Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013474.1 Corchorus capsularis cultivar CVL-1 contig13495, 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: 34318
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:11 original size:2 final size:2
Alignment explanation
Indices: 5--52 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1 CTCN
5 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
47 CT CT CT
1 CT CT CT
53 GTATTGGCTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3656 original size:189 final size:189
Alignment explanation
Indices: 3336--3716 Score: 762
Period size: 189 Copynumber: 2.0 Consensus size: 189
3326 AAGATACAGA
3336 TTGTACTCTTTCTAAAACAATATTAGCAGCCAAAATAAGCGAAACTCTAGACAAGTAAACAGATT
1 TTGTACTCTTTCTAAAACAATATTAGCAGCCAAAATAAGCGAAACTCTAGACAAGTAAACAGATT
3401 TGAATGAATCCACGATGACGACACCGTTAACATTCTTATAGATATATTTAAGCAACTTAACCTTG
66 TGAATGAATCCACGATGACGACACCGTTAACATTCTTATAGATATATTTAAGCAACTTAACCTTG
3466 ACTTAGAGGTTGTTATGGCTCATACCACTAATGGAGGGTCAACATCTAGGGTTCAATCT
131 ACTTAGAGGTTGTTATGGCTCATACCACTAATGGAGGGTCAACATCTAGGGTTCAATCT
3525 TTGTACTCTTTCTAAAACAATATTAGCAGCCAAAATAAGCGAAACTCTAGACAAGTAAACAGATT
1 TTGTACTCTTTCTAAAACAATATTAGCAGCCAAAATAAGCGAAACTCTAGACAAGTAAACAGATT
3590 TGAATGAATCCACGATGACGACACCGTTAACATTCTTATAGATATATTTAAGCAACTTAACCTTG
66 TGAATGAATCCACGATGACGACACCGTTAACATTCTTATAGATATATTTAAGCAACTTAACCTTG
3655 ACTTAGAGGTTGTTATGGCTCATACCACTAATGGAGGGTCAACATCTAGGGTTCAATCT
131 ACTTAGAGGTTGTTATGGCTCATACCACTAATGGAGGGTCAACATCTAGGGTTCAATCT
3714 TTG
1 TTG
3717 CCCTGCCTTT
Statistics
Matches: 192, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
189 192 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (189 bp):
TTGTACTCTTTCTAAAACAATATTAGCAGCCAAAATAAGCGAAACTCTAGACAAGTAAACAGATT
TGAATGAATCCACGATGACGACACCGTTAACATTCTTATAGATATATTTAAGCAACTTAACCTTG
ACTTAGAGGTTGTTATGGCTCATACCACTAATGGAGGGTCAACATCTAGGGTTCAATCT
Found at i:7243 original size:48 final size:48
Alignment explanation
Indices: 7172--7266 Score: 172
Period size: 48 Copynumber: 2.0 Consensus size: 48
7162 TAACACGAGG
*
7172 ATCAAACCCTGCACTCCTAGGTGTTTATTGTCTTGCAGGTCTTCCACT
1 ATCAAACCCTGCACTCCTAGGTGTTTATTGCCTTGCAGGTCTTCCACT
*
7220 ATCAAACCTTGCACTCCTAGGTGTTTATTGCCTTGCAGGTCTTCCAC
1 ATCAAACCCTGCACTCCTAGGTGTTTATTGCCTTGCAGGTCTTCCAC
7267 CTTCCTAAGT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.19, C:0.29, G:0.17, T:0.35
Consensus pattern (48 bp):
ATCAAACCCTGCACTCCTAGGTGTTTATTGCCTTGCAGGTCTTCCACT
Found at i:17576 original size:23 final size:25
Alignment explanation
Indices: 17533--17578 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
17523 CAAGTCCTCC
17533 TTTTTAAATAAAACAATAATTAATT
1 TTTTTAAATAAAACAATAATTAATT
*
17558 TTTTTAAA-AAAATAA-AATTAA
1 TTTTTAAATAAAACAATAATTAA
17579 AAAATTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (25 bp):
TTTTTAAATAAAACAATAATTAATT
Found at i:17580 original size:14 final size:14
Alignment explanation
Indices: 17561--17590 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17551 ATTAATTTTT
17561 TTAAAAAAATAAAA
1 TTAAAAAAATAAAA
*
17575 TTAAAAAATTAAAA
1 TTAAAAAAATAAAA
17589 TT
1 TT
17591 TATATATAAT
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
TTAAAAAAATAAAA
Found at i:21786 original size:2 final size:2
Alignment explanation
Indices: 21774--21812 Score: 51
Period size: 2 Copynumber: 18.0 Consensus size: 2
21764 GTACGGGATC
21774 AT AT CAT AT AT AT CAT AT AT AT AT AT CAT AT AT AT AT AT
1 AT AT -AT AT AT AT -AT AT AT AT AT AT -AT AT AT AT AT AT
21813 TTAAAACAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 28 0.82
3 6 0.18
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:21788 original size:9 final size:8
Alignment explanation
Indices: 21774--21812 Score: 51
Period size: 9 Copynumber: 4.5 Consensus size: 8
21764 GTACGGGATC
21774 ATATCATAT
1 ATAT-ATAT
21783 ATATCATAT
1 ATAT-ATAT
21792 ATATATAT
1 ATATATAT
21800 CATATATAT
1 -ATATATAT
21809 ATAT
1 ATAT
21813 TTAAAACAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.28
9 21 0.72
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (8 bp):
ATATATAT
Found at i:21797 original size:13 final size:13
Alignment explanation
