Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019422.1 Corchorus olitorius cultivar O-4 contig19455, 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: 87666
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:778 original size:320 final size:319
Alignment explanation
Indices: 12--1061 Score: 1116
Period size: 320 Copynumber: 3.2 Consensus size: 319
2 AACTGAGCCT
* * * *
12 GGGGCCCTAAAACGC-TTTTCTAGCCAAAAACTGTGATGGTTATTACACGATTTCGGCTAAAATT
1 GGGGCCCCAGAACGCGTTTT-TAGCCAAAAACCGTGATGGTTATTACACGATTTTGGCTAAAATT
* *** * *
76 TTGTAAAAATTGATTAGAAAAATATTTCCTCAATTTTAGGATAAAATACTTATAAAAAATATATA
65 TTGCAAAAATTGACCCG--AAATATTT-CTC-----T--GATAAAATACTCATAAAATATATATA
* * * * * * **
141 ATTCAACGCCAAAAAGATTGAAGGGCTTTTGACATTTCCAATATCGTTTTTCGTATGTTTTCCAA
120 ATTTAACGCCAAAAAGATTG-AGGACTTTTCACCTTT-TAATATCGTTTTTCATAT-TTTTCTGA
* * * * *
206 ATTAAGTTCTAATTAAATCGAAACAAGATTCAGATGCTCGCAAAAA-AAATCCTTAAATCTAATG
182 ATTAAATTCTAGTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATG
* * * *
270 TGGCAGAGATTTTG-TTAGATGAATATAGATAT-TACAAGGAGTGTTGGCACCAAAAATCATGCA
247 TGGCTGAGA-TTTGATTAGATGAATATGGATATCT-CAAGGAGTCTTGGCGCCAAAAATCATGCA
333 AAACTTAGTC
310 AAACTTAGTC
* * * *
343 -GGGCCCCAGAATGCGTTTTTAGCCGAAAACCGTGATGGTTATTACATGATTTCGGCTAAAATTT
1 GGGGCCCCAGAACGCGTTTTTAGCCAAAAACCGTGATGGTTATTACACGATTTTGGCTAAAATTT
* * ** *
407 TGCAAAAATTGACCCGAAATATTTTTCTG-TCAAATTTTGCATAAAATATATACAATTTAACGCC
66 TGCAAAAATTGACCCGAAATATTTCTCTGATAAAATACT-CATAAAATATATATAATTTAACGCC
* *
471 AAAAATATTAGAGGACTTTTCACGCTTTTAATATTGTTTTTCATATTTTTCTGAATTAAATTCTA
130 AAAAAGATT-GAGGACTTTTCAC-CTTTTAATATCGTTTTTCATATTTTTCTGAATTAAATTCTA
* * *
536 GTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTCAATCCAATGTAGCTGACATT
193 GTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATT
* * *
601 AGATTAAATGAATATGGATATCTCAAAGAGTCTTGGCGCC-AAAATCATGCAAAACTTAGTC
258 TGATTAGATGAATATGGATATCTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTTAGTC
* * *
662 GGGGCCCCAGAACGCGTTTTTAGCCAAAAAACCGTGATGGTTAGTCCACGATTTTGGCTAAAACT
1 GGGGCCCCAGAACGCGTTTTTAGCC-AAAAACCGTGATGGTTATTACACGATTTTGGCTAAAATT
*** ***
727 TTGCAGAAAACTT-TTTC-TTCTA-TTCT-TGATAAAATACTCATAAATATATATATAATTTAAC
65 TTGCA-AAAA-TTGACCCGAAATATTTCTCTGATAAAATACTCATAAA-ATATATATAATTTAAC
* * * *
788 ACCAAAAGGATTGGAGAACTTTTCACACTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTT
127 GCCAAAAAGATT-GAGGACTTTTCAC-CTTTTAATATCGTTTTTCATATTTTTCTGAATTAAATT
* * * *
853 CTAAG-AAAATCGAAACAAGATTCAGATGCTTGTAAAAACAAATTCTTAAATTCAATGCGGCTGA
190 CT-AGTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGA
* * * * *
917 GATTTGATTAGATGAATATGGATATCTCAAGGAGTCTTCGTGCCAAAAATCATGCAAGACTGAGC
254 GATTTGATTAGATGAATATGGATATCTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTTAGT
982 C
319 C
* * * * *
983 GGGACCCCAAAACGCTTTTTTAGCCAAAAACTGTGATGGTTATTGCACGATTTTCGGCTAAAATT
1 GGGGCCCCAGAACGCGTTTTTAGCCAAAAACCGTGATGGTTATTACACGATTTT-GGCTAAAATT
*
1048 TTGTAAAAAATTGA
65 TTG-CAAAAATTGA
1062 TTAGAAAAAT
Statistics
Matches: 609, Mismatches: 92, Indels: 46
0.82 0.12 0.06
Matches are distributed among these distances:
319 87 0.14
320 331 0.54
321 103 0.17
322 7 0.01
323 2 0.00
327 2 0.00
328 8 0.01
330 65 0.11
331 4 0.01
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (319 bp):
GGGGCCCCAGAACGCGTTTTTAGCCAAAAACCGTGATGGTTATTACACGATTTTGGCTAAAATTT
TGCAAAAATTGACCCGAAATATTTCTCTGATAAAATACTCATAAAATATATATAATTTAACGCCA
AAAAGATTGAGGACTTTTCACCTTTTAATATCGTTTTTCATATTTTTCTGAATTAAATTCTAGTT
AAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGA
TTAGATGAATATGGATATCTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTTAGTC
Found at i:2182 original size:14 final size:14
Alignment explanation
