Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001162.1 Hibiscus syriacus cultivar Beakdansim tig00002317_pilon, 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: 1560963
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 9
Found at i:1138 original size:2 final size:2
Alignment explanation
Indices: 1131--1170 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1121 ATACATAAAT
1131 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1171 AGCATACATA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4369 original size:19 final size:19
Alignment explanation
Indices: 4345--4382 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
4335 GAAAACCGTC
*
4345 TGCATAACTGCACGCCTAA
1 TGCATAACAGCACGCCTAA
*
4364 TGCATAACAGCATGCCTAA
1 TGCATAACAGCACGCCTAA
4383 CTGACTAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.21
Consensus pattern (19 bp):
TGCATAACAGCACGCCTAA
Found at i:8934 original size:19 final size:19
Alignment explanation
Indices: 8910--8947 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
8900 GAAAACCGTC
*
8910 TGCATAACTGCACGCCTAA
1 TGCATAACAGCACGCCTAA
*
8929 TGCATAACAGCATGCCTAA
1 TGCATAACAGCACGCCTAA
8948 CTGACTAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.21
Consensus pattern (19 bp):
TGCATAACAGCACGCCTAA
Found at i:16617 original size:22 final size:22
Alignment explanation
Indices: 16589--16663 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 22
16579 TAGCCCAAAA
16589 AAAAAGTATTATTGTCAAATGT
1 AAAAAGTATTATTGTCAAATGT
*
16611 AAAAAGTATTAAATATAGCCCCAAA---
1 AAAAAGTATT--AT-T-G--TCAAATGT
16636 AAAAAGTATTATTGTCAAATGT
1 AAAAAGTATTATTGTCAAATGT
16658 AAAAAG
1 AAAAAG
16664 AGGAAAAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 18
0.68 0.03 0.29
Matches are distributed among these distances:
19 4 0.10
21 1 0.02
22 17 0.40
23 2 0.05
24 2 0.05
25 11 0.26
26 1 0.02
28 4 0.10
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.28
Consensus pattern (22 bp):
AAAAAGTATTATTGTCAAATGT
Found at i:16637 original size:47 final size:47
Alignment explanation
Indices: 16568--16663 Score: 183
Period size: 47 Copynumber: 2.0 Consensus size: 47
16558 TAAAGGCAAT
16568 AGTATTAAATATAGCCCAAAAAAAAAGTATTATTGTCAAATGTAAAA
1 AGTATTAAATATAGCCCAAAAAAAAAGTATTATTGTCAAATGTAAAA
*
16615 AGTATTAAATATAGCCCCAAAAAAAAGTATTATTGTCAAATGTAAAA
1 AGTATTAAATATAGCCCAAAAAAAAAGTATTATTGTCAAATGTAAAA
16662 AG
1 AG
16664 AGGAAAAAAC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.52, C:0.09, G:0.11, T:0.27
Consensus pattern (47 bp):
AGTATTAAATATAGCCCAAAAAAAAAGTATTATTGTCAAATGTAAAA
Found at i:17970 original size:18 final size:18
Alignment explanation
Indices: 17927--17976 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 18
17917 CTTGATTTAC
17927 AGAATATAAGATTATTAGT
1 AGAA-ATAAGATTATTAGT
17946 -GAGAATAAGATTATT-GAT
1 AGA-AATAAGATTATTAG-T
*
17964 AGAAATAAAATTA
1 AGAAATAAGATTA
17977 CTGAGAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
17 1 0.04
18 23 0.85
19 3 0.11
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (18 bp):
AGAAATAAGATTATTAGT
Found at i:18253 original size:29 final size:29
Alignment explanation
Indices: 18221--18292 Score: 108
Period size: 29 Copynumber: 2.4 Consensus size: 29
18211 TAATGAAATG
* *
18221 ATAAAATTTAATTTTAACCTGAGCTTTAT
1 ATAAAATTTAATTTTAACCTAAACTTTAT
*
18250 ATAAAATTTTATTTTAACCTAAACTTTAT
1 ATAAAATTTAATTTTAACCTAAACTTTAT
18279 ATAAAATTCTAATT
1 ATAAAATT-TAATT
18293 ATGAATTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
29 34 0.89
30 4 0.11
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.46
Consensus pattern (29 bp):
ATAAAATTTAATTTTAACCTAAACTTTAT
Found at i:24259 original size:45 final size:45
Alignment explanation
Indices: 24209--24452 Score: 276
Period size: 45 Copynumber: 5.4 Consensus size: 45
24199 TTAGTAAAGG
*
24209 CTTTTGATTATTGGGTTGTCAAAAATAAAATCAAATGATTAATTC
1 CTTTTGATTATTGGGTTGTCAAAATTAAAATCAAATGATTAATTC
* * *
24254 CTTTTGATTATTGTGTTGCCAAAAATAAAATCAAATGATTAATTC
1 CTTTTGATTATTGGGTTGTCAAAATTAAAATCAAATGATTAATTC
* *
24299 CTTTTGATTATTGAGTTGTCAAAATTAAAAATCAAATGATTAGTTC
1 CTTTTGATTATTGGGTTGTCAAAATT-AAAATCAAATGATTAATTC
* * * *
24345 TTTTTTATTAATT-GGATG-CGAAAATTAAAATCAAATGATTATTTC
1 CTTTTGATT-ATTGGGTTGTC-AAAATTAAAATCAAATGATTAATTC
* * * ** * * *
24390 CTTTCGATTATTAGATTGAGAAAATTAAAATCAAAGGATTAGTTT
1 CTTTTGATTATTGGGTTGTCAAAATTAAAATCAAATGATTAATTC
*
24435 CTTTTGATTATTAGGTTG
1 CTTTTGATTATTGGGTTG
24453 GTAAGATTAA
Statistics
Matches: 172, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
44 3 0.02
45 132 0.77
46 34 0.20
47 3 0.02
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (45 bp):
CTTTTGATTATTGGGTTGTCAAAATTAAAATCAAATGATTAATTC
Found at i:24391 original size:91 final size:90
Alignment explanation
Indices: 24209--24446 Score: 302
Period size: 91 Copynumber: 2.6 Consensus size: 90
24199 TTAGTAAAGG
* * * * *
24209 CTTTTGATTATTGGGTTGTCAAAAATAAAATCAAATGATTAATTCCTTTTGATTATTGTGTTGCC
1 CTTTTGATTATTGAGTTGTCAAAATTAAAATCAAATGATTAGTTCTTTTTGATTATTGTGATGCC
24274 AAAAATAAAATCAAATGATTAATTC
66 AAAAATAAAATCAAATGATTAATTC
*
24299 CTTTTGATTATTGAGTTGTCAAAATTAAAAATCAAATGATTAGTTCTTTTTTATTAATTG-GATG
1 CTTTTGATTATTGAGTTGTCAAAATT-AAAATCAAATGATTAGTTCTTTTTGATT-ATTGTGATG
* * *
24363 CGAAAATTAAAATCAAATGATTATTTC
64 CCAAAAATAAAATCAAATGATTAATTC
* ** *
24390 CTTTCGATTATT-AGATTGAGAAAATTAAAATCAAAGGATTAGTT-TCTTTTGATTATT
1 CTTTTGATTATTGAG-TTGTCAAAATTAAAATCAAATGATTAGTTCT-TTTTGATTATT
24447 AGGTTGGTAA
Statistics
Matches: 130, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
89 4 0.03
90 50 0.38
91 72 0.55
92 4 0.03
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (90 bp):
CTTTTGATTATTGAGTTGTCAAAATTAAAATCAAATGATTAGTTCTTTTTGATTATTGTGATGCC
AAAAATAAAATCAAATGATTAATTC
Found at i:24765 original size:58 final size:58
Alignment explanation
Indices: 24627--24766 Score: 149
Period size: 58 Copynumber: 2.4 Consensus size: 58
24617 TTCATAAGGA
* * * * * * *
24627 AAATAAATTGTTGAATGTATTTCCTTGAGAATCTTGAATGATTCTATTTTGTAAAAAT
1 AAATAAATAGTTGAATTTATTTTCTTGAGAATCTTGAAGGATCCTATTATGCAAAAAT
* *
24685 AAATAAATTAGTT-AACTTATTTTCTT-AGGAATCTTGAAGGATCCTATTATGCAAAACT
1 AAATAAA-TAGTTGAATTTATTTTCTTGA-GAATCTTGAAGGATCCTATTATGCAAAAAT
* *
24743 AAATAAATCGTTGGATTTATTTTC
1 AAATAAATAGTTGAATTTATTTTC
24767 CTATTTTGTA
Statistics
Matches: 67, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
57 5 0.07
58 58 0.87
59 4 0.06
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.41
Consensus pattern (58 bp):
AAATAAATAGTTGAATTTATTTTCTTGAGAATCTTGAAGGATCCTATTATGCAAAAAT
Found at i:24786 original size:39 final size:39
Alignment explanation
Indices: 24743--24915 Score: 170
Period size: 39 Copynumber: 4.2 Consensus size: 39
24733 ATGCAAAACT
24743 AAATAAATCGTTGGATTTATTTTCCTATTTTGTAAAAGA
1 AAATAAATCGTTGGATTTATTTTCCTATTTTGTAAAAGA
*
24782 AAATAAATCGAAACAAATTGTTAGA-TTATTTTCCTATTTTGTAAAAGT
1 AAATAAATCG-------TTG---GATTTATTTTCCTATTTTGTAAAAGA
** *
24830 AAATAAATCGTTAAATTTATTTTCCTATATTGTAAAAGA
1 AAATAAATCGTTGGATTTATTTTCCTATTTTGTAAAAGA
* * *
24869 AAATAAATTGTTTGATTTATTTTCATGA-TTTGTAAAAGA
1 AAATAAATCGTTGGATTTATTTTCCT-ATTTTGTAAAAGA
24908 AAATAAAT
1 AAATAAAT
24916 TATTTGATTA
Statistics
Matches: 112, Mismatches: 10, Indels: 24
0.77 0.07 0.16
Matches are distributed among these distances:
38 1 0.01
39 71 0.63
40 1 0.01
41 2 0.02
46 3 0.03
48 32 0.29
49 2 0.02
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (39 bp):
AAATAAATCGTTGGATTTATTTTCCTATTTTGTAAAAGA
Found at i:31836 original size:18 final size:17
Alignment explanation
Indices: 31797--31839 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
31787 ATTATATGGA
31797 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
31813 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
31831 TATTATTAT
1 TATTATTAT
31840 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:33544 original size:5 final size:5
Alignment explanation
Indices: 33534--33562 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
33524 TTCATCTTTC
33534 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
33563 CATCACTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:35455 original size:9 final size:9
Alignment explanation
Indices: 35443--35496 Score: 60
Period size: 9 Copynumber: 6.3 Consensus size: 9
35433 TAAAAAGGGC
35443 AAAAAGAAA
1 AAAAAGAAA
*
35452 AAAAAG--C
1 AAAAAGAAA
35459 AAAAAG-AA
1 AAAAAGAAA
*
35467 AAAAAGCAA
1 AAAAAGAAA
*
35476 AAAAAGAAC
1 AAAAAGAAA
35485 AAAAAGAAA
1 AAAAAGAAA
35494 AAA
1 AAA
35497 GAAATGCAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
7 6 0.16
8 6 0.16
9 26 0.68
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:35460 original size:16 final size:16
Alignment explanation
Indices: 35441--35500 Score: 77
Period size: 16 Copynumber: 3.7 Consensus size: 16
35431 AATAAAAAGG
35441 GCAAAAAGAAAAAAAA
1 GCAAAAAGAAAAAAAA
35457 GCAAAAAG-AAAAAAA
1 GCAAAAAGAAAAAAAA
*
35472 GCAAAAAAAGAACAAAAA
1 GC--AAAAAGAAAAAAAA
*
35490 GAAAAAAGAAA
1 GCAAAAAGAAA
