Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014720.1 Corchorus olitorius cultivar O-4 contig14753, 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: 120786
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:106 original size:24 final size:25
Alignment explanation
Indices: 67--113 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
57 AATTTCAGCT
**
67 AAAAACTGACCCGAAAA-TTTTTGC
1 AAAAACTGACAAGAAAAGTTTTTGC
91 AAAAACTGACAAGAAAAGTTTTT
1 AAAAACTGACAAGAAAAGTTTTT
114 CCTCAATTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.47, C:0.15, G:0.13, T:0.26
Consensus pattern (25 bp):
AAAAACTGACAAGAAAAGTTTTTGC
Found at i:1856 original size:334 final size:327
Alignment explanation
Indices: 1186--1883 Score: 835
Period size: 334 Copynumber: 2.1 Consensus size: 327
1176 AGATTTCGGA
* * * * ** *
1186 TAAAATTTTGCAAAAATTGACTCGAAAAGATATTTCCTCAATTTTTCGCTAAATTACTCATAAAA
1 TAAAATTTTGCAAAAATTGACCCG-AAAGATTTTTCCTCAATTTCTAGAGAAAATACTCATAAAA
* * * *
1251 AATATATAATTCGACATCAAAAAGATCGAAGGTTTTTAACGCTTCTAATATCGTTTTTCCTATTT
65 AATATATAATTCAACACCAAAAAAATCGAAGCTTTTTAACGCTTCTAATATCGTTTTTCCTATTT
* * ** * **
1316 TTTCTAAATAATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATCCTTAAAT
130 TTTCCAAATAATTTCTAATTAAATCGAAACAAAATTCAAATGCGAGTAAAAACAAAACCCCAAAT
* *
1381 CCAATATAGCTGAGATTTGGTTAGACGAATACATAAATTTCAAGGAGTCTTGGCACCAAAAATCA
195 ACAATATAGCTGAGATTTGGTTAGACGAATACATAAATTTCAAGGAGTCTTCGCACCAAAAATCA
* **
1446 TGCAAAACTGAGCCGAGCCCCGGAACGAGTTTTTAGCCGAAAATCGTGATGGTTAGTACACGATT
260 TGCAAAACTGACCCGAGCCCCGGAACGAGTTTTTAGCAAAAAATCGTGATGG-T-GTACACGATT
* **
1511 TCGGG
323 ACGAC
*
1516 TAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCTTCAATTTCTAGAGAAAATACTCATAAAAA
1 TAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTCTAGAGAAAATACTCATAAAAA
* * *
1581 ATATATAATTCAACGCCAAAAAAATTGAAAGTCTTTTTCAC-CATTCTAATATCGTTTTTCCTAT
66 ATATATAATTCAACACCAAAAAAATCG-AAG-CTTTTTAACGC-TTCTAATATCGTTTTTCCTA-
* * * *
1645 TTTATTTCCAAATCAATTTCTGATTAAATCGAAACAAGATTTAAATTCGAGTAAAAACAAAACCC
127 TTT-TTTCCAAAT-AATTTCTAATTAAATCGAAACAAAATTCAAATGCGAGTAAAAACAAAACCC
* * * * * * * * *
1710 CAAATACAATGTGGCTGATATTTGGTTAGATGAATATAGATATATTTTAAGGATTCTTCGCGCCA
190 CAAATACAATATAGCTGAGATTTGGTTAGACG-A-ATACATAAATTTCAAGGAGTCTTCGCACCA
* *
1775 AAAATCATGCAAAACTGACCCGAGTCCTCGGAACGCGTTTTTAGCTAAAAAATCGTGAT-G-GTA
253 AAAATCATGCAAAACTGACCCGAG-CCCCGGAACGAGTTTTTAGC-AAAAAATCGTGATGGTGTA
*
1838 CATGATTACGAC
316 CACGATTACGAC
*
1850 TAAAATTTTGCAAAAATTGACCCGAAATATTTTT
1 TAAAATTTTGCAAAAATTGACCCGAAAGATTTTT
1884 TTTTCTAATT
Statistics
Matches: 311, Mismatches: 47, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
329 56 0.18
330 27 0.09
331 27 0.09
332 3 0.01
333 8 0.03
334 112 0.36
335 1 0.00
336 47 0.15
337 19 0.06
338 11 0.04
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (327 bp):
TAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTCTAGAGAAAATACTCATAAAAA
ATATATAATTCAACACCAAAAAAATCGAAGCTTTTTAACGCTTCTAATATCGTTTTTCCTATTTT
TTCCAAATAATTTCTAATTAAATCGAAACAAAATTCAAATGCGAGTAAAAACAAAACCCCAAATA
CAATATAGCTGAGATTTGGTTAGACGAATACATAAATTTCAAGGAGTCTTCGCACCAAAAATCAT
GCAAAACTGACCCGAGCCCCGGAACGAGTTTTTAGCAAAAAATCGTGATGGTGTACACGATTACG
AC
Found at i:1921 original size:2 final size:2
Alignment explanation
Indices: 1914--1938 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1904 GATACTCATA
1914 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 A
