Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012616.1 Corchorus capsularis cultivar CVL-1 contig12637, 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: 59955
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:6184 original size:64 final size:65
Alignment explanation
Indices: 6107--6254 Score: 217
Period size: 69 Copynumber: 2.2 Consensus size: 65
6097 GCCTTTTTAA
* *
6107 AGAGTTTAGGGGCTTCTTTGTTGATG-ACAAAAAAAAAGAGTTCACGGCTAATTTGGCTGCAATT
1 AGAGTTCAGGGGCTTCTTTGTTGATGAACAAAAAAAAAGAGTTCAAGGCTAATTTGGCTGCAATT
*
6171 AGAGTTCATGGGCTTCTTTGTTGATGATCAAACAAAAAAAAAGAGTTCAAGGCTAATTTGGCTGC
1 AGAGTTCAGGGGCTTCTTTGTTGATG----AACAAAAAAAAAGAGTTCAAGGCTAATTTGGCTGC
6236 AATT
62 AATT
*
6240 AGAGTTCAGAGGCTT
1 AGAGTTCAGGGGCTT
6255 ATTAGGCTAT
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
64 24 0.32
69 50 0.68
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.30
Consensus pattern (65 bp):
AGAGTTCAGGGGCTTCTTTGTTGATGAACAAAAAAAAAGAGTTCAAGGCTAATTTGGCTGCAATT
Found at i:8319 original size:436 final size:436
Alignment explanation
Indices: 7595--8404 Score: 1115
Period size: 436 Copynumber: 1.9 Consensus size: 436
7585 TTGGCTTTTA
* * *
7595 TTTTTGTATTTTTTTTTCTATTTGTCTGAGTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTC
1 TTTTTGTATTCTTTGTTCTATTTGTCCGAGTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTC
* * * * * * **
7660 ATTATCTACAATTTTCATGCGGAACTCAAAAGCCAATTTTAATGTTTTGATTCTAAAAAATGTTT
66 ATGATCTACAACTTTCATGAGGAACTCAAAAGCAAATTTTAATGTTTTAATTCAAAAAAATACTT
* * * * * * **
7725 CCGAAATTTTGTGGTTTTAATTGCCGGTCAATTTAATTTCGTATAATTTTTCGTCCACATGTCCG
131 CCCAAATTTGGTCGTTTCAATTGCCAGTCAATTTAATATAATATAATTTTTCGTCCACATGTCCG
* * * * *
7790 ATTGAAGTTATTGAAGTGTCAGTTAAAAGGTTATTGCATGATTTACGACTTTCATGAAGGACCAG
196 ATTAAAGTTATTCAAGTGTCAGTTAAAAGGTTACTGCATGATCTACGACTTTCATGAAGAACCAG
* ** *
7855 AAAACTAAATTTGATTTGTGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGCTTCAAGATCT
261 AAAACTAAATTTGATATACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGCTTCAAGATAT
* *
7920 CCATTAACAAACATTTTCTTATTTGGATTATTTATCAAATGACCCTCATATTTTTCTACTTTATA
326 CCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATGACCCTCATATTTTTCTACTTTATA
7985 CTATTTAGTCCTTTACAAATTCTATCTTAATCTAACGTTTAAGATT
391 CTATTTAGTCCTTTACAAATTCTATCTTAATCTAACGTTTAAGATT
* * * *
8031 TTTTTTTATTCTTTGTTCTATTTGTCCGATTAAGTTGATTCATGTGTCTATTAAAAGGTAATTTC
1 TTTTTGTATTCTTTGTTCTATTTGTCCGAGTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTC
*
8096 ATGATCTACAACTTTCATGAAGG-ACTCAAAAGCAAATTTTTATGTTTTAATTCAAAAAAAATAC
66 ATGATCTACAACTTTCATG-AGGAACTCAAAAGCAAATTTTAATGTTTTAATTC-AAAAAAATAC
* ** * *
8160 TTCCCAAATTTGGTCGTTTCGATTGTTAGTCTATTTAATATAATATAA-TTTTCGATCCACATTT
129 TTCCCAAATTTGGTCGTTTCAATTGCCAGTCAATTTAATATAATATAATTTTTCG-TCCACATGT
** *
8224 CCGATTAAAGTTATTCAAGTGTTGGTTAAAAGGTTACTGTATGATCTACGACTTTCATGAAGAAT
193 CCGATTAAAGTTATTCAAGTGTCAGTTAAAAGGTTACTGCATGATCTACGACTTTCATGAAGAA-
* * * *
8289 CC-G-AAAGTTAATTTGATATACGAGTTTCATGAAGGGTTTAAAAGGGAATTTTTATGTTTCAAG
257 CCAGAAAACTAAATTTGATATACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGCTTCAAG
* *
8352 ATATCCATTAAGAAATATTTTCTTATTTGAATTAGTTATCAAATGACCCTCAT
322 ATATCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATGACCCTCAT
8405 GCTTTCAAAT
Statistics
Matches: 321, Mismatches: 49, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
436 209 0.65
437 110 0.34
438 2 0.01
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (436 bp):
TTTTTGTATTCTTTGTTCTATTTGTCCGAGTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTC
ATGATCTACAACTTTCATGAGGAACTCAAAAGCAAATTTTAATGTTTTAATTCAAAAAAATACTT
CCCAAATTTGGTCGTTTCAATTGCCAGTCAATTTAATATAATATAATTTTTCGTCCACATGTCCG
ATTAAAGTTATTCAAGTGTCAGTTAAAAGGTTACTGCATGATCTACGACTTTCATGAAGAACCAG
AAAACTAAATTTGATATACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGCTTCAAGATAT
CCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATGACCCTCATATTTTTCTACTTTATA
CTATTTAGTCCTTTACAAATTCTATCTTAATCTAACGTTTAAGATT
Found at i:9102 original size:64 final size:64
Alignment explanation
Indices: 9001--9122 Score: 235
Period size: 64 Copynumber: 1.9 Consensus size: 64
8991 TGATGTATTC
9001 ACATGTACCCATTGTGATCCAATAGTATTCAACCACAATTTATAGTTTTATAAACTATATCAAA
1 ACATGTACCCATTGTGATCCAATAGTATTCAACCACAATTTATAGTTTTATAAACTATATCAAA
*
9065 ACATGTACCCATTGTGATTCAATAGTATTCAACCACAATTTATAGTTTTATAAACTAT
1 ACATGTACCCATTGTGATCCAATAGTATTCAACCACAATTTATAGTTTTATAAACTAT
9123 TCTATCAAGT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (64 bp):
ACATGTACCCATTGTGATCCAATAGTATTCAACCACAATTTATAGTTTTATAAACTATATCAAA
Found at i:9442 original size:78 final size:77
Alignment explanation
Indices: 9360--9598 Score: 350
Period size: 78 Copynumber: 3.2 Consensus size: 77
9350 TTGTTTAGGT
* *
9360 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATAT-CTT-T-A-T
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACT
*
9420 AAT-TATTTT--A
65 ATTATATTTTACA
*
9430 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAACATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
9495 TTATATTTTACCA
66 TTATATTTTA-CA
*
9508 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
9573 TTATATTTTACAA
66 TTATATTTTAC-A
9586 TTTTACTATTTTA
1 TTTTACTATTTTA
9599 ATTAAAAAAA
Statistics
Matches: 153, Mismatches: 6, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
70 48 0.31
71 5 0.03
72 1 0.01
73 1 0.01
74 3 0.02
75 6 0.04
77 1 0.01
78 88 0.58
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.49
Consensus pattern (77 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
TTATATTTTACA
Found at i:9443 original size:70 final size:70
Alignment explanation
Indices: 9360--9592 Score: 297
Period size: 70 Copynumber: 3.2 Consensus size: 70
9350 TTGTTTAGGT
* *
9360 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAATT
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATT
9424 ATTTTA
65 ATTTTA
*
9430 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAACATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATAT-CTT-T-A-TA
*
9495 TTATATTTTACCA
62 AT-TATTTT---A
* * *
9508 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATTA
*
9573 TTATA
66 TTTTA
*
9578 TTTTACAATTTTACT
1 TTTTACTATTTTACT
9593 ATTTTAATTA
Statistics
Matches: 143, Mismatches: 11, Indels: 18
0.83 0.06 0.10
Matches are distributed among these distances:
70 63 0.44
71 5 0.03
72 1 0.01
73 6 0.04
74 5 0.03
75 7 0.05
76 1 0.01
77 2 0.01
78 53 0.37
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.49
Consensus pattern (70 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATTA
TTTTA
Found at i:18362 original size:26 final size:26
Alignment explanation
Indices: 18326--18384 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
18316 AAGAAAATAT
18326 ATAGCATTCTACTAATTATTTTTGAC
1 ATAGCATTCTACTAATTATTTTTGAC
* * *
18352 ATAGTATTCTACTAGTTATTTTTTAC
1 ATAGCATTCTACTAATTATTTTTGAC
18378 AT-GCATT
1 ATAGCATT
18385 TTAAACAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 4 0.14
26 25 0.86
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.49
Consensus pattern (26 bp):
ATAGCATTCTACTAATTATTTTTGAC
Found at i:20707 original size:711 final size:703
Alignment explanation
Indices: 19344--21427 Score: 2545
Period size: 711 Copynumber: 2.9 Consensus size: 703
19334 TCTCACCTAT
* * * * *
19344 GAACATATATACCATTAGATTCTAAATTGGGTCAATTTACTTAGATGACAGTTGAATCTCCATCT
1 GAACATATATACCGTTAGATTCTAAATTTGGTCAATTTGCTTAGTTGACAATTGAATCTCCATCT
* * * * *
19409 TACCGTTCCTTTTTCATTGGACC-AAAAGTCATTATTTAATCACTCGATAGAA-TTTTATGAGGT
66 TACTG-TCCTTTTTTATTGAACCAAAAAG-CATTATTTCATCACTCGATAGAATTTTTAGGAGGT
*