35501 TGCAAAGATT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
15 9 0.24
16 16 0.42
17 6 0.16
18 7 0.18
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (16 bp):
GCAAAAAGAAAAAAAA
Found at i:35495 original size:7 final size:8
Alignment explanation
Indices: 35443--35500 Score: 66
Period size: 8 Copynumber: 7.1 Consensus size: 8
35433 TAAAAAGGGC
35443 AAAAAGAA
1 AAAAAGAA
*
35451 AAAAA-AGC
1 AAAAAGA-A
35459 AAAAAGAA
1 AAAAAGAA
35467 AAAAAGCAA
1 AAAAAG-AA
35476 AAAAAGAA
1 AAAAAGAA
35484 CAAAAAG-A
1 -AAAAAGAA
35492 AAAAAGAA
1 AAAAAGAA
35500 A
1 A
35501 TGCAAAGATT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
7 7 0.16
8 21 0.49
9 15 0.35
ACGTcount: A:0.83, C:0.05, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:36111 original size:22 final size:22
Alignment explanation
Indices: 36083--36126 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
36073 AGCTACCCCA
36083 TCAAACC-TTTGAGCATCAAATG
1 TCAAACCATTT-AGCATCAAATG
36105 TCAAACCATTTAGCATCAAATG
1 TCAAACCATTTAGCATCAAATG
36127 AACAAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (22 bp):
TCAAACCATTTAGCATCAAATG
Found at i:37120 original size:36 final size:36
Alignment explanation
Indices: 37077--37496 Score: 352
Period size: 36 Copynumber: 12.0 Consensus size: 36
37067 ACTAGAAGAG
*
37077 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* *
37113 TTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* *
37149 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * * *
37185 ------ATAT-TTGA-ATATGTTTTCTTTGAAACAAA
1 TTTTGTCTCTCTTGAGACA-GTTTCCCTTGAAACAAA
* * ** * *
37214 TTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA
* *
37251 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAATC-AA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
37286 TTTTCGTCTATCTTGAGACAGTTTCTCTTGAAATAAA
1 TTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
37323 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * * * *
37359 ------ATAT-TTGA-ATATGTTTTCTTTGAAATAAA
1 TTTTGTCTCTCTTGAGACA-GTTTCCCTTGAAACAAA
* * ** * *
37388 TTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA
*
37425 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* *
37461 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
37497 ATCTTTGAAT
Statistics
Matches: 308, Mismatches: 54, Indels: 44
0.76 0.13 0.11
Matches are distributed among these distances:
28 4 0.01
29 37 0.12
30 5 0.02
35 7 0.02
36 184 0.60
37 71 0.23
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.41
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:37140 original size:15 final size:16
Alignment explanation
Indices: 37120--37152 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
37110 AAATTTTGTC
*
37120 TCTCTTGAGAC-AATT
1 TCTCTTGAAACAAATT
37135 TCTCTTGAAACAAATT
1 TCTCTTGAAACAAATT
37151 TC
1 TC
37153 GTCTATCTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.39
Consensus pattern (16 bp):
TCTCTTGAAACAAATT
Found at i:37272 original size:174 final size:174
Alignment explanation
Indices: 37075--37496 Score: 729
Period size: 174 Copynumber: 2.4 Consensus size: 174
37065 TCACTAGAAG
* * *
37075 AGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAATTTCTCT
1 AGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCTCT
37140 TGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCTT
66 TGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCTT
37205 TGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTA
131 TGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTA
*
37249 AGTTTTGTCTCTCTTGAGACAGTTTCTCTTG-AATCAATTTTCGTCTATCTTGAGACAGTTTCTC
1 AGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAAATTTT-GTCTATCTTGAGACAGTTTCTC
* * *
37313 TTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCT
65 TTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCT
*
37378 TTGAAATAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTA
130 TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTA
* * *
37423 AGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCT
1 AGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCTCT
37488 TGAAACAAA
66 TGAAACAAA
37497 ATCTTTGAAT
Statistics
Matches: 233, Mismatches: 13, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
173 9 0.04
174 217 0.93
175 7 0.03
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.41
Consensus pattern (174 bp):
AGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCTCT
TGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCTT
TGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTA
Found at i:37438 original size:138 final size:137
Alignment explanation
Indices: 37255--37556 Score: 419
Period size: 138 Copynumber: 2.2 Consensus size: 137
37245 ACTAAGTTTT
* *
37255 GTCTCTCTTGAGACAGTTTCTCTTGAATCAATTTTCGTCTATCTTGAGACAGTTTCTCTTGAAAT
1 GTCTCCCTTGAGACAGTTTCTCTTGAATCAATTTTCGTCTATCTTGAGACAGTTTCTCTTGAAAC
* * * * ** * *
37320 AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCTTTGAAAT
66 AAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATATTTCCCCTAAAAC
37385 AAATTTC
131 AAATTTC
* *
37392 GTCTCCCTTGAGACAGTTTCTTTTGGAA-CTAAGTTTT-GTCTCTCTTGAGACAGTTTCTCTTGA
1 GTCTCCCTTGAGACAGTTTCTCTT-GAATC-AA-TTTTCGTCTATCTTGAGACAGTTTCTCTTGA
* *
37455 AACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCTAA
63 AACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATATTTCCCCTAA
*
37520 AACAAATTTT
128 AACAAATTTC
*
37530 GTCTCCCTTGAGACAGTTACTCTTGAA
1 GTCTCCCTTGAGACAGTTTCTCTTGAA
37557 ACACAAAATC
Statistics
Matches: 145, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
137 26 0.18
138 115 0.79
139 4 0.03
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (137 bp):
GTCTCCCTTGAGACAGTTTCTCTTGAATCAATTTTCGTCTATCTTGAGACAGTTTCTCTTGAAAC
AAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATATTTCCCCTAAAAC
AAATTTC
Found at i:37558 original size:65 final size:65
Alignment explanation
Indices: 37454--37628 Score: 217
Period size: 65 Copynumber: 2.6 Consensus size: 65
37444 GTTTCTCTTG
* ** * **
37454 AAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCTA
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
* *
37519 AAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG-AA-ACAAAATCTTCAAATTTATTTCCCC
37584 TA
64 TA
* *
37586 AAACATAATTTTGTTTCCCTTGAGATC-GTTTCTCATGAAACAA
1 AAACA-AATTTTGTCTCCCTTGAGA-CAGTTTCTCTTGAAACAA
37629 CATATATCTT
Statistics
Matches: 95, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
65 31 0.33
66 6 0.06
67 31 0.33
68 26 0.27
69 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.37
Consensus pattern (65 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
Found at i:38407 original size:59 final size:60
Alignment explanation
Indices: 38276--38419 Score: 227
Period size: 59 Copynumber: 2.4 Consensus size: 60
38266 CGAGACAATG
* *
38276 CAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGAGC
1 CAAGTTCAACTTCACAACGAAGGGACCGCTGCCTGT--ACAACAACTTCTCAATTTCAGAAC
38338 CAAGTTCAACTTCACAACGAAGGGACCGCTGCCTGT-CAACAACTTCTCAATTTCAGAAC
1 CAAGTTCAACTTCACAACGAAGGGACCGCTGCCTGTACAACAACTTCTCAATTTCAGAAC
* *
38397 CAATTTCAACTTCACAATGAAGG
1 CAAGTTCAACTTCACAACGAAGG
38420 ATATTGGACT
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
59 43 0.55
62 35 0.45
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (60 bp):
CAAGTTCAACTTCACAACGAAGGGACCGCTGCCTGTACAACAACTTCTCAATTTCAGAAC
Found at i:38524 original size:105 final size:105
Alignment explanation
Indices: 38338--38845 Score: 816
Period size: 105 Copynumber: 4.9 Consensus size: 105
38328 ATTTCAGAGC
* * *
38338 CAAGTTCAACTTCACAACGAAGGGACCGCTGCCTGT---CAACAACTTCTCAATTTCAGAACCAA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAA
* *
38400 TTTCAACTTCACAATGAAGGATATTGGACTTCAGACAACG
66 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
38440 CAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAA
*
38505 TTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACG
66 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* **
38545 CAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCGCAGAGCCAA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAA
*
38610 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATG
66 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
38650 CAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAA
38715 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
66 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
**
38755 CAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-A-AACTT-TC-A-TTCAGATTCAA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAA
* *
38815 TTTCAACTTCACGACGGAGGATATTGGACTC
66 TTTCAACTTCACAACGAAGGATATTGGACTC
38846 TGAACAATGC
Statistics
Matches: 386, Mismatches: 17, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
100 37 0.10
101 1 0.00
102 35 0.09
103 5 0.01
104 1 0.00
105 307 0.80
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.22
Consensus pattern (105 bp):
CAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAA
TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
Found at i:41176 original size:2 final size:2
Alignment explanation
Indices: 41169--41204 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
41159 GAGGAGCCTA
41169 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41205 ATTAATTCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41878 original size:7 final size:7
Alignment explanation
Indices: 41866--41898 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
41856 TTCTATTAAG
41866 TCAACAT
1 TCAACAT
41873 TCAACAT
1 TCAACAT
41880 TCAACAT
1 TCAACAT
41887 TCAACAT
1 TCAACAT
*
41894 CCAAC
1 TCAAC
41899 TCCTACCCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.42, C:0.33, G:0.00, T:0.24
Consensus pattern (7 bp):
TCAACAT
Found at i:46605 original size:12 final size:12
Alignment explanation
Indices: 46588--46616 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
46578 ATTCATATTG
46588 TATTTAAATTAT
1 TATTTAAATTAT
46600 TATTTAAATTAT
1 TATTTAAATTAT
46612 TATTT
1 TATTT
46617 TTCGCGATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TATTTAAATTAT
Found at i:48679 original size:55 final size:55
Alignment explanation
Indices: 48613--48813 Score: 179
Period size: 55 Copynumber: 3.5 Consensus size: 55
48603 AGCCATCAAC
*
48613 GATTTCAACTTCACGATGAAGGATATCGTGCCCACAAGCAACAATGCAACACTTG
1 GATTTCAACTTCACGATGAAGGATATCGTTCCCACAAGCAACAATGCAACACTTG
* * * * * *
48668 GATTTCAACTTCACGATGAAGGATATCCAATTCAAAGCTCAA-CTTCACAATGAAGGAACCATCC
1 GATTTCAACTTCACGATGAAGGATAT-C-GTTC---CCACAAGC--AACAAT---GCAA-CA-CT
**
48732 AC
54 TG
* *
48734 GATTTCATCTTCACGATGAAGGATATCGTTCCCACAAGCAACAATGCAACCCTTG
1 GATTTCAACTTCACGATGAAGGATATCGTTCCCACAAGCAACAATGCAACACTTG
*
48789 GATTTCAACTTCACGACGAAGGATA
1 GATTTCAACTTCACGATGAAGGATA
48814 CCCAATTCAA
Statistics
Matches: 112, Mismatches: 21, Indels: 26
0.70 0.13 0.16
Matches are distributed among these distances:
55 50 0.45
56 2 0.02
57 5 0.04
59 1 0.01
60 9 0.08
61 9 0.08
62 1 0.01
64 6 0.05
65 3 0.03
66 26 0.23
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.23
Consensus pattern (55 bp):
GATTTCAACTTCACGATGAAGGATATCGTTCCCACAAGCAACAATGCAACACTTG
Found at i:48746 original size:66 final size:66
Alignment explanation
Indices: 48668--48881 Score: 209
Period size: 66 Copynumber: 3.4 Consensus size: 66
48658 GCAACACTTG
*
48668 GATTTCAACTTCACGATGAAGGATATCCAATTCAAAGCTCAACTTCACAATGAAGGAACCATCCA
1 GATTTCAACTTCACGATGAAGGATATCCAATTCAAAGCTCAACTTAACAATGAAGGAACCATCCA
48733 C
66 C
* * * * * *
48734 GATTTCATCTTCACGATGAAGGATAT-C-GTTC---CCACAAGC--AACAAT---GCAACC--CT
1 GATTTCAACTTCACGATGAAGGATATCCAATTCAAAGCTCAA-CTTAACAATGAAGGAACCATCC
**
48787 TG
65 AC
* * * * *
48789 GATTTCAACTTCACGACGAAGGATACCCAATTCAAAGCTCAACTTTATAATGAAGGAGCCATCCA
1 GATTTCAACTTCACGATGAAGGATATCCAATTCAAAGCTCAACTTAACAATGAAGGAACCATCCA
48854 C
66 C
48855 GATTTCAACTTCACGATGAAGGATATC
1 GATTTCAACTTCACGATGAAGGATATC
48882 GTGCCTAACG
Statistics
Matches: 111, Mismatches: 24, Indels: 26
0.69 0.15 0.16
Matches are distributed among these distances:
55 24 0.22
56 1 0.01
57 8 0.07
59 1 0.01
60 9 0.08
61 8 0.07
62 1 0.01
64 7 0.06
65 1 0.01
66 51 0.46
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.24
Consensus pattern (66 bp):
GATTTCAACTTCACGATGAAGGATATCCAATTCAAAGCTCAACTTAACAATGAAGGAACCATCCA
C
Found at i:48746 original size:121 final size:121
Alignment explanation
Indices: 48527--48886 Score: 630
Period size: 121 Copynumber: 3.0 Consensus size: 121
48517 TCATATTTGG
48527 AAGCAACAATGCAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTT
1 AAGCAACAATGCAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTT
* *
48592 CACAACGAAGGAGCCATCAACGATTTCAACTTCACGATGAAGGATATCGTGCCCAC
66 CACAATGAAGGAGCCATCCACGATTTCAACTTCACGATGAAGGATATCGTGCCCAC
* *
48648 AAGCAACAATGCAACACTTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAAGCTCAACTT
1 AAGCAACAATGCAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTT
* * *
48713 CACAATGAAGGAACCATCCACGATTTCATCTTCACGATGAAGGATATCGTTCCCAC
66 CACAATGAAGGAGCCATCCACGATTTCAACTTCACGATGAAGGATATCGTGCCCAC
*
48769 AAGCAACAATGCAACCCTTGGATTTCAACTTCACGACGAAGGATACCCAATTCAAAGCTCAACTT
1 AAGCAACAATGCAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTT
* *
48834 TATAATGAAGGAGCCATCCACGATTTCAACTTCACGATGAAGGATATCGTGCC
66 CACAATGAAGGAGCCATCCACGATTTCAACTTCACGATGAAGGATATCGTGCC
48887 TAACGGATCG
Statistics
Matches: 224, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
121 224 1.00
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (121 bp):
AAGCAACAATGCAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTT
CACAATGAAGGAGCCATCCACGATTTCAACTTCACGATGAAGGATATCGTGCCCAC
Found at i:49186 original size:85 final size:85
Alignment explanation
Indices: 48943--49231 Score: 336
Period size: 85 Copynumber: 3.5 Consensus size: 85
48933 TAGCCCAGTG
** * * * * *
48943 CAACATAATTCAAGGTGAGAAGGGTTATCTGTCATCAAAGACCTTCGAGTTTGATTACATTCAGC
1 CAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGC
* * *
49008 TCAAAGGCATATCCAACTTA
66 TCAAAGGCACATCAAATTTA
* * * * * *
49028 CATCATAACTCAAGGTGAGAAGGGTTATCTGT---C-AAGACCTTCGAGTTCGATTATACTAAGC
1 CAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGC
* *
49089 TTAAAGGAACATCAAATTTA
66 TCAAAGGCACATCAAATTTA
* * *
49109 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTTAACAAAGACCTTAGAGTTCGATTACACTCAGC
1 CAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGC
49174 TCAAAGGCACATCAAATTTA
66 TCAAAGGCACATCAAATTTA
* *
49194 CAACATAGCTCAAAGCGAGAA-GGCTATCTATCAACAAA
1 CAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAA
49232 AGCAGTAGCA
Statistics
Matches: 176, Mismatches: 24, Indels: 9
0.84 0.11 0.04
Matches are distributed among these distances:
81 67 0.38
82 1 0.01
84 16 0.09
85 92 0.52
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25
Consensus pattern (85 bp):
CAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGC
TCAAAGGCACATCAAATTTA
Found at i:50860 original size:29 final size:30
Alignment explanation
Indices: 50805--50868 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
50795 CTTTAATCCA
50805 TTATTATTATATATATATAATTATATT-TT
1 TTATTATTATATATATATAATTATATTATT
*
50834 TGTATTA-TATATATATATTAGTT-TATTATT
1 T-TATTATTATATATATA-TAATTATATTATT
50864 TTATT
1 TTATT
50869 TTCTTTATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
29 19 0.61
30 12 0.39
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (30 bp):
TTATTATTATATATATATAATTATATTATT
Found at i:51017 original size:14 final size:14
Alignment explanation
Indices: 50998--51024 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
50988 TATTATTTTA
50998 TTATTTTGTATATT
1 TTATTTTGTATATT
51012 TTATTTTGTATAT
1 TTATTTTGTATAT
51025 GTTTTTATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.70
Consensus pattern (14 bp):
TTATTTTGTATATT
Found at i:51031 original size:34 final size:34
Alignment explanation
Indices: 50988--51085 Score: 98
Period size: 34 Copynumber: 2.9 Consensus size: 34
50978 CTTTAATTTT
50988 TATTATTTTATTATTTTGTATATTTTATTT-TGTA
1 TATT-TTTTATTATTTTGTATATTTTATTTATGTA
*
51022 TATGTTTTTATTATTTAT-TAT-TTTTATTTATGTT
1 TAT-TTTTTATTATTT-TGTATATTTTATTTATGTA
*
51056 TATTTATTT-TCT-TTTTGTTTATTTTATTTA
1 TATTT-TTTAT-TATTTTGTATATTTTATTTA
51086 CTTTTTATAT
Statistics
Matches: 55, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
32 1 0.02
33 16 0.29
34 36 0.65
35 2 0.04
ACGTcount: A:0.20, C:0.01, G:0.05, T:0.73
Consensus pattern (34 bp):
TATTTTTTATTATTTTGTATATTTTATTTATGTA
Found at i:51052 original size:10 final size:10
Alignment explanation
Indices: 51028--51102 Score: 52
Period size: 10 Copynumber: 7.8 Consensus size: 10
51018 TGTATATGTT
51028 TTTATTATTTA
1 TTTATT-TTTA
51039 -TTATTTTTA
1 TTTATTTTTA
*
51048 TTTATGTTTA
1 TTTATTTTTA
51058 TTTATTTTCT-
1 TTTATTTT-TA
*
51068 TTT-TGTTTA
1 TTTATTTTTA
*
51077 TTT-TATTTA
1 TTTATTTTTA
* *
51086 CTT-TTTATA
1 TTTATTTTTA
51095 TTTATTTT
1 TTTATTTT
51103 ATTAATATTA
Statistics
Matches: 51, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
8 1 0.02
9 23 0.45
10 26 0.51
11 1 0.02
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.76
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:51059 original size:19 final size:18
Alignment explanation
Indices: 51035--51078 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 18
51025 GTTTTTATTA
51035 TTTATTATTTT-TATTTATG
1 TTTATTATTTTCT-TTT-TG
51054 TTTATTTATTTTCTTTTTG
1 TTTA-TTATTTTCTTTTTG
51073 TTTATT
1 TTTATT
51079 TTATTTACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 2 0.09
19 10 0.43
20 10 0.43
21 1 0.04
ACGTcount: A:0.16, C:0.02, G:0.05, T:0.77
Consensus pattern (18 bp):
TTTATTATTTTCTTTTTG
Found at i:51062 original size:47 final size:47
Alignment explanation
Indices: 50986--51105 Score: 122
Period size: 47 Copynumber: 2.5 Consensus size: 47
50976 GTCTTTAATT
* *
50986 TTTATTATTTTATTATTT-TGTATATTTTATTTTGTATATGTTT-TTATTA
1 TTTATTA-TTT-TTATTTATGTTTA-TTTATTTTCTATATGTTTATT-TTA
* *
51035 TTTATTATTTTTATTTATGTTTATTTATTTTCTTTTTGTTTATTTTA
