Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007181.1 Corchorus capsularis cultivar CVL-1 contig07202, 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: 94155
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Found at i:1161 original size:331 final size:332
Alignment explanation
Indices: 1--2820 Score: 2868
Period size: 331 Copynumber: 8.5 Consensus size: 332
** * * *
1 TTTAACGTAAAAAATATTGGGGGACTTTTCAAAGCTTTTAATATCGTTTTTCATATTTTTCTTAA
1 TTTAACGCCAAAAAGATTGGAGGACTTTTC-ACGCTTTTAATATCGTTTTTCATATTTTTCTTAA
** * * *
66 TTAATTTCTAATTAAATCGAAACAAGATTTTGATGCTCCTAAAAACAAATCCTTTAATCCAATGT
65 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGT
* * * *
131 GGCTGATATTTGATTAGATGACTATCAAAATATTTCAAAGGAGTCTCGACGCCAAAAATCATGCA
130 GGCTGAGATTTGATTAGATGAATAT--AGATATTTC-AAGGAGTCTCGGCGCCAAAAATCATGCA
* * * * *
196 AAATCTGAGTCAAGTGCCCCGAAACT-CG-TTTTAGCAAAAAAC-GTGAATGGTTAATACAATGA
192 AAA-CTGAGTC-AGGGCCCTGAAACTGCGTTTTTAGCCAAAAACTGTG-ATGGTTATTAC-ACGA
*** * ** * *
258 TTTCAAATAAATGTTTTGCAAAAAAAAAATT-ACTAGAAATA-TTTTCCTAAAATTTTTTGGATA
253 TTTCGGCTAAA-ATTTTG-----AAAAAATTGACCCGAAAAATTTTTCCT-CAA-TTTTTGGATA
*
321 AAA-ACTTCATGAAATATATATAA
310 AAATAC-TCATAAAATATATATAA
*** * * *
344 TTTATTTCCAAAAAGATTGGAGGACTTTTCACGCTTTTCATATCGTTTTTAAT-TTTTTTTTGAA
1 TTTAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTT-AA
* * * * *
408 TTACTTTTTAATT-AATGTGAAATAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAATG
65 TTAATTTCTAATTAAAT-CGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATG
* * * ** ** * *
472 TGGCTGAGATTAGATTAGATGAATATGGATATCTCAAGGAGTCTTAGAACGAAAAATAATGCAAA
129 TGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAA
*** * * * * * *
537 ACTGCCCCTGGG-CCTGTAA-TGCTTTTTTAGACAAAAA-TCGTGATGATTATTATACGATTTCG
194 ACTGAGTCAGGGCCCTGAAACTGCGTTTTTAGCCAAAAACT-GTGATGGTTATTACACGATTTCG
* * * * * *
599 GCTAAAATTTTGTAAAAGTTGACCGGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAA
258 GCTAAAATTTTGAAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGATAAAATACTCATAAA
*
664 AGAATATATAA
323 A-TATATATAA
* * * * * * *
675 TTCAACGCCAAAAAGATAGAAGGACTTTTCGCGTTTTTAATATTGTTTTTCATATTTTTTCTGAA
1 TTTAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTCTTAA
* * * *
740 TTAATTTTTATTTAAATCGAAACAAGATTCAGATGCTGGTAAAAACAAATTCTTAAATGCAATGT
65 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGT
* * * * * * **
805 CGCTAAGATTTTATTAGATGAATATAGATATTTCAAGGAATGTCGGTGCCAAAAATCATGCAATG
130 GGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAA
* * *
870 TTGAGTCAGGGCCCTG-AACTGCGTTTTTAGCCAAAAACTGTGATGGTTACTACACGATTTTGGC
195 CTGAGTCAGGGCCCTGAAACTGCGTTTTTAGCCAAAAACTGTGATGGTTATTACACGATTTCGGC
*
934 TAAAATTCTGAAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGATAAAATACTCATAAAAT
260 TAAAATTTTGAAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGATAAAATACTCATAAAAT
*
999 ATTTATAA
325 ATATATAA
* *
1007 TTTAACGCCAAAAAGATTGGGGGACTTTTCAAGCTTTTAATATCGTTTTTCATATTTTTCTTAAT
1 TTTAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTTAAT
* *
1072 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTTAATCCAATGTG
66 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTG
* *
1137 GCTGATATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGACGCCAAAAATCATGCAAAAC
131 GCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAAC
* * * * * *
1202 TGAGTCAGTGCCCCGAAACT-CGTTTTTAGCAAAAAAAACTGTGATGGTTAATACATGATTTCAG
196 TGAGTCAGGGCCCTGAAACTGCGTTTTTAGC--CAAAAACTGTGATGGTTATTACACGATTTCGG
* * * **
1266 CTAAAGTTCTGCAAAAAAAAATGACTGGAAAAATATTTTCCT-ACATTTTTGGATAAAATACTCA
259 CTAAAATTTTG---AAAAAATTGACCCGAAAAAT-TTTTCCTCA-ATTTTTGGATAAAATACTCA
* *
1330 TGAAATATATATGA
319 TAAAATATATATAA
** * *
1344 TTTATTGCCAAAAAGATTGGAGGACTTTTCACGCTTTTCATATCGTTTTTCAT-TTTTTTTTAAT
1 TTTAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTTAAT
* * * * * * *
1408 TACTTTTTAATT-AATGTGATATAAGATTCAAATGCTTGTAAAAACAAATCCTTAAATGCAATGT
66 TAATTTCTAATTAAAT-CGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGT
** * * ** * *
1472 CCCTGAGATTTGATTAGATGAATATGGATATCTCAAGGAGTCTTAGCGCGAAAAATAATGCAAAA
130 GGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAA
*** * * * * * *
1537 CTGCCCCTGGG-CCTGTAA-TGCTTTTTTAGCCAAAAA-TCGTGATGATTATTATATGATTTCGG
195 CTGAGTCAGGGCCCTGAAACTGCGTTTTTAGCCAAAAACT-GTGATGGTTATTACACGATTTCGG
* * * *
1599 CTAAAATTTTGTAAAAATT-AACCGAAAAGATATTTCCTCAA-TTTTGGCTAAAATACTCATAAA
259 CTAAAATTTTGAAAAAATTGACCCGAAAA-ATTTTTCCTCAATTTTTGGATAAAATACTCATAAA
1662 CGA-ATATATAA
323 --ATATATATAA
* * * * * * *
1673 TTCAACGCCAAAAAGATAGAAGGAATTTTCATCGTTTTTAATAT-TTTTTTCATATTTTTTCTGA
1 TTTAACGCCAAAAAGATTGGAGGACTTTTCA-CGCTTTTAATATCGTTTTTCATA-TTTTTCTTA
* *
1737 ATTAATTTTTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATG
64 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATG
* * * * *
1802 TGGCTAAGATTTTATTAGATGAATATAGATATTTCAAGGAGTGTCAGCGCCAAAAATCATGCAAT
129 TGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAA
* * *
1867 GCTGAGTCAGGGCCC-GAAA-TGCGTTTTTAGCCAAAAACTGTGATGGTTACTACACGATTTTGG
194 ACTGAGTCAGGGCCCTGAAACTGCGTTTTTAGCCAAAAACTGTGATGGTTATTACACGATTTCGG
*
1930 CTAAAATTTTGAAAAAA-TGACCCGAAACATTTTTCCTCAATTTTTGGATAAAATACTCATAAAA
259 CTAAAATTTTGAAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGATAAAATACTCATAAAA
*
1994 TATTTATAA
324 TATATATAA
* *
2003 TTTAACGCCAAAAAGATTGGGGGACTTTTCAAGCTTTTAATATCGTTTTTCATATTTTTCTTAAT
1 TTTAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTTAAT
* *
2068 TAATTACTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATGCAATGTG
66 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTG
* * * * *
2133 GCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTTTTGACGGCAAAAATCATGCAAAAC
131 GCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAAC
* ** * ** * *
2198 TGAG-CCGGGACCCCAAAAC-GCTTTTTTAGCCAATAAAACTGTGATAATTATTACACTATTTTG
196 TGAGTCAGGG-CCCTGAAACTGCGTTTTTAGCC-A-AAAACTGTGATGGTTATTACACGATTTCG
* * * * * *
2261 GCTAAAATTTTGTAAAAATGGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATAGTCATAAA
258 GCTAAAATTTTGAAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGATAAAATACTCATAAA
*
2326 AAATATATAA
323 ATATATATAA
* * * * * **
2336 TTCAGCACCAAAAATATT-GACGGGA-TTTTGACG-TTTCTAATATCGTTTTTCATATTTTTCCA