19472 GATAACTTAAAAACTAGACTTTTTTGAGAGAATAATTGTGAAATACAAGTTGTAGGAAACTCATC
129 GATAACTTAAAAACTAGAC-TTTTTGAGAGAATAGTTGTGAAATACAAGTTGTAGGAAACTCATC
* * * * * * *
19537 AAAGATTCACCAGATAAGATTTCATGACAAACAGAGATTGTTTGTGTTTGATTATATGTTTATAT
193 AAAGA-TCACCGGATAAGATTTCATGGCAAACAGAGGTTGATT-TGTTTGATTTTATATTCATAT
* * *
19602 AAAGTAATTGAGAAATCAGTACGTTTAATCAGGGACGGATCCAAAATGGGTTAAATTAGATAAGT
256 AAA-TGATT-AG-AATCAGTACG-TTAATCAGGG-CGGATCCAAAAGGGGTTAAATTAAATAAGT
* *
19667 AAATATTTCTCAAACAAAAAGTTTCAAAATTCTACCTTGGCCCCTCTTGACTTTTTAATTTGTTC
316 AAATATTTCTCAAACAAAAAGTTTCAAAATT-AACCTTGGCCCCTCTTGACTTTTTAATTTGTCC
*
19732 CTCTTGGTAAATTTCGTAAGTTAACTCTTTATCTTTTAATATTTAAATCCTTCGCCTTATTATTG
380 CTCTTGGTAAATTTCGTAAGTTAACTCTTTATCTTTTAATATTTAAATCCTTTGCCTTATTA---
* *
19797 TTTATACTAGTATATTATAGTTGTATTTTTTTTGCTGATAAAAAAAAGACTTTT---ATCTTAGA
442 -TTATA-TA-T-TA-TATAGTT-TATTTTTTTAGCTGATAAAAAAATGACTTTTAGAATCTTAGA
*
19859 AGGTCCTTATTCAATTTTACCTTTTTATTTATCTAAAATTTCATTTAAATACAAAATATTCTTGT
501 AGGTCCTTATTCAATTTTACCTTTTTATTTATCTAAAATTTCATTTAAATAGAAAATATTCTTGT
* *
19924 AGAACTCAAGATTATGTTTGAATCAATATTACTTTCTAATTTATACTTTAAACATATTTATGATT
566 AGAACTCAAAATTATGTTTGAATCAATGTTACTTTCTAATTTATACTTTAAACATATTTATGATT
* **
19989 GGAAATTAGGTACTTATATGGAAAAATGTACTGTTGATAATGAGAGCATATCTCTATGCTCACCT
631 GGAAATTAGGTACATATATGGAAAAATGTACAATTGATAATGAGAGCATATCTCTATGCTCACCT
20054 ATGATTAC
696 ATGATTAC
* * * * *
20062 GAACATATGTACTGTTAGATTCTAAATTTGGTCAATTTGCTTAGTTGATAACTGAATCTTCATCT
1 GAACATATATACCGTTAGATTCTAAATTTGGTCAATTTGCTTAGTTGACAATTGAATCTCCATCT
* *
20127 TACTGTCCATTTTTTATTGAACCAAAAAGCATTATTTCATCACTTGTTAGAATTTTTAGGAGGTG
66 TACTGTCC-TTTTTTATTGAACCAAAAAGCATTATTTCATCACTCGATAGAATTTTTAGGAGGTG
*
20192 ATAACTTAAAAACTAGGCATTTTTGAGAGAATAGTTGTGAAATACAAGTTGTAGGAAACTCATCA
130 ATAACTTAAAAACTAGAC-TTTTTGAGAGAATAGTTGTGAAATACAAGTTGTAGGAAACTCATCA
20257 AAGATCCACCGGATAAGATTTCATGGCAAACAGAGGTTGATTATGTTTGATTTTATATTCATATG
194 AAGAT-CACCGGATAAGATTTCATGGCAAACAGAGGTTGATT-TGTTTGATTTTATATTCATAT-
20322 AAATGATTAAGAATCAGTACGTTCAATCAGGAGCGGATCCAAAAGGGGGTTAAATTAAATAAGTA
256 AAATGATT-AGAATCAGTACGTT-AATCAGG-GCGGATCCAAAA-GGGGTTAAATTAAATAAGTA
20387 AATATTTCTCAAACAAAAAGTTTCAAAATTAACCTTGGCCCCTCTTGAC-TTTTAATTTGTCCCT
317 AATATTTCTCAAACAAAAAGTTTCAAAATTAACCTTGGCCCCTCTTGACTTTTTAATTTGTCCCT
* * * *
20451 CTTGGTAAATTTCATAAGTTAACTCTTTATTTTTTAATATTTAAATCTTTTGTCTTATTATTATA
382 CTTGGTAAATTTCGTAAGTTAACTCTTTATCTTTTAATATTTAAATCCTTTGCCTTATTATTATA
20516 TATTATATAGTTATATTTTTTTAGCTGAT-AAAAAATGACTTTTAGAATCTTAGAAGGTCCTTAT
447 TATTATATAGTT-TATTTTTTTAGCTGATAAAAAAATGACTTTTAGAATCTTAGAAGGTCCTTAT
** *
20580 TCAATTTTACCTTTTTATTTATCTAAAATTTCATTTGGATAGAAAATATTCTCGTAGAACTCAAA
511 TCAATTTTACCTTTTTATTTATCTAAAATTTCATTTAAATAGAAAATATTCTTGTAGAACTCAAA
*
20645 ATTATGTTTGAATCAATGTAACTTTCTAATTTATACTTTAAACATATTTATGATTGGAAATTAGG
576 ATTATGTTTGAATCAATGTTACTTTCTAATTTATACTTTAAACATATTTATGATTGGAAATTAGG
* *
20710 TACATAAATGGAAAAATGTACAATTGATAATGAGAGCATATCTCTATGCTCACCTATGATTAT
641 TACATATATGGAAAAATGTACAATTGATAATGAGAGCATATCTCTATGCTCACCTATGATTAC
*
20773 GAACATATATACCGATTAGATTCTAAA-TTGG---GTTTGCTTAGTTGACAATTGAATCTCCATC
1 GAACATATATACCG-TTAGATTCTAAATTTGGTCAATTTGCTTAGTTGACAATTGAATCTCCATC
* * * * * *
20834 TTACCATCTTACCGTCCTTTTTCCATAGAATCAAAAGGCATGATTTCATCACTCCATAGAATTTT
65 TT---A-C-T---GTCCTTTTT-TATTGAACCAAAAAGCATTATTTCATCACTCGATAGAATTTT
* * * *
20899 TAGGAGGCGATAACTTAAAAACTAGACTTTCTT-AGGAGAATAGTTGTGAAATACAAGTTCTTGA
121 TAGGAGGTGATAACTTAAAAACTAGACTTT-TTGA-GAGAATAGTTGTGAAATACAAGTTGTAGG
* * * * * *
20963 AAATTCATCAAAGTATCACCGGATAAAATTTCATGGCCAACGGAAGTT-ATTTGCGTTTGAATTT
184 AAACTCATCAAAG-ATCACCGGATAAGATTTCATGGCAAACAGAGGTTGATTT--GTTTGATTTT
* ** * *
21027 ATATTCATAT--A-G----G-AT-A--A--TT-AT---GTCGGATCCACATTGGAGCTAAATTAA
246 ATATTCATATAAATGATTAGAATCAGTACGTTAATCAGGGCGGATCCA-AAAGGGGTTAAATTAA
* * * * * * *