1 TTTATTATTTTTATTTATGTTTATTTATTTTCTATATGTTTATTTTA
*
51082 TTTACTT-TTTATATTTAT-TTTATT
1 TTTA-TTATTTTTATTTATGTTTATT
51106 AATATTATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
46 6 0.10
47 38 0.60
48 12 0.19
49 7 0.11
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (47 bp):
TTTATTATTTTTATTTATGTTTATTTATTTTCTATATGTTTATTTTA
Found at i:51079 original size:19 final size:19
Alignment explanation
Indices: 51035--51091 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
51025 GTTTTTATTA
51035 TTTA-TTATTTT-TATTTATG
1 TTTATTTATTTTCT-TTT-TG
51054 TTTATTTATTTTCTTTTTG
1 TTTATTTATTTTCTTTTTG
*
51073 TTTATTTTATTTACTTTTT
1 TTTA-TTTATTTTCTTTTT
51092 ATATTTATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
19 10 0.29
20 23 0.68
21 1 0.03
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.77
Consensus pattern (19 bp):
TTTATTTATTTTCTTTTTG
Found at i:51971 original size:121 final size:121
Alignment explanation
Indices: 51805--52027 Score: 392
Period size: 121 Copynumber: 1.8 Consensus size: 121
51795 TCTTGAGCAC
*
51805 GATATCCTTCGTCGTGAAGTTGAAATTATGGACGGCTCATTCGTTGTGAAGTTGAGCTTTGAATT
1 GATATCCTTCGTCGTGAAGTTGAAATTATGGACGACTCATTCGTTGTGAAGTTGAGCTTTGAATT
51870 GGATATCCTTCGTCGTGAAGTTAAAATCCAAGGGTTGCATTGCTGCTTGTGGGCAT
66 GGATATCCTTCGTCGTGAAGTTAAAATCCAAGGGTTGCATTGCTGCTTGTGGGCAT
* * *
51926 GATATCCTTCGTCGTGAAGTTGAAATTGTGGATGACTCTTTCGTTGTGAAGTTGAGCTTTGAATT
1 GATATCCTTCGTCGTGAAGTTGAAATTATGGACGACTCATTCGTTGTGAAGTTGAGCTTTGAATT
* *
51991 GGATATCCTTCGTTGTGAAGTTGAAATCCAAGGGTTG
66 GGATATCCTTCGTCGTGAAGTTAAAATCCAAGGGTTG
52028 TTTAACCAAA
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
121 96 1.00
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.36
Consensus pattern (121 bp):
GATATCCTTCGTCGTGAAGTTGAAATTATGGACGACTCATTCGTTGTGAAGTTGAGCTTTGAATT
GGATATCCTTCGTCGTGAAGTTAAAATCCAAGGGTTGCATTGCTGCTTGTGGGCAT
Found at i:52121 original size:65 final size:64
Alignment explanation
Indices: 51981--52156 Score: 234
Period size: 65 Copynumber: 2.8 Consensus size: 64
51971 GTGAAGTTGA
* * *
51981 GCTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAA---GGGT-TGTTTAACCAAATTG
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTGAGTAAGTTTAACCAAATTG
* * * *
52041 GTTTTGAGTTGGATATCCTTCATCGTGAAGTTGAAATCCAATCTTGAGTAAGTTTCACCAAATTG
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATC-TGAGTAAGTTTAACCAAATTG
*
52106 GCTTTGAGTTGGATATCATTCGTTGTGAAGTTGAAATCCAATCTCGAGTAA
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCT-GAGTAA
52157 ATTGTGTTGT
Statistics
Matches: 99, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
60 37 0.37
64 4 0.04
65 58 0.59
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.36
Consensus pattern (64 bp):
GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTGAGTAAGTTTAACCAAATTG
Found at i:52256 original size:64 final size:64
Alignment explanation
Indices: 52171--52527 Score: 493
Period size: 64 Copynumber: 5.6 Consensus size: 64
52161 TGTTGTTTCA
* * * * *
52171 AGTCCAATATCCTTCGTTGTGAAGCTGAAATTGACTTTGAATGAAACTGAAAAGTTGTTTGTTG
1 AGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTG
* *
52235 AGTCCAATATCATTCGATGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTTTTTGTTG
1 AGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTG
*
52299 AGTCCAATATCATTCGCTGTGAAGTTAAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTG
1 AGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTG
* * * ** *
52363 ACTCCAATAT-ACTTTGCTGTGAAGTTGAAATTGACTCTGAATGAAAGTAAAAAGTTGTTT-TTA
1 AGTCCAATATCA-TTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTG
* * * *
52426 AGTCCAATATCATTCACTGTGAAGTTGAAATTGACTATGAAGGAAACTGGAAAGTTATTTGTTG
1 AGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTG
* * * *
52490 AGTCCAATGTCCTCCGCTGTGAAGTTGAAATTGGCTCT
1 AGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCT
52528 AAAAGCTGCA
Statistics
Matches: 258, Mismatches: 32, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
63 52 0.20
64 206 0.80
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (64 bp):
AGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTG
Found at i:52479 original size:191 final size:192
Alignment explanation
Indices: 52173--52527 Score: 543
Period size: 191 Copynumber: 1.9 Consensus size: 192
52163 TTGTTTCAAG
* * * * *
52173 TCCAATATCCTTCGTTGTGAAGCTGAAATTGACTTTGAATGAAACTGAAAAGTTGTTTGTTGAGT
1 TCCAATATACTTCGCTGTGAAGCTGAAATTGACTCTGAATGAAACTAAAAAGTTGTTTGTTAAGT
* * *
52238 CCAATATCATTCGATGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTTTTTGTTGAGTC
66 CCAATATCATTCGATGTGAAGTTGAAATTGACTATGAAGGAAACTGGAAAGTTATTTGTTGAGTC
*
52303 CAATATCATTCGCTGTGAAGTTAAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTGAC
131 CAATATCATCCGCTGTGAAGTTAAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTGAC
* * *
52365 TCCAATATACTTTGCTGTGAAGTTGAAATTGACTCTGAATGAAAGTAAAAAGTTGTTT-TTAAGT
1 TCCAATATACTTCGCTGTGAAGCTGAAATTGACTCTGAATGAAACTAAAAAGTTGTTTGTTAAGT
52429 CCAATATCATTC-ACTGTGAAGTTGAAATTGACTATGAAGGAAACTGGAAAGTTATTTGTTGAGT
66 CCAATATCATTCGA-TGTGAAGTTGAAATTGACTATGAAGGAAACTGGAAAGTTATTTGTTGAGT
* * * *
52493 CCAATGTCCTCCGCTGTGAAGTTGAAATTGGCTCT
130 CCAATATCATCCGCTGTGAAGTTAAAATTGACTCT
52528 AAAAGCTGCA
Statistics
Matches: 146, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
190 1 0.01
191 94 0.64
192 51 0.35
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (192 bp):
TCCAATATACTTCGCTGTGAAGCTGAAATTGACTCTGAATGAAACTAAAAAGTTGTTTGTTAAGT
CCAATATCATTCGATGTGAAGTTGAAATTGACTATGAAGGAAACTGGAAAGTTATTTGTTGAGTC
CAATATCATCCGCTGTGAAGTTAAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTGAC
Found at i:57289 original size:33 final size:37
Alignment explanation
Indices: 57252--57326 Score: 97
Period size: 36 Copynumber: 2.1 Consensus size: 37
57242 AAGAGTAAAG
*
57252 AAAGAT-AAAAG-AAA-AAAATAATA-TTAAT-AAAAT
1 AAAGATAAAAAGTAAATAAAATAA-ACATAATGAAAAT
57285 AAAGATAAAAAGTAAATAAAATAAACATAATGAAAAT
1 AAAGATAAAAAGTAAATAAAATAAACATAATGAAAAT
57322 AAAGA
1 AAAGA
57327 AACAAAAACA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
33 6 0.17
34 5 0.14
35 4 0.11
36 11 0.31
37 10 0.28
ACGTcount: A:0.72, C:0.01, G:0.08, T:0.19
Consensus pattern (37 bp):
AAAGATAAAAAGTAAATAAAATAAACATAATGAAAAT
Found at i:57292 original size:6 final size:5
Alignment explanation
Indices: 57277--57398 Score: 55
Period size: 5 Copynumber: 24.4 Consensus size: 5
57267 AAATAATATT
57277 AATAA AATAA AGATAA AA-AGTA AATAA AATAA ACAT-- AATGAA AATAA
1 AATAA AATAA A-ATAA AATA--A AATAA AATAA A-ATAA AAT-AA AATAA
* * *
57324 AGA-AA CA-AA AACAA AAGTAA AAAATA AATAA AAT-A AAT-A AATAA
1 A-ATAA AATAA AATAA AA-TAA AATA-A AATAA AATAA AATAA AATAA
* *
57368 AATAA TA-AA AATAAA AATAA AA-AT AATAA AA
1 AATAA AATAA AAT-AA AATAA AATAA AATAA AA
57399 ATTAAAGACA
Statistics
Matches: 92, Mismatches: 9, Indels: 32
0.69 0.07 0.24
Matches are distributed among these distances:
3 2 0.02
4 20 0.22
5 42 0.46
6 27 0.29
7 1 0.01
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.17
Consensus pattern (5 bp):
AATAA
Found at i:57321 original size:51 final size:49
Alignment explanation
Indices: 57234--57398 Score: 138
Period size: 51 Copynumber: 3.2 Consensus size: 49
57224 TAAAGAAGAT
* * **
57234 AAAATAAAAAGAGTAAAGAAAGATAAA-AGAAAAAAATAATATTAATAAAATA
1 AAAATAAAAA-A-TAAATAAA-ATAAACA-AATAAAATAATAAAAATAAAATA
* * *
57286 AAGATAAAAAGTAAATAAAATAAACATAATGAAAATAA-AGAAACA-AAAACA
1 AAAATAAAAAATAAATAAAATAAACA-AAT-AAAATAATA-AAA-ATAAAATA
* *
57337 AAAGTAAAAAATAAATAAAATAAATAAATAAAATAATAAAAATAAAAATA
1 AAAATAAAAAATAAATAAAATAAACAAATAAAATAATAAAAAT-AAAATA
57387 AAAATAATAAAA
1 AAAATAA-AAAA
57399 ATTAAAGACA
Statistics
Matches: 91, Mismatches: 14, Indels: 17
0.75 0.11 0.14
Matches are distributed among these distances:
48 1 0.01
49 15 0.16
50 26 0.29
51 39 0.43
52 10 0.11
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.17
Consensus pattern (49 bp):
AAAATAAAAAATAAATAAAATAAACAAATAAAATAATAAAAATAAAATA
Found at i:57361 original size:9 final size:9
Alignment explanation
Indices: 57197--57397 Score: 57
Period size: 9 Copynumber: 21.8 Consensus size: 9
57187 ATAATAAAGG
*
57197 AAATAAAAA
1 AAATAAATA
57206 CAAATAAA-A
1 -AAATAAATA
57215 CAAATGAAATA
1 -AAAT-AAATA
*
57226 AAGA-AGATA
1 AA-ATAAATA
57235 AAATAAA-A
1 AAATAAATA
* *
57243 AGAGTAAAGA
1 A-AATAAATA
57253 AAGATAAA-A
1 AA-ATAAATA
*
57262 GAAAAAAATA
1 -AAATAAATA
* *
57272 ATATTAATA
1 AAATAAATA
*
57281 AAATAAAGA
1 AAATAAATA
*
57290 TAAA-AAGT-
1 -AAATAAATA
57298 AAATAAAATA
1 AAAT-AAATA
57308 AACAT-AATGA
1 AA-ATAAAT-A
*
57318 AAATAAAGA
1 AAATAAATA
* *
57327 AACAAAAACA
1 AA-ATAAATA
57337 AAAGT-AA-A
1 AAA-TAAATA
57345 AAATAAATA
1 AAATAAATA
57354 AAATAAAT-
1 AAATAAATA
57362 AAATAAAATA
1 AAAT-AAATA
57372 ATAA-AAATAA
1 A-AATAAAT-A
57382 AAATAAA-A
1 AAATAAATA
57390 ATAATAAA
1 A-AATAAA
57398 AATTAAAGAC
Statistics
Matches: 147, Mismatches: 18, Indels: 53
0.67 0.08 0.24
Matches are distributed among these distances:
7 4 0.03
8 15 0.10
9 78 0.53
10 44 0.30