1939 ATTCAACGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2968 original size:333 final size:323
Alignment explanation
Indices: 2167--3934 Score: 1530
Period size: 333 Copynumber: 5.4 Consensus size: 323
2157 GTTTTTAGCT
* * * * * *
2167 AAAAAGATTGGA-GGACTTTTCACTCTTTTAATATCCTTTTT-CATATTTTTCTGAATTAATTTT
1 AAAAAGATT-GATGGATTTTTCACGCTTCTAATATCGTTTTTCCAT-TTTTTCCGAATTAATTTC
* *
2230 TAATTAAATCGAAATAAGATTCAGATGCACGTAAAAAAAAATCCTTAAATCCAATGTGGCTGAGA
64 TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAAAT-CTTAAATCCAATGTGGCTGAGA
* * * **** * * *
2295 TTTTGATTAGATAAATAAAGATATTTCAAGGAGTCTCGGTGCTAAAAATCATGCAAAA-AGAGCC
128 -TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTACGCAAAAAATCATGCAAAACTGAGCT
* * * * * * *
2359 GTGGCCCCGTAACGCGTTTTTAGTTCAAAATCATGATGTAACATACACGATTTCGGC------T-
192 GAGGCCCCGAAACGCGTTTTTAG-CCAAAAACGTGATATAA-GTACACGATTTCGGCTAAATTTG
* * * **
2417 -AAAAACTGACCCGAAGAGTTTTT-CTCAATTTTTTGGCACAATACTTTGAAAAAATATATAATT
255 CAAAAACTGA-CCGAA-AATTTTTCCTCAATTTTTAGCCACAATACTCAGAAAAAATATATAATT
2480 CAACGCC
318 CAACG-C
** ** * * * *
2487 AAAAAGATTGGCGGGCTTTTCACGCTTATAATATTGTTTTTCCATTTTCTCCGAATTAATTTCTT
1 AAAAAGATTGATGGATTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCGAATTAATTTCTA
* * * *
2552 ATTAAATCGAAACAAGTTTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCCGAGATT
66 ATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAAAT-CTTAAATCCAATGTGGCTGAGATT
* * * * * *
2617 CGGTTCA-ATGAATATAGATATTTCAAGGAGTCTTTGCGCAAAAAATAATGCAACATTGAGCTGG
130 TGGTT-AGATGAATATAGATATTTCAAGGAGTCTTTACGCAAAAAATCATGCAAAACTGAGCTGA
* * * * *
2681 GGCTCCGGAACACATTTTTAGCCAAAAACTGTGATATAAAGTACACGATTTTGGCTAAAATTTTG
194 GGCCCCGAAACGCGTTTTTAGCCAAAAAC-GTGATAT-AAGTACACGATTTCGGCT-AAA-TTTG
* * *
2746 CAAAATACCGACCTGAAAACTTTTTCCTCAATTTTCAGCCACAATACTCAGAAAAAATATATGAT
255 CAAAA-ACTGACC-GAAAA-TTTTTCCTCAATTTTTAGCCACAATACTCAGAAAAAATATATAAT
*
2811 TCAATGC
317 TCAACGC
* * * *
2818 TATATAA-ATTGATGGATTTTTCACGCTTCTAATATCGTTTTCCCATTTTTTTTCGAATTTATTT
1 -A-AAAAGATTGATGGATTTTTCACGCTTCTAATATCGTTTTTCCA-TTTTTTCCGAATTAATTT
* * *
2882 CTAATTAAATCGAAACAAGATTCAGATGTTCGTAAAAATAAATCTGTAAATCCAATGTAGCTGAG
63 CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAAATCT-TAAATCCAATGTGGCTGAG
* * * *
2947 ATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTACGC-CAAAACCATGAAAAACTGA-AT
127 ATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTACGCAAAAAATCATGCAAAACTGAGCT
*
3010 CGAGGCCCCGAAACGCG-TTTTAGCCAAAAAC----CAT--G--CACGATTAT-GGC------T-
192 -GAGGCCCCGAAACGCGTTTTTAGCCAAAAACGTGATATAAGTACACGATT-TCGGCTAAATTTG
* *
3058 -AAAAACTGACCCGAAAATTTTTTCTCAATTTTTTTTA-CCACAATACTCATAAAAAATATATAA
255 CAAAAACTGA-CCGAAAATTTTTCCTCAA---TTTTTAGCCACAATACTCAGAAAAAATATATAA
3121 TTCAACGCC
316 TTCAACG-C
* * * *
3130 AAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATCTTTTCCGAATTAATATTGT
1 AAAAAGATTGATGGATTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCGAATTAAT-TTCT
* * *
3195 AATTAAATCGAAACAAGATTCAGATGGTCGTAAAAAAAAAATCGTTAAATCGAATGTGGCTGGGA
65 AATTAAATCGAAACAAGATTCAGATGCTCGT-AAAAAAAAATC-TTAAATCCAATGTGGCTGAGA
* * * * * *
3260 TTTGGTTCGATGAATATAGATATTTCAAAGATTCTTTACACCAAAAATCATGCAAAACTGAGCCG
128 TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTACGCAAAAAATCATGCAAAACTGAGCTG
* * *
3325 GGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTG--ATGAGTAAACGATTTCGGCTAAAACTTTG