21075 CTAA--ATATATTTCCTTAAACAAAAATTTTC-AAATTACTACCTTGGGCCCGCATGACTTTTTA
310 ATAAGTAAATATTT-CTCAAACAAAAAGTTTCAAAATTA--ACCTTGGCCCCTCTTGACTTTTTA
* * * * *
21137 ATTTGCCCCTCTTGGTCAAA-TT-GTAAGTTAACCCTCTACCTTTTAATA-TTAAACCCTTTGCC
372 ATTTGTCCCTCTTGGT-AAATTTCGTAAGTTAACTCTTTATCTTTTAATATTTAAATCCTTTGCC
* * * * *
21199 TTATTTTTATTTATT-TATACTTT-TATTTTTAGCTGATAAAAAAATGACTTTTAGATTCTTAGA
436 TTATTATTATATATTATATAGTTTATTTTTTTAGCTGATAAAAAAATGACTTTTAGAATCTTAGA
* * * * * *
21262 AGGTACTTATTCAATTTTACCTTTTCA-TTATCTTAAATTTCACTTAAATAGAAAATATTTTTGA
501 AGGTCCTTATTCAATTTTACCTTTTTATTTATCTAAAATTTCATTTAAATAGAAAATATTCTTGT
* *
21326 AGAACTCAAAATTATGTTTGAATCAATGTTACTTTCTAATTTATACTTAAAACATATCTATGATT
566 AGAACTCAAAATTATGTTTGAATCAATGTTACTTTCTAATTTATACTTTAAACATATTTATGATT
* * *
21391 GGAAATTAGGAACAAATATGGAAAAATGTAAAATTGA
631 GGAAATTAGGTACATATATGGAAAAATGTACAATTGA
21428 GGAAAGCTAA
Statistics
Matches: 1212, Mismatches: 121, Indels: 93
0.85 0.08 0.07
Matches are distributed among these distances:
691 138 0.11
692 50 0.04
693 19 0.02
694 39 0.03
695 58 0.05
696 24 0.02
697 3 0.00
699 2 0.00
701 2 0.00
703 1 0.00
705 1 0.00
706 2 0.00
707 1 0.00
708 41 0.03
709 22 0.02
710 2 0.00
711 217 0.18
712 16 0.01
713 7 0.01
714 1 0.00
715 12 0.01
716 150 0.12
717 76 0.06
718 138 0.11
719 187 0.15
720 3 0.00
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (703 bp):
GAACATATATACCGTTAGATTCTAAATTTGGTCAATTTGCTTAGTTGACAATTGAATCTCCATCT
TACTGTCCTTTTTTATTGAACCAAAAAGCATTATTTCATCACTCGATAGAATTTTTAGGAGGTGA
TAACTTAAAAACTAGACTTTTTGAGAGAATAGTTGTGAAATACAAGTTGTAGGAAACTCATCAAA
GATCACCGGATAAGATTTCATGGCAAACAGAGGTTGATTTGTTTGATTTTATATTCATATAAATG
ATTAGAATCAGTACGTTAATCAGGGCGGATCCAAAAGGGGTTAAATTAAATAAGTAAATATTTCT
CAAACAAAAAGTTTCAAAATTAACCTTGGCCCCTCTTGACTTTTTAATTTGTCCCTCTTGGTAAA
TTTCGTAAGTTAACTCTTTATCTTTTAATATTTAAATCCTTTGCCTTATTATTATATATTATATA
GTTTATTTTTTTAGCTGATAAAAAAATGACTTTTAGAATCTTAGAAGGTCCTTATTCAATTTTAC
CTTTTTATTTATCTAAAATTTCATTTAAATAGAAAATATTCTTGTAGAACTCAAAATTATGTTTG
AATCAATGTTACTTTCTAATTTATACTTTAAACATATTTATGATTGGAAATTAGGTACATATATG
GAAAAATGTACAATTGATAATGAGAGCATATCTCTATGCTCACCTATGATTAC
Found at i:22867 original size:51 final size:51
Alignment explanation
Indices: 22791--22892 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
22781 TCAGGAGCAT
22791 TAATGAAAAGTCCTTTGAAGTTCTTATAATGTCCAATAGGGCACCATATCA
1 TAATGAAAAGTCCTTTGAAGTTCTTATAATGTCCAATAGGGCACCATATCA
22842 TAATGAAAAGTCCTTTGAAGTTCTTATAATGTCCAATAGGGCACCATATCA
1 TAATGAAAAGTCCTTTGAAGTTCTTATAATGTCCAATAGGGCACCATATCA
22893 CAATAAACTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (51 bp):
TAATGAAAAGTCCTTTGAAGTTCTTATAATGTCCAATAGGGCACCATATCA
Found at i:27011 original size:13 final size:13
Alignment explanation
Indices: 26977--27002 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
26967 ACTGTGTATT
26977 GAATAATTTTCCA
1 GAATAATTTTCCA
26990 GAATAATTTTCCA
1 GAATAATTTTCCA
27003 TACAAATTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
GAATAATTTTCCA
Found at i:29519 original size:38 final size:37
Alignment explanation
Indices: 29447--29542 Score: 138
Period size: 38 Copynumber: 2.6 Consensus size: 37
29437 AATTTGACTT
*
29447 TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTGTC
1 TTTGTTTCCAACGTCCTATTTAATTTAGCCTTTTGTC
** *
29484 TTTGTTTCCAATCGTTGTATTTAATTTAGCTTTTTGTC
1 TTTGTTTCCAA-CGTCCTATTTAATTTAGCCTTTTGTC
*
29522 TTTGTCTCCAACGTCCTATTT
1 TTTGTTTCCAACGTCCTATTT
29543 GAGCTTAGAT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
37 19 0.37
38 32 0.63
ACGTcount: A:0.15, C:0.20, G:0.11, T:0.54
Consensus pattern (37 bp):
TTTGTTTCCAACGTCCTATTTAATTTAGCCTTTTGTC
Found at i:31387 original size:22 final size:22
Alignment explanation
Indices: 31362--31444 Score: 71
Period size: 22 Copynumber: 3.8 Consensus size: 22
31352 TTTTCGATGT