11 6 0.04
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.16
Consensus pattern (9 bp):
AAATAAATA
Found at i:57376 original size:21 final size:21
Alignment explanation
Indices: 57298--57400 Score: 78
Period size: 20 Copynumber: 5.2 Consensus size: 21
57288 GATAAAAAGT
* *
57298 AAAT-AAAATAAACATAATGA
1 AAATAAAAATAAAAATAATAA
* *
57318 AAATAAAGAA-ACAAA-AACAA
1 AAATAAA-AATAAAAATAATAA
* *
57338 AAGTAAAAA-ATAAATAA-AA
1 AAATAAAAATAAAAATAATAA
57357 TAAAT--AAAT-AAAATAATAA
1 -AAATAAAAATAAAAATAATAA
57376 AAATAAAAATAAAAATAATAA
1 AAATAAAAATAAAAATAATAA
57397 AAAT
1 AAAT
57401 TAAAGACAAG
Statistics
Matches: 66, Mismatches: 8, Indels: 17
0.73 0.09 0.19
Matches are distributed among these distances:
18 13 0.20
19 10 0.15
20 22 0.33
21 19 0.29
22 2 0.03
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.17
Consensus pattern (21 bp):
AAATAAAAATAAAAATAATAA
Found at i:57399 original size:22 final size:22
Alignment explanation
Indices: 57342--57404 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
57332 AAACAAAAGT
*
57342 AAAAAATAA-ATAAAATAAATA
1 AAAAAATAATAAAAAATAAATA
57363 AATAAAATAAT-AAAAATAAA-A
1 AA-AAAATAATAAAAAATAAATA
*
57384 ATAAAAATAATAAAAATTAAA
1 A-AAAAATAATAAAAAATAAA
57405 GACAAGAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
21 12 0.33
22 24 0.67
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (22 bp):
AAAAAATAATAAAAAATAAATA
Found at i:57537 original size:29 final size:30
Alignment explanation
Indices: 57502--57583 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 30
57492 ATAAAAATTA
57502 ATAAATAAATAAAATAGATATA-ATGAAAAT
1 ATAAATAAATAAAATA-ATATATATGAAAAT
* *
57532 A-AAAT-AATAAAATAATATATATGTATAT
1 ATAAATAAATAAAATAATATATATGAAAAT
57560 ATAAATAAA-AAATATAATTATATA
1 ATAAATAAATAAA-ATAA-TATATA
57584 ATAATAATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
27 5 0.11
28 16 0.36
29 11 0.24
30 7 0.16
31 6 0.13
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.32
Consensus pattern (30 bp):
ATAAATAAATAAAATAATATATATGAAAAT
Found at i:57589 original size:23 final size:26
Alignment explanation
Indices: 57534--57597 Score: 82
Period size: 25 Copynumber: 2.5 Consensus size: 26
57524 ATGAAAATAA
57534 AATAATAAAATAATATATATGTATAT
1 AATAATAAAATAATATATATGTATAT
57560 -ATAAATAAAA-AATATA-AT-TATAT
1 AAT-AATAAAATAATATATATGTATAT
57583 AATAATAATAATAAT
1 AATAATAA-AATAAT
57598 GGATTAAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
23 10 0.29
24 6 0.18
25 11 0.32
26 7 0.21
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (26 bp):
AATAATAAAATAATATATATGTATAT
Found at i:57644 original size:17 final size:17
Alignment explanation
Indices: 57624--57658 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
57614 GAAATAAAAT
* *
57624 AAGAAGCCAAATTTAAA
1 AAGAAACCAAAGTTAAA
57641 AAGAAACCAAAGTTAAA
1 AAGAAACCAAAGTTAAA
57658 A
1 A
57659 TCGGATTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.63, C:0.11, G:0.11, T:0.14
Consensus pattern (17 bp):
AAGAAACCAAAGTTAAA
Found at i:58689 original size:2 final size:2
Alignment explanation
Indices: 58682--58722 Score: 59
Period size: 2 Copynumber: 21.0 Consensus size: 2
58672 ATATGTAATA
58682 AT AT AT AT -T GAT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58723 TTATGTTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 2 0.06
2 33 0.92
3 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:64609 original size:19 final size:19
Alignment explanation
Indices: 64585--64624 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
64575 AAAAAGAAAC
* *
64585 AAAAAAATCAACGAAAAAG
1 AAAAAAAGCAAAGAAAAAG
64604 AAAAAAAGCAAAGAAAAAG
1 AAAAAAAGCAAAGAAAAAG
64623 AA
1 AA
64625 GACAAGAAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.78, C:0.07, G:0.12, T:0.03
Consensus pattern (19 bp):
AAAAAAAGCAAAGAAAAAG
Found at i:65978 original size:43 final size:39
Alignment explanation
Indices: 65865--65978 Score: 102
Period size: 40 Copynumber: 2.8 Consensus size: 39
65855 CTAAAGATGG
* * *
65865 CCAGAACTCTTCATCACATATGAGCCGTGTCATCCACCGA
1 CCAGAACTCTTCATCACGTATGAG-CGTGTCACCCAACGA
* * * *
65905 CCAGATCTCCTCATCATGTAGGAGTCGTGTCACCCTTAAACGA
1 CCAGAACTCTTCATCACGTATGAG-CGTGTCACCC---AACGA
*
65948 CCAGAACTTTTCATCACGTATGAGCAGTGTC
1 CCAGAACTCTTCATCACGTATGAGC-GTGTC
65979 GTCTCCACCA
Statistics
Matches: 57, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
40 28 0.49
42 1 0.02
43 28 0.49
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (39 bp):
CCAGAACTCTTCATCACGTATGAGCGTGTCACCCAACGA
Found at i:66026 original size:3 final size:3
Alignment explanation
Indices: 66018--66051 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
66008 AGGACAAAAA
66018 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
66052 CAACATTTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:69460 original size:29 final size:29
Alignment explanation
Indices: 69428--69485 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
69418 AAAAAATATA
* * *
69428 ATTTAGACTCTTATTTTTTTTTAAAATTT
1 ATTTAGACCCCTAATTTTTTTTAAAATTT
* *
69457 ATTTTGCCCCCTAATTTTTTTTAAAATTT
1 ATTTAGACCCCTAATTTTTTTTAAAATTT
69486 CAGATTTAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.26, C:0.12, G:0.03, T:0.59
Consensus pattern (29 bp):
ATTTAGACCCCTAATTTTTTTTAAAATTT
Found at i:70143 original size:21 final size:21
Alignment explanation
Indices: 70117--70164 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
70107 TGCATTCCGT
*
70117 GTTGCGATAGTTGGAAATCGC
1 GTTGCGATAGTTGAAAATCGC
70138 GTTGCGATAGTTGAAAATCGC
1 GTTGCGATAGTTGAAAATCGC
70159 GTTGCG
1 GTTGCG
70165 GTTTTCCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.15, G:0.33, T:0.29
Consensus pattern (21 bp):
GTTGCGATAGTTGAAAATCGC
Found at i:70237 original size:18 final size:18
Alignment explanation
Indices: 70191--70240 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 18
70181 TGCGATAGTC
70191 TACAGTGTCGTTGCGATT
1 TACAGTGTCGTTGCGATT
* *
70209 TTC--CG-CGTTGCGATT
1 TACAGTGTCGTTGCGATT
70224 TACAGTGTCGTTGCGAT
1 TACAGTGTCGTTGCGAT
70241 AGTTGCGATA
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
15 12 0.48
16 1 0.04
17 1 0.04
18 11 0.44
ACGTcount: A:0.14, C:0.20, G:0.28, T:0.38
Consensus pattern (18 bp):
TACAGTGTCGTTGCGATT
Found at i:71089 original size:12 final size:11
Alignment explanation
Indices: 71059--71092 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
71049 CGCCGCCGTC
71059 TCGGGTCG-GG
1 TCGGGTCGTGG
71069 TCGGGTCGTGG
1 TCGGGTCGTGG
71080 TCGTGGTCGTGG
1 TCG-GGTCGTGG
71092 T
1 T
71093 AATACGTGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
11 5 0.23
12 9 0.41
ACGTcount: A:0.00, C:0.18, G:0.53, T:0.29
Consensus pattern (11 bp):
TCGGGTCGTGG
Found at i:71220 original size:41 final size:41
Alignment explanation
Indices: 71175--71329 Score: 265
Period size: 41 Copynumber: 3.8 Consensus size: 41
71165 CATTTTTAAA
*
71175 ACTATCGCAACGCGAAATGGAAAATTGCAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
71216 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
* * *
71257 ACTATTGTAACGTGAAATGGAAAATCGCAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
*
71298 ACTATCGCAACGCGAAATGGAAAACCGCAACG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACG
71330 CGAAACTGCG
Statistics
Matches: 106, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 106 1.00
ACGTcount: A:0.39, C:0.23, G:0.22, T:0.16
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
Found at i:71227 original size:21 final size:21
Alignment explanation
Indices: 71201--71309 Score: 68
Period size: 21 Copynumber: 5.3 Consensus size: 21
71191 ATGGAAAATT
71201 GCAACGACACTGTAGACTATC
1 GCAACGACACTGTAGACTATC
* **
71222 GCAACG-CGAAATG--GAAAATC
1 GCAACGAC--ACTGTAGACTATC
*
71242 GCAACGACACTGTAGACTATT
1 GCAACGACACTGTAGACTATC
* * **
71263 GTAACGTGA-AATG--GAAAATC
1 GCAAC--GACACTGTAGACTATC
71283 GCAACGACACTGTAGACTATC
1 GCAACGACACTGTAGACTATC
71304 GCAACG
1 GCAACG
71310 CGAAATGGAA
Statistics
Matches: 62, Mismatches: 16, Indels: 20
0.63 0.16 0.20
Matches are distributed among these distances:
18 2 0.03
19 6 0.10
20 20 0.32
21 26 0.42
22 6 0.10
23 2 0.03
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (21 bp):
GCAACGACACTGTAGACTATC
Found at i:74131 original size:21 final size:21
Alignment explanation
Indices: 74105--74174 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
74095 TAGCATTATC
*
74105 CAATAAACTTGACATCCATAA
1 CAATAAACTTGAAATCCATAA
* *
74126 CAATAAATTTGAAATTCATAA
1 CAATAAACTTGAAATCCATAA
* *
74147 CAAGAAACTTGAAATCAATAA
1 CAATAAACTTGAAATCCATAA
*
74168 TAATAAA
1 CAATAAA
74175 TCAAAGTTTA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.54, C:0.14, G:0.06, T:0.26
Consensus pattern (21 bp):
CAATAAACTTGAAATCCATAA
Found at i:87589 original size:31 final size:31
Alignment explanation
Indices: 87553--87615 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
87543 GATTGGAGTA
*
87553 AGAATTGGTTGCTTTAAGGTATGAGAGGTTG
1 AGAATTGGTTACTTTAAGGTATGAGAGGTTG
87584 AGAATTGGTTACTTTAAGGTATGAGAGGTTG