Indices: 21771--21812 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
21761 CTTGTACGGG
21771 ATCATATCATATAT
1 ATCATAT-ATATAT
21785 ATCATATATATAT
1 ATCATATATATAT
21798 ATCATATATATAT
1 ATCATATATATAT
21811 AT
1 AT
21813 TTAAAACAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 21 0.75
14 7 0.25
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (13 bp):
ATCATATATATAT
Found at i:23570 original size:194 final size:194
Alignment explanation
Indices: 23174--24201 Score: 1186
Period size: 201 Copynumber: 5.2 Consensus size: 194
23164 TAGAAAATTA
* * * *
23174 TCCAAAATTCACACTGAC-GATGTATTTTATAATAACCCTATAAGAAAATTTATACAATACACCG
1 TCCAAAATTTACACTGACAG-TGTATTGTATAATAATCCTATAAGAAAAATTATACAATACACCG
* * * * *
23238 TTAGTGGAGTTTAGCAAATTGCATGTGCGGGGTTTAACTTTAAGGGTTGACATGTGTACCCTTAG
65 TCAGTGGAGTTTAGCAGACTGCACGTGC-AGG------TTTAAGGGTTGACATGTGT-CCC-T--
23303 GGAATATGTATTAATATTAAATA--T--TTAATTATGAAATAGGGTATGTGTCAACTTCTTAACC
119 GGAATATGTATTAATATTAAATATTTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACC
23364 CGCTTATGGAG
184 CGCTTATGGAG
* * * *
23375 TCCAAAATTTACACTGATAGTGTAATATATAATAATTCTATAAGAAAAATTATACAATAC-CCGT
1 TCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATACAATACACCGT
* * *
23439 CAGTGGATTTTAGCAGACTGCATGTGCAGGATTTAAAAGGTTGACATGTGTCCC-GGAATATGTA
66 CAGTGGAGTTTAGCAGACTGCACGTGCAGG-TTT-AAGGGTTGACATGTGTCCCTGGAATATGTA
*
23503 TTAATATTAAATATTTAATTAATTATGAAAT-GGAGTATGTGTCAACTTCTTAACCCGTTTATGG
129 TTAATATTAAATATTTAATTAATTATGAAATAGG-GTATGTGTCAACTTCTTAACCCGCTTATGG
23567 AG
193 AG
* * * *
23569 TCCAAAATTTATATTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTCTGCAATACACCGT
1 TCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATACAATACACCGT
* * * * *
23634 CAGTGAAGTTTAGCAGACAGCACGTGCGGGGTTTAAGGGTTGACATGTATTCACTTAGGGAATAT
66 CAGTGGAGTTTAGCAGACTGCACGTGC-AGGTTTAAGGGTTGACATGT-GTC-CCT--GGAATAT
*
23699 GTATTAATA-T---TATTTAATTAATTATGAAATAGGGTATGTGTCAACTTTTTAACCCGCTTAT
126 GTATTAATATTAAATATTTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACCCGCTTAT
*
23760 GGAA
191 GGAG
* * *
23764 TCCAAAATTTACACTGACAGTGTATTGTGTATAATAATCATATAA-AAAAATTATACGATATACC
1 TCCAAAATTTACACTGACAGTGTA-T-TGTATAATAATCCTATAAGAAAAATTATACAATACACC
* ** *
23828 GTTAGTGGAGTTTAGCAGACTGCACGCACGAGGTTTTTAGGGTTGACATGTGTCCTCTTAGGGAA
64 GTCAGTGGAGTTTAGCAGACTGCACGTGC-AGG-TTTAAGGGTTGACATGTGTCC-C-T--GGAA
* ** *
23893 TATGTATTGATATTTTATATTTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTATCCCGCT
123 TATGTATTAATATTAAATATTTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACCCGCT
23958 TATGGAG
188 TATGGAG
* * * * * *
23965 TTCAAAATTTACCCTAACAGTGCATTGTATAATAATCCTATAA-AAAGATTATACAATACACTGT
1 TCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATACAATACACCGT
*
24029 CAGTGGAGTTTAGTAGACTGCACGTGCATGGTTTAAGGGTTGACATGTGTCCCCTTTGGAAATAT
66 CAGTGGAGTTTAGCAGACTGCACGTGCA-GGTTTAAGGGTTGACATGTGT-CCC--TGG-AATAT
* *
24094 GTATTAATATTAAATATTTAATTAATTATGAAAT-GGGATATGTGTCAACTTCTTAACTCACTTA
126 GTATTAATATTAAATATTTAATTAATTATGAAATAGGG-TATGTGTCAACTTCTTAACCCGCTTA
*
24158 TGAAG
190 TGGAG
* *
24163 TCCAAAATTTACATTGACAGTGTATTGTATAATACTCCT
1 TCCAAAATTTACACTGACAGTGTATTGTATAATAATCCT
24202 TATTATAAAG
Statistics
Matches: 717, Mismatches: 81, Indels: 61
0.83 0.09 0.07
Matches are distributed among these distances:
190 23 0.03
192 1 0.00
193 2 0.00
194 115 0.16
195 119 0.17
196 50 0.07
197 56 0.08
198 118 0.16
199 81 0.11
200 28 0.04
201 123 0.17
202 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (194 bp):
TCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATACAATACACCGT
CAGTGGAGTTTAGCAGACTGCACGTGCAGGTTTAAGGGTTGACATGTGTCCCTGGAATATGTATT
AATATTAAATATTTAATTAATTATGAAATAGGGTATGTGTCAACTTCTTAACCCGCTTATGGAG
Found at i:24982 original size:27 final size:27
Alignment explanation
Indices: 24945--25008 Score: 110
Period size: 27 Copynumber: 2.3 Consensus size: 27
24935 TAATTATTAC
*
24945 TCCCTCTGTTCCTTTTTAATTGTCTCTT
1 TCCCT-TGTTCCTTTTTAATTGTCCCTT
24973 TCCCTTGTTCCTTTTTAATTGTCCCTT
1 TCCCTTGTTCCTTTTTAATTGTCCCTT
25000 TCCCTTGTT
1 TCCCTTGTT
25009 TTCCAGAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 30 0.86
28 5 0.14
ACGTcount: A:0.06, C:0.30, G:0.08, T:0.56