193 AGGCCCCGAAACGCGTTTTTAGCCAAAAA-CGTGATATAAGTACACGATTTCGGCT-AAA-TTTG
* * * *
3388 CAAAAACTGAACCGAAAATGTTTACCTCAATTTTTTGCCACAATACTCATAAAAAATATATAATC
255 CAAAAACTG-ACCGAAAAT-TTTTCCTCAATTTTTAGCCACAATACTCAGAAAAAATATATAATT
3453 CAACGC
318 CAACGC
* * *
3459 AAAAAAGATTGA-AGAGTTTTTCACGTTTCTAATATCGTTTTTCCTTTTTTTCCCGAATTAATTT
1 -AAAAAGATTGATGGA-TTTTTCACGCTTCTAATATCGTTTTTCCATTTTTT-CCGAATTAATTT
* * *
3523 CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCGAATGTGGTTGAG
63 CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA-AAAATCTTAAATCCAATGTGGCTGAG
* * * * ** *** * *
3588 ATTTGATTCGATGAATATAGATATTTCATGTAGTCTCAAAATAAAAAATCATGCAAAATTGAGGT
127 ATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTACGCAAAAAATCATGCAAAACTGAGCT
* * * * * *
3653 -AGGTTCCCGGAACGCGTTTTTAGCGAAAAATCGTGATGGTTAGTACACGATTTCGACTAGAATT
192 GAGG-CCCCGAAACGCGTTTTTAGCCAAAAA-CGTGAT-ATAAGTACACGATTTCGGCTA-AA-T
* * * ** * * * * *
3717 TTGCAAAAAATTGAAACGACAGATTACTCCTTAATTTTTGGCTAAAATACTCA-TAAAAATATAT
252 TTGC-AAAAACTG-ACCGA-AAATTTTTCCTCAATTTTTAGCCACAATACTCAGAAAAAATATAT
* *
3781 AATTTAAAGGC
314 AA-TTCAACGC
* * * * * **
3792 AAAAAGATTGGATGGA-TGTTCACGCTTTTTATATCATATTTCCTATTTTTTTCTAAATTAATTT
1 AAAAAGATT-GATGGATTTTTCACGCTTCTAATATCGTTTTTCC-A-TTTTTTCCGAATTAATTT
* * * *
3856 CTAATTAAATCGAAACAAGATTCAGATGCTTGTAAAATCAAATTCTTAAATCCAATGTTGCTGAG
63 CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA-AAAAATCTTAAATCCAATGTGGCTGAG
3921 ATTTGGTTAGATGA
127 ATTTGGTTAGATGA
3935 TGTAAAGTAT
Statistics
Matches: 1191, Mismatches: 179, Indels: 143
0.79 0.12 0.09
Matches are distributed among these distances:
309 10 0.01
310 25 0.02
311 105 0.09
312 70 0.06
313 33 0.03
314 13 0.01
315 1 0.00
317 2 0.00
319 53 0.04
320 148 0.12
321 24 0.02
322 1 0.00
323 1 0.00
326 2 0.00
328 3 0.00
329 110 0.09
330 120 0.10
331 55 0.05
332 171 0.14
333 233 0.20
334 11 0.01
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (323 bp):
AAAAAGATTGATGGATTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCGAATTAATTTCTA
ATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAAATCTTAAATCCAATGTGGCTGAGATTT
GGTTAGATGAATATAGATATTTCAAGGAGTCTTTACGCAAAAAATCATGCAAAACTGAGCTGAGG
CCCCGAAACGCGTTTTTAGCCAAAAACGTGATATAAGTACACGATTTCGGCTAAATTTGCAAAAA
CTGACCGAAAATTTTTCCTCAATTTTTAGCCACAATACTCAGAAAAAATATATAATTCAACGC
Found at i:3445 original size:641 final size:644
Alignment explanation
Indices: 2212--3624 Score: 1719
Period size: 641 Copynumber: 2.2 Consensus size: 644
2202 CTTTTTCATA
* * *
2212 TTTTTCTGAATTAATTTTTAATTAAATCGAAATAAGATTCAGATGCACGTAAAAAAAAATCCTTA
1 TTTTTC-GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAAAT-CTTA
* * **
2277 AATCCAATGTGGCTGAGATTTTGATTAGATAAATAAAGATATTTCAAGGAGTCTCGGTGCTAAAA
64 AATCCAATGTGGCTGAGA-TTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGACGCTAAAA
* * * *
2342 ATCATGCAAAAAGAGCCGTGGCCCCGTAACGCGTTTTTAGTTCAAAATCATGATGTAACATACAC
128 ACCATGCAAAAAGAACCGAGGCCCCGAAACGCGTTTTTAG-TCAAAA-CA-GA--TAACATACAC
* ** *
2407 GATTTCGGCTAAAAACTGACCCGAAGAGTTTTTCTCAATTTTTTGGCACAATACTTTGAAAAAAT
188 GATTTCGGCTAAAAACTGACCCGAAAAGTTTTTCTCAATTTTTTACCACAATACTATGAAAAAAT
** *
2472 ATATAATTCAACGCCAAAAAGATTGGCGGGCTTTTCACGCTTATAATATTGTTTTTCCATTTTCT
253 ATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTATAATATCGTTTTTCCATTTTCT
* * * *
2537 CCGAATTAATTTCTTATTAAATCGAAACAAGTTTCAGATGCTCGTAAAAACAAATCCTTATATCC
318 CCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAAATCCTTAAATCC
* * *
2602 AATGTGGCCGAGATTCGGTTCAATGAATATAGATATTTCAAGGAGTCTTTGCGCAAAAAATAATG
383 AATGTGGCCGAGATTCGGTTCAATGAATATAGATATTTCAAAGAGTCTTTACACAAAAAATAATG
* * * * * * *
2667 CAACATTGAGCTGGGGCTCCGGAACACATTTTTAGCCAAAAACTGTGATATAAAGTACACGATTT
448 CAAAACTGAGCCGGGGCCCCGAAACACATTTTTAGCCAAAAACCGTGA-ATAAAGTAAACGATTT
* * *
2732 TGGCTAAAATTTTGCAAAATACCGACCTGAAAACTTTTTCCTCAATTTTCAGCCACAATACTCAG
512 CGGCTAAAACTTTGCAAAATACCGACCTGAAAACTTTTACCTCAATTTTCAGCCACAATACTCAG
* * * * * *
2797 AAAAAATATATGATTCAATGCTATATAA-ATTGATG-GATTTTTCACGCTTCTAATATCGTTTTC
577 AAAAAATATATAATCCAACGC-AAAAAAGATTGAAGAG-TTTTTCACGCTTCTAATATCGTTTTC
2860 CCATTT
640 CC-TTT
* * *
2866 TTTTTCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGTTCGTAAAAATAAATCTGTAA
1 TTTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAAATCT-TAA
* * ** *
2931 ATCCAATGTAGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTACGC-CAAAAC
65 ATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGACGCTAAAAAC
* * * *
2995 CATG-AAAAACTGAATCGAGGCCCCGAAACGCG-TTTTAG-C-CAA-A-A-ACCATGCACGATTA
130 CATGCAAAAA--GAACCGAGGCCCCGAAACGCGTTTTTAGTCAAAACAGATAACATACACGATT-
*
3053 T-GGCTAAAAACTGACCCGAAAATTTTTTCTCAATTTTTTTTACCACAATACTCAT-AAAAAATA
192 TCGGCTAAAAACTGACCCGAAAAGTTTTTCTCAA--TTTTTTACCACAATACT-ATGAAAAAATA
* *
3116 TATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATCTTT-T
254 TATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTATAATATCGTTTTTCCAT-TTTCT
* * *
3180 CCGAATTAATATTGTAATTAAATCGAAACAAGATTCAGATGGTCGTAAAAAAAAAATCGTTAAAT
318 CCGAATTAAT-TTCTAATTAAATCGAAACAAGATTCAGATGCTCGT-AAAAAAAAATCCTTAAAT
* * * * * * * *
3245 CGAATGTGGCTGGGATTTGGTTCGATGAATATAGATATTTCAAAGATTCTTTACACCAAAAATCA
381 CCAATGTGGCCGAGATTCGGTTCAATGAATATAGATATTTCAAAGAGTCTTTACACAAAAAATAA
* * *
3310 TGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTG-AT-GAGTAAACGATT
446 TGCAAAACTGAGCCGGGGCCCCGAAACACATTTTTAGCCAAAAACCGTGAATAAAGTAAACGATT
* **
3373 TCGGCTAAAACTTTGCAAAA-ACTGAACC-GAAAA-TGTTTACCTCAATTTTTTGCCACAATACT
511 TCGGCTAAAACTTTGCAAAATACCG-ACCTGAAAACT-TTTACCTCAATTTTCAGCCACAATACT
* *
3435 CATAAAAAATATATAATCCAACGCAAAAAAGATTGAAGAGTTTTTCACGTTTCTAATATCGTTTT
574 CAGAAAAAATATATAATCCAACGCAAAAAAGATTGAAGAGTTTTTCACGCTTCTAATATCGTTTT
*
3500 TCCTTT
639 CCCTTT
* *
3506 TTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTA
1 TTTT-TCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA-AAAATCTTA
* * * * *
3571 AATCGAATGTGGTTGAGATTTGATTCGATGAATATAGATATTTCATGTAGTCTC
64 AATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTC
3625 AAAATAAAAA
Statistics
Matches: 654, Mismatches: 89, Indels: 45
0.83 0.11 0.06
Matches are distributed among these distances:
640 12 0.02
641 220 0.34
642 38 0.06
643 90 0.14
644 36 0.06
645 110 0.17
646 1 0.00
648 2 0.00
649 1 0.00
650 5 0.01
651 14 0.02
652 53 0.08
653 66 0.10
654 6 0.01
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (644 bp):
TTTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAAATCTTAAA
TCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGACGCTAAAAACC
ATGCAAAAAGAACCGAGGCCCCGAAACGCGTTTTTAGTCAAAACAGATAACATACACGATTTCGG
CTAAAAACTGACCCGAAAAGTTTTTCTCAATTTTTTACCACAATACTATGAAAAAATATATAATT
CAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTATAATATCGTTTTTCCATTTTCTCCGAATTA
ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAAATCCTTAAATCCAATGTGGC
CGAGATTCGGTTCAATGAATATAGATATTTCAAAGAGTCTTTACACAAAAAATAATGCAAAACTG
