTAGCCAAAAAC
122 GTC-TTAGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCAAAAAC
* * * **
26852 CGTGAT-G--AGTAAACGATTTTGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTATTCA
186 CGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCA
* * * *
26914 ATTCTTT-GCCACAATACTCAGAAAAAATATATAATTCAACG-CAAAAAAATTG-ATGTGTTTTC
251 ATT-TTTGGCCAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGT-TTTTC
*
26976 ACG-TTTCTAATATTGTT
314 ACGCTTT-TAATATCGTT
** * * *
26993 TTTCAT-TTTTTTCCTGTCTTTATTTATAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAAC
1 TTTCATATTTTTT--TGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC
* * * * * *
27057 AAATCCTTAAA-TCAATTGTGGCTTACATTTGGTTAGATGAATATTGATATTTCAAGGAGTCTTT
64 AAATTCTTAAATTCAA-TGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTA
** * ** *
27121 TTGCCAAAAATCATGCACAACTGAGCTAGGGCCCCGAAACGCGTTTTTAGCCAAAAACCATGATG
128 GCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATG
* * * ** * *
27186 ATTTAGGTACACAATTTCGGCT--AA------AAACA--GACTTGAAAAGTTGTAT-CTCAATTT
193 -GTTA-GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATT-TTTCCTCAA-TT
* * * * * *
27240 TTTTGCCATAATACTCAAAAAAAACTATATAATTCAACGGCAAAAA-ATTGATGGGTTTTCACGC
254 TTTGGCCAAAATACTCATAAAAAA-TATATAATTCAACGCCAAAAAGATTGAAGGTTTTTCACGC
* *
27304 CTCTAATATCGTT
318 TTTTAATATCGTT
* * * * * * * *
27317 TTTCCTTTTTTTTTTCAAATTAAGTTCTAATTAAATCAAAATAAGATTTAGATCCTCGTAAAAAC
1 TTT-CATATTTTTTT-GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC
* * * * * * *
27382 AAATCCTTATATGCAATGTGGCTGAGATTTGGTT-GATGAATAAAGATATTTCAGGGAGTCTTTG
64 AAATTCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTAG
* * * * * *
27446 CACCAAAAATCATGCAAAATTGAGTCGGGGCTCCGGAACACGTTTTTAGCCAAAAACCGTGATGG
129 CGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGG
* * * * *
27511 TTAGTACACGATTTAGACTAAAGTTTTGCAAAAACTGACTCGAAAAATTTTTTCCTCAATTTTTT
194 TTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAA-TTTTTCCTCAA-TTTTT
* * * * * * * * *
27576 GG-CACAATACTC--AAAATATATATGATTAAAAGCCAAGAAGATTGGAGGACTCTTCACGCTTT
257 GGCCAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGG-TTTTTCACGCTTT
27638 TAATATCGTT
321 TAATATCGTT
* * * * * *
27648 TTTCATATTTTTCTGAATTAATTTCTAGTTAAATCGAAATAAGATTCAGATACTCGAAAAAACAT
1 TTTCATATTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
* * * *
27713 ATCCTTAAATTCAATGTGCCTGAGATTTGATTAGATGAATATAGATATTCCATGGAGTCTTAGCG
66 ATTCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTAGCG
* * ** * * * *
27778 TCAAAAATAAAACAAAACTAAGCCGGGGTCTCGAAACGCATTTTTAGCCAAAAACCGTGATGGTT
131 CCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTT
*
27843 AGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCGTCAATTTTTGGA
196 AGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCC-TCAATTTTTGGC
* * * * * * * **
27908 TAAAATAGTCATAAAATATATATAATTTAATGCTAAGAAGATTGGAAAATTTTTCACGCTTTTAA
260 CAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATT-GAAGGTTTTTCACGCTTTTAA
*
27973 TATCATT
324 TATCGTT
* *
27980 TTTCATATTTTTTTAAATTAATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
1 TTTCATATTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
* * * * * * *
28045 ATTCTTAAATGCAATGTAGTTGAGATTTGGTTAGATGAATATGGATATCTCAAAGAGTCTTGAG-
66 ATTCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTT-AGC
* * * * ** *
28109 GCCAAAAATCATGCAAAACTTAGCCGGGGCCTCGGAACGTGTTTTTAGTAAAAAACCGTGATGAT
130 GCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGT
* * * *
28174 TATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTCG-AAAGTTATTTCCTCAATTTTTAG
195 TAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATT-TTTCCTCAATTTTTGG
* * * * * *
28238 CCACAATACTCATAAAAATTATATAATTCAACGCCAATAAGATTGAAGGGCTTTTCATGCTTCTA
259 CCAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAA-GGTTTTTCACGCTTTTA
*
28303 ATATCATT
323 ATATCGTT
* * * * ***
28311 TTTCCTATTATTTTCCGAATTAATTTCTAATTAAATCGAAACATA-ATTTAGATGCTTGT-TTTA
1 TTTCATATT-TTTT-TGAATTAATTTCTAATTAAATCGAAACA-AGATTCAGATGCTCGTAAAAA
