Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010545.1 Corchorus capsularis cultivar CVL-1 contig10566, 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: 39645
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:127 original size:30 final size:29
Alignment explanation
Indices: 100--156 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
90 TGTACTTATT
*
100 AAAAAAG-TCAATTTGGTCCCTTTACTTA
1 AAAAAAGATCAATTTAGTCCCTTTACTTA
*
128 AAAAAAGATCAATTTAGTCCCTCTACTTA
1 AAAAAAGATCAATTTAGTCCCTTTACTTA
157 CATGTTGAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (29 bp):
AAAAAAGATCAATTTAGTCCCTTTACTTA
Found at i:8129 original size:29 final size:28
Alignment explanation
Indices: 8066--8131 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
8056 GTCCTTTCCT
* *
8066 GTTGTAATTTTTGGTTTAAGTTTTGATC
1 GTTGTAATTTTTAGTTCAAGTTTTGATC
* *
8094 TTCTGTAATTTTTAGTTCAAGTTTTTATCC
1 GT-TGTAATTTTTAGTTCAAGTTTTGAT-C
8124 GTTGTAAT
1 GTTGTAAT
8132 GCCATACAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 1 0.03
29 28 0.90
30 2 0.06
ACGTcount: A:0.20, C:0.08, G:0.17, T:0.56
Consensus pattern (28 bp):
GTTGTAATTTTTAGTTCAAGTTTTGATC
Found at i:10200 original size:322 final size:323
Alignment explanation
Indices: 8890--12563 Score: 4483
Period size: 322 Copynumber: 11.3 Consensus size: 323
8880 GTTTTGGTCC
* * * * * * * * * *
8890 ATGTAATTTAACGCCAAAATGATTTAAGGACTTTTTACGTTTCTAATATCGTTTTTCTATTTTTT
1 ATGTAATTCAATGCCAAAATAATTAAAGGGCTTTTCATGCTTCTAAAATCGTTTTTCCA----TT
* * * ** * *
8955 TTTTTCCGTATTAGA-TTCTAATTAGATCGAAA-CCATTT-ATGATGCCTCGTACAAACAATTCC
62 TTTTTCCG-AATAAATTTCTAATTAAATCGAAATTGATTTCA-GATG-CTCGTAAAAACAAATCC
* *** * * *
9017 TTAAATCCAATATAACTGAGATTTGATTAGATGAATATAGATATTTCAATAAGTCTTGGTGTCAA
124 TTAAATCCAATGTGGTTGAGATTTGGTTAGATGAATATAGATATTTCAATAAGTCTTGG-GGC-C
* * * * **
9082 AAATAATGCAAAGCAAAACTGATCTGGAGTCCCGGAACGCG-TTTTTAGCCAAAAACCGTGAAAG
187 AAA-AAT-C-AGGCAAAACTGAGCCGGAGCCCCGGAACGCGTTTTTTAGCCAAAAACCGTGATGG
* * * * * ** ** * *
9146 -T-ACAT--GATTTAGGCTAACATTTTGCAAAATCTGACTTGACTCAATTTTTTTC-CACAATAC
249 TTAATATACGATTTCGGCTAAAATTTTGAAAAAACTGACCCGACTCAATTTTTCACTGA-AATAA
9206 TCAA-AAAAAAT
313 T-AATAAAAAAT
* * * * * *
9217 ATATAATTCAACGCCAAAA-AGATTAAAGGGCTTTTTACGCTTCTAATATAGTTTTTTTCCATTT
1 ATGTAATTCAATGCCAAAATA-ATTAAAGGGCTTTTCATGCTTCTAAAATCG--TTTTTCCATTT
* * **
9281 TTTTCCGAATTAATTTTTAATTAAATCGAAACAAGA-TTCAGATGCTCGTAAAAACAAATCCTTA
63 TTTTCCGAATAAATTTCTAATTAAATCGAAA-TTGATTTCAGATGCTCGTAAAAACAAATCCTTA
* * * ** *
9345 AGTCCAATGTGGTTGAGATTTGGTTAGATGAATATAGATACTTCAATGAGTCTTGGCACAAAAAA
127 AATCCAATGTGGTTGAGATTTGGTTAGATGAATATAGATATTTCAATAAGTCTTGGGGCCAAAAA
* * * * * *
9410 TCAGGCGAAACTGAGCCGGGGTCCCGGAACGCG-TTTTTAACAAAAAACCGTGATGGTTAGTATA
192 TCAGGCAAAACTGAGCCGGAGCCCCGGAACGCGTTTTTTAGCCAAAAACCGTGATGGTTAATATA
* * * ** * * *
9474 CGATTTCGGCTAAATTTTTGCAAAAAA-TGACCCGGCTCAATTTCTGGCTAAAATACTCA-AAAA
257 CGATTTCGGCTAAAATTTTG-AAAAAACTGACCCGACTCAATTTTTCACTGAAATAATAATAAAA
*
9537 AGT
321 AAT
* * * * * * * * *
9540 ATTTAATTCAACGCCAAAAT-GTTCGAAGGGTTTTTTCATACTTCCAATAA-CGGTTTTCCTTTT
1 ATGTAATTCAATGCCAAAATAATT-AAAGGG-CTTTTCATGCTTCTAA-AATCGTTTTTCC-ATT
* * * * * * * * * * *
9603 TTTTTATCGTATCAATTTCTAAATAAATCAAAATTGGTTTTAGATGCTTGTGAAAACAAATCATG
62 TTTTT-CCGAATAAATTTCTAATTAAATCGAAATTGATTTCAGATGCTCGTAAAAACAAATCCTT
* * * * * *
9668 AAATCCAATGTGGTTCAGATTAGCTTAGATGAATATAGATATTTCAATGAGTCTTGGCGCAAAAA
126 AAATCCAATGTGGTTGAGATTTGGTTAGATGAATATAGATATTTCAATAAGTCTTGGGGCCAAAA
* * * * * * * **
9733 ATAAGGCAAAACTAAGTCGGGGCCCCGTAACGCGTTTTTT-GACAAAAACCGTGATGATTAGCAT
191 ATCAGGCAAAACTGAGCCGGAGCCCCGGAACGCGTTTTTTAGCCAAAAACCGTGATGGTTAATAT
* *
9797 ACGATTTCGGCTAAAATTTTGAAAAAACTGACCCGACTCAATATTTCACTGAAATAATAATAAAG
256 ACGATTTCGGCTAAAATTTTGAAAAAACTGACCCGACTCAATTTTTCACTGAAATAATAATAAAA
9862 AAT
321 AAT
*
9865 ATGTAATTCAATGCCAAAAT-ATTAAAAGGGCTTTT-ATGCTTCTAAAATCGTTTTTCCATTTTC
1 ATGTAATTCAATGCCAAAATAATT-AAAGGGCTTTTCATGCTTCTAAAATCGTTTTTCCATTTTT
*
9928 TTCCAAATAAATTTCTAATTAAATCGAAATTGATTTCAGATGCTCGTAAAAACAAATCCTTAAAT
65 TTCCGAATAAATTTCTAATTAAATCGAAATTGATTTCAGATGCTCGTAAAAACAAATCCTTAAAT
* *
9993 TCGATGTGGTTGAGATTTGGTTAGATGAATATAGATATTTCAATAAGTCTTGGGGCCAAAAATCA
130 CCAATGTGGTTGAGATTTGGTTAGATGAATATAGATATTTCAATAAGTCTTGGGGCCAAAAATCA
**
10058 GGCAAAACTGAGCCGGAGCCCCGGAACGCGTTTTTTAGCCAAAAACCGTGATAATTAATATACGA
195 GGCAAAACTGAGCCGGAGCCCCGGAACGCGTTTTTTAGCCAAAAACCGTGATGGTTAATATACGA
10123 TTTCGGCTAAAATTTTGAAAAAACTGACCCGACTCAATTTTTCACTGAAATAATAATAAAAAAT
260 TTTCGGCTAAAATTTTGAAAAAACTGACCCGACTCAATTTTTCACTGAAATAATAATAAAAAAT
* * *
10187 ATGTAATTCAATGCCAAAATAATTAAAGGCCTTTTCATGCTTTTAAAATCGTTTTCCCATTTTTT
1 ATGTAATTCAATGCCAAAATAATTAAAGGGCTTTTCATGCTTCTAAAATCGTTTTTCCATTTTTT
* * * *