AGCCGGGGCCCCGAAACACATTTTTAGCCAAAAACCGTGAATAAAGTAAACGATTTCGGCTAAAA
CTTTGCAAAATACCGACCTGAAAACTTTTACCTCAATTTTCAGCCACAATACTCAGAAAAAATAT
ATAATCCAACGCAAAAAAGATTGAAGAGTTTTTCACGCTTCTAATATCGTTTTCCCTTT
Found at i:29923 original size:14 final size:16
Alignment explanation
Indices: 29899--29930 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
29889 AAAAACTTTT
29899 TTTTTTGTAAAA-TCA
1 TTTTTTGTAAAAGTCA
29914 TTTTTT-TAAAAGTCA
1 TTTTTTGTAAAAGTCA
29929 TT
1 TT
29931 GGATTGATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.56
Consensus pattern (16 bp):
TTTTTTGTAAAAGTCA
Found at i:38249 original size:7 final size:7
Alignment explanation
Indices: 38239--38264 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
38229 TTTAGCAAAC
38239 AAAAAAG
1 AAAAAAG
38246 AAAAAAG
1 AAAAAAG
38253 AAAAAAG
1 AAAAAAG
38260 AAAAA
1 AAAAA
38265 TGGGTGGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:38814 original size:44 final size:45
Alignment explanation
Indices: 38751--38839 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 45
38741 CTAGTCAGAG
* *
38751 TTTGAGATTTTTTATCAGAA-TTTCGAGTTCGAATTTTGAAAATT
1 TTTGAGATCTTTTATCAGAATTTTCGAGTTCGAATCTTGAAAATT
* *
38795 TTTGAGATCTTTTATCAGAATTTTGGAGTTCGAATCTTGAGAATT
1 TTTGAGATCTTTTATCAGAATTTTCGAGTTCGAATCTTGAAAATT
38840 GACGAATAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.28, C:0.08, G:0.18, T:0.46
Consensus pattern (45 bp):
TTTGAGATCTTTTATCAGAATTTTCGAGTTCGAATCTTGAAAATT
Found at i:39625 original size:2 final size:2
Alignment explanation
Indices: 39618--39649 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
39608 TTGGAACTTT
39618 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39650 CCCAAAGTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42409 original size:22 final size:22
Alignment explanation
Indices: 42381--42429 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
42371 CATGGCACGG
42381 CACGATCCACGTGCCGACACAA
1 CACGATCCACGTGCCGACACAA
*
42403 CACGATCCACGTGCCGACGCAA
1 CACGATCCACGTGCCGACACAA
42425 CACGA
1 CACGA
42430 CCCATTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.41, G:0.20, T:0.08
Consensus pattern (22 bp):
CACGATCCACGTGCCGACACAA
Found at i:55233 original size:20 final size:20
Alignment explanation
Indices: 55208--55249 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
55198 TTATTATGAA
55208 ACACATTATCATTTGGTAGT
1 ACACATTATCATTTGGTAGT
55228 ACACATTATCATTTGGTAGT
1 ACACATTATCATTTGGTAGT
55248 AC
1 AC
55250 TCATAAGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (20 bp):
ACACATTATCATTTGGTAGT
Found at i:74696 original size:24 final size:23
Alignment explanation
Indices: 74637--74701 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
74627 GAGAGCCGAG
* * *
74637 AAGAGAAGGAAAATGAAGAAAGT
1 AAGAGAAGGATAGTGAAGAAAAT
* *
74660 AAGAACAATGATAGTGAAGAAAAT
1 AAG-AGAAGGATAGTGAAGAAAAT
74684 AAAGAGAAGGATAGTGAA
1 -AAGAGAAGGATAGTGAA
74702 AATAAAGAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
23 3 0.09
24 27 0.82
25 3 0.09
ACGTcount: A:0.58, C:0.02, G:0.28, T:0.12
Consensus pattern (23 bp):
AAGAGAAGGATAGTGAAGAAAAT
Found at i:75943 original size:57 final size:56
Alignment explanation
Indices: 75856--76136 Score: 291
Period size: 57 Copynumber: 4.9 Consensus size: 56
75846 ATGAAAACAG
* * *
75856 CAACAACAATGAAAATGCAGGTCCGAATGAGAATAATGCTGCTCAGAGCTACACAGA