Indices: 2163--2192 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2153 TTGCTTATTA
2163 TTATCATTATTATG
1 TTATCATTATTATG
*
2177 TTATCATTATTCTG
1 TTATCATTATTATG
2191 TT
1 TT
2193 TGTCAATTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.10, G:0.07, T:0.60
Consensus pattern (14 bp):
TTATCATTATTATG
Found at i:2437 original size:14 final size:14
Alignment explanation
Indices: 2418--2447 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2408 TTGCTTATTA
2418 TTATCATTATTCTG
1 TTATCATTATTCTG
2432 TTATCATTATTCTG
1 TTATCATTATTCTG
2446 TT
1 TT
2448 TGTCAATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.13, G:0.07, T:0.60
Consensus pattern (14 bp):
TTATCATTATTCTG
Found at i:2533 original size:255 final size:245
Alignment explanation
Indices: 2073--2580 Score: 854
Period size: 255 Copynumber: 2.0 Consensus size: 245
2063 GTAGTTTGTT
*
2073 GATGATTTTTAGCATTGATTACTTTACATGGAATGGCAGAAATCAGAATGCATGATTAAGTCAGT
1 GATGATTTTTAGCATTGATTACTTTACATGGAATGACAGAAATCAGAATGCATGATTAAGTCAGT
*
2138 TTTTGATGCATTTTTTTGCTTATTATTATCATTATTATGTTATCATTATTCTGTTTGTCAATTCG
66 TTTTGATGCATTTTTTTGCTTATTATTATCATTATTATGTTATCATTATTCTGTTTGTCAATTCA
*
2203 AATACTAAGCTGCCTTAAGTTGAATTAAATATGTTGAATTGAAACTCTGATATTGAGTTTAAGTT
131 AATACTAAGCTGCCTTAAGTTGAATTAAATATGTTGAATTGAAACTCTGATATTGAGCTTAA---
* *
2268 GTGTTGTTGTGCTGTTGTGTTGTTCAATTCGAATATTAAGCTTTGAAATGATCCTCAA
193 -----CTTGTGCTGTTGTGCTGTTCAATTCGAATATTAAGCTTTGAAATGATCCTCAA
2326 GATGATTTTTAGCATTGATTACTTTACATGGAATGACAGAAATCAGAATGCATGATTAAGTCAGT
1 GATGATTTTTAGCATTGATTACTTTACATGGAATGACAGAAATCAGAATGCATGATTAAGTCAGT
* *
2391 TTTTTATGCATTTTTTTTTGCTTATTATTATCATTATTCTGTTATCATTATTCTGTTTGTCAATT
66 TTTTGATGCA--TTTTTTTGCTTATTATTATCATTATTATGTTATCATTATTCTGTTTGTCAATT
*
2456 CAAATACTAAGCTGCCTTAAGTTGAATTAAATGTGTTGAATTGAAACTCTGATATTGAGCTTAAC
129 CAAATACTAAGCTGCCTTAAGTTGAATTAAATATGTTGAATTGAAACTCTGATATTGAGCTTAAC
2521 TTGTGCTGTTGTGCTGTTCAATTCGAATATTAAGCTTTGAAATGATCCTCAA
194 TTGTGCTGTTGTGCTGTTCAATTCGAATATTAAGCTTTGAAATGATCCTCAA
2573 GATGATTT
1 GATGATTT
2581 ACCAACCTGA
Statistics
Matches: 245, Mismatches: 8, Indels: 10
0.93 0.03 0.04
Matches are distributed among these distances:
247 59 0.24
253 73 0.30
255 113 0.46
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.43
Consensus pattern (245 bp):
GATGATTTTTAGCATTGATTACTTTACATGGAATGACAGAAATCAGAATGCATGATTAAGTCAGT
TTTTGATGCATTTTTTTGCTTATTATTATCATTATTATGTTATCATTATTCTGTTTGTCAATTCA
AATACTAAGCTGCCTTAAGTTGAATTAAATATGTTGAATTGAAACTCTGATATTGAGCTTAACTT
GTGCTGTTGTGCTGTTCAATTCGAATATTAAGCTTTGAAATGATCCTCAA
Found at i:6929 original size:8 final size:8
Alignment explanation
Indices: 6916--6967 Score: 86
Period size: 8 Copynumber: 6.2 Consensus size: 8
6906 TTTTGTATAG
6916 TAGTAAGA
1 TAGTAAGA
6924 TAGTAAGA
1 TAGTAAGA
6932 TAGTAAGA
1 TAGTAAGA
6940 TAGTAAGA
1 TAGTAAGA
6948 TAGTAAGA
1 TAGTAAGA
6956 TAAGATAAGA
1 T-AG-TAAGA
6966 TA
1 TA
6968 AGATTTATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
8 33 0.79
9 3 0.07
10 6 0.14
ACGTcount: A:0.52, C:0.00, G:0.23, T:0.25
Consensus pattern (8 bp):
TAGTAAGA
Found at i:6943 original size:24 final size:26
Alignment explanation
Indices: 6919--7045 Score: 88
Period size: 24 Copynumber: 5.0 Consensus size: 26
6909 TGTATAGTAG
6919 TAAGATAGTAAGATAGTAAGAT-AG-
1 TAAGATAGTAAGATAGTAAGATAAGA
6943 TAAGATAGTAAGATAAGATAAGATAAGA
1 TAAGATAGTAAGAT-AG-TAAGATAAGA
** * * * * *
6971 T-TTATAAT-ATATAATAATATAATAA
1 TAAGATAGTAAGATAGTAAGATAA-GA
* *
6996 TAATATAGTAAAATAGTAAGATAAGA
1 TAAGATAGTAAGATAGTAAGATAAGA
*
7022 TAAG--A-TAAGATAGTATGATAAGA
1 TAAGATAGTAAGATAGTAAGATAAGA
7045 T
1 T
7046 GAACAAATAC
Statistics
Matches: 80, Mismatches: 16, Indels: 15
0.72 0.14 0.14