1 AGAATTGGTTACTTTAAGGTATGAGAGGTTG
87615 A
1 A
87616 TTCTTCTCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.03, G:0.33, T:0.35
Consensus pattern (31 bp):
AGAATTGGTTACTTTAAGGTATGAGAGGTTG
Found at i:88887 original size:26 final size:26
Alignment explanation
Indices: 88836--88891 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
88826 AATATACAAC
* *
88836 ACAACTTTTATAAATCACATTTAAGG
1 ACAACTTTTATAAATCACACTAAAGG
88862 ACAACTTTTATAAAAT-ACACTAAAGG
1 ACAACTTTTAT-AAATCACACTAAAGG
88888 ACAA
1 ACAA
88892 AACATTTTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 23 0.85
27 4 0.15
ACGTcount: A:0.48, C:0.16, G:0.07, T:0.29
Consensus pattern (26 bp):
ACAACTTTTATAAATCACACTAAAGG
Found at i:88947 original size:29 final size:28
Alignment explanation
Indices: 88905--88982 Score: 111
Period size: 29 Copynumber: 2.7 Consensus size: 28
88895 ATTTTAGTAA
*
88905 AAGGACAAAACTTTATATAAATTAAAATT
1 AAGGAAAAAACTTT-TATAAATTAAAATT
88934 AAGGAAAAAACTTTTTATAAATTAAAATT
1 AAGGAAAAAAC-TTTTATAAATTAAAATT
*
88963 AAGGATAAAACCTTTTATAA
1 AAGGA-AAAAACTTTTATAA
88983 GTTATAATAG
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
29 37 0.82
30 8 0.18
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.32
Consensus pattern (28 bp):
AAGGAAAAAACTTTTATAAATTAAAATT
Found at i:89855 original size:13 final size:13
Alignment explanation
Indices: 89837--89862 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
89827 CTGCACAACG
89837 AGTGCCAAAAAAT
1 AGTGCCAAAAAAT
89850 AGTGCCAAAAAAT
1 AGTGCCAAAAAAT
89863 TGAATTATTC
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:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (13 bp):
AGTGCCAAAAAAT
Found at i:91425 original size:6 final size:6
Alignment explanation
Indices: 91416--92979 Score: 1467
Period size: 6 Copynumber: 261.8 Consensus size: 6
91406 ACTACTAGTA
* * * * ** *
91416 ACTACT ACTACC ACTACC ACTACC ACTACT ACCACT ACTATT ACTACG
1 ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC
* * * * * *
91464 ACTA-- ACTACT ACTACT ACTACT ACTACT ACTACC ACCACC ACCACC
1 ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC
* * * * * * *
91510 ACTACC ACTACT A-TCACT ACTACC ACTACT ACTACT ACGACTA ACTACT
1 ACTACC ACTACC ACT-ACC ACTACC ACTACC ACTACC ACTAC-C ACTACC
* * * * * * *
91559 ACTACT ACTACT ACTACG ACTA-- ACTACT ACTACT ACTACG ACTAACT
1 ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACT-ACC
* * * * * * *
91606 ACTACT AATACC ACTACT ACTAACT ACTACC ACCACC ACCACC ACCACC
1 ACTACC ACTACC ACTACC ACT-ACC ACTACC ACTACC ACTACC ACTACC
* * * * * * *
91655 ACCACC ACCACC ACCACC ACCACC ACCACC ACTACT ACTACG ACTA--
1 ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC
* * * * * * * *
91701 ACTACT ACTACT ACTACT ACTACT ACTACT ACTACT ACTACT ACTACT
1 ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC
* * * * * * *
91749 ACTACT ACTACTA ACTACT ACAACC ACTACT ACTACC ACTACT ACCACC
1 ACTACC ACTAC-C ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC
* * ** * * * * * * *
91798 ACTACT ACTACG ACTAAAT ACTACT AATATC ACTGCT ACCACT ACTACC
1 ACTACC ACTACC ACT-ACC ACTACC ACTACC ACTACC ACTACC ACTACC
* * * * * *
91847 ACTACT ACTA-- ACTACC ACCACC ACCACC ACCACC ACCACC ACCACC
1 ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC
* *
91893 ACTACC ACTACC ACTACC ACTACC ACTACC ACCACT ACTACC ACTACC
1 ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC
* * * *
91941 ACTACC ACTACC ACCACT ACTACC ACTACC ACTACT ACTACC ACTACT
1 ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC
* * * * * * * *
91989 ACCACC ACTACT ACTACG ACTAACT ACTACT ACTACT ACTACT ACTACT
1 ACTACC ACTACC ACTACC ACT-ACC ACTACC ACTACC ACTACC ACTACC
* * * * * *
92038 ACTAACT ACTACC ACTACC ACCACC ACCACT ACTACC ACTACG ACTAACT
1 ACT-ACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACT-ACC
* * * * *
92088 ACTACT ACTACG ACTAACT ACTACC ACCACC ACT--- ACTACC ACTACT
1 ACTACC ACTACC ACT-ACC ACTACC ACTACC ACTACC ACTACC ACTACC
* * ** ** * * *
92134 ACCACT ACTACC ACTATG ACTAATT ACTACC ACTACT ACCACT ACTACC
1 ACTACC ACTACC ACTACC ACT-ACC ACTACC ACTACC ACTACC ACTACC
* * * * * *
92183 ACTACG ACTA-- ACTACC ACTACC ACCACT ACCACC ACCACC ACTACT
1 ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC
* * * * * * * * *
92229 ACTAACT ACTACT ACTACT ACTACT ACTACT ACTACTA ATTACT ACTACT
1 ACT-ACC ACTACC ACTACC ACTACC ACTACC ACTAC-C ACTACC ACTACC
* * * * * * * *
92279 ACTACT ACTACT ACTACT ACTACT ACTACT ACTACC ACCACT ACTACT
1 ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC
* * * * * * * *
92327 ACTACT ACTACT ACTACT ACTACT ACTACT ACTACT ACTACT ACTACT
1 ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC
* * * * * * * *
92375 ACTACT ACTACT ACTACT ACTACT ACTACT ACTACT ACTACT ACTACT
1 ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC
* * * * * * * *
92423 ACTACT ACTACT ACTACT ACTACT ACTACT ACTACT ACTACG ACTACT
1 ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC
* *
92471 ACTACT ACTACT ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC
1 ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC
92519 ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC
1 ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC
92567 ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC
1 ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC
92615 ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC
1 ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC
92663 ACTACC ACTACC -CTACC ACTACC ACTACC ACTACC ACTACC ACTACC
1 ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC
92710 ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC
1 ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC
92758 ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC
1 ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC
92806 ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC
1 ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC
92854 ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC
1 ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC
92902 ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTA-C
1 ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC ACTACC
92949 -CTACC ACTA-C -C-ACC ACTACC ACTACC ACTAC
1 ACTACC ACTACC ACTACC ACTACC ACTACC ACTAC
92980 GCTCTTATGA
Statistics
Matches: 1407, Mismatches: 118, Indels: 66
0.88 0.07 0.04
Matches are distributed among these distances:
3 4 0.00
4 25 0.02
5 10 0.01
6 1307 0.93
7 61 0.04
ACGTcount: A:0.34, C:0.43, G:0.01, T:0.22
Consensus pattern (6 bp):
ACTACC
Found at i:97067 original size:29 final size:30
Alignment explanation
Indices: 97020--97087 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
97010 CAAATTTTGG
** * *
97020 TTAGTGACCAAAATGTAAATTTTG-AAAGT
1 TTAGTGACCAAAACATAAAGTTGGAAAAGT
97049 TTAGTGACCAAAACATAAAGTTGGAAAAGT
1 TTAGTGACCAAAACATAAAGTTGGAAAAGT
*
97079 TTAGGGACC
1 TTAGTGACC
97088 TAAGTGGTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
29 20 0.61
30 13 0.39
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (30 bp):
TTAGTGACCAAAACATAAAGTTGGAAAAGT
Found at i:109226 original size:21 final size:22
Alignment explanation
Indices: 109202--109242 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
109192 ATTGATTGTT
109202 ATATATGAT-GTTATCATGAAC
1 ATATATGATAGTTATCATGAAC
* *
109223 ATATATTATATTTATCATGA
1 ATATATGATAGTTATCATGA
109243 GTGATATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (22 bp):
ATATATGATAGTTATCATGAAC
Found at i:119205 original size:21 final size:21
Alignment explanation
Indices: 119163--119206 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
119153 ACTCCGGGAG
* *
119163 CTAGTTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
119184 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
119205 CT
1 CT
119207 CCTGGCACCG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.39, G:0.16, T:0.36
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:120373 original size:65 final size:64
Alignment explanation
Indices: 120304--120462 Score: 178
Period size: 65 Copynumber: 2.5 Consensus size: 64
120294 GAATAAATTG
* *
120304 AACATCCAATGCATTTCATGCATCGATGCA-CATACTATGCATCGATGCACACAGAGTT-TTATG
1 AACATCAAATGCATTTCATGCATCGATGCACCA-ACCATGCATCGATGCACACAG-GTTATTATG
120367 AA
64 -A
* * * * * * * *
120369 AACATCGAATACATTTGATGAATCGATACACCAACCATGCATCGATGCACTCTGGTTATTTTGA
1 AACATCAAATGCATTTCATGCATCGATGCACCAACCATGCATCGATGCACACAGGTTATTATGA
*
120433 AACATCAAATGCACTTCATGCATCGATGCA
1 AACATCAAATGCATTTCATGCATCGATGCA
120463 TTCTTAGTGC
Statistics
Matches: 77, Mismatches: 15, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
64 28 0.36
65 47 0.61
66 2 0.03
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (64 bp):
AACATCAAATGCATTTCATGCATCGATGCACCAACCATGCATCGATGCACACAGGTTATTATGA
Found at i:121169 original size:20 final size:21
Alignment explanation
Indices: 121131--121179 Score: 82
Period size: 20 Copynumber: 2.4 Consensus size: 21
121121 AATTTTAATT
*
121131 GCCAATTCACCCCCCCTCTTG