1 TTTAACGCCAAAAAGATTGGA--GGACTTTTCACGCTTT-TAATATCGTTTTTCATATTTTTCTT
* * *
2398 AATTAATTTCTAATTAAATCGAAACAAGATTCGGATGCTCGTAAAAACAAATCCTTTAATCCAAT
63 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAAT
* * * * ** * *
2463 GTGGCTGAAATTTGTTTAAATGAATATAGATATTTTAAATAGTCTCGGAGCTAAAAATCATGCAA
128 GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAA
* * * * * * * * *
2528 AATTGAG-CCGGGTCTTCGGAA-TGCGGTTTTAGCTGAAAACCT-TGATGGTTTGTTAGTACACG
193 AACTGAGTCAGGGCCCT-GAAACTGCGTTTTTAGC-CAAAAACTGTGAT-G---GTTATTACACG
* * * *
2590 ATTTCGGCTAAAATTTTGCAAAAATTGACACGAAAGATTTCTT-CTCAATTTTTGGCTAAAATAC
252 ATTTCGGCTAAAATTTTGAAAAAATTGACCCGAAAAATTT-TTCCTCAATTTTTGGATAAAATAC
2654 TCATAAAA-ATATATAA
316 TCATAAAATATATATAA
* * * * * * * *
2670 TTCAATGCCAAAAAGATTTGAGGACTTTTTATGCTTTTAATATCGTATTTCTTATTTTTTCTAAA
1 TTTAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTCTTAA
* ** * * *
2735 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAGAACAAATTTTTATATCCAATAT
65 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGT
* **
2800 TGCTGAGATTTGGCTAGATGA
130 GGCTGAGATTTGATTAGATGA
2821 TGTAAAATAT
Statistics
Matches: 2056, Mismatches: 359, Indels: 132
0.81 0.14 0.05
Matches are distributed among these distances:
328 24 0.01
329 197 0.10
330 113 0.05
331 418 0.20
332 235 0.11
333 408 0.20
334 48 0.02
335 182 0.09
336 159 0.08
337 107 0.05
338 7 0.00
339 24 0.01
340 6 0.00
341 10 0.00
342 95 0.05
343 23 0.01
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (332 bp):
TTTAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTTAAT
TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTG
GCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAAC
TGAGTCAGGGCCCTGAAACTGCGTTTTTAGCCAAAAACTGTGATGGTTATTACACGATTTCGGCT
AAAATTTTGAAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGATAAAATACTCATAAAATA
TATATAA
Found at i:3196 original size:15 final size:16
Alignment explanation
Indices: 3178--3207 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3168 ATAAAGAATA
3178 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
3193 ATATTATAATCTAAA
1 ATATTATAATCTAAA
3208 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:17338 original size:20 final size:21
Alignment explanation
Indices: 17299--17340 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
17289 TGAATGGTAA
*
17299 CCAATTTTTTCATTTTTTTAGG
1 CCAATTTTTT-ATTTATTTAGG
17321 CCAATTTTTT-TTTATTTAGG
1 CCAATTTTTTATTTATTTAGG
17341 AGCTAAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
22 10 0.53
ACGTcount: A:0.19, C:0.12, G:0.10, T:0.60
Consensus pattern (21 bp):
CCAATTTTTTATTTATTTAGG
Found at i:19974 original size:18 final size:18
Alignment explanation
Indices: 19951--19985 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
19941 CACATGAATC
19951 CATTTCTTTATTAGTGCT
1 CATTTCTTTATTAGTGCT
19969 CATTTCTTTATTAGTGC
1 CATTTCTTTATTAGTGC
19986 CCGTTTGGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (18 bp):
CATTTCTTTATTAGTGCT
Found at i:21533 original size:18 final size:18
Alignment explanation
Indices: 21498--21537 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
21488 TGATTTAGAA