10252 TCCGGATAAATTTCTAATTAAATCGAAATTG-GTTCAGATGCTCATAAAAATAAATCCTTAAATC
66 TCCGAATAAATTTCTAATTAAATCGAAATTGATTTCAGATGCTCGTAAAAACAAATCCTTAAATC
* * * *
10316 CAATGTGGTTGAGATTTGATTAGATAAATATAGATATTTCAATAAGTCATGGGGTCAAAAATCAG
131 CAATGTGGTTGAGATTTGGTTAGATGAATATAGATATTTCAATAAGTCTTGGGGCCAAAAATCAG
* *
10381 GCAAAACTGAGCCGGAGCCCCGGAACACGTTTTTT-GCCAAAAACCGTGAT-GTAACATATACGA
196 GCAAAACTGAGCCGGAGCCCCGGAACGCGTTTTTTAGCCAAAAACCGTGATGGTTA-ATATACGA
*** *
10444 TTTCGGCTAAAATTTTGAAAAGTGTGACCCGACTCAATTTTTCACTGAAATAATAATAAAAAGT
260 TTTCGGCTAAAATTTTGAAAAAACTGACCCGACTCAATTTTTCACTGAAATAATAATAAAAAAT
* *
10508 ATGTAATTCAATGCCAAAATAATTAAAGGGCTTTTCATGTTTCTAAAATCGTTATTCCA-TTTTT
1 ATGTAATTCAATGCCAAAATAATTAAAGGGCTTTTCATGCTTCTAAAATCGTTTTTCCATTTTTT
* * * * *
10572 TCCGGATAAATTTCTAATTAAATCGAAATTGGTTTCAGATGCACTTAAAAACAAATACTTAAATC
66 TCCGAATAAATTTCTAATTAAATCGAAATTGATTTCAGATGCTCGTAAAAACAAATCCTTAAATC
* * *
10637 CAATGTGGTTGAGATTTGGTTAGATGAATATAGATACTTCAATGAGTCTTGGCGCCAAAAATCAG
131 CAATGTGGTTGAGATTTGGTTAGATGAATATAGATATTTCAATAAGTCTTGGGGCCAAAAATCAG
* * * ** *
10702 GCGAAACTGAGCCGGGGCCCCGGAACGC-ATTTTTAGTAAAAAACCGTGATGGTTAGTATACGAT
196 GCAAAACTGAGCCGGAGCCCCGGAACGCGTTTTTTAGCCAAAAACCGTGATGGTTAATATACGAT
* * * * * ** *
10766 TTCGGCTAAAATTTTGCAAAAACTGACCCAACTCAATTTCTT-GCTAAAATACTCCTTAAAAAT
261 TTCGGCTAAAATTTTGAAAAAACTGACCCGACTCAATTT-TTCACTGAAATAATAATAAAAAAT
* *
10829 ATGTAATTCAATGCCAAAATATTTGAAGGGCTTTTCATGCTTCTAAAATCGTTTTTCCATTTTTT
1 ATGTAATTCAATGCCAAAATAATTAAAGGGCTTTTCATGCTTCTAAAATCGTTTTTCCATTTTTT
* *
10894 TCCAAATAAATTTCTAATTAAATCGAAATTGATTTCAGATGCTCGTAAAAAAAAATCCTTAAATC
66 TCCGAATAAATTTCTAATTAAATCGAAATTGATTTCAGATGCTCGTAAAAACAAATCCTTAAATC
*** * * *
10959 TGTTGTGGTTGAGATTTTGTTAGATGATTATAGATATTTCAATAAGTGTTGGGGCCAAAAATCAG
131 CAATGTGGTTGAGATTTGGTTAGATGAATATAGATATTTCAATAAGTCTTGGGGCCAAAAATCAG
* * *
11024 GCAAAACTGAGTCGGAGCCTCGAAACGCGTTTTTTAGCCAAAAACCGTGATGGTGTTAATATACG
196 GCAAAACTGAGCCGGAGCCCCGGAACGCGTTTTTTAGCCAAAAACCGTGAT-G-GTTAATATACG
* * * *
11089 ATTTCGGCTAAAATTTTGAAAAAAACTGACCTGACTCAATTTTGCACTTAAATAATAATAGAAAA
259 ATTTCGGCTAAAATTTTG-AAAAAACTGACCCGACTCAATTTTTCACTGAAATAATAATAAAAAA
11154 T
323 T
11155 ATGTAATTCAATGCCAAAATAATTAAAGGGCTTTTCATGCTTCTAAAATCGTTTTTCCATTTTTT
1 ATGTAATTCAATGCCAAAATAATTAAAGGGCTTTTCATGCTTCTAAAATCGTTTTTCCA-TTTTT
* * * *
11220 TTCCGGATAAATTTCTAATTAAATCTAAATTGATTTTAGATGCTCGTAAAAACAAATCGTTAAAT
65 TTCCGAATAAATTTCTAATTAAATCGAAATTGATTTCAGATGCTCGTAAAAACAAATCCTTAAAT
11285 CCAATGTGGTTGAGATTTGGTTAGATGAATATAGATATTTCAATAAGTCTTGGGGCCAAAAATCA
130 CCAATGTGGTTGAGATTTGGTTAGATGAATATAGATATTTCAATAAGTCTTGGGGCCAAAAATCA
* * * * *
11350 GGGAAAATTGAGCCAGAGCCCCGAAACGCGTTTTTTAGCCGAAAACCGTGATGGTTAATATACGA
195 GGCAAAACTGAGCCGGAGCCCCGGAACGCGTTTTTTAGCCAAAAACCGTGATGGTTAATATACGA
* * * *
11415 TTTCGGCTAAAATTTTGTAAAAACTGACCTGACTC-ATTTTTGCACTTAAATAATAATAGAAAAT
260 TTTCGGCTAAAATTTTGAAAAAACTGACCCGACTCAATTTTT-CACTGAAATAATAATAAAAAAT
* * * *
11479 CTGTAATTCAAAGACAAATTAATTAAAGGGCTTTTCATGCTTCTAAAATCGTTTTTCCATTTTTT
1 ATGTAATTCAATGCCAAAATAATTAAAGGGCTTTTCATGCTTCTAAAATCGTTTTTCCA--TTTT
*
11544 TTTCCGGATAAATTTCTAATTAAATCGAAATTTG-TTTCAGATGCTCGTAAAAACAAATCCTTAA
64 TTTCCGAATAAATTTCTAATTAAATCGAAA-TTGATTTCAGATGCTCGTAAAAACAAATCCTTAA
*
11608 ATCCAATGTGGTTGAGATTTGGTTAGATGAATATAGATATTTCAATAAGTCTAT-GGGCCAGAAA
128 ATCCAATGTGGTTGAGATTTGGTTAGATGAATATAGATATTTCAATAAGTCT-TGGGGCCAAAAA
* * *
11672 TCAGGCAAAACTGAGCCGAAGCCCCGAAACGCGTTTTTTAGCCAAAAACCGTGACGGTTAATATA
192 TCAGGCAAAACTGAGCCGGAGCCCCGGAACGCGTTTTTTAGCCAAAAACCGTGATGGTTAATATA
* *
11737 CGATTTCGGCT-AAATTTTGTAAAAACTGACCCGACTCAATTTTTCACTAAAATAATAATAAAAA
257 CGATTTCGGCTAAAATTTTGAAAAAACTGACCCGACTCAATTTTTCACTGAAATAATAATAAAAA
11801 AT
322 AT
* * *
11803 ATGTAATTCAAAGACAAAATAATTAAAGGACTTTTCATGCTTCTAAAATCGTTTTTCCATTTTTT
1 ATGTAATTCAATGCCAAAATAATTAAAGGGCTTTTCATGCTTCTAAAATCGTTTTTCCATTTTTT
* *
11868 TCCAAATAAATTTCTAATTAAATCGAAATTGATTTCAGATGCTCGTAAAAATAAATCCTTAAATC
66 TCCGAATAAATTTCTAATTAAATCGAAATTGATTTCAGATGCTCGTAAAAACAAATCCTTAAATC
* * * *
11933 CAATGTGGTTGAAATTTGGTTAGATGATTATAGATATTTCAATAAGTCTTGGAGCCAAAAATTAG
131 CAATGTGGTTGAGATTTGGTTAGATGAATATAGATATTTCAATAAGTCTTGGGGCCAAAAATCAG
***
11998 GCAAAACTGAGCAAAAGCCCCGGAACGCGTTTTTTAGCCAAAAACCGTGATGGTTAATATACGAT
196 GCAAAACTGAGCCGGAGCCCCGGAACGCGTTTTTTAGCCAAAAACCGTGATGGTTAATATACGAT
* * *
12063 TTCGGCTAACATTTTGTAAAAACTGACCCGACTCAATTTTTCACTGAAATAATAATATAAAAT
261 TTCGGCTAAAATTTTGAAAAAACTGACCCGACTCAATTTTTCACTGAAATAATAATAAAAAAT
* * *
12126 TTGTAATTCAATGCCAAAATAATTAAAGGGCTTTTCATGTTTCTAAAATCGTTATTCCATTTTTT
1 ATGTAATTCAATGCCAAAATAATTAAAGGGCTTTTCATGCTTCTAAAATCGTTTTTCCATTTTTT
*
12191 TCCGGATAAATTTCTAATTAAATCGAAATTGGTTTCAGATGCTCTTAAAAATTCAGATGCTCGTA
66 TCCGAATAAATTTCTAATTAAATCGAAA-----TT--GA------T-----TTCAGATGCTCGTA