* * * * * * **
28374 CAAATCCTTAAATCCATTGTGGATGAGATTTGGTTAGATTAATATAGATATTTCAAGGAGTCTCG
63 CAAATTCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTA
* * * * *
28439 GCGCAAAAAATCAAGCAACATTGAACCGGGGCCCC-ATAACGCGTTTTTAG-CAAAAA-----A-
128 GCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGA-AACGCGTTTTTAGCCAAAAACCGTGAT
* * * ** * *
28496 --CT-GT----GATTTCGAC-AAATATTTTGCAAAAAATGACTAGAAATAGTTTTCCTCAATTTT
192 GGTTAGTACACGATTTCGGCTAAA-ATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTT
** * * * ** * *
28553 TATCTAAAATACTCATAAAATATTTATAATTCAATTCAAAAAATATT-ACAGTGTTTTTCA-GCT
256 TGGCCAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGA-AG-GTTTTTCACGCT
28616 TTTAATATCGTT
319 TTTAATATCGTT
* * * * * *
28628 TTTAATATTTTTCTGAATTAATTTCTAATCAAATTGAAACAAGATTCAAATGCTCGTAAAAAGAA
1 TTTCATATTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
* * *
28693 A-TCTTTAAATGCAATGTGGTTGAGATTTGATT--A-G---AT-GATATTTCAAGGAGTC-TCGA
66 ATTC-TTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTAG-
* * * * * * * *
28749 CGACAAAAATCATGCAAAATTGAGCTGAGGCCTC-ATAACGTGTTTTTAGCAAAAAAAAAAACTG
129 CGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGA-AACGCGTTTTTAGC-----CAAAAACCG
* * * * * *
28813 TGATGGTTAGTACATGATTTCGCCTAAAATTTTGCAAAATACTGACCAGAATATTTTTTCCTCAA
188 TGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAA-ATTGACCCGAAAAATTTTTCCTCAA
* * * *
28878 TTTTTGGCTAAAATACTCATGAAATATATATATATATATAATTTAACGCAAAAAAGATTGGAGGA
252 TTTTTGGCCAAAATACTCAT---A-A-A-A-A-ATATATAATTCAACGCCAAAAAGATTGAAGG-
* * *
28943 CTTTTCACGCTTTTCATATCATT
308 TTTTTCACGCTTTTAATATCGTT
* * *
28966 TTTTATATTTTTTTGAATTAATTTCTAATTAAATCGAAATAAGATTTAGATGCTCGTAAAAACAA
1 TTTCATATTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
* * * * * *
29031 ATTCTTAAATGCATTGTGACTGAGATTTGATTAGATGAATATGGATATCTCAAGTAGTCTTAGCG
66 ATTCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTAGCG
* * * * * * *
29096 CCAAAAATCATGCAAAACTGACCCAGGGCCCTGGAGCGCATTTTTAGCCAAAAACCGTGATGATT
131 CCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTT
* * * * * * * *
29161 ATTACACGATTTCGGCTAACATTTTGCAAAAATTGAGCGGAAAGATATTTCCTCAATTTTTTGCT
196 AGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCC
* * * * * * * * *
29226 AAATTA-TGATGAAAAAAAATATAATTCTACACCAAAAATATTGAAGGGTTTTTTACTCTTCTAA
261 AAAATACTCAT-AAAAAATATATAATTCAACGCCAAAAAGATTGAA-GGTTTTTCACGCTTTTAA
29290 TATCGTT
324 TATCGTT
* ** ** *
29297 TTTCCTACTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTTTGATACTCGTAAAAACA
1 TTTCATA-TTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACA
* * * * *
29362 AATCCTTAAATCCAATGTGGCCGAGATTTGATTAGATGAATATAGATAGTTT-AAGGAGTTTTGG
65 AATTCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATA-TTTCAAGGAGTCTTAG
* * * ** * * * **** *
29426 CGCCAAAAACCATGCAATACTGATCCGGGGTACCGGAACACATTTTTAGCCAAAAA-AAAAATCG
129 CGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGG
* * * * * * *
29490 TGATGTTACACGATTTCAGCTAATATTTTACAAAAAATGACTCGAAATATTTTTCCTCAATTTTT
194 TTA-G-TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTT
* * * * * *
29555 AGCCACAATAATCATAAGAAATATATAATTTAACGCCAAAAAGTTTGAAGGGTTTTTCACG-TTT
257 GGCCAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAA-GGTTTTTCACGCTTT
*
29619 CTAATACCGTT
321 -TAATATCGTT
* * *
29630 TTTCCTATATTTTTTTTGAATTAATTTCTAATTAAAACGAAACATGATTCGGATGCT--T----A
1 TTT-C-ATA-TTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
* * * *
29689 -TAA-----AAA--CAA--TGGCTG-GAATTTGGTTAGATGAATATAGATAATTCAAGGAGTCTC
63 CAAATTCTTAAATTCAATGTGGCTGAG-ATTTGATTAGATGAATATAGATATTTCAAGGAGTCTT
* * * * *** *
29743 GGTGCCAAAAATTATTCAAAACTGA-AATGGGCCCCGAAACGCGTTTTTTTGCCAAAAACCGTGA
127 AGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCG-TTTTTAGCCAAAAACCGTGA
* * * * * ***
29807 TGATTATTATACGATTTTGGCTAAAATTTTGCAAAAATTGACCCGAAAGATAAATCCTCAATTTT
191 TGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTT
** * * * *
29872 CAGCCATAATACTCATAAAAAATATATAATTCAACGTCAAAAATATTGAAGGTCTTTTGACGCTT