31362 GGTTAACAAAATTTTATTAGGA
1 GGTTAACAAAATTTTATTAGGA
* * **
31384 GGTT-ACTAATATTTCATGGGGA
1 GGTTAAC-AAAATTTTATTAGGA
* *
31406 GGTTATCAAAATTTTA-TAGTA
1 GGTTAACAAAATTTTATTAGGA
*
31427 TGGTTATCAAAATTTTAT
1 -GGTTAACAAAATTTTAT
31445 ATGAAGGTTA
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
21 4 0.09
22 42 0.89
23 1 0.02
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (22 bp):
GGTTAACAAAATTTTATTAGGA
Found at i:31453 original size:22 final size:22
Alignment explanation
Indices: 31405--31459 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
31395 TTTCATGGGG
31405 AGGTTATCAAAATTTTATAGTA
1 AGGTTATCAAAATTTTATAGTA
*
31427 TGGTTATCAAAATTTTATA-TGA
1 AGGTTATCAAAATTTTATAGT-A
31449 AGGTTAT-AAAA
1 AGGTTATCAAAA
31460 GTCTCAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 5 0.17
22 25 0.83
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.40
Consensus pattern (22 bp):
AGGTTATCAAAATTTTATAGTA
Found at i:31534 original size:22 final size:22
Alignment explanation
Indices: 31482--31668 Score: 102
Period size: 22 Copynumber: 8.4 Consensus size: 22
31472 TTAGGAGTAC
*
31482 CAAAATTTTATAGAAG-G-TTAT
1 CAAAATTTCATAG-AGTGATTAT
*
31503 C-AAATCTCATAGAGTGATTAT
1 CAAAATTTCATAGAGTGATTAT
* *
31524 CGAAATTTCATAGAATTCAGATTAT
1 CAAAATTTCATAG-AGT--GATTAT
*
31549 CAAAATTT-ATAG-GAAGATTAT
1 CAAAATTTCATAGAG-TGATTAT
31570 CAAAATTTCATA-ATGTTG-TTAT
1 CAAAATTTCATAGA-G-TGATTAT
* * * *
31592 CAAAATTTCAAAGCGAGGTTAT
1 CAAAATTTCATAGAGTGATTAT
*
31614 CAAAATTACATA-ATGTGATTAT
1 CAAAATTTCATAGA-GTGATTAT
* * *
31636 CAGAAATATTTCATAGAGGGGTTAA
1 C--AAA-ATTTCATAGAGTGATTAT
31661 CAAAATTT
1 CAAAATTT
31669 TATTTTTATA
Statistics
Matches: 128, Mismatches: 21, Indels: 33
0.70 0.12 0.18
Matches are distributed among these distances:
19 2 0.02
20 10 0.08
21 21 0.16
22 54 0.42
23 7 0.05
24 7 0.05
25 26 0.20
26 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAGAGTGATTAT
Found at i:31554 original size:25 final size:22
Alignment explanation
Indices: 31482--31581 Score: 89
Period size: 21 Copynumber: 4.5 Consensus size: 22
31472 TTAGGAGTAC
* *
31482 CAAAATTTTATAG-AAGGTTAT
1 CAAAATTTCATAGAAAGATTAT
* **
31503 C-AAATCTCATAGAGTGATTAT
1 CAAAATTTCATAGAAAGATTAT
*
31524 CGAAATTTCATAGAATTCAGATTAT
1 CAAAATTTCATAGAA---AGATTAT
*
31549 CAAAATTT-ATAGGAAGATTAT
1 CAAAATTTCATAGAAAGATTAT
31570 CAAAATTTCATA
1 CAAAATTTCATA
31582 ATGTTGTTAT
Statistics
Matches: 63, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
20 9 0.14
21 22 0.35
22 14 0.22
24 5 0.08
25 13 0.21
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAGAAAGATTAT
Found at i:31626 original size:44 final size:43
Alignment explanation
Indices: 31543--31642 Score: 123
Period size: 44 Copynumber: 2.3 Consensus size: 43
31533 ATAGAATTCA
* *
31543 GATTATCAAAATTTATAGGAAGATTATCAAAATTTCATAATGTT
1 GATTATCAAAATTTAAAGGAAGATTATCAAAATTACATAATG-T
*
31587 G-TTATCAAAATTTCAAAGCG-AGGTTATCAAAATTACATAATGT
1 GATTATCAAAATTT-AAAG-GAAGATTATCAAAATTACATAATGT
31630 GATTATCAGAAAT
1 GATTATCA-AAAT
31643 ATTTCATAGA
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
43 14 0.29
44 30 0.61
45 5 0.10
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (43 bp):
GATTATCAAAATTTAAAGGAAGATTATCAAAATTACATAATGT
Found at i:31719 original size:22 final size:23
Alignment explanation
Indices: 31670--31720 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
31660 ACAAAATTTT
*
31670 ATTTTTATAAAGAGGTTATCGAA
1 ATTTTCATAAAGAGGTTATCGAA
31693 A-TTTCATAAAGAGGTTATC-AA
1 ATTTTCATAAAGAGGTTATCGAA
31714 ATTTTCA
1 ATTTTCA
31721 AAATGTGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 3 0.12
22 22 0.85
23 1 0.04
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (23 bp):
ATTTTCATAAAGAGGTTATCGAA
Found at i:31944 original size:22 final size:22
Alignment explanation
Indices: 31919--32287 Score: 100