* * *
12256 AAAATAAATCCTTAAATCCACTGTGGTTGAGATTTGGTTAGATGAATATAGATATTTCAGTAAGT
113 AAAACAAATCCTTAAATCCAATGTGGTTGAGATTTGGTTAGATGAATATAGATATTTCAATAAGT
* * * * * *
12321 CTTGGGGTCAAAAATCAAGCAAAACTAAGCCGGAGCCCCGAAACGCGTTTTTTAACCAAAACCCG
178 CTTGGGGCCAAAAATCAGGCAAAACTGAGCCGGAGCCCCGGAACGCGTTTTTTAGCCAAAAACCG
* * * * * *
12386 TGATGGTTAATATACGATGTCGACTAAAATTTTGAAAATACCGACACGACTCAATATTTCACTGA
243 TGATGGTTAATATACGATTTCGGCTAAAATTTTGAAAAAACTGACCCGACTCAATTTTTCACTGA
*
12451 AATACTAATAAAAAAT
308 AATAATAATAAAAAAT
* * * * * * *
12467 ATGTAATTCAAAGACAAAATATTTGAGGGGCTATTCATGCTTCTAAAATCATTTTTCCATTTTTT
1 ATGTAATTCAATGCCAAAATAATTAAAGGGCTTTTCATGCTTCTAAAATCGTTTTTCCA-TTTTT
*
12532 TTCCAAATAAATTTCTAATTAAATCGAAATTG
65 TTCCGAATAAATTTCTAATTAAATCGAAATTG
12564 GTACAGATGC
Statistics
Matches: 2932, Mismatches: 349, Indels: 124
0.86 0.10 0.04
Matches are distributed among these distances:
320 88 0.03
321 517 0.18
322 597 0.20
323 283 0.10
324 446 0.15
325 389 0.13
326 102 0.03
327 214 0.07
328 2 0.00
329 7 0.00
330 2 0.00
335 1 0.00
336 1 0.00
337 2 0.00
341 249 0.08
342 32 0.01
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (323 bp):
ATGTAATTCAATGCCAAAATAATTAAAGGGCTTTTCATGCTTCTAAAATCGTTTTTCCATTTTTT
TCCGAATAAATTTCTAATTAAATCGAAATTGATTTCAGATGCTCGTAAAAACAAATCCTTAAATC
CAATGTGGTTGAGATTTGGTTAGATGAATATAGATATTTCAATAAGTCTTGGGGCCAAAAATCAG
GCAAAACTGAGCCGGAGCCCCGGAACGCGTTTTTTAGCCAAAAACCGTGATGGTTAATATACGAT
TTCGGCTAAAATTTTGAAAAAACTGACCCGACTCAATTTTTCACTGAAATAATAATAAAAAAT
Found at i:10522 original size:643 final size:644
Alignment explanation
Indices: 8995--12563 Score: 4456
Period size: 643 Copynumber: 5.5 Consensus size: 644
8985 AACCATTTAT
* * * ***
8995 GATGCCTCGTACAAACAATTCCTTAAATCCAATATAACTGAGATTTGATTAGATGAATATAGATA
1 GATG-CTCGTAAAAACAAATCCTTAAATCCAATGTGGTTGAGATTTGATTAGATGAATATAGATA
* * * * * *
9060 TTTCAATAAGTCTTGGTGTCAAAAATAATGCAAAGCAAAACTGATCTGGAGTCCCGGAACGCG-T
65 TTTCAATAAGTCTTGGGGTC--AAA-AAT-C-AGGCAAAACTGAGCCGGAGCCCCGAAACGCGTT
* * * * * * **
9124 TTTTAGCCAAAAACCGTGA----AAGTACATGATTTAGGCTAACATTTTGCAAAATCTGACTTGA
125 TTTTAGCCAAAAACCGTGATGTTAA-TATACGATTTCGGCTAAAATTTTGAAAAAACTGACCCGA
** * * * *
9185 CTCAATTTTTTTC-CACAATACTCAA-AAAAAATATATAATTCAACGCCAAAA-AGATTAAAGGG
189 CTCAATTTTTCACTGA-AATAAT-AATAAAAAATATGTAATTCAATGCCAAAATA-ATTAAAGGG
* * * * * * *
9247 CTTTTTACGCTTCTAATATAGTTTTTTTCCATTTTTTTCCGAATTAATTTTTAATTAAATCGAAA
251 CTTTTCATGCTTCTAAAATCG--TTTTTCCATTTTTTTCCAAATAAATTTCTAATTAAATCGAAA
** *
9312 CAAGA-TTCAGATGCTCGTAAAAACAAATCCTTAAGTCCAATGTGGTTGAGATTTGGTTAGATGA
314 -TTGATTTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGTTGAGATTTGGTTAGATGA
* * * * * * *
9376 ATATAGATACTTCAATGAGTCTTGGCACAAAAAATCAGGCGAAACTGAGCCGGGGTCCCGGAACG
378 ATATAGATATTTCAATAAGTCTTGGCGCCAAAAATCAGGCAAAACTGAGCCGGAGCCCCGGAACG
* * * *
9441 CG-TTTTTAACAAAAAACCGTGATGGTTAGTATACGATTTCGGCTAAATTTTTGCAAAAAA-TGA
443 CGTTTTTTAGCCAAAAACCGTGATGGTTAATATACGATTTCGGCTAAAATTTTG-AAAAAACTGA
* * ** * * * * * * *
9504 CCCGGCTCAATTTCTGGCTAAAATACTCA-AAAAAGTATTTAATTCAACGCCAAAAT-GTTCGAA
507 CCCGACTCAATTTTTCACTAAAATAATAATAAAAAATATGTAATTCAATGCCAAAATAATT-AAA
* * * ** * * * *
9567 GGGTTTTTTCATACTTCCAATAA-CGGTTTTCCTTTTTTTTTATCGTATCAATTTCTAAATAAAT
571 GGG-CTTTTCATGCTTCTAA-AATC-GTTTTCCCATTTTTTT-CCGGATAAATTTCTAATTAAAT
* *
9631 CAAAATTGGTTTTA
632 CGAAATTGG-TTCA
* * * * * * *
9645 GATGCTTGTGAAAACAAATCATGAAATCCAATGTGGTTCAGATTAGCTTAGATGAATATAGATAT
1 GATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGTTGAGATTTGATTAGATGAATATAGATAT
* * * * * * *
9710 TTCAATGAGTCTTGGCG-CAAAAAATAAGGCAAAACTAAGTCGGGGCCCCGTAACGCGTTTTTT-
66 TTCAATAAGTCTTGGGGTC-AAAAATCAGGCAAAACTGAGCCGGAGCCCCGAAACGCGTTTTTTA
* **
9773 GACAAAAACCGTGATGATTAGCATACGATTTCGGCTAAAATTTTGAAAAAACTGACCCGACTCAA
130 GCCAAAAACCGTGATG-TTAATATACGATTTCGGCTAAAATTTTGAAAAAACTGACCCGACTCAA
* *
9838 TATTTCACTGAAATAATAATAAAGAATATGTAATTCAATGCCAAAAT-ATTAAAAGGGCTTTT-A
194 TTTTTCACTGAAATAATAATAAAAAATATGTAATTCAATGCCAAAATAATT-AAAGGGCTTTTCA
*
9901 TGCTTCTAAAATCGTTTTTCCATTTTCTTCCAAATAAATTTCTAATTAAATCGAAATTGATTTCA
258 TGCTTCTAAAATCGTTTTTCCATTTTTTTCCAAATAAATTTCTAATTAAATCGAAATTGATTTCA
* *
9966 GATGCTCGTAAAAACAAATCCTTAAATTCGATGTGGTTGAGATTTGGTTAGATGAATATAGATAT
323 GATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGTTGAGATTTGGTTAGATGAATATAGATAT
*
10031 TTCAATAAGTCTTGGGGCCAAAAATCAGGCAAAACTGAGCCGGAGCCCCGGAACGCGTTTTTTAG
388 TTCAATAAGTCTTGGCGCCAAAAATCAGGCAAAACTGAGCCGGAGCCCCGGAACGCGTTTTTTAG
**
10096 CCAAAAACCGTGATAATTAATATACGATTTCGGCTAAAATTTTGAAAAAACTGACCCGACTCAAT
453 CCAAAAACCGTGATGGTTAATATACGATTTCGGCTAAAATTTTGAAAAAACTGACCCGACTCAAT
* *
10161 TTTTCACTGAAATAATAATAAAAAATATGTAATTCAATGCCAAAATAATTAAAGGCCTTTTCATG