* *
21498 GATGATGATTATCTTTAT
1 GATGATGATGATCATTAT
*
21516 GATGATGATGATGATTAT
1 GATGATGATGATCATTAT
21534 GATG
1 GATG
21538 GAGATGGTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.03, G:0.25, T:0.42
Consensus pattern (18 bp):
GATGATGATGATCATTAT
Found at i:26222 original size:92 final size:92
Alignment explanation
Indices: 26065--26248 Score: 368
Period size: 92 Copynumber: 2.0 Consensus size: 92
26055 CTAGGAGAAA
26065 TTATTAGGTGGGACCACACGTCATTCATGGGACTAATCAATGGAATCTTGCCATGCCAAATGATC
1 TTATTAGGTGGGACCACACGTCATTCATGGGACTAATCAATGGAATCTTGCCATGCCAAATGATC
26130 TCTTTAAATTTAGGCACGATTTTAACT
66 TCTTTAAATTTAGGCACGATTTTAACT
26157 TTATTAGGTGGGACCACACGTCATTCATGGGACTAATCAATGGAATCTTGCCATGCCAAATGATC
1 TTATTAGGTGGGACCACACGTCATTCATGGGACTAATCAATGGAATCTTGCCATGCCAAATGATC
26222 TCTTTAAATTTAGGCACGATTTTAACT
66 TCTTTAAATTTAGGCACGATTTTAACT
26249 AAGGGTTTAG
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (92 bp):
TTATTAGGTGGGACCACACGTCATTCATGGGACTAATCAATGGAATCTTGCCATGCCAAATGATC
TCTTTAAATTTAGGCACGATTTTAACT
Found at i:27050 original size:157 final size:157
Alignment explanation
Indices: 26764--27065 Score: 577
Period size: 157 Copynumber: 1.9 Consensus size: 157
26754 GCAACCAATC
26764 TCTAAGATTGGGTAGCAACCATAATTTATTAGACTAATAGCTTAGGTGTTGGGTTGGTCATATTA
1 TCTAAGATTGGGTAGCAACCATAATTTATTAGACTAATAGCTTAGGTGTTGGGTTGGTCATATTA
*
26829 ATATACACACAATAGTTATTAAGAGTATATTTTTTTTGGTATATTCTTAATGTTATTAAGAATAT
66 ATATACACACAATAGTTATTAAGAATATATTTTTTTTGGTATATTCTTAATGTTATTAAGAATAT
26894 ATATAGCATTAGTTTATTAGACTAATT
131 ATATAGCATTAGTTTATTAGACTAATT
* *
26921 TCTAAGATTGGGTAGCAATCTTAATTTATTAGACTAATAGCTTAGGTGTTGGGTTGGTCATATTA
1 TCTAAGATTGGGTAGCAACCATAATTTATTAGACTAATAGCTTAGGTGTTGGGTTGGTCATATTA
26986 ATATACACACAATAGTTATTAAGAATATATTTTTTTTGGTATATTCTTAATGTTATTAAGAATAT
66 ATATACACACAATAGTTATTAAGAATATATTTTTTTTGGTATATTCTTAATGTTATTAAGAATAT
27051 ATATAGCATTAGTTT
131 ATATAGCATTAGTTT
27066 CTAACATACA
Statistics
Matches: 142, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
157 142 1.00
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (157 bp):
TCTAAGATTGGGTAGCAACCATAATTTATTAGACTAATAGCTTAGGTGTTGGGTTGGTCATATTA
ATATACACACAATAGTTATTAAGAATATATTTTTTTTGGTATATTCTTAATGTTATTAAGAATAT
ATATAGCATTAGTTTATTAGACTAATT
Found at i:28210 original size:11 final size:11
Alignment explanation
Indices: 28196--28233 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
28186 ATTCATAACA
28196 AATTTATAATT
1 AATTTATAATT
28207 AATTTATAATT
1 AATTTATAATT
28218 -ATTTGATAATT
1 AATTT-ATAATT
*
28229 TATTT
1 AATTT
28234 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:34315 original size:19 final size:19
Alignment explanation
Indices: 34291--34336 Score: 74
Period size: 21 Copynumber: 2.3 Consensus size: 19
34281 TTTCAGCAGA
34291 AAAAGACTCTTTTGCCAAC
1 AAAAGACTCTTTTGCCAAC
34310 AAAAGAAACTCTTTTGCCAAC
1 AAAAG--ACTCTTTTGCCAAC
34331 AAAAGA
1 AAAAGA
34337 AGTCACAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.24
21 19 0.76
ACGTcount: A:0.46, C:0.22, G:0.11, T:0.22
Consensus pattern (19 bp):
AAAAGACTCTTTTGCCAAC
Found at i:34322 original size:21 final size:21