1 CAACAACAATGAGAATGCAAGTCAGAATGAGAATAATGCTGCTCAGAGCTACACA-A
* *
75913 CAGCAACAATGAGAATGCAAGTCAGAATGAGAATAATGCTTCTCAGAGCTACACAGA
1 CAACAACAATGAGAATGCAAGTCAGAATGAGAATAATGCTGCTCAGAGCTACACA-A
* * * * *
75970 CAGCAACAATGAGAATACAAGTCAGAATGAGAACAATGATGCGGCTCAGAGC-A-ACAC
1 CAACAACAATGAGAATGCAAGTCAGAATGAG---AATAATGCTGCTCAGAGCTACACAA
* * *
76027 CAACAACAATGAGAATGCAAGTCAGAATGAGAACAATGATGCGGCTCAGAGC-A-ACAC
1 CAACAACAATGAGAATGCAAGTCAGAATGAG---AATAATGCTGCTCAGAGCTACACAA
* ** * * *
76084 CAACAACAATGAAAACACAAGTCAGAATGAGAACAATGATGCTCAGACCTACA
1 CAACAACAATGAGAATGCAAGTCAGAATGAGAATAATGCTGCTCAGAGCTACA
76137 ATAATGAAAA
Statistics
Matches: 199, Mismatches: 20, Indels: 11
0.87 0.09 0.05
Matches are distributed among these distances:
54 13 0.07
55 1 0.01
56 1 0.01
57 165 0.83
58 3 0.02
59 1 0.01
60 15 0.08
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.14
Consensus pattern (56 bp):
CAACAACAATGAGAATGCAAGTCAGAATGAGAATAATGCTGCTCAGAGCTACACAA
Found at i:80091 original size:23 final size:23
Alignment explanation
Indices: 80044--80204 Score: 197
Period size: 23 Copynumber: 7.0 Consensus size: 23
80034 CCTGAGTAAC
80044 GTAACGTATGTGATGA--TCTAA
1 GTAACGTATGTGATGATTTCTAA
*
80065 GTAACGTATGTGATGATTTCTAG
1 GTAACGTATGTGATGATTTCTAA
*
80088 GTAACGTTTGTGAT-ATTTTCTAA
1 GTAACGTATGTGATGA-TTTCTAA
80111 GTAACGTATGTGATGATTTCT-A
1 GTAACGTATGTGATGATTTCTAA
*
80133 GATAACGTTTGTGAT-ATTTTCTAA
1 G-TAACGTATGTGATGA-TTTCTAA
80157 GTAACGTATGTGATGATGTTTTCTAA
1 GTAACGTATGTGATGA---TTTCTAA
*
80183 GTAACGTATGTGATAATTTCTA
1 GTAACGTATGTGATGATTTCTA
80205 CGAGGCATAA
Statistics
Matches: 123, Mismatches: 7, Indels: 18
0.83 0.05 0.12
Matches are distributed among these distances:
21 16 0.13
22 4 0.03
23 76 0.62
24 4 0.03
26 23 0.19
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.42
Consensus pattern (23 bp):
GTAACGTATGTGATGATTTCTAA
Found at i:80118 original size:46 final size:46
Alignment explanation
Indices: 80060--80204 Score: 227
Period size: 46 Copynumber: 3.1 Consensus size: 46
80050 TATGTGATGA
80060 TCTAAGTAACGTATGTGATGATTTCTAGGTAACGTTTGTGATATTT
1 TCTAAGTAACGTATGTGATGATTTCTAGGTAACGTTTGTGATATTT
*
80106 TCTAAGTAACGTATGTGATGATTTCTAGATAACGTTTGTGATATTT
1 TCTAAGTAACGTATGTGATGATTTCTAGGTAACGTTTGTGATATTT
* * *
80152 TCTAAGTAACGTATGTGATGATGTTTTCTAAGTAACGTATGTGATAATT
1 TCTAAGTAACGTATGTGATGA---TTTCTAGGTAACGTTTGTGATATTT
80201 TCTA
1 TCTA
80205 CGAGGCATAA
Statistics
Matches: 91, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
46 66 0.73
49 25 0.27
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.43
Consensus pattern (46 bp):
TCTAAGTAACGTATGTGATGATTTCTAGGTAACGTTTGTGATATTT
Found at i:101729 original size:29 final size:29
Alignment explanation
Indices: 101694--101766 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
101684 ACTTGTAGCA
*
101694 TTTGGACGTTTTGCTCTATGAACTT-CAAT
1 TTTGGACGTTTTGCTCCATGAA-TTCCAAT
* *
101723 TTTGGACATTTTAC-CCATGAATTCCAAT
1 TTTGGACGTTTTGCTCCATGAATTCCAAT
101751 TTTGTGACGTTTTGCT
1 TTTG-GACGTTTTGCT
101767 ACGTCAGCGC
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
27 2 0.06
28 14 0.39
29 20 0.56
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.45
Consensus pattern (29 bp):
TTTGGACGTTTTGCTCCATGAATTCCAAT
Found at i:102582 original size:49 final size:50
Alignment explanation
Indices: 102524--102626 Score: 190
Period size: 49 Copynumber: 2.1 Consensus size: 50
102514 TGGATTAATA