1 GCCAATTCACCCCCACTCTTG
121152 GCCAATTCA-CCCCACTCTTG
1 GCCAATTCACCCCCACTCTTG
121172 GCCAATTC
1 GCCAATTC
121180 CATCGATCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 18 0.67
21 9 0.33
ACGTcount: A:0.18, C:0.47, G:0.10, T:0.24
Consensus pattern (21 bp):
GCCAATTCACCCCCACTCTTG
Found at i:125444 original size:40 final size:40
Alignment explanation
Indices: 125400--125479 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
125390 ACGGTGTACA
* * *
125400 AGGTGGGTAAAGCCCAACCTCAGCACTATGGTGCAGTATT
1 AGGTGAGTAAAGCCCAACCTCAGCACTACGGTGCAATATT
* * *
125440 AGGTGAGTAAATCTCGACCTCAGCACTACGGTGCAATATT
1 AGGTGAGTAAAGCCCAACCTCAGCACTACGGTGCAATATT
125480 TGACTCCTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.24
Consensus pattern (40 bp):
AGGTGAGTAAAGCCCAACCTCAGCACTACGGTGCAATATT
Found at i:131806 original size:20 final size:20
Alignment explanation
Indices: 131770--131808 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
131760 TCAAAATTAG
*
131770 TTTTCAAAATTTCATTTTGC
1 TTTTCAAAATTCCATTTTGC
131790 TTTTCAAAA-TCCAATTTTG
1 TTTTCAAAATTCC-ATTTTG
131809 GTTTCAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.28, C:0.15, G:0.05, T:0.51
Consensus pattern (20 bp):
TTTTCAAAATTCCATTTTGC
Found at i:132872 original size:20 final size:20
Alignment explanation
Indices: 132849--132894 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
132839 TGGTGCATTA
132849 ATGCACAACAGGATGCATCG
1 ATGCACAACAGGATGCATCG
*
132869 ATGCACAGCAGGATGCATCG
1 ATGCACAACAGGATGCATCG
132889 ATGCAC
1 ATGCAC
132895 TAAGTGCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.26, G:0.26, T:0.15
Consensus pattern (20 bp):
ATGCACAACAGGATGCATCG
Found at i:132967 original size:23 final size:20
Alignment explanation
Indices: 132914--133013 Score: 69
Period size: 21 Copynumber: 4.8 Consensus size: 20
132904 TTGAAATGGA
132914 GTGCATGGATGCACTACATG
1 GTGCATGGATGCACTACATG
*
132934 GTGCATCGATGCACTAGTGGCA-G
1 GTGCATGGATGCACTA----CATG
* **
132957 GTGCATGGATGCATTGTA-G
1 GTGCATGGATGCACTACATG
* *
132976 GTGTACATGGATGCACTGCAGGG
1 GTG--CATGGATGCACTACA-TG
132999 GTGCATGGATGCACT
1 GTGCATGGATGCACT
133014 TTGACACCCT
Statistics
Matches: 65, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
19 5 0.08
20 15 0.23
21 25 0.38
23 18 0.28
24 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.35, T:0.25
Consensus pattern (20 bp):
GTGCATGGATGCACTACATG
Found at i:132986 original size:21 final size:21
Alignment explanation
Indices: 132960--133013 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
132950 GTGGCAGGTG
* * *
132960 CATGGATGCATTGTAGGTGTA
1 CATGGATGCACTGCAGGGGTA
*
132981 CATGGATGCACTGCAGGGGTG
1 CATGGATGCACTGCAGGGGTA
133002 CATGGATGCACT
1 CATGGATGCACT
133014 TTGACACCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.22, C:0.17, G:0.35, T:0.26
Consensus pattern (21 bp):
CATGGATGCACTGCAGGGGTA
Found at i:133256 original size:21 final size:21
Alignment explanation
Indices: 133232--133271 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
133222 ATGTTTAATG
133232 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
* *
133253 AAAATGATATCAATTGTTA
1 AAAAAGATACCAATTGTTA
133272 CCAATTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTAAC
Found at i:134410 original size:20 final size:20
Alignment explanation
Indices: 134375--134412 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
134365 TCTAAATCCT
* *
134375 TTTCAAAATTTTATTTTGGC
1 TTTCAAAATCTAATTTTGGC
134395 TTTCAAAATCTAATTTTG
1 TTTCAAAATCTAATTTTG
134413 TTTACAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.53
Consensus pattern (20 bp):
TTTCAAAATCTAATTTTGGC
Found at i:135796 original size:43 final size:42
Alignment explanation
Indices: 135748--135847 Score: 123
Period size: 43 Copynumber: 2.4 Consensus size: 42
135738 TCGAAATGGA
* *
135748 GTGCATGGATGCACTACA-TGGTGCATCGATGCACTAGT-GGCAG
1 GTGCATGGATGCACTACAGGGGTGCATAGATGCACT-GTAGG--G
* *
135791 GTGCATGGATGCACTGCAGGGGTGTATAGATGCACTGTAGGG
1 GTGCATGGATGCACTACAGGGGTGCATAGATGCACTGTAGGG
135833 GTGCATGGATGCACT
1 GTGCATGGATGCACT
135848 TTGACACCCT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
42 16 0.31
43 19 0.37
44 16 0.31
ACGTcount: A:0.22, C:0.18, G:0.36, T:0.24
Consensus pattern (42 bp):
GTGCATGGATGCACTACAGGGGTGCATAGATGCACTGTAGGG
Found at i:135801 original size:23 final size:20
Alignment explanation
Indices: 135748--135847 Score: 67
Period size: 21 Copynumber: 4.8 Consensus size: 20
135738 TCGAAATGGA
135748 GTGCATGGATGCACTACATG
1 GTGCATGGATGCACTACATG
*
135768 GTGCATCGATGCACTAGTGGCA-G
1 GTGCATGGATGCACTA----CATG
* *
135791 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTACA-TG
* * ** *
135812 GTGTATAGATGCACTGTAGGG
1 GTGCATGGATGCACTACA-TG
135833 GTGCATGGATGCACT
1 GTGCATGGATGCACT
135848 TTGACACCCT
Statistics
Matches: 66, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
19 2 0.03
20 15 0.23
21 32 0.48
23 15 0.23
24 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.36, T:0.24
Consensus pattern (20 bp):
GTGCATGGATGCACTACATG
Found at i:135822 original size:21 final size:21
Alignment explanation
Indices: 135790--135847 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
135780 ACTAGTGGCA
*
135790 GGTGCATGGATGCACTGCAGG
1 GGTGCATAGATGCACTGCAGG
* *
135811 GGTGTATAGATGCACTGTAGG
1 GGTGCATAGATGCACTGCAGG
*
135832 GGTGCATGGATGCACT
1 GGTGCATAGATGCACT
135848 TTGACACCCT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.21, C:0.16, G:0.40, T:0.24
Consensus pattern (21 bp):
GGTGCATAGATGCACTGCAGG
Found at i:138295 original size:12 final size:12
Alignment explanation
Indices: 138274--138304 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
138264 ATTAGTTGTC
*
138274 TTTACAATGAAA
1 TTTACGATGAAA
138286 TTTACGATGAAA
1 TTTACGATGAAA
138298 TTTACGA
1 TTTACGA
138305 GTTCAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (12 bp):
TTTACGATGAAA
Found at i:140847 original size:2 final size:2
Alignment explanation
Indices: 140836--140873 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
140826 TTATTATTAT
*
140836 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
140874 TTGATTTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:141090 original size:31 final size:31
Alignment explanation
Indices: 141028--141102 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
141018 CCTATATAAT
141028 TAATAATA-ATATAACCATAAATATAACTAA
1 TAATAATATATATAACCATAAATATAACTAA
* * *
141058 TAGTAATATATATAACCATAACTA-ATAGTAA
1 TAATAATATATATAACCATAAATATA-ACTAA
141089 TAATAAT-TA-ATAAC
1 TAATAATATATATAAC
141103 TAACACATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
29 5 0.13
30 10 0.26
31 24 0.62
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.32
Consensus pattern (31 bp):
TAATAATATATATAACCATAAATATAACTAA
Found at i:142711 original size:24 final size:25
Alignment explanation
Indices: 142684--142731 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
142674 TATTATTTAT
*
142684 AATTTATATATATATAA-TTAATAA
1 AATTTATATATAAATAATTTAATAA
*
142708 AATTTGTATATAAATAATTTAATA
1 AATTTATATATAAATAATTTAATA
142732 TATATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (25 bp):
AATTTATATATAAATAATTTAATAA
Found at i:143311 original size:24 final size:23
Alignment explanation
Indices: 143255--143318 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 23
143245 TTTATGAATA
*
143255 TGTTCATTTAATGTTCACAAACG
1 TGTTTATTTAATGTTCACAAACG
*
143278 T-TTTCTTTTATATGTTCA-AGAACG
1 TGTTT-ATTTA-ATGTTCACA-AACG
*
143302 TGTTTATTTAGTGTTCA
1 TGTTTATTTAATGTTCA
143319 TGAATATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 16 0.48
25 3 0.09
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.48
Consensus pattern (23 bp):
TGTTTATTTAATGTTCACAAACG
Found at i:147397 original size:21 final size:21
Alignment explanation
Indices: 147373--147436 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
147363 GTGAATTGTC
147373 AAGTTGAATTATCATATCAAT
1 AAGTTGAATTATCATATCAAT
* * * *
147394 AAGTT-AATTGTTAAATCAGT
1 AAGTTGAATTATCATATCAAT
* *
147414 AAGCTGAAGTATCATATCAAT
1 AAGTTGAATTATCATATCAAT
147435 AA
1 AA
147437 TAATTTTTGC
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.34
Consensus pattern (21 bp):
AAGTTGAATTATCATATCAAT
Found at i:151537 original size:194 final size:192
Alignment explanation
Indices: 151200--151552 Score: 498
Period size: 194 Copynumber: 1.8 Consensus size: 192
151190 AATTTCCTGG
* * *
151200 ATAATGATATTTAGAAATCCAAAATTGACAGAACTTACCAAACAGTTATTAAATGCAAAGTTCCA
1 ATAATAATATTTAGAAATCCAAAATTGACAGAACTTACCAAACAGATAATAAATGCAAAGTTCCA
* * * *
151265 CCACATACAGGAATTAACCTGAGCCAACTAAGATCCACTTAAAAGAGAATGAGGATGAGACTAAT
66 CCACATACAGGAATTAACCTGAACCAACCAACATCCACTTAAAAGAGAATGAGGAAGAGACTAAT
*
151330 CTATAAAGGCCAATATTACGTTCAACTCACAGAATATGTTTGTAAATGAAAATCCCTGGATA
131 CTATAAAGGCCAATATTACATTCAACTCACAGAATATGTTTGTAAATGAAAATCCCTGGATA
*
151392 ATAATAATATTTAGAAATCCAAAATTGACAGAACTTCACCAAACAGATAATAAATGCCAAGTTTC
1 ATAATAATATTTAGAAATCCAAAATTGACAGAACTT-ACCAAACAGATAATAAATGCAAAG-TTC