Consensus pattern (27 bp):
TCCCTTGTTCCTTTTTAATTGTCCCTT
Found at i:26772 original size:139 final size:139
Alignment explanation
Indices: 26540--26939 Score: 477
Period size: 139 Copynumber: 2.9 Consensus size: 139
26530 CCAAAAGCTA
* * * *
26540 ATGATTATTTAATTTTGCCAAAAATAAATGAATCAATTTGT-ATTATGTTACAAAAAAATAAATT
1 ATGATTATTTATTTTTTCCATAAATAAATGAATCAATTAGTAATTATGTTAC-AAAAAA-AAATT
* * * *
26604 GATTGAACATCCAAAATAAGTAAATGAATCAAGTTAGTCCTTAGTTAACTTTGCCAATCAAAGTT
64 GATTGAACATACTAAATAAATAAATGAATCAAGTTAGTCGTTAGTTAACTTTGCCAATCAAAGTT
26669 ATAATTGATGG
129 ATAATTGATGG
* * *
26680 ATGATTATTTATTTTTTCCATAAATAAATAAATCAATTAGTAATTATATTACCAAAAAAAATTGA
1 ATGATTATTTATTTTTTCCATAAATAAATGAATCAATTAGTAATTATGTTACAAAAAAAAATTGA
* * * ** *
26745 TTGAGCATGCTAAATAAATAAATGAATCAAGTTAGTCGTT-GATCAACTTTATCAATTAAAGTTA
66 TTGAACATACTAAATAAATAAATGAATCAAGTTAGTCGTTAG-TTAACTTTGCCAATCAAAGTTA
*
26809 TAATTGATTG
130 TAATTGATGG
* *
26819 ATGATTATTTGATTTTAT-CATAAATAAATGAATAAATTAGTAATTATGTTAGCAAAAAAATAGA
1 ATGATTATTT-ATTTTTTCCATAAATAAATGAATCAATTAGTAATTATGTTA-CAAAAAAA-A-A
* ** * *
26883 TTGATTGAACATACTAAATAAATTAGGGAATCAAATTAGTCGTTAATTAA--TTGCCAA
62 TTGATTGAACATACTAAATAAATAAATGAATCAAGTTAGTCGTTAGTTAACTTTGCCAA
26940 AAAAATTAGT
Statistics
Matches: 221, Mismatches: 32, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
138 1 0.00
139 109 0.49
140 59 0.27
141 10 0.05
142 42 0.19
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.36
Consensus pattern (139 bp):
ATGATTATTTATTTTTTCCATAAATAAATGAATCAATTAGTAATTATGTTACAAAAAAAAATTGA
TTGAACATACTAAATAAATAAATGAATCAAGTTAGTCGTTAGTTAACTTTGCCAATCAAAGTTAT
AATTGATGG
Found at i:30274 original size:14 final size:15
Alignment explanation
Indices: 30257--30294 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
30247 TCGAAAAAAA
*
30257 TTTCAAGAAAATG-C
1 TTTCAAAAAAATGAC
30271 TTTCAAAAAAATGAC
1 TTTCAAAAAAATGAC
30286 TTTCAAAAA
1 TTTCAAAAA
30295 TGAGTTTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.50, C:0.13, G:0.08, T:0.29
Consensus pattern (15 bp):
TTTCAAAAAAATGAC
Found at i:30308 original size:15 final size:14
Alignment explanation
Indices: 30257--30308 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
30247 TCGAAAAAAA
30257 TTTCAAGAAAATG-C
1 TTTCAA-AAAATGAC
30271 TTTCAAAAAAATGAC
1 TTTC-AAAAAATGAC
*
30286 TTTC-AAAAATGAGT
1 TTTCAAAAAATGA-C
30300 TTTCAAAAA
1 TTTCAAAAA
30309 GGTTTTCAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
13 8 0.24
14 14 0.42
15 11 0.33
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.31
Consensus pattern (14 bp):
TTTCAAAAAATGAC
Found at i:30315 original size:12 final size:14
Alignment explanation
Indices: 30277--30316 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
30267 ATGCTTTCAA
*
30277 AAAAATGA-CTTTC
1 AAAAATGAGTTTTC
30290 AAAAATGAGTTTTC
1 AAAAATGAGTTTTC
30304 AAAAA-G-GTTTTC
1 AAAAATGAGTTTTC
30316 A
1 A
30317 GTTTTCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 7 0.28
13 9 0.36
14 9 0.36
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (14 bp):
AAAAATGAGTTTTC
Found at i:31906 original size:12 final size:12
Alignment explanation
Indices: 31889--31922 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
31879 GCATTGCATC
31889 TCATAAACATAA
1 TCATAAACATAA
*
31901 TCATAATCATAA
1 TCATAAACATAA
*
31913 TCATCAACAT
1 TCATAAACAT
31923 TTACATCCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (12 bp):
TCATAAACATAA
Found at i:32142 original size:37 final size:37
Alignment explanation
Indices: 32087--32510 Score: 446
Period size: 37 Copynumber: 11.6 Consensus size: 37
32077 AAATTCAGTC
*
32087 CTTGTTTAAG-GTCTCTGTTTAGGTGTCTCATCAAAAT
1 CTTGTTTAAGATTC-CTGTTTAGGTGTCTCATCAAAAT
* * *
32124 CTTGTTTAAGATTCCTGTTTAGATTTCTTATC-AAAT
1 CTTGTTTAAGATTCCTGTTTAGGTGTCTCATCAAAAT
*** *
32160 CCTTGTTTAAGGCCCCTGTTTAGGTTTCTCATCAAAAT
1 -CTTGTTTAAGATTCCTGTTTAGGTGTCTCATCAAAAT
* * * * *
32198 CTTGTTTAACAATCCTGTTTAGGTTTCTTAT-TAAAT
1 CTTGTTTAAGATTCCTGTTTAGGTGTCTCATCAAAAT
* *
32234 CCTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCAAAAT
1 -CTTGTTTAAGATTCCTGTTTAGGTGTCTCATCAAAAT
* * *
32272 CTTGTTTAAGATTCCTGTTTAGGTTTCTTAT-TAAAT
1 CTTGTTTAAGATTCCTGTTTAGGTGTCTCATCAAAAT