Matches are distributed among these distances:
23 17 0.21
24 22 0.28
25 5 0.06
26 18 0.22
27 17 0.21
28 1 0.01
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (26 bp):
TAAGATAGTAAGATAGTAAGATAAGA
Found at i:6961 original size:5 final size:5
Alignment explanation
Indices: 6919--7045 Score: 52
Period size: 5 Copynumber: 28.2 Consensus size: 5
6909 TGTATAGTAG
6919 TAAGA T-AG- TAAGA T-AG- TAAGA T-AG- TAAGA T-AG- TAAGA TAAGA
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA
** * * * * *
6961 TAAGA TAAGA T-TTA TAATA TATA-A TAATA TAATAA TAATA T-AG- TAAAA
1 TAAGA TAAGA TAAGA TAAGA TA-AGA TAAGA TAA-GA TAAGA TAAGA TAAGA
*
7009 T-AG- TAAGA TAAGA TAAGA TAAGA T-AG- TATGA TAAGA T
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA T
7046 GAACAAATAC
Statistics
Matches: 94, Mismatches: 10, Indels: 36
0.67 0.07 0.26
Matches are distributed among these distances:
3 7 0.07
4 27 0.29
5 55 0.59
6 5 0.05
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (5 bp):
TAAGA
Found at i:6997 original size:11 final size:11
Alignment explanation
Indices: 6974--7002 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
6964 GATAAGATTT
6974 ATAATAT-ATA
1 ATAATATAATA
6984 ATAATATAATA
1 ATAATATAATA
6995 ATAATATA
1 ATAATATA
7003 GTAAAATAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
ATAATATAATA
Found at i:15165 original size:6 final size:6
Alignment explanation
Indices: 15156--15185 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
15146 CATATATTTA
15156 TATATC TATATC TATATC TATATAC TATAT
1 TATATC TATATC TATATC TATAT-C TATAT
15186 AAGTCTAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (6 bp):
TATATC
Found at i:15500 original size:141 final size:141
Alignment explanation
Indices: 15292--15695 Score: 625
Period size: 141 Copynumber: 2.8 Consensus size: 141
15282 TCCAATCAGA
* * * * * *
15292 TTTTATTTCCATATTAAAAAAGTCTAAAATAATAAC-AATTATTTTTATA-TTAAACAACTTATT
1 TTTTCTTTCCATATTACAAAAGTCTTAAATGAT-ACTAATAATTTTTTTACTTAAACAACTTATT
15355 ATTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTTTTT-AGGAAT
65 ATTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTTTTTGAGGAAT
*
15419 TAGTCATTAGGT
130 TAGTCATTACGT
15431 TTTTCTTTCCATATTACAAAAGTCTTAAATGATACTAATAATTTTTTTACGTTAAACAACTTATT
1 TTTTCTTTCCATATTACAAAAGTCTTAAATGATACTAATAATTTTTTTAC-TTAAACAACTTATT
15496 ATTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTTTTTTTTTGAG
65 ATTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACG----TTTTTTTTGAG
15561 GAATTAGTCATTACGT
126 GAATTAGTCATTACGT
**
15577 TTTTCTTTCTGTATTACAAAAGTCTTAAATGATACTAATAATTTTTTTACTTAAACAACTTATTA
1 TTTTCTTTCCATATTACAAAAGTCTTAAATGATACTAATAATTTTTTTACTTAAACAACTTATTA
* * *
15642 TTATAATTATTAAAATTATTATTAGTTATATATATTATTAATCACTACGTTTTT
66 TTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTT
15696 CTTTCCATAT
Statistics
Matches: 245, Mismatches: 12, Indels: 14
0.90 0.04 0.05
Matches are distributed among these distances:
138 2 0.01
139 40 0.16
141 69 0.28
145 69 0.28
146 65 0.27
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.49
Consensus pattern (141 bp):
TTTTCTTTCCATATTACAAAAGTCTTAAATGATACTAATAATTTTTTTACTTAAACAACTTATTA
TTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTTTTTGAGGAATT
AGTCATTACGT
Found at i:15668 original size:145 final size:144
Alignment explanation
Indices: 15292--15695 Score: 631
Period size: 145 Copynumber: 2.8 Consensus size: 144
15282 TCCAATCAGA
* * * * * *
15292 TTTTATTTCCATATTAAAAAAGTCTAAAATAATAAC-AATTATTTTTATA-TTAAACAACTTATT
1 TTTTCTTTCCATATTACAAAAGTCTTAAATGAT-ACTAATAATTTTTTTACTTAAACAACTTATT
15355 ATTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACG----TTTTTTTTAGG