518 TTTTCACTAAAATAATAATAAAAAATATGTAATTCAATGCCAAAATAATTAAAGGGCTTTTCATG
*
10226 CTTTTAAAATCGTTTTCCCATTTTTTTCCGGATAAATTTCTAATTAAATCGAAATTGGTTCA
583 CTTCTAAAATCGTTTTCCCATTTTTTTCCGGATAAATTTCTAATTAAATCGAAATTGGTTCA
* * *
10288 GATGCTCATAAAAATAAATCCTTAAATCCAATGTGGTTGAGATTTGATTAGATAAATATAGATAT
1 GATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGTTGAGATTTGATTAGATGAATATAGATAT
* * *
10353 TTCAATAAGTCATGGGGTCAAAAATCAGGCAAAACTGAGCCGGAGCCCCGGAACACGTTTTTT-G
66 TTCAATAAGTCTTGGGGTCAAAAATCAGGCAAAACTGAGCCGGAGCCCCGAAACGCGTTTTTTAG
* ***
10417 CCAAAAACCGTGATGTAACATATACGATTTCGGCTAAAATTTTGAAAAGTGTGACCCGACTCAAT
131 CCAAAAACCGTGATGTTA-ATATACGATTTCGGCTAAAATTTTGAAAAAACTGACCCGACTCAAT
*
10482 TTTTCACTGAAATAATAATAAAAAGTATGTAATTCAATGCCAAAATAATTAAAGGGCTTTTCATG
195 TTTTCACTGAAATAATAATAAAAAATATGTAATTCAATGCCAAAATAATTAAAGGGCTTTTCATG
* * ** *
10547 TTTCTAAAATCGTTATTCCA-TTTTTTCCGGATAAATTTCTAATTAAATCGAAATTGGTTTCAGA
260 CTTCTAAAATCGTTTTTCCATTTTTTTCCAAATAAATTTCTAATTAAATCGAAATTGATTTCAGA
* * * *
10611 TGCACTTAAAAACAAATACTTAAATCCAATGTGGTTGAGATTTGGTTAGATGAATATAGATACTT
325 TGCTCGTAAAAACAAATCCTTAAATCCAATGTGGTTGAGATTTGGTTAGATGAATATAGATATTT
* * * * **
10676 CAATGAGTCTTGGCGCCAAAAATCAGGCGAAACTGAGCCGGGGCCCCGGAACGC-ATTTTTAGTA
390 CAATAAGTCTTGGCGCCAAAAATCAGGCAAAACTGAGCCGGAGCCCCGGAACGCGTTTTTTAGCC
* * *
10740 AAAAACCGTGATGGTTAGTATACGATTTCGGCTAAAATTTTGCAAAAACTGACCCAACTCAATTT
455 AAAAACCGTGATGGTTAATATACGATTTCGGCTAAAATTTTGAAAAAACTGACCCGACTCAATTT
* * ** * * *
10805 CTT-GCTAAAATACTCCTTAAAAATATGTAATTCAATGCCAAAATATTTGAAGGGCTTTTCATGC
520 -TTCACTAAAATAATAATAAAAAATATGTAATTCAATGCCAAAATAATTAAAGGGCTTTTCATGC
* ** *
10869 TTCTAAAATCGTTTTTCCATTTTTTTCCAAATAAATTTCTAATTAAATCGAAATTGATTTCA
584 TTCTAAAATCGTTTTCCCATTTTTTTCCGGATAAATTTCTAATTAAATCGAAATTG-GTTCA
* *** *
10931 GATGCTCGTAAAAAAAAATCCTTAAATCTGTTGTGGTTGAGATTTTG-TTAGATGATTATAGATA
1 GATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGTTGAGA-TTTGATTAGATGAATATAGATA
* * * *
10995 TTTCAATAAGTGTTGGGGCCAAAAATCAGGCAAAACTGAGTCGGAGCCTCGAAACGCGTTTTTTA
65 TTTCAATAAGTCTTGGGGTCAAAAATCAGGCAAAACTGAGCCGGAGCCCCGAAACGCGTTTTTTA
*
11060 GCCAAAAACCGTGATGGTGTTAATATACGATTTCGGCTAAAATTTTGAAAAAAACTGACCTGACT
130 GCCAAAAACCGTGA---TGTTAATATACGATTTCGGCTAAAATTTTG-AAAAAACTGACCCGACT
* * *
11125 CAATTTTGCACTTAAATAATAATAGAAAATATGTAATTCAATGCCAAAATAATTAAAGGGCTTTT
191 CAATTTTTCACTGAAATAATAATAAAAAATATGTAATTCAATGCCAAAATAATTAAAGGGCTTTT
** *
11190 CATGCTTCTAAAATCGTTTTTCCATTTTTTTTCCGGATAAATTTCTAATTAAATCTAAATTGATT
256 CATGCTTCTAAAATCGTTTTTCCA-TTTTTTTCCAAATAAATTTCTAATTAAATCGAAATTGATT
* *
11255 TTAGATGCTCGTAAAAACAAATCGTTAAATCCAATGTGGTTGAGATTTGGTTAGATGAATATAGA
320 TCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGTTGAGATTTGGTTAGATGAATATAGA
* * * * *
11320 TATTTCAATAAGTCTTGGGGCCAAAAATCAGGGAAAATTGAGCCAGAGCCCCGAAACGCGTTTTT
385 TATTTCAATAAGTCTTGGCGCCAAAAATCAGGCAAAACTGAGCCGGAGCCCCGGAACGCGTTTTT
* * *
11385 TAGCCGAAAACCGTGATGGTTAATATACGATTTCGGCTAAAATTTTGTAAAAACTGACCTGACTC
450 TAGCCAAAAACCGTGATGGTTAATATACGATTTCGGCTAAAATTTTGAAAAAACTGACCCGACTC
* * * * * *
11450 -ATTTTTGCACTTAAATAATAATAGAAAATCTGTAATTCAAAGACAAATTAATTAAAGGGCTTTT
515 AATTTTT-CACTAAAATAATAATAAAAAATATGTAATTCAATGCCAAAATAATTAAAGGGCTTTT
* *
11514 CATGCTTCTAAAATCGTTTTTCCATTTTTTTTTCCGGATAAATTTCTAATTAAATCGAAATTTGT
579 CATGCTTCTAAAATCGTTTTCCCA--TTTTTTTCCGGATAAATTTCTAATTAAATCGAAA-TTGG
11579 TTCA
641 TTCA
*
11583 GATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGTTGAGATTTGGTTAGATGAATATAGATAT
1 GATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGTTGAGATTTGATTAGATGAATATAGATAT
* * *
11648 TTCAATAAGTCTAT-GGGCCAGAAATCAGGCAAAACTGAGCCGAAGCCCCGAAACGCGTTTTTTA
66 TTCAATAAGTCT-TGGGGTCAAAAATCAGGCAAAACTGAGCCGGAGCCCCGAAACGCGTTTTTTA
* *
11712 GCCAAAAACCGTGACGGTTAATATACGATTTCGGCT-AAATTTTGTAAAAACTGACCCGACTCAA
130 GCCAAAAACCGTGA-TGTTAATATACGATTTCGGCTAAAATTTTGAAAAAACTGACCCGACTCAA
* * * *
11776 TTTTTCACTAAAATAATAATAAAAAATATGTAATTCAAAGACAAAATAATTAAAGGACTTTTCAT
194 TTTTTCACTGAAATAATAATAAAAAATATGTAATTCAATGCCAAAATAATTAAAGGGCTTTTCAT
11841 GCTTCTAAAATCGTTTTTCCATTTTTTTCCAAATAAATTTCTAATTAAATCGAAATTGATTTCAG
259 GCTTCTAAAATCGTTTTTCCATTTTTTTCCAAATAAATTTCTAATTAAATCGAAATTGATTTCAG
* * *
11906 ATGCTCGTAAAAATAAATCCTTAAATCCAATGTGGTTGAAATTTGGTTAGATGATTATAGATATT
324 ATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGTTGAGATTTGGTTAGATGAATATAGATATT
* * ***
11971 TCAATAAGTCTTGGAGCCAAAAATTAGGCAAAACTGAGCAAAAGCCCCGGAACGCGTTTTTTAGC
389 TCAATAAGTCTTGGCGCCAAAAATCAGGCAAAACTGAGCCGGAGCCCCGGAACGCGTTTTTTAGC
* *
12036 CAAAAACCGTGATGGTTAATATACGATTTCGGCTAACATTTTGTAAAAACTGACCCGACTCAATT
454 CAAAAACCGTGATGGTTAATATACGATTTCGGCTAAAATTTTGAAAAAACTGACCCGACTCAATT
* * * *
12101 TTTCACTGAAATAATAATATAAAATTTGTAATTCAATGCCAAAATAATTAAAGGGCTTTTCATGT