* *
32308 CCTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCAAAAT
1 -CTTGTTTAAGATTCCTGTTTAGGTGTCTCATCAAAAT
32346 CTTGTTTAAGATTCCTGTTTA-G-G--T--T--AAAT
1 CTTGTTTAAGATTCCTGTTTAGGTGTCTCATCAAAAT
*
32375 CCTTGTTTAAG-GTCACTGTTTAGGTGTCTCATCAAAAT
1 -CTTGTTTAAGATTC-CTGTTTAGGTGTCTCATCAAAAT
* * *
32413 CTTGTTTAAGATTCCTGTTTAGGTTTCTTAT-TAAAT
1 CTTGTTTAAGATTCCTGTTTAGGTGTCTCATCAAAAT
*
32449 CCTTGTTTAAG-GTCCATGTTTAGGTGTCTCATCAAAAT
1 -CTTGTTTAAGATTCC-TGTTTAGGTGTCTCATCAAAAT
32487 CTTGTTTAAGATTCCTGTTTAGGT
1 CTTGTTTAAGATTCCTGTTTAGGT
32511 TTCTTAACAA
Statistics
Matches: 321, Mismatches: 44, Indels: 44
0.78 0.11 0.11
Matches are distributed among these distances:
29 6 0.02
30 17 0.05
31 2 0.01
32 1 0.00
33 1 0.00
34 1 0.00
35 1 0.00
36 21 0.07
37 244 0.76
38 27 0.08
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.45
Consensus pattern (37 bp):
CTTGTTTAAGATTCCTGTTTAGGTGTCTCATCAAAAT
Found at i:32206 original size:74 final size:74
Alignment explanation
Indices: 32085--32531 Score: 746
Period size: 74 Copynumber: 6.1 Consensus size: 74
32075 CAAAATTCAG
* *
32085 TCCTTGTTTAAGGTCTCTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGATTT
1 TCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTT
*
32150 CTTATCAAA
66 CTTATTAAA
* * * *
32159 TCCTTGTTTAAGGCCCCTGTTTAGGTTTCTCATCAAAATCTTGTTTAACAATCCTGTTTAGGTTT
1 TCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTT
32224 CTTATTAAA
66 CTTATTAAA
32233 TCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTT
1 TCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTT
32298 CTTATTAAA
66 CTTATTAAA
32307 TCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGG---
1 TCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTT
32369 ----TTAAA
66 CTTATTAAA
*
32374 TCCTTGTTTAAGGTCACTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTT
1 TCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTT
32439 CTTATTAAA
66 CTTATTAAA
*
32448 TCCTTGTTTAAGGTCCATGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTT
1 TCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTT
**
32513 CTTAACAAA
66 CTTATTAAA
32522 TCCTTGTTTA
1 TCCTTGTTTA
32532 GGTTTCAAAA
Statistics
Matches: 350, Mismatches: 16, Indels: 14
0.92 0.04 0.04
Matches are distributed among these distances:
67 66 0.19
74 284 0.81
ACGTcount: A:0.23, C:0.17, G:0.16, T:0.45
Consensus pattern (74 bp):
TCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTT
CTTATTAAA
Found at i:32380 original size:30 final size:29
Alignment explanation
Indices: 32342--32399 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
32332 TGTCTCATCA
*
32342 AAATCTTGTTTAAGATTC-CTGTTTAGGTT
1 AAATCTTGTTTAAG-GTCACTGTTTAGGTT
32371 AAATCCTTGTTTAAGGTCACTGTTTAGGT
1 AAAT-CTTGTTTAAGGTCACTGTTTAGGT
32400 GTCTCATCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.24, C:0.12, G:0.19, T:0.45
Consensus pattern (29 bp):
AAATCTTGTTTAAGGTCACTGTTTAGGTT
Found at i:32410 original size:67 final size:66
Alignment explanation
Indices: 32302--32511 Score: 330
Period size: 67 Copynumber: 3.0 Consensus size: 66
32292 AGGTTTCTTA
32302 TTAAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGTTTA
1 TTAAATCCTTGTTTAAGGT-CCTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGTTTA
32367 GG
65 GG
32369 TTAAATCCTTGTTTAAGGTCACTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGTTTA
1 TTAAATCCTTGTTTAAGGTC-CTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGTTTA
32434 GG
65 GG
32436 TTTCTTATTAAATCCTTGTTTAAGGTCCATGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTC
1 -------TTAAATCCTTGTTTAAGGTCC-TGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTC
32501 CTGTTTAGG
58 CTGTTTAGG
32510 TT
1 TT
32512 TCTTAACAAA
Statistics
Matches: 134, Mismatches: 0, Indels: 18
0.88 0.00 0.12
Matches are distributed among these distances:
66 1 0.01
67 67 0.50
73 1 0.01
74 65 0.49
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.45
Consensus pattern (66 bp):
TTAAATCCTTGTTTAAGGTCCTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAG
G
Found at i:32441 original size:141 final size:141
Alignment explanation
Indices: 32085--32511 Score: 710