Alignment explanation
Indices: 34296--34337 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
34286 GCAGAAAAAG
34296 ACTCTTTTGCCAACAAAAGAA
1 ACTCTTTTGCCAACAAAAGAA
34317 ACTCTTTTGCCAACAAAAGAA
1 ACTCTTTTGCCAACAAAAGAA
34338 GTCACAGGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.24, G:0.10, T:0.24
Consensus pattern (21 bp):
ACTCTTTTGCCAACAAAAGAA
Found at i:34869 original size:287 final size:287
Alignment explanation
Indices: 34317--34867 Score: 1014
Period size: 286 Copynumber: 1.9 Consensus size: 287
34307 AACAAAAGAA
34317 ACTCTTTTGCCAACAAAAGAAGTCACAGGAGGGGTGCCACCTCACCCTCCCATTTATTCAAGAAA
1 ACTCTTTTGCCAACAAAAGAAGTCACAGGAGGGGTGCCACCTCACCCTCCCATTTATTCAAGAAA
** *
34382 TCTTAATTAAGGTTGTTAAAATTTAGGTTGTTCTTTGATTAGCTGTTGGGCTTATGCCTATTAGG
66 TCTTAATTAAGGTTGTTAAAATTTAAATCGTTCTTTGATTAGCTGTTGGGCTTATGCCTATTAGG
*
34447 TCCAACCCACATTTTAGCTTACTTTCAAGTGGGCTTTATGGCCTTGATAATTGGATGGCTAAGAT
131 TCCAACCCACATTTTAGCTCACTTTCAAGTGGGCTTTATGGCCTTGATAATTGGATGGCTAAGAT
34512 TTGATTTTAATCAAATCATCCAATGGTCATAATTAAAAAGAGATATGGATTAAATGAGATAAAAA
196 TTGATTTTAATCAAATCATCCAATGGTCATAATTAAAAAGAGATATGGATTAAATGAGATAAAAA
34577 AAAAACTTAAATTTTCAGCAGAAAAAG
261 AAAAACTTAAATTTTCAGCAGAAAAAG
*
34604 ACTCTTTTGCCAACAAAAGAAGTCACGGGAGGGGTGCCACCTCACCCTCCCATTTATTCAAGAAA
1 ACTCTTTTGCCAACAAAAGAAGTCACAGGAGGGGTGCCACCTCACCCTCCCATTTATTCAAGAAA
*
34669 TTTTAATTAAGGTTGTTAAAATTTAAATCGTTCTTTGATTAGCTGTTGGGCTTATGCCTATT-GG
66 TCTTAATTAAGGTTGTTAAAATTTAAATCGTTCTTTGATTAGCTGTTGGGCTTATGCCTATTAGG
* *
34733 TCCAACCCACATTTTGGCTCGCTTTCAAGTGGGCTTTATGGCCTTGATAATTGGATGGCTAAGAT
131 TCCAACCCACATTTTAGCTCACTTTCAAGTGGGCTTTATGGCCTTGATAATTGGATGGCTAAGAT
*
34798 TTGATTTTAATCAAATCATCCAATGGTCATAATTAAAAAGAGATATGGATTAAATGAGTTAAAAA
196 TTGATTTTAATCAAATCATCCAATGGTCATAATTAAAAAGAGATATGGATTAAATGAGATAAAAA
34863 AAAAA
261 AAAAA
34868 ACAAACTTTG
Statistics
Matches: 255, Mismatches: 9, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
286 133 0.52
287 122 0.48
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (287 bp):
ACTCTTTTGCCAACAAAAGAAGTCACAGGAGGGGTGCCACCTCACCCTCCCATTTATTCAAGAAA
TCTTAATTAAGGTTGTTAAAATTTAAATCGTTCTTTGATTAGCTGTTGGGCTTATGCCTATTAGG
TCCAACCCACATTTTAGCTCACTTTCAAGTGGGCTTTATGGCCTTGATAATTGGATGGCTAAGAT
TTGATTTTAATCAAATCATCCAATGGTCATAATTAAAAAGAGATATGGATTAAATGAGATAAAAA
AAAAACTTAAATTTTCAGCAGAAAAAG
Found at i:40392 original size:80 final size:80
Alignment explanation
Indices: 40259--40420 Score: 281
Period size: 80 Copynumber: 2.0 Consensus size: 80
40249 ACAGATATCC
*
40259 AAGGCCTTAAACTCGAAATCGTACCGAATCCGCGTCGGATTGTAATCTCACTATCCAAAACCACA
1 AAGGCCTTAAACTCGAAATCGCACCGAATCCGCGTCGGATTGTAATCTCACTATCCAAAACCACA
40324 CAAAAACCGTTTAAT
66 CAAAAACCGTTTAAT
* *
40339 AAGGCCTTAAACTCGAAA-CAGCATCGAATCCGCGTCGGATTGTAATCTCACTATTCAAAACCAC
1 AAGGCCTTAAACTCGAAATC-GCACCGAATCCGCGTCGGATTGTAATCTCACTATCCAAAACCAC
40403 ACAAAAACCGTTTAAT
65 ACAAAAACCGTTTAAT
40419 AA
1 AA
40421 ACGGAATCGG
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
79 1 0.01
80 77 0.99
ACGTcount: A:0.38, C:0.27, G:0.14, T:0.22
Consensus pattern (80 bp):
AAGGCCTTAAACTCGAAATCGCACCGAATCCGCGTCGGATTGTAATCTCACTATCCAAAACCACA