256 TGGCCAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGT-TTTTCACGCTT
29937 TT-A-A-----
320 TTAATATCGTT
* *
29941 --T-AT-TTTTTTTGAATTAATTTCTAAATAAATCGAAACATGATTCAGATGCTCGT-AAAA-AA
1 TTTCATATTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
* * * * * * **
30000 A-TATTAAATTCAATGTGGCTAAGATTTTATTAGATGAATATAGTTATTTCAAGGTGTGTCGGCG
66 ATTCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTAGCG
* * * ** *
30064 CCAAAAATCTTGTAAAACTGAGCTGGTACCCCGAAACGCGTTTTTAGCCAAAAATCGTGATGGTT
131 CCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTT
* * * * *
30129 AGTACACGATTTTGGCTAAAATTTTGCAAAAAAATGACTCGAAAATTTTTTCCTCAATTTTTGGA
196 AGTACACGATTTCGGCTAAAATTTTGC-AAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGC
* * * * * *
30194 TAAAATACTCATAAAATATATAT-AGTCTAACGGCAAAAAGATTGGAGGACTTTTCACGCTTTTA
260 CAAAATACTCATAAAAAATATATAATTC-AACGCCAAAAAGATTGAAGG-TTTTTCACGCTTTTA
* *
30258 TTATTGTT
323 ATATCGTT
* * * * *
30266 TTTCATATTTTTCTGTATTAATTTCCAATTAAATCGAAACAAGATTTAGATGCTTGTAAAAACAA
1 TTTCATATTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
* * * *
30331 ATTTTTATATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTT-GAC
66 ATTCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTAG-C
* * * ** * * * * * *
30395 GTCAAAAATGATGCAAAACTCAGCTTGGGCCCTAGGAA-G-TTTTTTATCCAAAATCTGTGATGG
130 GCCAAAAATCATGCAAAACTGAGCCGGGGCCC-CGAAACGCGTTTTTAGCCAAAAACCGTGATGG
* * * * * *
30458 TTAATACACGATTTCAGCTAAAATTTTGTAAAAAATGACCCGAAAGATATTTCCTCAATTTTTGG
194 TTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGG
** * * * *
30523 GTAAAATACTCATAAAAAATATATAACTCAACGGCAAAAAGATTGAAGGGCTTTTGACG-TTTCT
259 CCAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAA-GGTTTTTCACGCTTT-T
*
30587 AATATCATT
322 AATATCGTT
* *** * *
30596 TTTCCA-AATTTTCCAAATTAATTTCCAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACA
1 TTT-CATATTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACA
* * * * *
30660 AATTCTTAAATT-TATGGTGGGTGAGATATGATTAGATGAATATAGATATTTCAAGTAGTC-TCG
65 AATTCTTAAATTCAAT-GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTAG
* * ** * * * * *
30723 AAGCCAGAAATCAAACAAAATTAAGCCAGGTCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATG
129 -CGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGAT-
** * * *
30788 GTTTGTTAGTACACGA-TTCAACTAAAATTTTTCAAAAATTGACACGAAAGATTTCTT-CTCAAT
192 G---GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTT-TTCCTCAAT
** * *
30851 TTTTGGCTTAAATACTCAT-AAAAATATATAATTCAACGCTAAAAAGATTGGAGGGCTTTTT-AC
253 TTTTGGCCAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATT-GAAGG-TTTTTCAC
* * *
30914 GTTTTTAATATCCTA
316 GCTTTTAATATCGTT
* * * *
30929 TTTCTTATTTTTTTTGTAAATTAATTTCTAATTAAAAT-GAAATAAGATTTAGATGCTCGTAATA
1 TTTCATA-TTTTTTTG--AATTAATTTCTAATT-AAATCGAAACAAGATTCAGATGCTCGTAAAA
* * **
30993 ACAAATTCTTAAATCCAATGTTGCTGAGATTTGGGTAGATGA
62 ACAAATTCTTAAATTCAATGTGGCTGAGATTTGATTAGATGA
31035 TGTAAAGTAT
Statistics
Matches: 4020, Mismatches: 768, Indels: 441
0.77 0.15 0.08
Matches are distributed among these distances:
304 44 0.01
306 3 0.00
308 1 0.00
309 60 0.01
310 2 0.00
313 3 0.00
314 37 0.01
315 60 0.01
316 53 0.01
317 144 0.04
318 300 0.07
319 194 0.05
320 13 0.00
321 123 0.03
322 34 0.01
323 73 0.02
324 151 0.04
325 173 0.04
326 105 0.03
327 110 0.03
328 24 0.01
329 318 0.08
330 406 0.10
331 238 0.06
332 656 0.16
333 226 0.06
334 75 0.02
335 57 0.01
336 72 0.02
337 35 0.01
338 99 0.02
339 33 0.01
340 42 0.01
341 1 0.00
344 2 0.00
345 51 0.01
346 2 0.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (330 bp):
TTTCATATTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
ATTCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTAGCG
CCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTT
AGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCC
AAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGTTTTTCACGCTTTTAATA
TCGTT
Found at i:28155 original size:986 final size:980