Period size: 141 Copynumber: 3.0 Consensus size: 141
32075 CAAAATTCAG
* *
32085 TCCTTGTTTAAGGTCTCTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGATTT
1 TCCTTGTTTAAGGTCACTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTT
* * * * *
32150 CTTATCAAATCCTTGTTTAAGGCCCCTGTTTAGGTTTCTCATCAAAATCTTGTTTAACAATCCTG
66 CTTATTAAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTG
32215 TTTAGGTTTCTTATTAAA
131 TTTAGG-------TTAAA
*
32233 TCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTT
1 TCCTTGTTTAAGGTCACTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTT
32298 CTTATTAAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTG
66 CTTATTAAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTG
32363 TTTAGGTTAAA
131 TTTAGGTTAAA
32374 TCCTTGTTTAAGGTCACTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTT
1 TCCTTGTTTAAGGTCACTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTT
*
32439 CTTATTAAATCCTTGTTTAAGGTCCATGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTG
66 CTTATTAAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTG
32504 TTTAGGTT
131 TTTAGGTT
32512 TCTTAACAAA
Statistics
Matches: 270, Mismatches: 9, Indels: 7
0.94 0.03 0.02
Matches are distributed among these distances:
141 141 0.52
148 129 0.48
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.45
Consensus pattern (141 bp):
TCCTTGTTTAAGGTCACTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTT
CTTATTAAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTG
TTTAGGTTAAA
Found at i:32528 original size:37 final size:37
Alignment explanation
Indices: 32371--32531 Score: 186
Period size: 37 Copynumber: 4.4 Consensus size: 37
32361 TGTTTAGGTT
32371 AAATCCTTGTTTAAGGTCACTGTTTAGGTGTCTCATCA
1 AAATCCTTGTTTAAGGTC-CTGTTTAGGTGTCTCATCA
* * * *
32409 AAAT-CTTGTTTAAGATTCCTGTTTAGGTTTCTTAT-T
1 AAATCCTTGTTTAAG-GTCCTGTTTAGGTGTCTCATCA
32445 AAATCCTTGTTTAAGGTCCATGTTTAGGTGTCTCATCA
1 AAATCCTTGTTTAAGGTCC-TGTTTAGGTGTCTCATCA
* * * *
32483 AAAT-CTTGTTTAAGATTCCTGTTTAGGTTTCTTAAC-
1 AAATCCTTGTTTAAG-GTCCTGTTTAGGTGTCTCATCA
32519 AAATCCTTGTTTA
1 AAATCCTTGTTTA
32532 GGTTTCAAAA
Statistics
Matches: 105, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
36 11 0.10
37 81 0.77
38 13 0.12
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.45
Consensus pattern (37 bp):
AAATCCTTGTTTAAGGTCCTGTTTAGGTGTCTCATCA
Found at i:32621 original size:43 final size:43
Alignment explanation
Indices: 32550--32666 Score: 114
Period size: 43 Copynumber: 2.7 Consensus size: 43
32540 AATTCTTAGC
* * * *
32550 TCAAAAATCAAATTTCAAGACCTACATTT-ATG-ATT-TACTCT
1 TCAAAAATCAAAATTCAAAACTTGCATTTCA-GCATTCTACTCT
*
32591 TCAAAAAAATCAAAATTCAAAACTTGCATTTCAGCATTCTATTCT
1 TC--AAAAATCAAAATTCAAAACTTGCATTTCAGCATTCTACTCT
* * *
32636 TCGAAAATCAAAGTTCAAAATTTGCATTTCA
1 TCAAAAATCAAAATTCAAAACTTGCATTTCA
32667 TTCAAAAATC
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
41 2 0.03
43 50 0.79
44 4 0.06
45 7 0.11
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.34
Consensus pattern (43 bp):
TCAAAAATCAAAATTCAAAACTTGCATTTCAGCATTCTACTCT
Found at i:32743 original size:28 final size:28
Alignment explanation
Indices: 32675--32733 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
32665 CATTCAAAAA
*
32675 TCAAAATTCAAAATCAGCATCTCATGGT
1 TCAAAATTCAAAACCAGCATCTCATGGT
* *
32703 TCAAAATTCAAAACCTGCATTTCATGGT
1 TCAAAATTCAAAACCAGCATCTCATGGT
32731 TCA
1 TCA
32734 TTCTTCAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (28 bp):
TCAAAATTCAAAACCAGCATCTCATGGT
Found at i:32792 original size:148 final size:148
Alignment explanation
Indices: 32557--33288 Score: 1143
Period size: 148 Copynumber: 4.9 Consensus size: 148
32547 AGCTCAAAAA
* * * * * *
32557 TCAAATTTCAAGACCTACATTT-ATGATTTACTCTTCAAAAAAATCAAAATTCAAAACTTGCATT
1 TCAAAATTCAAAACCTGCATTTCATGGTTCATTCTTCAAAAAAATCAAAATTCAAAACTTGCATT
32621 TCAGCATTCTATTCTTCGAAAATCAAAGTTCAAAATTTGCATTTC-ATTCAAAAATCAAAATTCA
66 TCAGCATTCTATTCTTCGAAAATCAAAGTTCAAAATTTGCATTTCTATTCAAAAATCAAAATTCA
32685 AAATCAGCATCTCATGGT
131 AAATCAGCATCTCATGGT
32703 TCAAAATTCAAAACCTGCATTTCATGGTTCATTCTTCAAAAAAAATCAAAATTCAAAACTTGCAT
1 TCAAAATTCAAAACCTGCATTTCATGGTTCATTCTTC-AAAAAAATCAAAATTCAAAACTTGCAT