CAAAAACCGTTTAAT
Found at i:43480 original size:13 final size:13
Alignment explanation
Indices: 43464--43488 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43454 TGGCTATTTA
43464 TTTTTTTTCTAAT
1 TTTTTTTTCTAAT
43477 TTTTTTTTCTAA
1 TTTTTTTTCTAA
43489 CAACGGAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTTTTCTAAT
Found at i:52576 original size:12 final size:12
Alignment explanation
Indices: 52555--52587 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
52545 ATTTTTTCCC
52555 GCACGCGCTCCT
1 GCACGCGCTCCT
*
52567 GCATGCGCTCCT
1 GCACGCGCTCCT
52579 GCACGCGCT
1 GCACGCGCT
52588 AGGAATTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.09, C:0.45, G:0.27, T:0.18
Consensus pattern (12 bp):
GCACGCGCTCCT
Found at i:59247 original size:35 final size:36
Alignment explanation
Indices: 59201--59406 Score: 289
Period size: 35 Copynumber: 5.8 Consensus size: 36
59191 TTCTTACTAA
*
59201 ACTTAATTACCCTGAATTAAGTTATTTATTGAACT-
1 ACTTAATTACCCTGAATTAAGTTACTTATTGAACTC
*
59236 ACTTAATTACCCTGAATTAAGTTACTCATT-AACTC
1 ACTTAATTACCCTGAATTAAGTTACTTATTGAACTC
*
59271 ACTTAATTACCTTGAATTAAGTTACTTATTGAACT-
1 ACTTAATTACCCTGAATTAAGTTACTTATTGAACTC
*
59306 ACTTAATTACCCTGAATTAAGTTACATATT-AACTC
1 ACTTAATTACCCTGAATTAAGTTACTTATTGAACTC
* *
59341 ACTTAATTACCCCGAATTAAAGTTGA-TTACTG-ACTC
1 ACTTAATTACCCTGAATT-AAGTT-ACTTATTGAACTC
*
59377 ACTTAATTACCCTGAATTAAGTTGCTTATT
1 ACTTAATTACCCTGAATTAAGTTACTTATT
59407 ACTGATTCAC
Statistics
Matches: 152, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
34 8 0.05
35 110 0.72
36 33 0.22
37 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.39
Consensus pattern (36 bp):
ACTTAATTACCCTGAATTAAGTTACTTATTGAACTC
Found at i:65649 original size:21 final size:21
Alignment explanation
Indices: 65623--65667 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
65613 GAGTTCTGGA
65623 TTGCTAAACACCGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
** *
65644 TTGCTATTCATCGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
65665 TTG
1 TTG
65668 ACTTTTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.33, G:0.11, T:0.38
Consensus pattern (21 bp):
TTGCTAAACACCGCCCCATTT
Found at i:66386 original size:45 final size:46
Alignment explanation
Indices: 66305--66402 Score: 153
Period size: 45 Copynumber: 2.2 Consensus size: 46
66295 ATAATCAGAG
* * *
66305 ATTATAAACCCAACCCCAAATTTAGTTATGACTGAAAATTGATGCA
1 ATTATCAACCCAACCCCAAAATTAGTTATGAATGAAAATTGATGCA
*
66351 ATTATCAACCCAA-CCCAAAATTATTTATGAATGAAAATTGATGCA
1 ATTATCAACCCAACCCCAAAATTAGTTATGAATGAAAATTGATGCA
66396 ATTATCA
1 ATTATCA
66403 TTGTTGGAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
45 36 0.75
46 12 0.25
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (46 bp):
ATTATCAACCCAACCCCAAAATTAGTTATGAATGAAAATTGATGCA
Found at i:74036 original size:3 final size:3
Alignment explanation
Indices: 74030--74055 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
74020 AATAAAGAGA
74030 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
74056 TCAAAGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:83446 original size:12 final size:13