Alignment explanation
Indices: 25701--31034 Score: 4126
Period size: 986 Copynumber: 5.4 Consensus size: 980
25691 ATTTTTGTTT
* * * * * *
25701 CATATTTTTTTGAATTAATTTCTAATTAAATCGAAACAAAATTTAAATACTCGTAAAAACAAATT
1 CATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGAAAAAACAAATC
* * * **
25766 CTTAAATACAATGTGGCTGATATTTGATTAGATGAATAAAGATATTTCAAGGAGTCTCGGTC-CC
66 CTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATA-TTCAAGGAGTCTTAG-CGCC
* * * ** * * ** ** *
25830 AAAAATCATGCAAAACAAAGCAGTGGCCCCCGAAACGCGTTCTTAGTAAAAAAAAAGTGATGATT
129 AAAAATCATACAAAACTAAGCCG-GGGTCTCGAAACGCGTTTTTAG-CCAAAAACCGTGATGGTT
* * * ** *
25895 AGTACACAATTTCGGC--------T--AAAAACTGACCCGAAAAGTTTTT-CTCAATTTTTTACC
192 AGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCT
** * * * * ** * *
25949 ACTATACTGA-GAAAAATATATAATTCAACGCCAAAAAGATTGGCAGGCTTTTCAAGCTTATAAT
257 AAAATACTCATAAAAAATATATAATTCAACGCTAAAAAGATTGGAAGATTTTTCACGCTTTTAAT
* *** * ** **
26013 ATCGTTTTTCCATTTTTCCCGAATTAATTTCTAATAAAATATAAACAAGATTCATCTGC-CTGTA
322 ATCATTTTT--ATTTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTC-GTA
* * * * * * * *
26077 AAAACAAATCCTTATATCCAATGTGCCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGT
384 AAAACAAATTCTTAAATGCAATGTGGCTGAGATTTGGTTAGATGAATATGGATATCTCAAAGAGT
** * * * * ** *
26142 -TTTTGCACCAAAAATCATGCAAAATTGAGTCGGGGTTCCG-AACACGTTTTTAGCCAAAAACCG
449 CTTGAGCGCCAAAAATCATGCAAAACTGAGCCAGGGCCCCGAAACGCGTTTTTAGCCAAAAACCG
* * *
26205 TGATG---AGTACATGATTTCGGCTAAAATTTTGCAAAAATTAACCCGAAAAGTT-TTTCCTCAA
514 TGATGATTAGTACACGATTTCGGCTAAAA----ACAAAAATTGA---G-AAAGTTATTTCCTCAA
* * * * **
26266 TTTTTTTCCATAATACTC-AAAAAAA-ATATAATTTAACGCCATAAAAGTTAAAGCATTTTTCAC
571 TTTTTTGCCATAATACTCAAAAAAAATATATAATTCAACGCCA-AAAAATTGAAG-GGTTTTCAC
* * *
26329 GCTTCTACTATCGTTTTTCATATTTTTTTTCCCGAATTTATTTCTAATTAAAT-AGAAACAAGAT
634 GCTTCTAATATCGTTTTTCCT-TTTTTTTT-CCGAATTAATTTCTAATTAAATCA-AAACAAGAT
*
26393 TTAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGCTGAGATTTGGTTAGATGAATATAGA
696 TTAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGA
** * * * * *
26458 TATTTCAAGGAGTCTTTATGTCAAAAACCATGCAAAACTGAGTCGAGGCCCTGAAACGCGTTTTT
761 TATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACTGAGTCGGGGCCC-GGAACACGTTTTT
* * ** *
26523 AGCCAAAAACCGTGATGGTTAGTATACGATTTCGGCTAAAAATTG------AT--C-CTAAAAAT
825 AGCCAAAAACCGTGATGGTTAGTACACGATTT-AGCTAAATTTTGCAAAAAATGACTCGAAAAAT
* * *
26579 TTTTTCTCAATTTTTTGCCAAAATACTCATAAAAAATATATAATTCAATGTCAAAAAGATTGAAG
889 TTTTCCTCAATTTTTTGCCAAAATACTCA-AAAAAATATATAATTCAACGCCAAAAAGATTGAAG
*
26644 AATTTTTCACG-------ATCGTTTTTC
953 GATTTTTCACGTTTTAATATCGTTTTTC
* * * *
26665 CATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAAATTCAGATGCATGCTTGGAAAAAAC
1 CATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGAT--A--C-TCGAAAAAAC
* * * * * * * *
26730 AAATCATTATA-TCGAATGTGACTGGGATTTGATTCGATAAATATTGGTATTTCAAGGAGTCTTT
61 AAATCCTTAAATTC-AATGTGGCTGAGATTTGATTAGATGAATATAGATA-TTCAAGGAGTC-TT
* * *
26794 A-CGCCAAAAATCATGCAAAACTGAA--CAGGGTCATCGGAACGCGTTTTTAGCCAAAAACCGTG
123 AGCGCCAAAAATCATACAAAACT-AAGCCGGGGTC-TCGAAACGCGTTTTTAGCCAAAAACCGTG
* * * **
26856 AT-G--AGTAAACGATTTTGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTATTCAATTC
186 ATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATT-
* * * * *
26918 TTT-GCCACAATACTCAGAAAAAATATATAATTCAACGC-AAAAAAATT-GATG-TGTTTTCACG
250 TTTGGCTAAAATACTCATAAAAAATATATAATTCAACGCTAAAAAGATTGGAAGAT-TTTTCACG
** ** * * *
26979 -TTTCTAATATTGTTTTTCATTTTTTTCCTGTCTTTATTTATAATTAAATCGAAACAAGATTCAA
314 CTTT-TAATATCATTTTT-ATTTTTTT--TGAATTAATTTCTAATTAAATCGAAACAAGATTCAG
* * * *
27043 ATGCTCGTAAAAACAAATCCTTAAAT-CAATTGTGGCTTACATTTGGTTAGATGAATATTGATAT
375 ATGCTCGTAAAAACAAATTCTTAAATGCAA-TGTGGCTGAGATTTGGTTAGATGAATATGGATAT
* * *** * *
27107 TTCAAGGAGTCTT-TTTGCCAAAAATCATGCACAACTGAGCTAGGGCCCCGAAACGCGTTTTTAG
439 CTCAAAGAGTCTTGAGCGCCAAAAATCATGCAAAACTGAGCCAGGGCCCCGAAACGCGTTTTTAG
* * * * * *
27171 CCAAAAACCATGATGATTTAGGTACACAATTTCGGCTAAAAAC-AGACTTGA-AAAGTTGTAT-C