65 ATTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTTTTTTTTTAGG
*
15416 AATTAGTCATTAGGT
130 AATTAGTCATTACGT
15431 TTTTCTTTCCATATTACAAAAGTCTTAAATGATACTAATAATTTTTTTACGTTAAACAACTTATT
1 TTTTCTTTCCATATTACAAAAGTCTTAAATGATACTAATAATTTTTTTAC-TTAAACAACTTATT
15496 ATTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTTTTTTTTTGAG
65 ATTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTTTTTTTTT-AG
15561 GAATTAGTCATTACGT
129 GAATTAGTCATTACGT
**
15577 TTTTCTTTCTGTATTACAAAAGTCTTAAATGATACTAATAATTTTTTTACTTAAACAACTTATTA
1 TTTTCTTTCCATATTACAAAAGTCTTAAATGATACTAATAATTTTTTTACTTAAACAACTTATTA
* * *
15642 TTATAATTATTAAAATTATTATTAGTTATATATATTATTAATCACTACGTTTTT
66 TTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTT
15696 CTTTCCATAT
Statistics
Matches: 245, Mismatches: 12, Indels: 10
0.92 0.04 0.04
Matches are distributed among these distances:
138 2 0.01
139 40 0.16
141 64 0.26
145 74 0.30
146 65 0.27
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.49
Consensus pattern (144 bp):
TTTTCTTTCCATATTACAAAAGTCTTAAATGATACTAATAATTTTTTTACTTAAACAACTTATTA
TTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTTTTTTTTTAGGA
ATTAGTCATTACGT
Found at i:15707 original size:115 final size:114
Alignment explanation
Indices: 15563--15785 Score: 333
Period size: 115 Copynumber: 1.9 Consensus size: 114
15553 TTTTTGAGGA
* * ** *
15563 ATTAGTCATTACGTTTTTCTTTCTGTATTACAAAAGTCTT-AAATGATACTAATAATTTTTTTAC
1 ATTAATCACTACGTTTTTCTTTCCATATTACAAAAGT-TTAAAATAATACTAAT-ATTTTTTTAC
15627 -TTAAACAACTTATTATTATAATTATTAAAATTATTATTAGTTATATATATT
64 GTTAAACAACTTATTATTATAATTATTAAAATTATTATTA-TTATATATATT
15678 ATTAATCACTACGTTTTTCTTTCCATATTACAAAAGTTTAAAATAATACTAATATTTTTTTACGT
1 ATTAATCACTACGTTTTTCTTTCCATATTACAAAAGTTTAAAATAATACTAATATTTTTTTACGT
* * *
15743 TAAACATCTTCTTATTATAATTATTAAACTTATTATTATTATA
66 TAAACAACTTATTATTATAATTATTAAAATTATTATTATTATA
15786 ACAATTATTA
Statistics
Matches: 98, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
114 17 0.17
115 81 0.83
ACGTcount: A:0.37, C:0.10, G:0.04, T:0.49
Consensus pattern (114 bp):
ATTAATCACTACGTTTTTCTTTCCATATTACAAAAGTTTAAAATAATACTAATATTTTTTTACGT
TAAACAACTTATTATTATAATTATTAAAATTATTATTATTATATATATT
Found at i:15780 original size:15 final size:16
Alignment explanation
Indices: 15757--15804 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
15747 CATCTTCTTA
*
15757 TTATAATTATTA-AAC
1 TTATTATTATTATAAC
15772 TTATTATTATTATAAC
1 TTATTATTATTATAAC
15788 AATTATTATTAGTTATA
1 --TTATTATTA-TTATA
15805 TGATCACTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 11 0.39
16 3 0.11
18 9 0.32
19 5 0.18
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (16 bp):
TTATTATTATTATAAC
Found at i:15793 original size:18 final size:17
Alignment explanation
Indices: 15754--15804 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
15744 AAACATCTTC
* *
15754 TTATTATAATTATTAAAC
1 TTATTATTATTA-TAAAA
15772 TTATTATTATTATAACAA
1 TTATTATTATTATAA-AA
15790 TTATTATTAGTTATA
1 TTATTATTA-TTATA
15805 TGATCACTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 3 0.10
18 21 0.72
19 5 0.17
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (17 bp):
TTATTATTATTATAAAA
Found at i:17155 original size:22 final size:22
Alignment explanation
Indices: 17130--17171 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
17120 AAGATAATAA
* *
17130 TATAGTTTTTAAAATAATCACT
1 TATACTTTTTAAAACAATCACT
*
17152 TATACTTTTTAGAACAATCA
1 TATACTTTTTAAAACAATCA
17172 TTGAAGCTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.43
Consensus pattern (22 bp):
TATACTTTTTAAAACAATCACT
Found at i:20433 original size:2 final size:2
Alignment explanation
Indices: 20426--20452 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20416 TTTGTTCGAT