Alignment explanation
Indices: 83429--83463 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
83419 GGATGAGTTC
83429 TTTTTTC-TTTTT
1 TTTTTTCATTTTT
83441 TTTTTTCCATTTTT
1 TTTTTT-CATTTTT
83455 TTTTTTCAT
1 TTTTTTCAT
83464 AATAGTAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.29
13 4 0.19
14 11 0.52
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTTCATTTTT
Found at i:84732 original size:2 final size:2
Alignment explanation
Indices: 84725--84763 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
84715 TGTAAATACA
* * *
84725 AT AT AT AT AT AT AT AC AC AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
84764 CTAATATTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:85019 original size:18 final size:19
Alignment explanation
Indices: 84982--85021 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
84972 TAACAATAAT
*
84982 TATCTATCTACAATTTATA
1 TATCCATCTACAATTTATA
*
85001 TATCCATCTATAA-TTATA
1 TATCCATCTACAATTTATA
85019 TAT
1 TAT
85022 TTACAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.47
Consensus pattern (19 bp):
TATCCATCTACAATTTATA
Found at i:85852 original size:24 final size:24
Alignment explanation
Indices: 85820--85893 Score: 85
Period size: 24 Copynumber: 3.1 Consensus size: 24
85810 CGATGATGCT
*
85820 CCGGCTGATGATGCACCTGCACCA
1 CCGGCTGATGATGCACCAGCACCA
* * *
85844 CCGGCTGATGATGTACCGGCACCG
1 CCGGCTGATGATGCACCAGCACCA
* * *
85868 CCAGCCGATGATGCACCAGCCCCA
1 CCGGCTGATGATGCACCAGCACCA
85892 CC
1 CC
85894 AACCAAAAAC
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.20, C:0.41, G:0.26, T:0.14
Consensus pattern (24 bp):
CCGGCTGATGATGCACCAGCACCA
Found at i:91464 original size:21 final size:19
Alignment explanation
Indices: 91432--91471 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
91422 TATAATTCAA
*
91432 AATATTTACTATCTAACAAT
1 AATAATTACTATCT-ACAAT
91452 AATAATTATCTATCTACAAT
1 AATAATTA-CTATCTACAAT
91472 TTATATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.40
Consensus pattern (19 bp):
AATAATTACTATCTACAAT
Found at i:92307 original size:24 final size:24
Alignment explanation
Indices: 92274--92344 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
92264 CAATGATGCT
92274 CCAGCAGATGATGCACCTGCACCG
1 CCAGCAGATGATGCACCTGCACCG
* *
92298 CCAGCTGATGATGCACCGGCACCG
1 CCAGCAGATGATGCACCTGCACCG
*
92322 CCAGCCGATGATGCACCTGCACC
1 CCAGCAGATGATGCACCTGCACC
92345 AGCAACCAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.23, C:0.39, G:0.25, T:0.13
Consensus pattern (24 bp):
CCAGCAGATGATGCACCTGCACCG
Found at i:92504 original size:33 final size:32
Alignment explanation
Indices: 92454--92527 Score: 98
Period size: 31 Copynumber: 2.3 Consensus size: 32
92444 GTTGCCTAGG
*
92454 GATTA-GTTTATGATTATGTTTTATTAGGAATGA
1 GATTATGTTTATGATTATG-ATT-TTAGGAATGA
*
92487 GATTATGTTTA-GTTTATGATTTTAGGAATGA
1 GATTATGTTTATGATTATGATTTTAGGAATGA
92518 GATTATGTTT
1 GATTATGTTT
92528 GTGTTTTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
31 20 0.53
32 2 0.05
33 11 0.29
34 5 0.13
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (32 bp):
GATTATGTTTATGATTATGATTTTAGGAATGA
Done.