519 TTTCACTAAAATAATAATAAAAAATATGTAATTCAATGCCAAAATAATTAAAGGGCTTTTCATGC
12166 TTCTAAAATCGTTATT-CCATTTTTTTCCGGATAAATTTCTAATTAAATCGAAATTGGTTTCAGA
584 TTCTAAAATCGTT-TTCCCATTTTTTTCCGGATAAATTTCTAATTAAATCGAAA-----TT--G-
12230 TGCTCTTAAAAATTCA
640 -G----------TTCA
* * *
12246 GATGCTCGTAAAAATAAATCCTTAAATCCACTGTGGTTGAGATTTGGTTAGATGAATATAGATAT
1 GATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGTTGAGATTTGATTAGATGAATATAGATAT
* * * *
12311 TTCAGTAAGTCTTGGGGTCAAAAATCAAGCAAAACTAAGCCGGAGCCCCGAAACGCGTTTTTTAA
66 TTCAATAAGTCTTGGGGTCAAAAATCAGGCAAAACTGAGCCGGAGCCCCGAAACGCGTTTTTTAG
* * * * * *
12376 CCAAAACCCGTGATGGTTAATATACGATGTCGACTAAAATTTTGAAAATACCGACACGACTCAAT
131 CCAAAAACCGTGAT-GTTAATATACGATTTCGGCTAAAATTTTGAAAAAACTGACCCGACTCAAT
* * * * * * * *
12441 ATTTCACTGAAATACTAATAAAAAATATGTAATTCAAAGACAAAATATTTGAGGGGCTATTCATG
195 TTTTCACTGAAATAATAATAAAAAATATGTAATTCAATGCCAAAATAATTAAAGGGCTTTTCATG
*
12506 CTTCTAAAATCATTTTTCCATTTTTTTTCCAAATAAATTTCTAATTAAATCGAAATTG
260 CTTCTAAAATCGTTTTTCCA-TTTTTTTCCAAATAAATTTCTAATTAAATCGAAATTG
12564 GTACAGATGC
Statistics
Matches: 2560, Mismatches: 297, Indels: 109
0.86 0.10 0.04
Matches are distributed among these distances:
642 173 0.07
643 484 0.19
644 107 0.04
645 214 0.08
646 111 0.04
647 437 0.17
648 190 0.07
649 227 0.09
650 153 0.06
651 5 0.00
652 163 0.06
653 4 0.00
662 1 0.00
663 153 0.06
664 101 0.04
665 37 0.01
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (644 bp):
GATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGTTGAGATTTGATTAGATGAATATAGATAT
TTCAATAAGTCTTGGGGTCAAAAATCAGGCAAAACTGAGCCGGAGCCCCGAAACGCGTTTTTTAG
CCAAAAACCGTGATGTTAATATACGATTTCGGCTAAAATTTTGAAAAAACTGACCCGACTCAATT
TTTCACTGAAATAATAATAAAAAATATGTAATTCAATGCCAAAATAATTAAAGGGCTTTTCATGC
TTCTAAAATCGTTTTTCCATTTTTTTCCAAATAAATTTCTAATTAAATCGAAATTGATTTCAGAT
GCTCGTAAAAACAAATCCTTAAATCCAATGTGGTTGAGATTTGGTTAGATGAATATAGATATTTC
AATAAGTCTTGGCGCCAAAAATCAGGCAAAACTGAGCCGGAGCCCCGGAACGCGTTTTTTAGCCA
AAAACCGTGATGGTTAATATACGATTTCGGCTAAAATTTTGAAAAAACTGACCCGACTCAATTTT
TCACTAAAATAATAATAAAAAATATGTAATTCAATGCCAAAATAATTAAAGGGCTTTTCATGCTT
CTAAAATCGTTTTCCCATTTTTTTCCGGATAAATTTCTAATTAAATCGAAATTGGTTCA
Found at i:12247 original size:18 final size:18
Alignment explanation
Indices: 12224--12260 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
12214 CGAAATTGGT
*
12224 TTCAGATGCTCTTAAAAA
1 TTCAGATGCTCGTAAAAA
12242 TTCAGATGCTCGTAAAAA
1 TTCAGATGCTCGTAAAAA
12260 T
1 T
12261 AAATCCTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (18 bp):
TTCAGATGCTCGTAAAAA
Found at i:13175 original size:4 final size:4
Alignment explanation
Indices: 13152--13282 Score: 52
Period size: 4 Copynumber: 34.2 Consensus size: 4
13142 GAGGATAAAT
* * * *
13152 ATAA AT-A ATCA ATAA TTAA ATAA A-AT ATAT ATAA AT-A ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
* *
13197 ATGTA ATAA ATATA CGATAA AT-- ATAA AT-A ATCA ATAA TTATAA AT--
1 AT-AA ATAA ATA-A --ATAA ATAA ATAA ATAA ATAA ATAA --ATAA ATAA
* *
13242 ATAA AT-A ATCA ATAA AT-- ATAA AT-A ATAA ATAA ATCA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
13283 AGGCCACTCC
Statistics
Matches: 98, Mismatches: 11, Indels: 36
0.68 0.08 0.25
Matches are distributed among these distances:
2 6 0.06
3 17 0.17
4 63 0.64
5 4 0.04
6 5 0.05
7 3 0.03
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.31
Consensus pattern (4 bp):
ATAA
Found at i:13184 original size:30 final size:32
Alignment explanation
Indices: 13150--13266 Score: 97
Period size: 30 Copynumber: 3.8 Consensus size: 32
13140 GAGAGGATAA
*
13150 ATATAAATAATCAAT-AAT-TAAATAAAATAT
1 ATATAAATAATAAATAAATATAAATAAAATAT
*
13180 ATATAAATAATAAATAAATGT-AAT-AAATAT
1 ATATAAATAATAAATAAATATAAATAAAATAT
* * * *
13210 ACGATAAAT-ATAAAT--A-ATCAATAATTATAA
1 A-TATAAATAATAAATAAATATAAATAA-AATAT
*
13240 ATATAAATAATCAATAAATATAAATAA
1 ATATAAATAATAAATAAATATAAATAA
13267 TAAATAAATC
Statistics
Matches: 69, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
27 1 0.01
28 4 0.06
29 7 0.10
30 36 0.52
31 12 0.17
32 2 0.03
33 7 0.10
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (32 bp):
ATATAAATAATAAATAAATATAAATAAAATAT
Found at i:13222 original size:17 final size:18
Alignment explanation
Indices: 13146--13275 Score: 73
Period size: 17 Copynumber: 7.3 Consensus size: 18
13136 GGCTGAGAGG
13146 ATAAATATAAATA-ATCA
1 ATAAATATAAATATATCA
13163 AT-AAT-TAAATA-A--A
1 ATAAATATAAATATATCA
* *
13176 ATATATATAAATA-ATAA
1 ATAAATATAAATATATCA
*
13193 ATAAATGTAATAAATATA-CG
1 ATAAA--T-ATAAATATATCA
13213 ATAAATATAAATA-ATCA
1 ATAAATATAAATATATCA
*
13230 ATAATTATAAATATAAATAATCA
1 ATAAATAT-AA-AT--AT-ATCA
*
13253 ATAAATATAAATA-ATAA
1 ATAAATATAAATATATCA
13270 ATAAAT
1 ATAAAT
13276 CAATAAAAGG
Statistics