102524 TGTTTTGATTTTTAATTAATTTAATAAGATCA-TTTTTTATCAAAAGTGT
1 TGTTTTGATTTTTAATTAATTTAATAAGATCATTTTTTTATCAAAAGTGT
102573 TGTTTTGATTTTTAATTAATTTAATAAGATCATTTTTTTTATCAAAAGTGT
1 TGTTTTGATTTTTAATTAATTTAATAAGATCA-TTTTTTTATCAAAAGTGT
102624 TGT
1 TGT
102627 GTAGGCATGA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
49 32 0.62
51 20 0.38
ACGTcount: A:0.31, C:0.04, G:0.11, T:0.54
Consensus pattern (50 bp):
TGTTTTGATTTTTAATTAATTTAATAAGATCATTTTTTTATCAAAAGTGT
Found at i:104941 original size:15 final size:15
Alignment explanation
Indices: 104921--104950 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
104911 GTACAACTTG
104921 CATATATATAGTATA
1 CATATATATAGTATA
104936 CATATATATAGTATA
1 CATATATATAGTATA
104951 GTCCATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (15 bp):
CATATATATAGTATA
Found at i:105665 original size:84 final size:84
Alignment explanation
Indices: 105524--105691 Score: 318
Period size: 84 Copynumber: 2.0 Consensus size: 84
105514 AGAAAATATG
*
105524 GTATTTTCCTTTGCCTAATTTCTCATCTATACTAATTGGCAAATTATACAATTAATACATCGTCA
1 GTATTTTCCTTTACCTAATTTCTCATCTATACTAATTGGCAAATTATACAATTAATACATCGTCA
105589 GTGGAGTTTAACAGACTAC
66 GTGGAGTTTAACAGACTAC
*
105608 GTATTTTCCTTTACCTAATTTCTCATCTATACTAATTGGCAAATTATACAATTAATACATCGTTA
1 GTATTTTCCTTTACCTAATTTCTCATCTATACTAATTGGCAAATTATACAATTAATACATCGTCA
105673 GTGGAGTTTAACAGACTAC
66 GTGGAGTTTAACAGACTAC
105692 ACAAGCGGGT
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 82 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (84 bp):
GTATTTTCCTTTACCTAATTTCTCATCTATACTAATTGGCAAATTATACAATTAATACATCGTCA
GTGGAGTTTAACAGACTAC
Found at i:113172 original size:33 final size:34
Alignment explanation
Indices: 113130--113204 Score: 107
Period size: 33 Copynumber: 2.2 Consensus size: 34
113120 AAAATTTAGA
*
113130 TCAGCCACCGTTCGCTGTTAGACGG-GGCGGTTG
1 TCAGCCACCGTTCGCTATTAGACGGCGGCGGTTG
* *
113163 TCAGCCACCGTTTGCTATTAGATGGCGGCGGTTG
1 TCAGCCACCGTTCGCTATTAGACGGCGGCGGTTG
*
113197 TCATCCAC
1 TCAGCCAC
113205 ATTGTTCTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 22 0.59
34 15 0.41
ACGTcount: A:0.15, C:0.28, G:0.31, T:0.27
Consensus pattern (34 bp):
TCAGCCACCGTTCGCTATTAGACGGCGGCGGTTG
Found at i:119501 original size:34 final size:34
Alignment explanation
Indices: 119463--119591 Score: 222
Period size: 34 Copynumber: 3.8 Consensus size: 34
119453 AGCACCACTG
* *
119463 TGTCTTCTCGTTTACCTTCGTGTCTGTCTTCCTC
1 TGTCTTCTCGTGTACCTTCGTGCCTGTCTTCCTC
* *
119497 TGTCTTCTCGTGTACCTTCGTGTCTGTCTTCCTG
1 TGTCTTCTCGTGTACCTTCGTGCCTGTCTTCCTC
119531 TGTCTTCTCGTGTACCTTCGTGCCTGTCTTCCTC
1 TGTCTTCTCGTGTACCTTCGTGCCTGTCTTCCTC
119565 TGTCTTCTCGTGTACCTTCGTGCCTGT
1 TGTCTTCTCGTGTACCTTCGTGCCTGT
119592 TGGCCTCGCC
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 91 1.00
ACGTcount: A:0.03, C:0.32, G:0.19, T:0.47
Consensus pattern (34 bp):
TGTCTTCTCGTGTACCTTCGTGCCTGTCTTCCTC
Found at i:119507 original size:24 final size:23
Alignment explanation
Indices: 119480--119577 Score: 64
Period size: 24 Copynumber: 4.3 Consensus size: 23
119470 TCGTTTACCT
119480 TCGTGTCTGTCTTCCTCTGTCTTC
1 TCGTGTCTGTCTT-CTCTGTCTTC
* *
119504 TCGTGTACCT-TCGTGTCTGTCTTC
1 TCGTGT--CTGTCTTCTCTGTCTTC
*
119528 -C-TG--TGTCTTCTCGTGTACCT-
1 TCGTGTCTGTCTTCTC-TGT-CTTC
*
119548 TCGTGCCTGTCTTCCTCTGTCTTC
1 TCGTGTCTGTCTT-CTCTGTCTTC
119572 TCGTGT
1 TCGTGT
119578 ACCTTCGTGC
Statistics
Matches: 56, Mismatches: 7, Indels: 22
0.66 0.08 0.26