504 CCAAAAACCGTGATGA-TTA-GTACACGATTTCGGCTAAAAACAAAAATTGAGAAAGTTATTTCC
* *
27233 TCAATTTTTTTGCCATAATACTCAAAAAAAACTATATAATTCAACGGCAAAAAATTGATGGGTTT
567 TCAA-TTTTTTGCCATAATACTCAAAAAAAA-TATATAATTCAACGCCAAAAAATTGAAGGGTTT
* * * * *
27298 TCACGCCTCTAATATCGTTTTTCCTTTTTTTTTTCAAATTAAGTTCTAATTAAATCAAAATAAGA
630 TCACGCTTCTAATATCGTTTTTCCTTTTTTTTTCCGAATTAATTTCTAATTAAATCAAAACAAGA
* * * *
27363 TTTAGATCCTCGTAAAAACAAATCCTTATATGCAATGTGGCTGAGATTTGGTT-GATGAATAAAG
695 TTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAG
* * *
27427 ATATTTCAGGGAGTCTTTGCACCAAAAATCATGCAAAATTGAGTCGGGGCTCCGGAACACGTTTT
760 ATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACTGAGTCGGGGC-CCGGAACACGTTTT
*
27492 TAGCCAAAAACCGTGATGGTTAGTACACGATTTAGACTAAAGTTTTGCAAAAACTGACTCGAAAA
824 TAGCCAAAAACCGTGATGGTTAGTACACGATTTAG-CTAAA-TTTTGCAAAAAATGACTCGAAAA
* * * * * * * *
27557 ATTTTTTCCTCAATTTTTTGGCACAATACTC-AAAATATATATGATTAAAAGCCAAGAAGATTGG
887 A-TTTTTCCTCAATTTTTTGCCAAAATACTCAAAAAAATATATAATTCAACGCCAAAAAGATTGA
* *
27621 AGGACTCTTCACGCTTTTAATATCGTTTTT-
951 AGGATTTTTCACG-TTTTAATATCGTTTTTC
* * *
27651 CATATTTTTCTGAATTAATTTCTAGTTAAATCGAAATAAGATTCAGATACTCGAAAAAACATATC
1 CATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGAAAAAACAAATC
* * *
27716 CTTAAATTCAATGTGCCTGAGATTTGATTAGATGAATATAGATATTCCATGGAGTCTTAGCGTCA
66 CTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATT-CAAGGAGTCTTAGCGCCA
* * *
27781 AAAATAAAACAAAACTAAGCCGGGGTCTCGAAACGCATTTTTAGCCAAAAACCGTGATGGTTAGT
130 AAAATCATACAAAACTAAGCCGGGGTCTCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGT
*
27846 ACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCGTCAATTTTTGGATAA
195 ACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCC-TCAATTTTTGGCTAA
* * * * * *
27911 AATAGTCATAAAATATATATAATTTAATGCTAAGAAGATTGGAAAATTTTTCACGCTTTTAATAT
259 AATACTCATAAAAAATATATAATTCAACGCTAAAAAGATTGGAAGATTTTTCACGCTTTTAATAT
* *
27976 CATTTTTCATATTTTTTTAAATTAATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
324 CATTTTT-AT-TTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
* *
28041 ACAAATTCTTAAATGCAATGTAGTTGAGATTTGGTTAGATGAATATGGATATCTCAAAGAGTCTT
387 ACAAATTCTTAAATGCAATGTGGCTGAGATTTGGTTAGATGAATATGGATATCTCAAAGAGTCTT
* * * * * **
28106 GAG-GCCAAAAATCATGCAAAACTTAGCCGGGGCCTCGGAACGTGTTTTTAGTAAAAAACCGTGA
452 GAGCGCCAAAAATCATGCAAAACTGAGCCAGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGA
* *
28170 TGATTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTCGAAAGTTATTTCCTCAATTTT
517 TGATTAGTACACGATTTCGGCTAAAA----ACAAAAATTGA---GAAAGTTATTTCCTCAATTTT
* * * * * *
28235 TAGCCACAATACTCATAAAAATTATATAATTCAACGCCAATAAGATTGAAGGGCTTTTCATGCTT
575 TTGCCATAATACTCAAAAAAAATATATAATTCAACGCCAA-AAAATTGAAGGG-TTTTCACGCTT
* * * *
28300 CTAATATCATTTTTCCTATTATTTTCCGAATTAATTTCTAATTAAATCGAAACATA-ATTTAGAT
638 CTAATATCGTTTTTCCTTTTTTTTTCCGAATTAATTTCTAATTAAATCAAAACA-AGATTTAGAT
* *** * * *
28364 GCTTGT-TTTACAAATCCTTAAATCCATTGTGGATGAGATTTGGTTAGATTAATATAGATATTTC
702 GCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTC
** * * * * ** ** * *
28428 AAGGAGTCTCGGCGCAAAAAATCAAGCAACATTGAACCGGGGCCCCATAACGCGTTTTTAGCAAA
767 AAGGAGTCTTTGCGCCAAAAATCATGCAAAACTGAGTCGGGG-CCCGGAACACGTTTTTAGCCAA
* * * * *
28493 AAACTGTGAT--TTCG-ACA--A---A--T--ATTTTGCAAAAAATGACTAGAAATAGTTTTCCT
831 AAACCGTGATGGTTAGTACACGATTTAGCTAAATTTTGCAAAAAATGACTCGAAAAATTTTTCCT
* * * ** * *
28546 CAATTTTTAT-CTAAAATACTCATAAAATATTTATAATTCAATTCAAAAAATATT-ACAGTG-TT
896 CAATTTTT-TGCCAAAATACTCA-AAAAAATATATAATTCAACGCCAAAAAGATTGA-AG-GATT
28608 TTTCA-GCTTTTAATATCGTTTTT-
957 TTTCACG-TTTTAATATCGTTTTTC
* * * * * * *
28631 AATATTTTTCTGAATTAATTTCTAATCAAATTGAAACAAGATTCAAATGCTCGTAAAAAGAAATC
1 CATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGAAAAAACAAATC
* * * * *
28696 TTTAAATGCAATGTGGTTGAGATTTGATTAGATG---AT--AT-TTCAAGGAGTC-TCGACGACA
66 CTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTCAAGGAGTCTTAG-CGCCA
* * * * * * * * *