Period size: 22 Copynumber: 16.6 Consensus size: 22
31909 TCGAAAGAGA
*
31919 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGCGAGG
* *
31941 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGCGAGG
* **
31963 TTAACAAAATTTCATTAG-GAAA
1 TTATCAAAATTTCA-TAGCGAGG
* * *
31985 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGCGAGG
*
32007 TTATCAAAATTTCATATG-AAGG
1 TTATCAAAATTTCATA-GCGAGG
* **
32029 TTATAAAAGTCTCAATTTCATAAGGA-G
1 TTAT-CAA-----AATTTCATAGCGAGG
* * * *
32056 -TACCAAAAATTGATAG-AAGG
1 TTATCAAAATTTCATAGCGAGG
* * * *
32076 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGCGAGG
*
32097 TTAT-AGAAATTTCATATAGATC-AGA
1 TTATCA-AAATTTC--ATAG--CGAGG
*
32122 TTATCAAAATTT-ATAG-GAAGA
1 TTATCAAAATTTCATAGCG-AGG
* * **
32143 TCATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAGCGAGG
* *
32165 TTATCAAAATTTCAAAGCGAGA
1 TTATCAAAATTTCATAGCGAGG
* ** * *
32187 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAGCGAGG
* * *
32209 TTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGCGAGG
* * *
32231 TCAACAAAATTT-AT-GAAGAGG
1 TTATCAAAATTTCATAG-CGAGG
**
32252 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGCGAGG
*
32274 TTATCAAATTTTCA
1 TTATCAAAATTTCA
32288 AAACAAAAAT
Statistics
Matches: 254, Mismatches: 62, Indels: 62
0.67 0.16 0.16
Matches are distributed among these distances:
19 1 0.00
20 17 0.07
21 43 0.17
22 151 0.59
23 10 0.04
24 4 0.02
25 14 0.06
26 3 0.01
27 1 0.00
28 10 0.04
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (22 bp):
TTATCAAAATTTCATAGCGAGG
Found at i:32213 original size:44 final size:45
Alignment explanation
Indices: 32120--32222 Score: 124
Period size: 44 Copynumber: 2.4 Consensus size: 45
32110 ATATAGATCA
* * *
32120 GATTATCAAAATTT-ATAGGAAGATCATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCAAAGGAAGATCATCAAAATTACATAATGTT
*
32164 G-TTATCAAAATTTCAAAGCG-AGATTATCAAAATTACATAATG-T
1 GATTATCAAAATTTCAAAG-GAAGATCATCAAAATTACATAATGTT
*
32207 GATTATCAGAATTTCA
1 GATTATCAAAATTTCA
32223 TAGAGGGGTC
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
43 14 0.27
44 36 0.71
45 1 0.02
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.35
Consensus pattern (45 bp):
GATTATCAAAATTTCAAAGGAAGATCATCAAAATTACATAATGTT
Found at i:32260 original size:21 final size:22
Alignment explanation
Indices: 32145--32287 Score: 110
Period size: 22 Copynumber: 6.5 Consensus size: 22
32135 TAGGAAGATC
** **
32145 ATCAAAATTTCATAGTGTTGTT
1 ATCAAAATTTCATAAAGAGGTT
* *
32167 ATCAAAATTTCA-AAGCGAGATT
1 ATCAAAATTTCATAA-AGAGGTT
* * * *
32189 ATCAAAATTACATAATGTGATT
1 ATCAAAATTTCATAAAGAGGTT
* * * *
32211 ATCAGAATTTCATAGAGGGGTC
1 ATCAAAATTTCATAAAGAGGTT
* *
32233 AACAAAATTT-ATGAAGAGGTT
1 ATCAAAATTTCATAAAGAGGTT
32254 ATCAAAATTTCATAAAGAGGTT
1 ATCAAAATTTCATAAAGAGGTT
*
32276 ATCAAATTTTCA
1 ATCAAAATTTCA
32288 AAACAAAAAT
Statistics
Matches: 94, Mismatches: 24, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
21 17 0.18
22 75 0.80
23 2 0.02
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (22 bp):
ATCAAAATTTCATAAAGAGGTT
Found at i:32453 original size:22 final size:22
Alignment explanation
Indices: 32385--32937 Score: 96
Period size: 22 Copynumber: 25.7 Consensus size: 22
32375 TTTTGGAGTA
* *
32385 ATCAAAATTTCAT-GGA-GGAT
1 ATCAAAATTTCATAAGAGGGTT
***
32405 ATCAAAATTTCAT-AGTTTAGTT
1 ATCAAAATTTCATAAG-AGGGTT
*
32427 TTCAAAATTTCATAAGAGGGTT
1 ATCAAAATTTCATAAGAGGGTT
*
32449 ATCAAAATTTCAT-AGTA-TG-T
1 ATCAAAATTTCATAAG-AGGGTT
**
32469 A-GGAAATTTCAT-AG-GGAGATT
1 ATCAAAATTTCATAAGAGG-G-TT
* *
32490 AACAAAATTCCATAATGA-GGTT
1 ATCAAAATTTCATAA-GAGGGTT
* ** *
32512 ATAAAAAAATCAT-AGGGAGGTT
1 ATCAAAATTTCATAAGAG-GGTT
*
32534 ATCAAAATTT--T--TA--GTT
1 ATCAAAATTTCATAAGAGGGTT
* **
32550 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCATAAGAGGGTT
* * * *
32572 ATCAAAATTTTATAGGGATGTTT
1 ATCAAAATTTCATA-AGAGGGTT
* **
32595 ATCAAAATTTTATAAGAAGATTT
1 ATCAAAATTTCATAAG-AGGGTT
* * *
32618 ATCAAAATTTTAT-AGCGAGATT
1 ATCAAAATTTCATAAGAG-GGTT
* *
32640 ATCAAAATTTCAT-AGTGTGATT
1 ATCAAAATTTCATAAGAG-GGTT
* * *
32662 ATCAAAATTTCA-GAGTGTGATT
1 ATCAAAATTTCATAAGAG-GGTT
*
32684 A-CTAACAATTTCATATG-GAGGTT
1 ATC-AA-AATTTCATAAGAG-GGTT
* * * *
32707 TTTAAATTTTCATAACG-TGGTT
1 ATCAAAATTTCATAA-GAGGGTT
* *
32729 ATCAATATTTCATATG-GAGGTT
1 ATCAAAATTTCATAAGAG-GGTT
* * *
32751 ATCAACATCTCAT-AGTGTTGGTT
1 ATCAAAATTTCATAAGAG--GGTT
*
32774 ATCAAAATTTCAT-TG-GGAAGTT
1 ATCAAAATTTCATAAGAGG--GTT
* *
32796 ATCAAAATTTCATATTGA-GGTC
1 ATCAAAATTTCATA-AGAGGGTT
*
32818 ATCAAAA-TTCATTA-A--GTT
1 ATCAAAATTTCATAAGAGGGTT
*
32836 AGT-AAAATTTCATAAGAAGGTT
1 A-TCAAAATTTCATAAGAGGGTT
** * * *
32858 AAAAAAATGT-ATAAAAAGGTT
1 ATCAAAATTTCATAAGAGGGTT
* * * ***
32879 CTCGAAATTCCAT-AGTATCATT
1 ATCAAAATTTCATAAG-AGGGTT
* *
32901 ATCAAAATTTCATAGGAAGGTT
1 ATCAAAATTTCATAAGAGGGTT
32923 ATCAAAATTTCATAA
1 ATCAAAATTTCATAA
32938 TGGGATCATA
Statistics
Matches: 395, Mismatches: 92, Indels: 90
0.68 0.16 0.16
Matches are distributed among these distances:
16 12 0.03
18 8 0.02
19 20 0.05
20 21 0.05
21 30 0.08
22 228 0.58
23 70 0.18
24 6 0.02
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAAGAGGGTT
Found at i:32598 original size:23 final size:23
Alignment explanation
Indices: 32570--32671 Score: 120
Period size: 22 Copynumber: 4.5 Consensus size: 23
32560 CATAAGAAAG
* *
32570 TTATCAAAATTTTATAGGGATGT
1 TTATCAAAATTTTATAGAGATGA
*
32593 TTATCAAAATTTTATA-AGAAGA
1 TTATCAAAATTTTATAGAGATGA
*
32615 TTTATCAAAATTTTATAGCGA-GA
1 -TTATCAAAATTTTATAGAGATGA
* *
32638 TTATCAAAATTTCATAGTG-TGA
1 TTATCAAAATTTTATAGAGATGA
32660 TTATCAAAATTT
1 TTATCAAAATTT
32672 CAGAGTGTGA
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
22 34 0.49
23 34 0.49
24 2 0.03
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.41
Consensus pattern (23 bp):
TTATCAAAATTTTATAGAGATGA
Found at i:32612 original size:45 final size:45
Alignment explanation
Indices: 32548--32653 Score: 151
Period size: 45 Copynumber: 2.4 Consensus size: 45
32538 AAATTTTTAG
* * *
32548 TTATCAAGATTTCATAAGAA-AGTTATCAAAATTTTATAGGGATGT
1 TTATCAAAATTTCATAAGAAGAGTTATCAAAATTTTATAGCGA-GA
* *
32593 TTATCAAAATTTTATAAGAAGATTTATCAAAATTTTATAGCGAGA
1 TTATCAAAATTTCATAAGAAGAGTTATCAAAATTTTATAGCGAGA
32638 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
32654 GTGTGATTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 34 0.63
46 20 0.37
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (45 bp):
TTATCAAAATTTCATAAGAAGAGTTATCAAAATTTTATAGCGAGA
Found at i:32797 original size:45 final size:43
Alignment explanation
Indices: 32547--32830 Score: 135
Period size: 45 Copynumber: 6.4 Consensus size: 43
32537 AAAATTTTTA
* * * * * *
32547 GTTATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAGGGATG
1 GTTATCAAAATTTCAT-TGGAAGTTATCAAAATCTCATAGTG-TG
* * ** * * * *
32592 TTTATCAAAATTTTATAAGAAGATTTATCAAAATTTTATAGCGAG
1 GTTATCAAAATTTCATTGGAAG--TTATCAAAATCTCATAGTGTG
* * *
32637 ATTATCAAAATTTCATAGTGTG-A-TTATCAAAATTTCAGAGTGTG
1 GTTATCAAAATTTCAT--TG-GAAGTTATCAAAATCTCATAGTGTG
* * * * * * **
32681 ATTA-CTAACAATTTCATATGGAGGTTTTTAAATTTTCATAACGTG
1 GTTATC-AA-AATTTCAT-TGGAAGTTATCAAAATCTCATAGTGTG
* * *
32726 GTTATCAATATTTCATATGGAGGTTATCAACATCTCATAGTGTTG
1 GTTATCAAAATTTCAT-TGGAAGTTATCAAAATCTCATAGTG-TG
* * *
32771 GTTATCAAAATTTCATTGGGAAGTTATCAAAATTTCATATTGAG
1 GTTATCAAAATTTCATT-GGAAGTTATCAAAATCTCATAGTGTG
*
32815 GTCATCAAAA-TTCATT
1 GTTATCAAAATTTCATT
32831 AAGTTAGTAA
Statistics
Matches: 188, Mismatches: 39, Indels: 26
0.74 0.15 0.10
Matches are distributed among these distances:
43 8 0.04
44 66 0.35
45 93 0.49
46 19 0.10
47 1 0.01