*
32768 TACAGCATTCTATTCTTCGAAAATCAAAGTTCAAAATTTGCATTTCATTATTCAAAAATCAAAAT
65 TTCAGCATTCTATTCTTCGAAAATCAAAGTTCAAAATTTGCATTTC--TATTCAAAAATCAAAAT
32833 TCAAAATCAGCATCTCATGGT
128 TCAAAATCAGCATCTCATGGT
*
32854 TCAAAATTCAAAACCTGCATTTCATGGTTCATTCTTAAAAAAAAAAATCAAAATTCAAAACTTGC
1 TCAAAATTCAAAACCTGCATTTCATGGTTCATTCTT---CAAAAAAATCAAAATTCAAAACTTGC
32919 ATTTCAGCATTCTATTCTTCGAAAATCAAAGTTCAAAATTTGCATTTCATTATTCAAAAATCAAA
63 ATTTCAGCATTCTATTCTTCGAAAATCAAAGTTCAAAATTTGCATTTC--TATTCAAAAATCAAA
*
32984 TTTCAAAATCAGCATCTCATGGT
126 ATTCAAAATCAGCATCTCATGGT
* * *
33007 TCAAAATTCAAAACCTGTATTTCACGGTTCATTCTTC--AAAAGTCAAAATTCAAAACTTGCATT
1 TCAAAATTCAAAACCTGCATTTCATGGTTCATTCTTCAAAAAAATCAAAATTCAAAACTTGCATT
* * *
33070 TCAGCATTCTATTCTTCTAAAATCAAAGTTCAAAGTTTGCATTTCATTATTCAAAAATAAAAATT
66 TCAGCATTCTATTCTTCGAAAATCAAAGTTCAAAATTTGCATTTC--TATTCAAAAATCAAAATT
33135 CAAAATCAGCATCTCATGGT
129 CAAAATCAGCATCTCATGGT
* * *
33155 TCAAAATTCAAAACCTGCATTTCACGGTTCATTCTTC--AAAAGTCAAAGTTCAAAACTTGCATT
1 TCAAAATTCAAAACCTGCATTTCATGGTTCATTCTTCAAAAAAATCAAAATTCAAAACTTGCATT
*
33218 TCAGCATTCTATTCTTCGAAAATCAAAGTTCAAAGTTTGCATTTCATTATTCAAAAATCAAAATT
66 TCAGCATTCTATTCTTCGAAAATCAAAGTTCAAAATTTGCATTTC--TATTCAAAAATCAAAATT
33283 CAAAAT
129 CAAAAT
33289 TTGCATTTCA
Statistics
Matches: 556, Mismatches: 22, Indels: 14
0.94 0.04 0.02
Matches are distributed among these distances:
146 19 0.03
147 11 0.02
148 308 0.55
151 73 0.13
153 145 0.26
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (148 bp):
TCAAAATTCAAAACCTGCATTTCATGGTTCATTCTTCAAAAAAATCAAAATTCAAAACTTGCATT
TCAGCATTCTATTCTTCGAAAATCAAAGTTCAAAATTTGCATTTCTATTCAAAAATCAAAATTCA
AAATCAGCATCTCATGGT
Found at i:32811 original size:35 final size:35
Alignment explanation
Indices: 32787--33422 Score: 212
Period size: 35 Copynumber: 17.3 Consensus size: 35
32777 CTATTCTTCG
*
32787 AAAATCAAAGTTCAAAATTTGCATTTCATTATTCA
1 AAAATCAAAATTCAAAATTTGCATTTCATTATTCA
** * **
32822 AAAATCAAAATTCAAAATCAGCATCTCATGGTTCA
1 AAAATCAAAATTCAAAATTTGCATTTCATTATTCA
* * *** * *
32857 AAATTCAAAA-CCTGCATTT-CATGGTTCATTCTTAAAAAAA
1 AAAATCAAAATTCAAAATTTGCAT--TTCATTATT-----CA
* *
32897 AAAATCAAAATTCAAAACTTGCATTTCAGCATTCTATTCTTCG
1 AAAATCAAAATTCAAAATTTGCATTT---CA-T-TA---TTCA
*
32940 AAAATCAAAGTTCAAAATTTGCATTTCATTATTCA
1 AAAATCAAAATTCAAAATTTGCATTTCATTATTCA
* ** * **
32975 AAAATCAAATTTCAAAATCAGCATCTCATGGTTCA
1 AAAATCAAAATTCAAAATTTGCATTTCATTATTCA
* * *** * *
33010 AAATTCAAAA-CCTGTATTT-CACGGTTCATTCTTCA
1 AAAATCAAAATTCAAAATTTGCA--TTTCATTATTCA
* * *
33045 AAAGTCAAAATTCAAAACTTGCATTTCAGCATTCTATTCTTCT
1 AAAATCAAAATTCAAAATTTGCATTT---CA-T-TA---TTCA
* *
33088 AAAATCAAAGTTCAAAGTTTGCATTTCATTATTCA
1 AAAATCAAAATTCAAAATTTGCATTTCATTATTCA
* ** * **
33123 AAAATAAAAATTCAAAATCAGCATCTCATGGTTCA
1 AAAATCAAAATTCAAAATTTGCATTTCATTATTCA
* * *** * *
33158 AAATTCAAAA-CCTGCATTT-CACGGTTCATTCTTCA
1 AAAATCAAAATTCAAAATTTGCA--TTTCATTATTCA
* * * *
33193 AAAGTCAAAGTTCAAAACTTGCATTTCAGCATTCTATTCTTCG
1 AAAATCAAAATTCAAAATTTGCATTT---CA-T-TA---TTCA
* *
33236 AAAATCAAAGTTCAAAGTTTGCATTTCATTATTCA
1 AAAATCAAAATTCAAAATTTGCATTTCATTATTCA
* *
33271 AAAATCAAAATTCAAAATTTGCATTTCAACATTCCGTTCG
1 AAAATCAAAATTCAAAATTTGCATTT---CATT--ATTCA
* *
33311 AAAATTAGAATTCAAAATTTGCATTTCA-T-TTCA
1 AAAATCAAAATTCAAAATTTGCATTTCATTATTCA
** * * * *
33344 AAGTTCAAAGTTCAAAATCTGCATCTCA-TGTTCA
1 AAAATCAAAATTCAAAATTTGCATTTCATTATTCA
* * * * * *
33378 AAACTCAAAATCCAGAATCTGCATCTCA-TGTTCA
1 AAAATCAAAATTCAAAATTTGCATTTCATTATTCA
*
33412 AAACTCAAAAT
1 AAAATCAAAAT
33423 CCTAATTGGT
Statistics
Matches: 440, Mismatches: 114, Indels: 95
0.68 0.18 0.15
Matches are distributed among these distances:
33 32 0.07
34 53 0.12
35 186 0.42
36 9 0.02
37 6 0.01
38 14 0.03
39 5 0.01
40 47 0.11
41 4 0.01
42 3 0.01
43 77 0.17
44 1 0.00
45 1 0.00
48 2 0.00
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (35 bp):
AAAATCAAAATTCAAAATTTGCATTTCATTATTCA
Found at i:32857 original size:28 final size:28
Alignment explanation
Indices: 32826--32884 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
32816 TATTCAAAAA
*
32826 TCAAAATTCAAAATCAGCATCTCATGGT
1 TCAAAATTCAAAACCAGCATCTCATGGT
* *
32854 TCAAAATTCAAAACCTGCATTTCATGGT
1 TCAAAATTCAAAACCAGCATCTCATGGT