Matches are distributed among these distances:
18 1 0.02
19 5 0.09
20 3 0.05
21 3 0.05
22 4 0.07
23 3 0.05
24 29 0.52
25 6 0.11
26 2 0.04
ACGTcount: A:0.02, C:0.32, G:0.19, T:0.47
Consensus pattern (23 bp):
TCGTGTCTGTCTTCTCTGTCTTC
Found at i:119632 original size:62 final size:62
Alignment explanation
Indices: 119558--119785 Score: 348
Period size: 62 Copynumber: 3.5 Consensus size: 62
119548 TCGTGCCTGT
*
119558 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTTC
1 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC
119620 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTCCTT
1 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGG----------
119685 CCTCTTC
56 CCTCTTC
*
119692 CTTCCTCTGGCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC
1 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC
119754 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCT
1 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCT
119786 CGTGTCTGTC
Statistics
Matches: 153, Mismatches: 3, Indels: 20
0.87 0.02 0.11
Matches are distributed among these distances:
62 92 0.60
72 61 0.40
ACGTcount: A:0.03, C:0.40, G:0.21, T:0.36
Consensus pattern (62 bp):
CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTC
Found at i:119689 original size:72 final size:72
Alignment explanation
Indices: 119613--119761 Score: 289
Period size: 72 Copynumber: 2.1 Consensus size: 72
119603 CCTGCGGAGG
*
119613 CCTCTTCCTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCT
1 CCTCTTCCTTCCTCTGGCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCT
119678 CTTCCTT
66 CTTCCTT
119685 CCTCTTCCTTCCTCTGGCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCT
1 CCTCTTCCTTCCTCTGGCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCT
119750 CTTCCTT
66 CTTCCTT
119757 CCTCT
1 CCTCT
119762 GTCTTCTCGT
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 76 1.00
ACGTcount: A:0.03, C:0.42, G:0.19, T:0.36
Consensus pattern (72 bp):
CCTCTTCCTTCCTCTGGCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCT
CTTCCTT
Found at i:119690 original size:10 final size:10
Alignment explanation
Indices: 119675--119699 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
119665 CCTGCGGAGG
119675 CCTCTTCCTT
1 CCTCTTCCTT
119685 CCTCTTCCTT
1 CCTCTTCCTT
119695 CCTCT
1 CCTCT
119700 GGCTTCTCGT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (10 bp):
CCTCTTCCTT
Found at i:120520 original size:20 final size:20
Alignment explanation
Indices: 120495--120554 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
120485 ATGAGACTCC
120495 TTTTCTACA-TATCACATGAT
1 TTTTCTACATTA-CACATGAT
* *
120515 TTTTCTGCATTACATATGAT
1 TTTTCTACATTACACATGAT
* *
120535 TTTTCTGCATTACATATGAT
1 TTTTCTACATTACACATGAT
120555 ATAGCTCAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 35 0.95
21 2 0.05
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (20 bp):
TTTTCTACATTACACATGAT
Found at i:120528 original size:25 final size:22
Alignment explanation
Indices: 120510--120551 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
120500 TACATATCAC
120510 ATGATTTTTCTGCATTAC--AT
1 ATGATTTTTCTGCATTACATAT
120530 ATGATTTTTCTGCATTACATAT
1 ATGATTTTTCTGCATTACATAT
120552 GATATAGCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 18 0.90
22 2 0.10
ACGTcount: A:0.26, C:0.14, G:0.10, T:0.50
Consensus pattern (22 bp):
ATGATTTTTCTGCATTACATAT
Done.