48 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (43 bp):
GTTATCAAAATTTCATTGGAAGTTATCAAAATCTCATAGTGTG
Found at i:34455 original size:19 final size:18
Alignment explanation
Indices: 34431--34466 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
34421 AGAATATTTA
34431 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
34450 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
34467 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:39852 original size:22 final size:23
Alignment explanation
Indices: 39814--39862 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 23
39804 ATTGACATAG
*
39814 ACATTACCAAAAGATTATCCCTA
1 ACATTACCAAAAAATTATCCCTA
39837 ACATTA-CAAAAAATTATCCCTA
1 ACATTACCAAAAAATTATCCCTA
39859 ACAT
1 ACAT
39863 AAAAATTGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.47, C:0.24, G:0.02, T:0.27
Consensus pattern (23 bp):
ACATTACCAAAAAATTATCCCTA
Found at i:39911 original size:48 final size:48
Alignment explanation
Indices: 39858--39955 Score: 178
Period size: 48 Copynumber: 2.0 Consensus size: 48
39848 AATTATCCCT
*
39858 AACATAAAAATTGGAATTAATATGAACAACATTCTCACATGTTACGTG
1 AACATAAAAATTGGAATTAATAAGAACAACATTCTCACATGTTACGTG
*
39906 AACATAAAAATTGGAATTAATAAGAACAACATTCTCACGTGTTACGTG
1 AACATAAAAATTGGAATTAATAAGAACAACATTCTCACATGTTACGTG
39954 AA
1 AA
39956 TAGCCAGTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.45, C:0.14, G:0.13, T:0.28
Consensus pattern (48 bp):
AACATAAAAATTGGAATTAATAAGAACAACATTCTCACATGTTACGTG
Found at i:42540 original size:22 final size:23
Alignment explanation
Indices: 42515--42558 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
42505 TTAAATCTAA
*
42515 TATCCTAATAC-AATTTTATTTT
1 TATCATAATACTAATTTTATTTT
**
42537 TATCATTTTACTAATTTTATTT
1 TATCATAATACTAATTTTATTT
42559 AAAAACTTAG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.59
Consensus pattern (23 bp):
TATCATAATACTAATTTTATTTT
Found at i:51308 original size:178 final size:178
Alignment explanation
Indices: 51004--51363 Score: 612
Period size: 178 Copynumber: 2.0 Consensus size: 178
50994 CGTGTTATGT
*
51004 ATGTTGACGACGCATACTATTCCCTATTCACGCAAAAGAATATCGTTTCCAACCTCAAACGGGTT
1 ATGTCGACGACGCATACTATTCCCTATTCACGCAAAAGAATATCGTTTCCAACCTCAAACGGGTT
* * * *
51069 CTCATAAAATGTGTATACGACATATTTAATAAAGTTGACAATAGGAGGGACAAAGCTGCCAATTA
66 CACATAAAACGTGTATACGACATACTTAATAAAGTAGACAATAGGAGGGACAAAGCTGCCAATTA
* * *
51134 TTGTTCTGATTAGGAAACATATGACAAAAATTCCTTTATAAAAAAAGG
131 TTGTTCCGATTAGGAAACATATAACAAAAATTCCTATATAAAAAAAGG
*
51182 ATGTCGACGACGCATACTATTCCCTCTTCACGCAAAAGAATATCGTTTCCAACCTCAAACGGGTT
1 ATGTCGACGACGCATACTATTCCCTATTCACGCAAAAGAATATCGTTTCCAACCTCAAACGGGTT
* *
51247 CACGTAAAACGTGTATACGACATACTTAATAAAGTAGACAATAGGAGGGAGAAAGCTGCCAATTA
66 CACATAAAACGTGTATACGACATACTTAATAAAGTAGACAATAGGAGGGACAAAGCTGCCAATTA
*
51312 TTGTTCCGATTAGGGAACATATAACAAAAATTCCTATATAAAAAAAGG
131 TTGTTCCGATTAGGAAACATATAACAAAAATTCCTATATAAAAAAAGG
51360 ATGT
1 ATGT
51364 AAGAAAAGAT
Statistics
Matches: 170, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
178 170 1.00
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.26
Consensus pattern (178 bp):
ATGTCGACGACGCATACTATTCCCTATTCACGCAAAAGAATATCGTTTCCAACCTCAAACGGGTT
CACATAAAACGTGTATACGACATACTTAATAAAGTAGACAATAGGAGGGACAAAGCTGCCAATTA
TTGTTCCGATTAGGAAACATATAACAAAAATTCCTATATAAAAAAAGG
Found at i:54801 original size:2 final size:2
Alignment explanation
Indices: 54724--54785 Score: 92
Period size: 2 Copynumber: 32.0 Consensus size: 2
54714 ATCACCAAAT
*
54724 TA TA TA TA TG TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
54765 TA -A TA TA TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
54786 AGCTAACACA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
1 2 0.04
2 52 0.96
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Done.