Matches: 90, Mismatches: 8, Indels: 30
0.70 0.06 0.23
Matches are distributed among these distances:
13 3 0.03
14 2 0.02
15 14 0.16
16 4 0.04
17 31 0.34
18 3 0.03
19 4 0.04
20 12 0.13
21 4 0.04
22 2 0.02
23 11 0.12
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.32
Consensus pattern (18 bp):
ATAAATATAAATATATCA
Found at i:13368 original size:25 final size:25
Alignment explanation
Indices: 13330--13659 Score: 225
Period size: 25 Copynumber: 12.9 Consensus size: 25
13320 CATACAAAAT
*
13330 ATGACCCCTACTGAATATGCAACTGC
1 ATGA-CCCTACTGAATATGCAACTAC
* *
13356 ATGACCATACTGAATATGCAACTAT
1 ATGACCCTACTGAATATGCAACTAC
* * ** * * * *
13381 TTCACCAAAATGAAAATGCGACTAT
1 ATGACCCTACTGAATATGCAACTAC
* *
13406 AAGACCCCACTGAATATG-ACACTAC
1 ATGACCCTACTGAATATGCA-ACTAC
* * *
13431 AAGACCCTACTGAATATGCGACTAT
1 ATGACCCTACTGAATATGCAACTAC
* * * *
13456 ATGATCTTACTGAATAT-AACACAAC
1 ATGACCCTACTGAATATGCA-ACTAC
* * *
13481 AAGATCCTACTGAATATGCGACTAC
1 ATGACCCTACTGAATATGCAACTAC
*
13506 ATGACCCCTACTGAATATGCCACTAC
1 ATGA-CCCTACTGAATATGCAACTAC
* * *
13532 ATGACCCCTACTAAATATGCCACTAA
1 ATGA-CCCTACTGAATATGCAACTAC
*
13558 ATGACCCCTACTGAATATGCAACTAT
1 ATGA-CCCTACTGAATATGCAACTAC
* *
13584 ATGATCTCCTA-TCGAATATGCAATTAT
1 ATGA-C-CCTACT-GAATATGCAACTAC
* * *
13611 AAGACCTGTACTGAATATGCAACTAT
1 ATGACC-CTACTGAATATGCAACTAC
* *
13637 ATCACCCCTATTGAATATGCAAC
1 ATGA-CCCTACTGAATATGCAAC
13660 CATATCACCC
Statistics
Matches: 244, Mismatches: 50, Indels: 20
0.78 0.16 0.06
Matches are distributed among these distances:
25 113 0.46
26 108 0.44
27 23 0.09
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.25
Consensus pattern (25 bp):
ATGACCCTACTGAATATGCAACTAC
Found at i:13521 original size:26 final size:26
Alignment explanation
Indices: 13328--15469 Score: 1875
Period size: 26 Copynumber: 82.2 Consensus size: 26
13318 TCCATACAAA
13328 ATATGACCCCTACTGAATATGCAACT
1 ATATGACCCCTACTGAATATGCAACT
** *
13354 GCATGA-CCATACTGAATATGCAACT
1 ATATGACCCCTACTGAATATGCAACT
* * ** * * *
13379 ATTTCA-CCAAAATGAAAATGCGACT
1 ATATGACCCCTACTGAATATGCAACT
*
13404 ATAAGACCCC-ACTGAATATG-ACACT
1 ATATGACCCCTACTGAATATGCA-ACT
* * *
13429 ACAAGA-CCCTACTGAATATGCGACT
1 ATATGACCCCTACTGAATATGCAACT
* * * *
13454 ATATGA-TCTTACTGAATAT-AACACA
1 ATATGACCCCTACTGAATATGCA-ACT
* * * *
13479 ACAAGA-TCCTACTGAATATGCGACT
1 ATATGACCCCTACTGAATATGCAACT
* *
13504 ACATGACCCCTACTGAATATGCCACT
1 ATATGACCCCTACTGAATATGCAACT
* * *
13530 ACATGACCCCTACTAAATATGCCACT
1 ATATGACCCCTACTGAATATGCAACT
*
13556 AAATGACCCCTACTGAATATGCAACT
1 ATATGACCCCTACTGAATATGCAACT
* *
13582 ATATGATCTCCTA-TCGAATATGCAATT
1 ATATGA-CCCCTACT-GAATATGCAACT
* **
13609 ATAAGACCTGTACTGAATATGCAACT
1 ATATGACCCCTACTGAATATGCAACT
* * *
13635 ATATCACCCCTATTGAATATGCAACC
1 ATATGACCCCTACTGAATATGCAACT
* *
13661 ATATCACCCCTACATGACGCTACTG-AA-T
1 ATATGACCCCTAC-TGA--ATA-TGCAACT
* *
13689 ATGCAACTACACGACCCTAATGAATATGCAACT
1 AT---A-T-GAC--CCCTACTGAATATGCAACT
** ** * *
13722 GCATGA-CATTACTAAATTTGCGAA-T
1 ATATGACCCCTACTGAATATGC-AACT
** *
13747 ATATGATGTCCTACTAAATATGCGAA-T
1 ATATGA-CCCCTACTGAATATGC-AACT
* *
13774 ATAAGA-CCCTACAGAATATGCAACT
1 ATATGACCCCTACTGAATATGCAACT
*
13799 ATATAACCCCTACTGAATATGCAACT
1 ATATGACCCCTACTGAATATGCAACT
* *
13825 ATATGA-CCCTATTGAATATGCAGCT
1 ATATGACCCCTACTGAATATGCAACT
* *
13850 ATATGACCCATTCTGAATATGCAACAAT
1 ATATGACCCCTACTGAATATGCAAC--T
* *
13878 ATAATG-TCCC-ACTGAATATGCAGCT
1 AT-ATGACCCCTACTGAATATGCAACT
* * * *
13903 TTATGACCCATTCTGAATATGCAGCT
1 ATATGACCCCTACTGAATATGCAACT
* ** *
13929 ATATGATGTCCC-ACAAAATATGCAGCT
1 ATATGA--CCCCTACTGAATATGCAACT
* **
13956 ACATGATGTCCTACTGAATATGCAACT
1 ATATGA-CCCCTACTGAATATGCAACT
13983 ATATGACCCCTACTGAATATGCGAA-T
1 ATATGACCCCTACTGAATATGC-AACT
* * ** ** *
14009 TTAAGATGTCAGACTGACA-ATGCGACT
1 ATATGA-CCCCTACTGA-ATATGCAACT
*
14036 ATATG-CACCCTACTGAATATGCAATT
1 ATATGAC-CCCTACTGAATATGCAACT
*
14062 ATATGTCCCCTACTGAATATGCAACT
1 ATATGACCCCTACTGAATATGCAACT
** * *
14088 ATATGGGCCCTACTGAATATTCTACT
1 ATATGACCCCTACTGAATATGCAACT
*
14114 ATAT-ACGGCCTACTGAATATGCAACT
1 ATATGAC-CCCTACTGAATATGCAACT
*
14140 ATATG-CGCCTTACTGAATATGCAACT
1 ATATGAC-CCCTACTGAATATGCAACT
* *
14166 ACATG-GCCCTACTGAATATGCAACT
1 ATATGACCCCTACTGAATATGCAACT
**
14191 ATATG-GGCCTCACTGAATATGCAACT
1 ATATGACCCCT-ACTGAATATGCAACT
* *
14217 ATATGTCCCCTACTGAATATCCAACT
1 ATATGACCCCTACTGAATATGCAACT
*
14243 ATATGTCCCCTACTGAATATGCAACT
1 ATATGACCCCTACTGAATATGCAACT
** * **
14269 ATATGGGCCCAACAAAATATGCAACT
1 ATATGACCCCTACTGAATATGCAACT
**
14295 ATATGGGCCCTACTGAATATGCAACT
1 ATATGACCCCTACTGAATATGCAACT
* *
14321 ATATGTCCCCTACTGAATATGAAACT
1 ATATGACCCCTACTGAATATGCAACT
* *
14347 ATATGAGCCCTCCTGAATATGCAACT
1 ATATGACCCCTACTGAATATGCAACT
14373 ATATGAGCCCTACTGATTTACTGAATATGCAACT