32882 TCA
1 TCA
32885 TTCTTAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (28 bp):
TCAAAATTCAAAACCAGCATCTCATGGT
Found at i:32944 original size:301 final size:295
Alignment explanation
Indices: 32588--33288 Score: 1163
Period size: 301 Copynumber: 2.3 Consensus size: 295
32578 TATGATTTAC
32588 TCTTCAAAAAAATCAAAATTCAAAACTTGCATTTCAGCATTCTATTCTTCGAAAATCAAAGTTCA
1 TCTT-AAAAAAATCAAAATTCAAAACTTGCATTTCAGCATTCTATTCTTCGAAAATCAAAGTTCA
32653 AAATTTGCATTTC-ATTCAAAAATCAAAATTCAAAATCAGCATCTCATGGTTCAAAATTCAAAAC
65 AAATTTGCATTTCTATTCAAAAATCAAAATTCAAAATCAGCATCTCATGGTTCAAAATTCAAAAC
*
32717 CTGCATTTCATGGTTCATTCTTCAAAAAAAATCAAAATTCAAAACTTGCATTACAGCATTCTATT
130 CTGCATTTCACGGTTCATTCTTC---AAAAATCAAAATTCAAAACTTGCATTACAGCATTCTATT
*
32782 CTTCGAAAATCAAAGTTCAAAATTTGCATTTCATTATTCAAAAATCAAAATTCAAAATCAGCATC
192 CTTCGAAAATCAAAGTTCAAAATTTGCATTTCATTATTCAAAAATAAAAATTCAAAATCAGCATC
*
32847 TCATGGTTCAAAATTCAAAACCTGCATTTCATGGTTCAT
257 TCATGGTTCAAAATTCAAAACCTGCATTTCACGGTTCAT
32886 TCTTAAAAAAAAAAATCAAAATTCAAAACTTGCATTTCAGCATTCTATTCTTCGAAAATCAAAGT
1 TCTT----AAAAAAATCAAAATTCAAAACTTGCATTTCAGCATTCTATTCTTCGAAAATCAAAGT
*
32951 TCAAAATTTGCATTTCATTATTCAAAAATCAAATTTCAAAATCAGCATCTCATGGTTCAAAATTC
62 TCAAAATTTGCATTTC--TATTCAAAAATCAAAATTCAAAATCAGCATCTCATGGTTCAAAATTC
* * *
33016 AAAACCTGTATTTCACGGTTCATTCTTCAAAAGTCAAAATTCAAAACTTGCATTTCAGCATTCTA
125 AAAACCTGCATTTCACGGTTCATTCTTCAAAAATCAAAATTCAAAACTTGCATTACAGCATTCTA
* *
33081 TTCTTCTAAAATCAAAGTTCAAAGTTTGCATTTCATTATTCAAAAATAAAAATTCAAAATCAGCA
190 TTCTTCGAAAATCAAAGTTCAAAATTTGCATTTCATTATTCAAAAATAAAAATTCAAAATCAGCA
33146 TCTCATGGTTCAAAATTCAAAACCTGCATTTCACGGTTCAT
255 TCTCATGGTTCAAAATTCAAAACCTGCATTTCACGGTTCAT
* * *
33187 TCTT-CAAAAGTCAAAGTTCAAAACTTGCATTTCAGCATTCTATTCTTCGAAAATCAAAGTTCAA
1 TCTTAAAAAAATCAAAATTCAAAACTTGCATTTCAGCATTCTATTCTTCGAAAATCAAAGTTCAA
*
33251 AGTTTGCATTTCATTATTCAAAAATCAAAATTCAAAAT
66 AATTTGCATTTC--TATTCAAAAATCAAAATTCAAAAT
33289 TTGCATTTCA
Statistics
Matches: 382, Mismatches: 15, Indels: 14
0.93 0.04 0.03
Matches are distributed among these distances:
296 93 0.24
298 4 0.01
301 214 0.56
304 71 0.19
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (295 bp):
TCTTAAAAAAATCAAAATTCAAAACTTGCATTTCAGCATTCTATTCTTCGAAAATCAAAGTTCAA
AATTTGCATTTCTATTCAAAAATCAAAATTCAAAATCAGCATCTCATGGTTCAAAATTCAAAACC
TGCATTTCACGGTTCATTCTTCAAAAATCAAAATTCAAAACTTGCATTACAGCATTCTATTCTTC
GAAAATCAAAGTTCAAAATTTGCATTTCATTATTCAAAAATAAAAATTCAAAATCAGCATCTCAT
GGTTCAAAATTCAAAACCTGCATTTCACGGTTCAT
Found at i:33053 original size:42 final size:43
Alignment explanation
Indices: 33007--33103 Score: 119
Period size: 42 Copynumber: 2.3 Consensus size: 43
32997 ATCTCATGGT
* *
33007 TCAAAATTCAAAACCTGTATTTCA-CGGTTC-ATTCTTC-AAAA
1 TCAAAATTCAAAACCTGCATTTCAGC-ATTCTATTCTTCTAAAA
*
33048 GTCAAAATTCAAAACTTGCATTTCAGCATTCTATTCTTCTAAAA
1 -TCAAAATTCAAAACCTGCATTTCAGCATTCTATTCTTCTAAAA
*
33092 TCAAAGTTCAAA
1 TCAAAATTCAAA
33104 GTTTGCATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
42 25 0.52
43 19 0.40
44 4 0.08
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (43 bp):
TCAAAATTCAAAACCTGCATTTCAGCATTCTATTCTTCTAAAA
Found at i:33102 original size:43 final size:42
Alignment explanation
Indices: 33007--33115 Score: 123
Period size: 43 Copynumber: 2.6 Consensus size: 42
32997 ATCTCATGGT
* * *
33007 TCAAAATTCAAAACCTGTATTTCACGGTTCATTCTTCAAAAG
1 TCAAAATTCAAAACTTGCATTTCACGATTCATTCTTCAAAAG
33049 TCAAAATTCAAAACTTGCATTTCA-GCATTCTATTCTTCTAAAA-
1 TCAAAATTCAAAACTTGCATTTCACG-ATTC-ATTCTTC-AAAAG
* **
33092 TCAAAGTTCAAAGTTTGCATTTCA
1 TCAAAATTCAAAACTTGCATTTCA
33116 TTATTCAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
41 1 0.02
42 25 0.43
43 28 0.48
44 4 0.07
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.36
Consensus pattern (42 bp):
TCAAAATTCAAAACTTGCATTTCACGATTCATTCTTCAAAAG
Found at i:33123 original size:78 final size:76
Alignment explanation
Indices: 32743--33304 Score: 363
Period size: 78 Copynumber: 7.5 Consensus size: 76
32733 ATTCTTCAAA
*
32743 AAAAATCAAAATTCAAAACTTGCATTACAGCATTCTATTCTTCGAAAATCAAAGTTCAAAATTTG
1 AAAAATCAAAATTCAAAACTTGCATTTCAGCATTCTATTCTTC-AAAATCAAAGTTC-AAATTTG
32808 CATTTCATTATTC
64 CATTTCATTATTC