28754 AAAATCATGCAAAATTGAGCTGAGGCCTC-ATAACGTGTTTTTAGCAAAAAAAAAAACTGTGATG
130 AAAATCATACAAAACTAAGCCGGGGTCTCGA-AACGCGTTTTTAGC-----CAAAAACCGTGATG
* * * * * *
28818 GTTAGTACATGATTTCGCCTAAAATTTTGCAAAATACTGACCAGAATATTTTTTCCTCAATTTTT
189 GTTAGTACACGATTTCGGCTAAAATTTTGCAAAA-ATTGACCCGAAAAATTTTTCCTCAATTTTT
* * * *
28883 GGCTAAAATACTCATGAAATATATATATATATATAATTTAACGCAAAAAAGATTGGAGGACTTTT
253 GGCTAAAATACTCAT---A-A-A-A-A-ATATATAATTCAACGCTAAAAAGATTGGAAGATTTTT
* * *
28948 CACGCTTTTCATATCATTTTTTATATTTTTTTGAATTAATTTCTAATTAAATCGAAATAAGATTT
310 CACGCTTTTAATATCA-TTTTTAT-TTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTC
* * *
29013 AGATGCTCGTAAAAACAAATTCTTAAATGCATTGTGACTGAGATTTGATTAGATGAATATGGATA
373 AGATGCTCGTAAAAACAAATTCTTAAATGCAATGTGGCTGAGATTTGGTTAGATGAATATGGATA
* * * * *
29078 TCTC-AAGTAGTCTT-AGCGCCAAAAATCATGCAAAACTGACCCAGGGCCCTGGAGCGCATTTTT
438 TCTCAAAG-AGTCTTGAGCGCCAAAAATCATGCAAAACTGAGCCAGGGCCCCGAAACGCGTTTTT
* ** *
29141 AGCCAAAAACCGTGATGATTATTACACGATTTCGGCTAACATTTTGCAAAAATTGAGCGGAAAGA
502 AGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAA-A---AACAAAAATTGA---GAAAGT
* * * *
29206 TATTTCCTCAATTTTTTGCTA-AATTA-TGATGAAAAAAA-ATATAATTCTACACCAAAAATATT
560 TATTTCCTCAATTTTTTGCCATAA-TACTCA--AAAAAAATATATAATTCAACGCCAAAAA-ATT
* * **
29268 GAAGGGTTTTTTACTCTTCTAATATCGTTTTTCC-TACTTTTTCCGAATTAATTTCTAATTAAAT
621 GAAGGG-TTTTCACGCTTCTAATATCGTTTTTCCTTTTTTTTTCCGAATTAATTTCTAATTAAAT
* * * * *
29332 CGAAACAAGATTTTGATACTCGTAAAAACAAATCCTTAAATCCAATGTGGCCGAGATTTGATTAG
685 CAAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAG
* * *
29397 ATGAATATAGATAGTTT-AAGGAGT-TTTGGCGCCAAAAACCATGCAATACTGA-TCCGGGGTAC
750 ATGAATATAGATA-TTTCAAGGAGTCTTT-GCGCCAAAAATCATGCAAAACTGAGT-CGGGG-CC
* **** * * *
29459 CGGAACACATTTTTAGCCAAAAA-AAAAATCGTGATGTTACACGATTTCAGCTAATATTTTACAA
811 CGGAACACGTTTTTAGCCAAAAACCGTGATGGTTA-G-TACACGATTT-AGCTAA-ATTTTGCAA
* * * * * *
29523 AAAATGACTCGAAATATTTTTCCTCAATTTTTAGCCACAATAATCATAAGAAATATATAATTTAA
872 AAAATGACTCGAAAAATTTTTCCTCAATTTTTTGCCAAAATACTCA-AAAAAATATATAATTCAA
* * *
29588 CGCCAAAAAGTTTGAAGGGTTTTTCACGTTTCTAATACCGTTTTTC
936 CGCCAAAAAGATTGAAGGATTTTTCACGTTT-TAATATCGTTTTTC
* * * * * * *
29634 CTATATTTTTTTTGAATTAATTTCTAATTAAAACGAAACATGATTCGGATGCT------TA-TAA
1 C-ATA-TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGAAAAAACAAA
* ** *
29692 -----AAA--CAA--TGGCTG-GAATTTGGTTAGATGAATATAGATAATTCAAGGAGTCTCGGTG
64 TCCTTAAATTCAATGTGGCTGAG-ATTTGATTAGATGAATATAGAT-ATTCAAGGAGTCTTAGCG
* * ** * * * *
29747 CCAAAAATTATTCAAAACTGAA--ATGGGCCCCGAAACGCGTTTTTTTGCCAAAAACCGTGATGA
127 CCAAAAATCATACAAAACT-AAGCCGGGGTCTCGAAACGCG-TTTTTAGCCAAAAACCGTGATGG
* * * * *** **
29810 TTATTATACGATTTTGGCTAAAATTTTGCAAAAATTGACCCGAAAGATAAATCCTCAATTTTCAG
190 TTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGG
* * * * *
29875 CCATAATACTCATAAAAAATATATAATTCAACG-TCAAAAATATT-GAAGGTCTTTTGACGC-TT
255 CTAAAATACTCATAAAAAATATATAATTCAACGCT-AAAAAGATTGGAAGAT-TTTTCACGCTTT
* *
29937 T--TA--A----TATTTTTTTTGAATTAATTTCTAAATAAATCGAAACATGATTCAGATGCTCGT
318 TAATATCATTTTTATTTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
* * * ** * * * * *
29994 -AAAA-AAA-TATTAAATTCAATGTGGCTAAGATTTTATTAGATGAATATAGTTATTTCAAGGTG
383 AAAAACAAATTCTTAAATGCAATGTGGCTGAGATTTGGTTAGATGAATATGGATATCTCAAAGAG
* * * * * * *
30056 TGTCG-GCGCCAAAAATCTTGTAAAACTGAG-CTGGTACCCCGAAACGCGTTTTTAGCCAAAAAT
448 TCTTGAGCGCCAAAAATCATGCAAAACTGAGCCAGG-GCCCCGAAACGCGTTTTTAGCCAAAAAC
* * * * * *
30119 CGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAAAATGACTCGAAAATTTTTTCCTC
512 CGTGATGATTAGTACACGATTTCGGCTAAAA----AC-AAAAATTGA---GAAAGTTATTTCCTC
* ** * * * * * * *
30184 AATTTTTGGATAAAATACTCATAAAATATATAT-AGTCTAACGGCAAAAAGATTGGAGGACTTTT
569 AATTTTTTGCCATAATACTCAAAAAAAATATATAATTC-AACGCCAAAAA-ATTGAAGG-GTTTT
* * * * * * * * *
30248 CACGCTTTTATTATTGTTTTT-C-ATATTTTTCTGTATTAATTTCCAATTAAATCGAAACAAGAT
631 CACGCTTCTAATATCGTTTTTCCTTTTTTTTTCCGAATTAATTTCTAATTAAATCAAAACAAGAT
* ** * *
30311 TTAGATGCTTGTAAAAACAAATTTTTATATCCAATGTGGCTGAGATTTGATTAGATGAATATAGA