20426 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 T
20453 TTTCATCATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20664 original size:32 final size:32
Alignment explanation
Indices: 20628--20691 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
20618 AAAGAAGATT
* * *
20628 ATATATTTTTTATGTTATATGCTATAAATTAA
1 ATATATTTTTTATGTCATATACTACAAATTAA
20660 ATATATTTTTTATGTCATATACTACAAATTAA
1 ATATATTTTTTATGTCATATACTACAAATTAA
20692 TGTAATTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.06, G:0.05, T:0.50
Consensus pattern (32 bp):
ATATATTTTTTATGTCATATACTACAAATTAA
Found at i:21205 original size:8 final size:8
Alignment explanation
Indices: 21192--21227 Score: 72
Period size: 8 Copynumber: 4.5 Consensus size: 8
21182 CATTTTAATA
21192 AAGTGGGC
1 AAGTGGGC
21200 AAGTGGGC
1 AAGTGGGC
21208 AAGTGGGC
1 AAGTGGGC
21216 AAGTGGGC
1 AAGTGGGC
21224 AAGT
1 AAGT
21228 ATCTGAACCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.28, C:0.11, G:0.47, T:0.14
Consensus pattern (8 bp):
AAGTGGGC
Found at i:22096 original size:128 final size:128
Alignment explanation
Indices: 21806--22062 Score: 315
Period size: 130 Copynumber: 2.0 Consensus size: 128
21796 ATCTCATCTG
* * * *
21806 GTGAAACTAGCGGCTAAACCTGGTGCAAAATTAATGCCTAAATTTTAGAAAGAAATCTGACTTGT
1 GTGAAACTAGGGGCTAAACATGGTCCCAAATTAATGCCTAAATTTTAGAAAGAAATCTGAC-T-T
* **
21871 CACAATCTTATTGATCACCATGGATGACGTGGTGGACCTGGTCCAACTAATAATTTCTCCATCTG
64 CACAATCTTATTGATCACCATGGATGACGTGGTGGACCTAGTCCAACTAATAATTTCTCCATCAA
* * * * *
21936 GTGAAACTAGGGGCTAAACATGGTGCTAAATTAGTGGCTAAATTTTAGGAAGAAATCTG-C-TCA
1 GTGAAACTAGGGGCTAAACATGGTCCCAAATTAATGCCTAAATTTTAGAAAGAAATCTGACTTCA
* *
21999 TAATCTTATTGATCGGGACCAT-GATGACGTGGTGGACCTAGTCCATCTAATAATTTCTCC-TCA
66 CAATCTTATTGATC---ACCATGGATGACGTGGTGGACCTAGTCCAACTAATAATTTCTCCATCA
22062 A
128 A
22063 ATTGCAAGTT
Statistics
Matches: 113, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
126 16 0.14
127 2 0.02
128 36 0.32
129 6 0.05
130 53 0.47
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.30
Consensus pattern (128 bp):
GTGAAACTAGGGGCTAAACATGGTCCCAAATTAATGCCTAAATTTTAGAAAGAAATCTGACTTCA
CAATCTTATTGATCACCATGGATGACGTGGTGGACCTAGTCCAACTAATAATTTCTCCATCAA
Found at i:27183 original size:45 final size:45
Alignment explanation
Indices: 27119--27219 Score: 202
Period size: 45 Copynumber: 2.2 Consensus size: 45
27109 AAAAAAGTAC
27119 GATGACAACTCAGACTCTAAAACTACCAACTACCAACTATAATAT
1 GATGACAACTCAGACTCTAAAACTACCAACTACCAACTATAATAT
27164 GATGACAACTCAGACTCTAAAACTACCAACTACCAACTATAATAT
1 GATGACAACTCAGACTCTAAAACTACCAACTACCAACTATAATAT
27209 GATGACAACTC
1 GATGACAACTC
27220 CATGATACTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.44, C:0.27, G:0.08, T:0.22
Consensus pattern (45 bp):
GATGACAACTCAGACTCTAAAACTACCAACTACCAACTATAATAT
Found at i:29618 original size:20 final size:20
Alignment explanation
Indices: 29593--29630 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
29583 ACGTTTGCTG
29593 TAAAGCTTAAAAGAACAAAA
1 TAAAGCTTAAAAGAACAAAA
29613 TAAAGCTTAAAAGAACAA
1 TAAAGCTTAAAAGAACAA
29631 CCAAGAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.63, C:0.11, G:0.11, T:0.16
Consensus pattern (20 bp):
TAAAGCTTAAAAGAACAAAA
Found at i:29752 original size:48 final size:48
Alignment explanation
Indices: 29681--29777 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
29671 CTACGTCCAC
* *
29681 GGGCAGAGAGAGATTCTAATTAATTTTTGGGAGAAAACGATATATCAA
1 GGGCAGAGAGAGACTCTAATTAATTTTTGGGAGAAAACAATATATCAA
29729 GGGCAGAGAGAGACTCTAATTAATTTTTGGGAGAAAACAATATATCAA
1 GGGCAGAGAGAGACTCTAATTAATTTTTGGGAGAAAACAATATATCAA
29777 G
1 G