* * * *** * ** * ***
32821 AAAAATCAAAATTCAAAA-TCAGCATCTCATG-GTTC-AAAATTCAAAACCTGCATTTCATGGTT
1 AAAAATCAAAATTCAAAACT-TGCATTTCA-GCATTCTATTCTTCAAAATC-AAAGTTCAAATTT
***
32883 -CA-TTC-TTAAAAAA
63 GCATTTCATT--ATTC
32896 AAAAATCAAAATTCAAAACTTGCATTTCAGCATTCTATTCTTCGAAAATCAAAGTTCAAAATTTG
1 AAAAATCAAAATTCAAAACTTGCATTTCAGCATTCTATTCTTC-AAAATCAAAGTTC-AAATTTG
32961 CATTTCATTATTC
64 CATTTCATTATTC
* ** ** **
32974 AAAAATCAAATTTC-AAA-----A--TCAGCA-TCTCATGGTTCAAAATTCAAA-ACCTGTATTT
1 AAAAATCAAAATTCAAAACTTGCATTTCAGCATTCT-ATTCTTCAAAA-TCAAAGTTC-AAATTT
* *
33029 -CACGGTTCATTCTTC
63 GCA--TTTCATTATTC
*
33044 AAAAGTCAAAATTCAAAACTTGCATTTCAGCATTCTATTCTTCTAAAATCAAAGTTCAAAGTTTG
1 AAAAATCAAAATTCAAAACTTGCATTTCAGCATTCTATTCTTC-AAAATCAAAGTTCAAA-TTTG
33109 CATTTCATTATTC
64 CATTTCATTATTC
* ** * *
33122 AAAAATAAAAATTC-AAA-----A--TCAGCA-TCTCATGGTTCAAAATTCAAAACCTGC--ATT
1 AAAAATCAAAATTCAAAACTTGCATTTCAGCATTCT-ATTCTTCAAAA-TC-AAA-GTTCAAATT
* *
33176 T-CACGGTTCATTCTTC
62 TGCA--TTTCATTATTC
* *
33192 AAAAGTCAAAGTTCAAAACTTGCATTTCAGCATTCTATTCTTCGAAAATCAAAGTTCAAAGTTTG
1 AAAAATCAAAATTCAAAACTTGCATTTCAGCATTCTATTCTTC-AAAATCAAAGTTCAAA-TTTG
33257 CATTTCATTATTC
64 CATTTCATTATTC
* *
33270 AAAAATCAAAATTCAAAATTTGCATTTCAACATTC
1 AAAAATCAAAATTCAAAACTTGCATTTCAGCATTC
33305 CGTTCGAAAA
Statistics
Matches: 360, Mismatches: 74, Indels: 100
0.67 0.14 0.19
Matches are distributed among these distances:
68 4 0.01
69 22 0.06
70 71 0.20
71 9 0.03
72 4 0.01
73 2 0.01
74 4 0.01
75 31 0.09
76 21 0.06
77 26 0.07
78 135 0.38
79 25 0.07
80 6 0.02
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.34
Consensus pattern (76 bp):
AAAAATCAAAATTCAAAACTTGCATTTCAGCATTCTATTCTTCAAAATCAAAGTTCAAATTTGCA
TTTCATTATTC
Found at i:33174 original size:28 final size:28
Alignment explanation
Indices: 33129--33185 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
33119 TTCAAAAATA
* *
33129 AAAATTCAAAATCAGCATCTCATGGTTC
1 AAAATTCAAAACCAGCATCTCACGGTTC
* *
33157 AAAATTCAAAACCTGCATTTCACGGTTC
1 AAAATTCAAAACCAGCATCTCACGGTTC
33185 A
1 A
33186 TTCTTCAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.28
Consensus pattern (28 bp):
AAAATTCAAAACCAGCATCTCACGGTTC
Found at i:33201 original size:42 final size:43
Alignment explanation
Indices: 33155--33251 Score: 128
Period size: 42 Copynumber: 2.3 Consensus size: 43
33145 ATCTCATGGT
* *
33155 TCAAAATTCAAAACCTGCATTTCA-CGGTTC-ATTCTTC-AAAA
1 TCAAAGTTCAAAACCTGCATTTCAGC-ATTCTATTCTTCGAAAA
*
33196 GTCAAAGTTCAAAACTTGCATTTCAGCATTCTATTCTTCGAAAA
1 -TCAAAGTTCAAAACCTGCATTTCAGCATTCTATTCTTCGAAAA
33240 TCAAAGTTCAAA
1 TCAAAGTTCAAA
33252 GTTTGCATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
42 25 0.51
43 20 0.41
44 4 0.08
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.32
Consensus pattern (43 bp):
TCAAAGTTCAAAACCTGCATTTCAGCATTCTATTCTTCGAAAA
Found at i:33246 original size:43 final size:42
Alignment explanation
Indices: 33155--33263 Score: 132
Period size: 43 Copynumber: 2.6 Consensus size: 42
33145 ATCTCATGGT
* * *
33155 TCAAAATTCAAAACCTGCATTTCACGGTTCATTCTTCAAAAG
1 TCAAAGTTCAAAACTTGCATTTCACGATTCATTCTTCAAAAG
33197 TCAAAGTTCAAAACTTGCATTTCA-GCATTCTATTCTTCGAAAA-
1 TCAAAGTTCAAAACTTGCATTTCACG-ATTC-ATTCTTC-AAAAG
**
33240 TCAAAGTTCAAAGTTTGCATTTCA
1 TCAAAGTTCAAAACTTGCATTTCA
33264 TTATTCAAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
41 1 0.02
42 25 0.42
43 29 0.49
44 4 0.07
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.34
Consensus pattern (42 bp):
TCAAAGTTCAAAACTTGCATTTCACGATTCATTCTTCAAAAG
Found at i:33386 original size:34 final size:34
Alignment explanation
Indices: 33319--33422 Score: 138
Period size: 34 Copynumber: 3.1 Consensus size: 34
33309 CGAAAATTAG
* * **
33319 AATTCAAAATTTGCATTTCAT-TTCAAAGTTCAA
1 AATTCAAAATCTGCATCTCATGTTCAAAACTCAA
*
33352 AGTTCAAAATCTGCATCTCATGTTCAAAACTCAA
1 AATTCAAAATCTGCATCTCATGTTCAAAACTCAA
* *
33386 AATCCAGAATCTGCATCTCATGTTCAAAACTCAA
1 AATTCAAAATCTGCATCTCATGTTCAAAACTCAA
33420 AAT
1 AAT
33423 CCTAATTGGT
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
33 18 0.29
34 44 0.71
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.32
Consensus pattern (34 bp):
AATTCAAAATCTGCATCTCATGTTCAAAACTCAA
Done.