1 ATATGA-CCC--C-----TACTGAATATGCAACT
14407 ATAT-ATCCCCTACTGAATATGCAACT
1 ATATGA-CCCCTACTGAATATGCAACT
* * * *
14433 GTATGTCCCCTTACAGAAAATGCAAC-
1 ATATGACCCC-TACTGAATATGCAACT
* * *
14459 -TATGTCCCCTTACAGAAAATGCAAC-
1 ATATGACCCC-TACTGAATATGCAACT
*
14484 -TATGTCCCCTACTGAATATGCAACT
1 ATATGACCCCTACTGAATATGCAACT
*
14509 ATATGAGCCCTACTGAATATGCAACT
1 ATATGACCCCTACTGAATATGCAACT
* *
14535 ATATGTCCCCTACTGAATATGTAACT
1 ATATGACCCCTACTGAATATGCAACT
** *
14561 ATATGGGCTCTACTGAATATGCAACT
1 ATATGACCCCTACTGAATATGCAACT
*
14587 ATATG-TCCCTACTGAATATGCAACT
1 ATATGACCCCTACTGAATATGCAACT
* *
14612 ATATGTCCCCTACTGAATATACAACT
1 ATATGACCCCTACTGAATATGCAACT
* *
14638 AT-T-TCCCCTAATGAATAT-----T
1 ATATGACCCCTACTGAATATGCAACT
*
14657 ATATGAGCCCTACTGAATATGCAACT
1 ATATGACCCCTACTGAATATGCAACT
* *
14683 ATATGTCCCCTACTTAATATGCAACT
1 ATATGACCCCTACTGAATATGCAACT
**
14709 ATATGGGCCCTACTGAATATGCAACT
1 ATATGACCCCTACTGAATATGCAACT
* *
14735 ATATGAGCCCTACAGAATATGCAACT
1 ATATGACCCCTACTGAATATGCAACT
*
14761 ATATGTCCCCTACTGAATATGCAACT
1 ATATGACCCCTACTGAATATGCAACT
** *
14787 ATATGGGCCCTACAGAATATGCAACT
1 ATATGACCCCTACTGAATATGCAACT
14813 ATATGGA-CCCTACTGAATATGCAACT
1 ATAT-GACCCCTACTGAATATGCAACT
14839 ATATGGA-CCCTACTGAATATGCAACT
1 ATAT-GACCCCTACTGAATATGCAACT
* *
14865 ATATGAGCCCTACTGAATATGCAATT
1 ATATGACCCCTACTGAATATGCAACT
14891 ATATGGA-CCCTACTGAATATGCAACT
1 ATAT-GACCCCTACTGAATATGCAACT
14917 ATATGGA-CCCTACTGAATATGCAACT
1 ATAT-GACCCCTACTGAATATGCAACT
14943 ATATGAACCCC-ACTGAATATGCAACT
1 ATATG-ACCCCTACTGAATATGCAACT
*
14969 ATATGTCCCCTACTGAATATGCAACT
1 ATATGACCCCTACTGAATATGCAACT
* *
14995 ATATGTCCCCTACTGAATATTCAACT
1 ATATGACCCCTACTGAATATGCAACT
*
15021 ATATGAGCCCCTACTGAGTA-GACAACT
1 ATATGA-CCCCTACTGAATATG-CAACT
** *
15048 ATATGGGCCCTACTGAGTA-GACAACT
1 ATATGACCCCTACTGAATATG-CAACT
** *
15074 ATATGGGCCCTACTGAGTA-GACAACT
1 ATATGACCCCTACTGAATATG-CAACT
** *
15100 ATATGGGCCCTACTGAATACGCAACT
1 ATATGACCCCTACTGAATATGCAACT
** *
15126 ATATGGGCCCTACTGAATACGCAACT
1 ATATGACCCCTACTGAATATGCAACT
** *
15152 ATATGGGCCCTACTGAATACGCAACT
1 ATATGACCCCTACTGAATATGCAACT
**
15178 ATATGGGCCCTACTGAATATGCAACT
1 ATATGACCCCTACTGAATATGCAACT
15204 ATATGTA-CCCTACTGAATATGCAACT
1 ATATG-ACCCCTACTGAATATGCAACT
* *
15230 ATATGTCCTCTACTGAATATGCAACT
1 ATATGACCCCTACTGAATATGCAACT
**
15256 ATATGGGCCC--CTGAATATGCAACT
1 ATATGACCCCTACTGAATATGCAACT
* *
15280 ATATGTCCTCTACTGAATATGCAACT
1 ATATGACCCCTACTGAATATGCAACT
* *
15306 ATATGTCCTCTACTGAATATGCAACT
1 ATATGACCCCTACTGAATATGCAACT
*
15332 ATATGGGCCCCTCCTACTGAATATGCAACT
1 ATAT--G-ACC-CCTACTGAATATGCAACT
*
15362 ATAT-ATCCCCTACAGAATATGCAACT
1 ATATGA-CCCCTACTGAATATGCAACT
*
15388 ATATGTCCCCTACTGAATATGCAACT
1 ATATGACCCCTACTGAATATGCAACT
**
15414 ATATGGGCCCTACTGAATATGCAACT
1 ATATGACCCCTACTGAATATGCAACT
** *
15440 ATATGGGCCCTACTGAATTTGCAACT
1 ATATGACCCCTACTGAATATGCAACT
15466 ATAT
1 ATAT
15470 AGGCCCTACT
Statistics
Matches: 1796, Mismatches: 233, Indels: 174
0.82 0.11 0.08
Matches are distributed among these distances:
19 3 0.00
20 1 0.00
21 12 0.01
24 56 0.03
25 258 0.14
26 1218 0.68
27 157 0.09
28 12 0.01
29 11 0.01
30 24 0.01
31 4 0.00
32 5 0.00
33 8 0.00
34 22 0.01
35 5 0.00
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (26 bp):
ATATGACCCCTACTGAATATGCAACT
Found at i:13973 original size:80 final size:77
Alignment explanation
Indices: 13807--14004 Score: 229
Period size: 80 Copynumber: 2.5 Consensus size: 77
13797 CTATATAACC
**
13807 CCTACTGAATATGCAACTATATGACCCTAT-TGAATATGCAGCTATATGACCCATTCTGAATATG
1 CCTACTGAATATGCAACTATATGACCCT-TCTGAATATGCAGCTATATGACCCA-TCAAAATATG
*
13871 CAACAATATAATGT
64 CAACAACATAATGT
* * *
13885 CCCACTGAATATGCAGCTTTATGACCCATTCTGAATATGCAGCTATATGATGTCCCA-CAAAATA
1 CCTACTGAATATGCAACTATATGACCC-TTCTGAATATGCAGCTATATGA---CCCATCAAAATA
* * *
13949 TGCAGCTACATGATGT
62 TGCAACAACATAATGT
*
13965 CCTACTGAATATGCAACTATATGACCCCTACTGAATATGC
1 CCTACTGAATATGCAACTATATGA-CCCTTCTGAATATGC
14005 GAATTTAAGA
Statistics
Matches: 101, Mismatches: 13, Indels: 10
0.81 0.10 0.08
Matches are distributed among these distances:
78 25 0.25
79 20 0.20
80 49 0.49
81 3 0.03
82 4 0.04
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.29
Consensus pattern (77 bp):
CCTACTGAATATGCAACTATATGACCCTTCTGAATATGCAGCTATATGACCCATCAAAATATGCA
ACAACATAATGT
Found at i:15726 original size:4 final size:4
Alignment explanation
Indices: 15717--15742 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
15707 TGTTTTAAAA
15717 AAAC AAAC AAAC AAAC AAAC AAAC AA
1 AAAC AAAC AAAC AAAC AAAC AAAC AA
15743 GTATTTACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:15927 original size:15 final size:15
Alignment explanation
Indices: 15909--15941 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