29778 AATACAAGAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.40, C:0.09, G:0.25, T:0.26
Consensus pattern (48 bp):
GGGCAGAGAGAGACTCTAATTAATTTTTGGGAGAAAACAATATATCAA
Found at i:32176 original size:54 final size:54
Alignment explanation
Indices: 32094--32256 Score: 308
Period size: 54 Copynumber: 3.0 Consensus size: 54
32084 TGTGAACATG
32094 AAATTAAATGATGGGCTACATAAAAGGAGGTAGCCTTCTCCCATCCCTACACCC
1 AAATTAAATGATGGGCTACATAAAAGGAGGTAGCCTTCTCCCATCCCTACACCC
*
32148 AAATTAAATGATGGGCTACATAAAAGGAGGTAGCCTTTTCCCATCCCTACACCC
1 AAATTAAATGATGGGCTACATAAAAGGAGGTAGCCTTCTCCCATCCCTACACCC
*
32202 AAATTAAATGATGGGCTACATAAAAGGAGATAGCCTTCTCCCATCCCTACACCC
1 AAATTAAATGATGGGCTACATAAAAGGAGGTAGCCTTCTCCCATCCCTACACCC
32256 A
1 A
32257 CTCCTCTCAT
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 106 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (54 bp):
AAATTAAATGATGGGCTACATAAAAGGAGGTAGCCTTCTCCCATCCCTACACCC
Found at i:33451 original size:22 final size:22
Alignment explanation
Indices: 33423--33466 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
33413 GTAAGCTTCG
*
33423 TCCCTTTTGAACAGTACGTCCA
1 TCCCTTTTGAACAGCACGTCCA
*
33445 TCCCTTTTGAAGAGCACGTCCA
1 TCCCTTTTGAACAGCACGTCCA
33467 ACAGCTTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.32, G:0.16, T:0.30
Consensus pattern (22 bp):
TCCCTTTTGAACAGCACGTCCA
Found at i:34711 original size:20 final size:20
Alignment explanation
Indices: 34686--34727 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
34676 TTCAATTCGA
34686 TTCGAAATAGAGACACAAGG
1 TTCGAAATAGAGACACAAGG
34706 TTCGAAATAGAGACACAAGG
1 TTCGAAATAGAGACACAAGG
34726 TT
1 TT
34728 GTGACACTGT
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:0.43, C:0.14, G:0.24, T:0.19
Consensus pattern (20 bp):
TTCGAAATAGAGACACAAGG
Found at i:36901 original size:23 final size:23
Alignment explanation
Indices: 36871--36916 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
36861 ACAAGAAACT
* *
36871 TAATTCCTCATTATTGAATATCC
1 TAATTCCTCATCATTGAAAATCC
36894 TAATTCCTCATCATTGAAAATCC
1 TAATTCCTCATCATTGAAAATCC
36917 CGTGTCACTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (23 bp):
TAATTCCTCATCATTGAAAATCC
Found at i:37153 original size:39 final size:39
Alignment explanation
Indices: 37090--37262 Score: 301
Period size: 39 Copynumber: 4.4 Consensus size: 39
37080 AAAACCTTCC
* * *
37090 TCTTCCTCTTCTTCTCCCATTGAGTTGTCTTGATCACTA
1 TCTTCCTCTTCATCTTCCACTGAGTTGTCTTGATCACTA
37129 TCTTCCTCTTCATCTTCCACTGAGTTGTCTTGATCACTA
1 TCTTCCTCTTCATCTTCCACTGAGTTGTCTTGATCACTA
*
37168 TCTTCCTCTTCATCTTCCACTGAGTTGTCTTTATCACTA
1 TCTTCCTCTTCATCTTCCACTGAGTTGTCTTGATCACTA
*
37207 TCTTCCTCTTCATCTTCCACTGAGTTGTCTTTATCACTA
1 TCTTCCTCTTCATCTTCCACTGAGTTGTCTTGATCACTA
37246 TCTTCCTCTTCATCTTC
1 TCTTCCTCTTCATCTTC
37263 ATTATCATTT
Statistics
Matches: 130, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 130 1.00
ACGTcount: A:0.14, C:0.32, G:0.08, T:0.46
Consensus pattern (39 bp):
TCTTCCTCTTCATCTTCCACTGAGTTGTCTTGATCACTA
Found at i:47921 original size:23 final size:23
Alignment explanation
Indices: 47863--47922 Score: 86
Period size: 23 Copynumber: 2.6 Consensus size: 23
47853 ACCGTTTAAC
*
47863 AATTATATATATTATTATTATAT
1 AATTATATATATAATTATTATAT
*
47886 AATTATATATATAA-TATATATTT
1 AATTATATATATAATTAT-TATAT
47909 AATTATATATATAA
1 AATTATATATATAA
47923 CTAAACGGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
22 3 0.09
23 31 0.91
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATTATATATATAATTATTATAT
Found at i:50886 original size:159 final size:161
Alignment explanation
Indices: 50589--50903 Score: 503
Period size: 159 Copynumber: 2.0 Consensus size: 161
50579 TTTGGTACAT
* *