696 TTAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGA
* * * * *
30376 TATCTCAAGGAGTC-TTGACGTCAAAAATGATGCAAAACTCAG-CTTGGGCCCTAGG-A-A-GTT
761 TATTTCAAGGAGTCTTTG-CGCCAAAAATCATGCAAAACTGAGTC-GGGGCCC--GGAACACG-T
* * * * * *
30436 TTTTATCCAAAATCTGTGATGGTTAATACACGATTTCAGCTAAAATTTTGTAAAAAATGACCCGA
821 TTTTAGCCAAAAACCGTGATGGTTAGTACACGATTT-AGCT-AAATTTTGCAAAAAATGACTCGA
* * * ** * *
30501 AAGATATTTCCTCAATTTTTGGGTAAAATACTCATAAAAAATATATAACTCAACGGCAAAAAGAT
884 AAAATTTTTCCTCAATTTTTTGCCAAAATACTCA-AAAAAATATATAATTCAACGCCAAAAAGAT
** * *
30566 TGAAGGGCTTTTGACGTTTCTAATATCATTTTTC
948 TGAAGGATTTTTCACGTTT-TAATATCGTTTTTC
* ** * * * * *
30600 CA-AATTTTCCAAATTAATTTCCAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATT
1 CATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGAAAAAACAAATC
* * * * * *
30664 CTTAAATT-TATGGTGGGTGAGATATGATTAGATGAATATAGATATTTCAAGTAGTC-TCGAAGC
66 CTTAAATTCAAT-GTGGCTGAGATTTGATTAGATGAATATAGATA-TTCAAGGAGTCTTAG-CGC
* * * * * *
30727 CAGAAATCAAACAAAATTAAGCC-AGGTCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTT
128 CAAAAATCATACAAAACTAAGCCGGGGT-CTCGAAACGCGTTTTTAGCCAAAAACCGTGAT-G--
** * * *
30791 TGTTAGTACACGA-TTCAACTAAAATTTTTCAAAAATTGACACGAAAGATTTCTT-CTCAATTTT
189 -GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTT-TTCCTCAATTTT
* * * *
30854 TGGCTTAAATACTCAT-AAAAATATATAATTCAACGCTAAAAAGATTGGAGGGCTTTTT-ACGTT
252 TGGCTAAAATACTCATAAAAAATATATAATTCAACGCTAAAAAGATTGGA-AGATTTTTCACGCT
* *
30917 TTTAATATCCTATTTCTTATTTTTTTTGTAAATTAATTTCTAATTAAAAT-GAAATAAGATTTAG
316 TTTAATAT-C-ATTT-TTATTTTTTTTG--AATTAATTTCTAATT-AAATCGAAACAAGATTCAG
* * * *
30981 ATGCTCGTAATAACAAATTCTTAAATCCAATGTTGCTGAGATTTGGGTAGATGA
375 ATGCTCGTAAAAACAAATTCTTAAATGCAATGTGGCTGAGATTTGGTTAGATGA
31035 TGTAAAGTAT
Statistics
Matches: 3502, Mismatches: 626, Indels: 450
0.76 0.14 0.10
Matches are distributed among these distances:
963 38 0.01
964 57 0.02
965 1 0.00
966 118 0.03
967 38 0.01
968 272 0.08
969 153 0.04
970 112 0.03
971 137 0.04
972 35 0.01
973 86 0.02
974 56 0.02
975 158 0.05
976 58 0.02
977 5 0.00
978 70 0.02
979 151 0.04
980 151 0.04
981 212 0.06
982 103 0.03
983 15 0.00
984 74 0.02
985 95 0.03
986 611 0.17
987 52 0.01
988 14 0.00
989 24 0.01
990 36 0.01
991 46 0.01
992 23 0.01
993 86 0.02
994 149 0.04
995 45 0.01
996 43 0.01
997 5 0.00
998 32 0.01
999 1 0.00
1000 1 0.00
1001 82 0.02
1002 14 0.00
1004 3 0.00
1005 40 0.01
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (980 bp):
CATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGAAAAAACAAATC
CTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTCAAGGAGTCTTAGCGCCAA
AAATCATACAAAACTAAGCCGGGGTCTCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTA
CACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCTAAAA
TACTCATAAAAAATATATAATTCAACGCTAAAAAGATTGGAAGATTTTTCACGCTTTTAATATCA
TTTTTATTTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
ATTCTTAAATGCAATGTGGCTGAGATTTGGTTAGATGAATATGGATATCTCAAAGAGTCTTGAGC
GCCAAAAATCATGCAAAACTGAGCCAGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGAT
TAGTACACGATTTCGGCTAAAAACAAAAATTGAGAAAGTTATTTCCTCAATTTTTTGCCATAATA
CTCAAAAAAAATATATAATTCAACGCCAAAAAATTGAAGGGTTTTCACGCTTCTAATATCGTTTT
TCCTTTTTTTTTCCGAATTAATTTCTAATTAAATCAAAACAAGATTTAGATGCTCGTAAAAACAA
ATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCG
CCAAAAATCATGCAAAACTGAGTCGGGGCCCGGAACACGTTTTTAGCCAAAAACCGTGATGGTTA
GTACACGATTTAGCTAAATTTTGCAAAAAATGACTCGAAAAATTTTTCCTCAATTTTTTGCCAAA
ATACTCAAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGATTTTTCACGTTTTAATATCGT
TTTTC
Found at i:31381 original size:21 final size:21
Alignment explanation
Indices: 31357--31408 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
31347 AATATCTTTA
31357 CATAATTAAAATAAAAAGT-TT
1 CATAATTAAAATAAAAA-TATT
* *
31378 CATAACTATAAATAATAATATT
1 CATAATTA-AAATAAAAATATT
31400 -ATAATTAAA
1 CATAATTAAA
31409 TATATTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 2 0.08
21 14 0.54
22 10 0.38