15899 TGAAAACATT
15909 AATTAAGAAATAAAA
1 AATTAAGAAATAAAA
*
15924 AATTATGAAATAAAA
1 AATTAAGAAATAAAA
15939 AAT
1 AAT
15942 AATAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (15 bp):
AATTAAGAAATAAAA
Found at i:24978 original size:41 final size:42
Alignment explanation
Indices: 24933--25016 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
24923 CAATCTAAAT
* *
24933 AAATATATAAATTCACAC-CAGGAAATGCTAAGTTGAGTGGA
1 AAATATATAAATCCACACTAAGGAAATGCTAAGTTGAGTGGA
* *
24974 AAATATATAAATCCACACTAAGGAAGTGTTAAGTTGAGTGGA
1 AAATATATAAATCCACACTAAGGAAATGCTAAGTTGAGTGGA
25016 A
1 A
25017 GGAGTTTAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
41 17 0.45
42 21 0.55
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.25
Consensus pattern (42 bp):
AAATATATAAATCCACACTAAGGAAATGCTAAGTTGAGTGGA
Found at i:25079 original size:24 final size:24
Alignment explanation
Indices: 25047--25096 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
25037 GGAGATCTTG
*
25047 GATTCGATCATTCACATATTGAGT
1 GATTCGATCATTCACAGATTGAGT
*
25071 GATTCGATCATTCACGGATTGAGT
1 GATTCGATCATTCACAGATTGAGT
25095 GA
1 GA
25097 AAAATAGCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (24 bp):
GATTCGATCATTCACAGATTGAGT
Found at i:32717 original size:27 final size:25
Alignment explanation
Indices: 32681--32750 Score: 104
Period size: 27 Copynumber: 2.7 Consensus size: 25
32671 ATTACTATAG
32681 AAAAAGGGCTCTGTTTTTACCTCAAAA
1 AAAAAGGGCTCTGTTTTTACCT--AAA
*
32708 AAAAAAGGCTCTGTTTTTACCTAAA
1 AAAAAGGGCTCTGTTTTTACCTAAA
*
32733 AAAAGGGGCTCTGTTTTT
1 AAAAAGGGCTCTGTTTTT
32751 CATCTGTGCC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
25 19 0.47
27 21 0.52
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (25 bp):
AAAAAGGGCTCTGTTTTTACCTAAA
Found at i:33888 original size:2 final size:2
Alignment explanation
Indices: 33881--33911 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
33871 TCCGACCTTG
33881 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
33912 GTTATTAGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:37082 original size:18 final size:18
Alignment explanation
Indices: 37059--37105 Score: 76
Period size: 20 Copynumber: 2.5 Consensus size: 18
37049 ATATCAATCA
37059 ATTTGTAATAATTTTAAT
1 ATTTGTAATAATTTTAAT
37077 ATTTGTGTAATAATTTTAAT
1 A-TT-TGTAATAATTTTAAT
37097 ATTTGTAAT
1 ATTTGTAAT
37106 GTAAAAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.26
19 4 0.15
20 16 0.59
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (18 bp):
ATTTGTAATAATTTTAAT
Found at i:37087 original size:20 final size:20
Alignment explanation
Indices: 37062--37102 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
37052 TCAATCAATT
37062 TGTAATAATTTTAATATTTG
1 TGTAATAATTTTAATATTTG
37082 TGTAATAATTTTAATATTTG
1 TGTAATAATTTTAATATTTG
37102 T
1 T
37103 AATGTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (20 bp):
TGTAATAATTTTAATATTTG
Found at i:37096 original size:9 final size:10
Alignment explanation
Indices: 37058--37105 Score: 57
Period size: 9 Copynumber: 5.0 Consensus size: 10
37048 TATATCAATC
37058 AATTTGTAAT
1 AATTTGTAAT
37068 AATTT-TAAT
1 AATTTGTAAT
*
37077 ATTTGTGTAAT
1 AATT-TGTAAT
37088 AATTT-TAAT
1 AATTTGTAAT
37097 -ATTTGTAAT
1 AATTTGTAAT
37106 GTAAAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
8 4 0.12
9 15 0.45
10 7 0.21
11 7 0.21
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (10 bp):
AATTTGTAAT
Found at i:37169 original size:2 final size:2
Alignment explanation
Indices: 37162--37192 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
37152 TGTACGGATT
37162 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
37193 TTAGACCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:37660 original size:27 final size:27
Alignment explanation
Indices: 37622--37679 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
37612 TTTATTTTAT
* *
37622 AAATTTTTTTAAGAAAAATCAGTTAGG
1 AAATTCTTTTAAGAAAAATCAGTTAAG
*
37649 AAATTCTTTTAAGAAAATTCAGTTAAG
1 AAATTCTTTTAAGAAAAATCAGTTAAG
37676 AAAT
1 AAAT
37680 GAAATTTTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.36
Consensus pattern (27 bp):
AAATTCTTTTAAGAAAAATCAGTTAAG
Found at i:37679 original size:13 final size:14
Alignment explanation
Indices: 37630--37678 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
37620 ATAAATTTTT
*
37630 TTAAGAAAAATCAG
1 TTAAGAAAATTCAG
* **
37644 TT-AGGAAATTCTT
1 TTAAGAAAATTCAG
37657 TTAAGAAAATTCAG
1 TTAAGAAAATTCAG
37671 TTAAGAAA
1 TTAAGAAA
37679 TGAAATTTTG
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
13 9 0.33
14 18 0.67
ACGTcount: A:0.49, C:0.06, G:0.14, T:0.31
Consensus pattern (14 bp):
TTAAGAAAATTCAG
Done.