50589 AAGAGACCAATAACGGCTTACAACCTTATACCAGGGATTCCATTTAAATCTTATTCTCTACTAAA
1 AAGAGACCAATAACAGCTTACAACCTTATACCAGGGACTCCATTTAAATCTTATTCTCTACTAAA
* *
50654 GGATTCAGATCCAAAGGAGGATCATTTAGCACCGATATTGGTAGTTCTGCTATGGAAGGGTTTGA
66 GGAATCAGATCCAAAGGAGGATCATTTAGCACCGATATTGGTAGTTCTGCCATGGAAGGGTTTGA
50719 ACATATGATTTAGTACTATATCAATCAATCC
131 ACATATGATTTAGTACTATATCAATCAATCC
* ** *
50750 AAGAGGCCAATAACAGCTTACAACCTTATACTTGGGGCTCCATTTAAATCTTATT-T-TACTAAA
1 AAGAGACCAATAACAGCTTACAACCTTATACCAGGGACTCCATTTAAATCTTATTCTCTACTAAA
*
50813 GGAATCAGATCCAAATGGA-GATCATTTAGCACCGA-AGTTGGTAGTTTTGCCATGGAAGGGTTT
66 GGAATCAGATCCAAA-GGAGGATCATTTAGCACCGATA-TTGGTAGTTCTGCCATGGAAGGGTTT
50876 GAACATATGATTTAGTACTATATCAATC
129 GAACATATGATTTAGTACTATATCAATC
50904 GATCATACAA
Statistics
Matches: 143, Mismatches: 9, Indels: 6
0.91 0.06 0.04
Matches are distributed among these distances:
158 1 0.01
159 89 0.62
160 4 0.03
161 49 0.34
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (161 bp):
AAGAGACCAATAACAGCTTACAACCTTATACCAGGGACTCCATTTAAATCTTATTCTCTACTAAA
GGAATCAGATCCAAAGGAGGATCATTTAGCACCGATATTGGTAGTTCTGCCATGGAAGGGTTTGA
ACATATGATTTAGTACTATATCAATCAATCC
Found at i:57385 original size:22 final size:22
Alignment explanation
Indices: 57357--57472 Score: 223
Period size: 22 Copynumber: 5.3 Consensus size: 22
57347 TATATTAAAA
57357 TGGGTCGTGCTGCGTCGGCACG
1 TGGGTCGTGCTGCGTCGGCACG
57379 TGGGTCGTGCTGCGTCGGCACG
1 TGGGTCGTGCTGCGTCGGCACG
57401 TGGGTCGTGCTGCGTCGGCACG
1 TGGGTCGTGCTGCGTCGGCACG
57423 TGGGTCGTGCTGCGTCGGCACG
1 TGGGTCGTGCTGCGTCGGCACG
*
57445 TGGGTCGTGCTGCGCCGGCACG
1 TGGGTCGTGCTGCGTCGGCACG
57467 TGGGTC
1 TGGGTC
57473 ATGCCGTGTC
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
22 93 1.00
ACGTcount: A:0.04, C:0.28, G:0.46, T:0.22
Consensus pattern (22 bp):
TGGGTCGTGCTGCGTCGGCACG
Found at i:59628 original size:61 final size:60
Alignment explanation
Indices: 59533--59717 Score: 237
Period size: 60 Copynumber: 3.1 Consensus size: 60
59523 TACTTATTGA
* * *
59533 TTCAATTAAAATG-TTTAGACTCAAATGGAGTAATTCGCGAAAGGGTTAACCTCAGATTTGT
1 TTCAATTAAAA-GATTTAAACTCAAATAGAGTAATTCGCGAAAGGGTTAACCTC-GATTTCT
* *
59594 TTCAATTAAAAGATTTAAACTCAAATAGAGTAATTCACGAAAGGGTTAATCTCGATTTCT
1 TTCAATTAAAAGATTTAAACTCAAATAGAGTAATTCGCGAAAGGGTTAACCTCGATTTCT
* * * * * * *
59654 TTCAATTAAAAGACTTAAATTCAAATAGAGTAATTCGAGAATGGATTAACCTCGGTTTAT
1 TTCAATTAAAAGATTTAAACTCAAATAGAGTAATTCGCGAAAGGGTTAACCTCGATTTCT
59714 TTCA
1 TTCA
59718 GATTTAAACT
Statistics
Matches: 109, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
60 62 0.57
61 47 0.43
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.34
Consensus pattern (60 bp):
TTCAATTAAAAGATTTAAACTCAAATAGAGTAATTCGCGAAAGGGTTAACCTCGATTTCT
Found at i:63649 original size:11 final size:10
Alignment explanation
Indices: 63633--63670 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
63623 TGGGCTATAG
63633 ATTATAGTATT
1 ATTATA-TATT
63644 ATTATATTATT
1 ATTATA-TATT
63655 ATTATATA-T
1 ATTATATATT
63664 ATTATAT
1 ATTATAT
63671 TATATCTATC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
9 8 0.31
10 2 0.08
11 16 0.62
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (10 bp):
ATTATATATT
Found at i:63653 original size:5 final size:5
Alignment explanation
Indices: 63633--63675 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
63623 TGGGCTATAG
*
63633 ATTAT AGTATT ATTAT ATTATT ATTAT A-TAT ATTAT ATTAT AT
1 ATTAT ATTA-T ATTAT ATTA-T ATTAT ATTAT ATTAT ATTAT AT
63676 CTATCTAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
4 4 0.12
5 20 0.61
6 9 0.27
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (5 bp):
ATTAT
Found at i:63674 original size:14 final size:15
Alignment explanation