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.35
Consensus pattern (21 bp):
CATAATTAAAATAAAAATATT
Found at i:31413 original size:15 final size:16
Alignment explanation
Indices: 31395--31424 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
31385 ATAAATAATA
31395 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
31410 ATATTATAATCTAAA
1 ATATTATAATCTAAA
31425 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:31444 original size:35 final size:37
Alignment explanation
Indices: 31386--31454 Score: 90
Period size: 35 Copynumber: 1.9 Consensus size: 37
31376 TTCATAACTA
* *
31386 TAAATAATAATATTATAATTAAAT-ATAT-TATAATC
1 TAAATAATAATATTAGAAGTAAATCATATATATAATC
31421 TAAA-AATAATTATTAGAAGTAAATCATATATATA
1 TAAATAATAA-TATTAGAAGTAAATCATATATATA
31455 TATATATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 5 0.17
35 16 0.55
36 4 0.14
37 4 0.14
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (37 bp):
TAAATAATAATATTAGAAGTAAATCATATATATAATC
Found at i:31651 original size:4 final size:4
Alignment explanation
Indices: 31642--31672 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
31632 ATGATATTAA
31642 ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATT
1 ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATT
31673 TGAATATCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
ATTG
Found at i:31668 original size:77 final size:75
Alignment explanation
Indices: 31577--31752 Score: 282
Period size: 77 Copynumber: 2.3 Consensus size: 75
31567 TATATATTAA
*
31577 ATTGATTGATTGATTTGAATATATTTTGATCCAATTAGAATCAATTAGTACTAAAATGATATTAA
1 ATTGATTGATTGATTTGAATATATCTTGATCCAATTAGAATCAATTAGTACT--AATGATATTAA
31642 ATTGATTGATTG
64 ATTGATTGATTG
*
31654 ATTGATTGATTGA-TTGATTTGAATATCTTGATCCAATTAGAATCAATTAGTACTAATGATATTA
1 ATTGATTGATTGATTTGA-AT--ATATCTTGATCCAATTAGAATCAATTAGTACTAATGATATTA
31718 AATTGATTGATTG
63 AATTGATTGATTG
31731 ATTGATTGATTGATTTGAATAT
1 ATTGATTGATTGATTTGAATAT
31753 TGATCAAATT
Statistics
Matches: 92, Mismatches: 3, Indels: 10
0.88 0.03 0.10
Matches are distributed among these distances:
75 2 0.02
76 4 0.04
77 51 0.55
78 4 0.04
79 31 0.34
ACGTcount: A:0.36, C:0.05, G:0.15, T:0.44
Consensus pattern (75 bp):
ATTGATTGATTGATTTGAATATATCTTGATCCAATTAGAATCAATTAGTACTAATGATATTAAAT
TGATTGATTG
Found at i:31728 original size:4 final size:4
Alignment explanation
Indices: 31719--31745 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
31709 ATGATATTAA
31719 ATTG ATTG ATTG ATTG ATTG ATTG ATT
1 ATTG ATTG ATTG ATTG ATTG ATTG ATT
31746 TGAATATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
ATTG
Found at i:31774 original size:10 final size:10
Alignment explanation
Indices: 31759--31783 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
31749 ATATTGATCA
31759 AATTAAAATC
1 AATTAAAATC
31769 AATTAAAATC
1 AATTAAAATC
31779 AATTA
1 AATTA
31784 GTATTAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (10 bp):
AATTAAAATC
Found at i:31779 original size:81 final size:77
Alignment explanation
Indices: 31577--31792 Score: 256
Period size: 81 Copynumber: 2.7 Consensus size: 77
31567 TATATATTAA
* **
31577 ATTGATTGATTGATTTGAATATATTTTGATCCAATTAGAATCAATTAGTACTAAAATGATATTAA
1 ATTGATTGATTGATTTGAA-A-ATCTAAATCCAATTAGAATCAATTAGTACT--AATGATATTAA
31642 ATTGATTGATTGATTG
62 ATTGATTGATTGATTG
* **
31658 ATTGATTGATTGATTTGAATATCTTGATCCAATTAGAATCAATTAGTACTAATGATATTAAATTG
1 ATTGATTGATTGATTTGAAAATCTAAATCCAATTAGAATCAATTAGTACTAATGATATTAAATTG
31723 ATTGATTGATTG
66 ATTGATTGATTG
* *
31735 ATTGATTGATTTGAATATTGATCAAAT-TAAAAT-CAATTAAAATCAATTAGTATTAATG
1 ATTGATTGA-TTG-AT-TTGA--AAATCT-AAATCCAATTAGAATCAATTAGTACTAATG
31793 TCATTTAATT
Statistics
Matches: 122, Mismatches: 7, Indels: 12
0.87 0.05 0.09
Matches are distributed among these distances:
77 36 0.30
78 3 0.02
79 31 0.25
80 4 0.03
81 43 0.35
82 5 0.04
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.42
Consensus pattern (77 bp):
ATTGATTGATTGATTTGAAAATCTAAATCCAATTAGAATCAATTAGTACTAATGATATTAAATTG
ATTGATTGATTG
Done.