Indices: 63640--63675 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
63630 TAGATTATAG
63640 TATTAT-TATATTAT
1 TATTATATATATTAT
63654 TATTATATATATTA-
1 TATTATATATATTAT
63668 TATTATAT
1 TATTATAT
63676 CTATCTAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTATATATATTAT
Found at i:63927 original size:19 final size:19
Alignment explanation
Indices: 63914--63951 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
63904 AAACAATTGT
63914 ATAGTTTAAGAACAAAAGA
1 ATAGTTTAAGAACAAAAGA
*
63933 ATAGTTTAAGAGCAAAAGA
1 ATAGTTTAAGAACAAAAGA
63952 GAGAAAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.05, G:0.18, T:0.21
Consensus pattern (19 bp):
ATAGTTTAAGAACAAAAGA
Found at i:64315 original size:36 final size:36
Alignment explanation
Indices: 64245--64315 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
64235 ACTTTCATTT
***
64245 ATGAAGAAAGATAACATTAATGGAACTTGGTTTTTC
1 ATGAAGAAAGATAACATTAATGGAACTCAATTTTTC
*
64281 ATGAAGTAAGATAACATTAATGGAACTCAATTTTT
1 ATGAAGAAAGATAACATTAATGGAACTCAATTTTT
64316 TCCCAACTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.34
Consensus pattern (36 bp):
ATGAAGAAAGATAACATTAATGGAACTCAATTTTTC
Found at i:67778 original size:6 final size:6
Alignment explanation
Indices: 67767--67802 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
67757 ACTCCAACAA
*
67767 CTGAAG CTGAAG CTGAAG CTGAAG CCGAAG CTGAAG
1 CTGAAG CTGAAG CTGAAG CTGAAG CTGAAG CTGAAG
67803 TTCTTGCTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.33, C:0.19, G:0.33, T:0.14
Consensus pattern (6 bp):
CTGAAG
Found at i:72075 original size:39 final size:39
Alignment explanation
Indices: 71959--72076 Score: 99
Period size: 39 Copynumber: 3.2 Consensus size: 39
71949 TCAATCGCCC
71959 ACCAACGAGAACTCCTGATAAGACTCGAATGCCAACTCA
1 ACCAACGAGAACTCCTGATAAGACTCGAATGCCAACTCA
*** * * *
71998 ACCAACCTCAA-T-CGGCAT-AGAACTCG--TG---ATTCCC
1 ACCAACGAGAACTCCTG-ATAAG-ACTCGAATGCCAACT-CA
72032 ACCAACGAGAACTCCTGATAAGACTCGAATGCCAACTCA
1 ACCAACGAGAACTCCTGATAAGACTCGAATGCCAACTCA
72071 ACCAAC
1 ACCAAC
72077 CTCAATCGGC
Statistics
Matches: 56, Mismatches: 12, Indels: 22
0.62 0.13 0.24
Matches are distributed among these distances:
33 2 0.04
34 9 0.16
35 8 0.14
36 6 0.11
37 6 0.11
38 8 0.14
39 15 0.27
40 2 0.04
ACGTcount: A:0.36, C:0.33, G:0.14, T:0.16
Consensus pattern (39 bp):
ACCAACGAGAACTCCTGATAAGACTCGAATGCCAACTCA
Found at i:72075 original size:73 final size:73
Alignment explanation
Indices: 71956--72102 Score: 294
Period size: 73 Copynumber: 2.0 Consensus size: 73
71946 TCGTCAATCG
71956 CCCACCAACGAGAACTCCTGATAAGACTCGAATGCCAACTCAACCAACCTCAATCGGCATAGAAC
1 CCCACCAACGAGAACTCCTGATAAGACTCGAATGCCAACTCAACCAACCTCAATCGGCATAGAAC
72021 TCGTGATT
66 TCGTGATT
72029 CCCACCAACGAGAACTCCTGATAAGACTCGAATGCCAACTCAACCAACCTCAATCGGCATAGAAC
1 CCCACCAACGAGAACTCCTGATAAGACTCGAATGCCAACTCAACCAACCTCAATCGGCATAGAAC
72094 TCGTGATT
66 TCGTGATT
72102 C
1 C
72103 GATCTGGCAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.34, C:0.33, G:0.15, T:0.18
Consensus pattern (73 bp):
CCCACCAACGAGAACTCCTGATAAGACTCGAATGCCAACTCAACCAACCTCAATCGGCATAGAAC
TCGTGATT
Found at i:84777 original size:29 final size:30
Alignment explanation
Indices: 84744--84816 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
84734 ACTTGTACTG
**
84744 TTTGGACGTTTTGTCCC-ATGAACTTCAAT
1 TTTGGACGTTTTACCCCTATGAACTTCAAT
* *
84773 TTTGGACATTTTACCCCTTTGAACTTCAAT
1 TTTGGACGTTTTACCCCTATGAACTTCAAT
*
84803 TTTGAGACGATTTA
1 TTTG-GACGTTTTA
84817 GCTCCTCAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
29 14 0.39
30 15 0.42
31 7 0.19
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.42
Consensus pattern (30 bp):
TTTGGACGTTTTACCCCTATGAACTTCAAT
Done.