* * * *
151457 TACCACAT-CAAGGCATT-ATCTAGAACCAACCAACATCCACTTGAAAGAGAATGAGGAA-AGGA
64 CACCACATAC-AGGAATTAACCT-GAACCAACCAACATCCACTTAAAAGAGAATGAGGAAGA-GA
*
151519 CTAATCT-TGAATGGCCAATATTACATTCAACTCA
126 CTAATCTAT-AAAGGCCAATATTACATTCAACTCA
151553 GTTTTTTTTT
Statistics
Matches: 141, Mismatches: 14, Indels: 10
0.85 0.08 0.06
Matches are distributed among these distances:
192 35 0.25
193 27 0.19
194 79 0.56
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (192 bp):
ATAATAATATTTAGAAATCCAAAATTGACAGAACTTACCAAACAGATAATAAATGCAAAGTTCCA
CCACATACAGGAATTAACCTGAACCAACCAACATCCACTTAAAAGAGAATGAGGAAGAGACTAAT
CTATAAAGGCCAATATTACATTCAACTCACAGAATATGTTTGTAAATGAAAATCCCTGGATA
Found at i:158928 original size:10 final size:10
Alignment explanation
Indices: 158913--158999 Score: 75
Period size: 10 Copynumber: 8.0 Consensus size: 10
158903 GAGGCGAAAA
158913 GTTCGTTTAT
1 GTTCGTTTAT
158923 GTTCGTTTATTGT
1 GTTCGTTTA---T
158936 GTTCGTTTAT
1 GTTCGTTTAT
*
158946 GTTCATTTATGTT
1 GTTCGTTTA---T
*
158959 CGTTCGTTTGT
1 -GTTCGTTTAT
*
158970 GTTCGTTTAC
1 GTTCGTTTAT
158980 GTTCGTTTAT
1 GTTCGTTTAT
*
158990 GTTCATTTAT
1 GTTCGTTTAT
159000 TATTTAAATG
Statistics
Matches: 63, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
10 44 0.70
11 1 0.02
13 11 0.17
14 7 0.11
ACGTcount: A:0.10, C:0.11, G:0.20, T:0.59
Consensus pattern (10 bp):
GTTCGTTTAT
Found at i:158972 original size:24 final size:24
Alignment explanation
Indices: 158913--158986 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
158903 GAGGCGAAAA
158913 GTTCGTTTATGTTCGTTTAT-TGT-
1 GTTCGTTTATGTTCGTTTATGT-TC
*
158936 GTTCGTTTATGTTCATTTATGTTC
1 GTTCGTTTATGTTCGTTTATGTTC
* *
158960 GTTCGTTTGTGTTCGTTTACGTTC
1 GTTCGTTTATGTTCGTTTATGTTC
158984 GTT
1 GTT
158987 TATGTTCATT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
23 20 0.44
24 25 0.56
ACGTcount: A:0.08, C:0.12, G:0.22, T:0.58
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTTATGTTC
Found at i:158975 original size:34 final size:33
Alignment explanation
Indices: 158913--158993 Score: 117
Period size: 34 Copynumber: 2.4 Consensus size: 33
158903 GAGGCGAAAA
* *
158913 GTTCGTTTATGTTCGTTTATTGTGTTCGTTTAT
1 GTTCGTTTATGTTCGTTGATTGTGTTCGTTTAC
* *
158946 GTTCATTTATGTTCGTTCGTTTGTGTTCGTTTAC
1 GTTCGTTTATGTTCGTT-GATTGTGTTCGTTTAC
158980 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
158994 ATTTATTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 16 0.38
34 26 0.62
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.58
Consensus pattern (33 bp):
GTTCGTTTATGTTCGTTGATTGTGTTCGTTTAC
Found at i:159685 original size:56 final size:56
Alignment explanation
Indices: 159624--159731 Score: 182
Period size: 56 Copynumber: 1.9 Consensus size: 56
159614 CAGTTTAGGA
159624 TTAAAAATAATATAAAAAATT-ATCATATTTAAAATGGAAGTCTAAGGTTAAATTTT
1 TTAAAAATAATATAAAAAATTAAT-ATATTTAAAATGGAAGTCTAAGGTTAAATTTT
* *
159680 TTAAAAATAATATAAAAAATTAATATATTTAAAATGGCAGTTTAAGGTTAAA
1 TTAAAAATAATATAAAAAATTAATATATTTAAAATGGAAGTCTAAGGTTAAA
159732 AATAATATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
56 47 0.96
57 2 0.04
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.36
Consensus pattern (56 bp):
TTAAAAATAATATAAAAAATTAATATATTTAAAATGGAAGTCTAAGGTTAAATTTT
Found at i:162952 original size:14 final size:14
Alignment explanation
Indices: 162933--162973 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
162923 AATGAACACG
162933 AACGAACAAATATA
1 AACGAACAAATATA
* *
162947 AACGAACGAACATA
1 AACGAACAAATATA
162961 AACGAACACAATA
1 AACGAACA-AATA
162974 AATGAACATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
14 19 0.86
15 3 0.14
ACGTcount: A:0.61, C:0.20, G:0.10, T:0.10
Consensus pattern (14 bp):
AACGAACAAATATA
Found at i:162995 original size:13 final size:13
Alignment explanation
Indices: 162974--162999 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
162964 GAACACAATA
162974 AATGAACATAAAC
1 AATGAACATAAAC
162987 AATGAACATAAAC
1 AATGAACATAAAC
163000 GAACAATACA
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:0.62, C:0.15, G:0.08, T:0.15
Consensus pattern (13 bp):
AATGAACATAAAC
Found at i:163293 original size:24 final size:26
Alignment explanation
Indices: 163264--163315 Score: 81
Period size: 24 Copynumber: 2.1 Consensus size: 26
163254 TGCCTCTGTT
*
163264 CGAACATAAATGAACATA-AAT-GAA
1 CGAACATAAACGAACATATAATCGAA
163288 CGAACATAAACGAACATATAATCGAA
1 CGAACATAAACGAACATATAATCGAA
163314 CG
1 CG
163316 TTCACGAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 17 0.68
25 3 0.12
26 5 0.20
ACGTcount: A:0.54, C:0.17, G:0.13, T:0.15
Consensus pattern (26 bp):
CGAACATAAACGAACATATAATCGAA
Found at i:165263 original size:16 final size:17
Alignment explanation
Indices: 165242--165274 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
165232 AGAAAATAAA
165242 TAAAAAC-TTAGAAAAG
1 TAAAAACATTAGAAAAG
*
165258 TAAAAACATTATAAAAG
1 TAAAAACATTAGAAAAG
165275 AAGAAAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.64, C:0.06, G:0.09, T:0.21
Consensus pattern (17 bp):
TAAAAACATTAGAAAAG
Found at i:165731 original size:22 final size:23
Alignment explanation
Indices: 165671--165731 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 23
165661 TTAAAATAAT
165671 TAATCAATGAGTAA-TTATCAACA
1 TAATCAATGA-TAATTTATCAACA
*
165694 TAAT-AATGCATGATTTAATC-AC-
1 TAATCAATG-ATAATTT-ATCAACA
165716 TAATCAATGATAATTT
1 TAATCAATGATAATTT
165732 TTATCCTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
22 16 0.50
23 13 0.41
24 3 0.09
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.36
Consensus pattern (23 bp):
TAATCAATGATAATTTATCAACA
Found at i:168714 original size:182 final size:182
Alignment explanation
Indices: 168443--168895 Score: 696
Period size: 182 Copynumber: 2.5 Consensus size: 182
168433 ATCCATATCA
* * ** *
168443 ATATAACAGGTAAAAATATCGATAAAACCGGTCA-CGAAAA-GACAATACCGGTAAA-TCCTTAT
1 ATATAACAGGTAAAAATAT-GATAAAACCGGT-ATC-AAAATGATAAAACCGGTAAAGAGC-TAC
*
168505 CGGATATATTGAACGTGTCGATACTTTAATATAAGGATCGACACTTTGTGAATTTAAAAGAGAAG
62 CGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTTGTGAATTTAAAAGAGAAG
* *
168570 CATTTTTAACGCCTATAAAGTGTCGATACTTTATAAAAATGTATCGATCCACAACG
127 CAGTTTTAACGCCTATAAAGTGTCGATACTTTATAAAAATATATCGATCCACAACG
*
168626 ATATAACAGGTAAAAATATGACAAAACCGGTATCAAAATGATAAAACCGGTAAAGAGCTACCGGA
1 ATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATAAAACCGGTAAAGAGCTACCGGA
* * *
168691 TATATTTAAAGTGTCGGTACTTTAATATAAGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGT
66 TATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTTGTGAATTTAAAAGAGAAGCAGT
*
168756 TTTAGCGCCTATAAAGTGTCGATACTTTATAAAAATATATCGATCCACAACG
131 TTTAACGCCTATAAAGTGTCGATACTTTATAAAAATATATCGATCCACAACG
* * * *
168808 ATATAATATGTAAAAATATGATAAAACCGGTATCAAAATGATAAAACTGGTAAAGCGCTACCGGA
1 ATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATAAAACCGGTAAAGAGCTACCGGA
168873 TATATTGAAAGTGTCGATACTTT
66 TATATTGAAAGTGTCGATACTTT
168896 CATAAGTACG
Statistics
Matches: 247, Mismatches: 20, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
181 5 0.02
182 222 0.90
183 20 0.08
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (182 bp):
ATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATAAAACCGGTAAAGAGCTACCGGA
TATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTTGTGAATTTAAAAGAGAAGCAGT
TTTAACGCCTATAAAGTGTCGATACTTTATAAAAATATATCGATCCACAACG
Found at i:171124 original size:21 final size:21
Alignment explanation
Indices: 171100--171143 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
171090 AAGACAATCA
171100 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
171121 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
171142 AG
1 AG
171144 GCATAAGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.11, G:0.32, T:0.16
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:171214 original size:33 final size:33
Alignment explanation
Indices: 171177--171242 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
171167 AAATAGATGG
*
171177 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
*
171210 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
171243 TCTTAAGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:172448 original size:4 final size:4
Alignment explanation
Indices: 172439--172465 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
172429 AGAGATTGGA
172439 ATGT ATGT ATGT ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATG
172466 AAAGGACATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:173062 original size:19 final size:19
Alignment explanation
Indices: 173038--173086 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
173028 AATGTAGGGT
*
173038 TAATTTTTTATAAGATTTA
1 TAATTTTGTATAAGATTTA
173057 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
173076 TAATTTTGTAT
1 TAATTTTGTAT
173087 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:173850 original size:180 final size:179
Alignment explanation
Indices: 173547--173915 Score: 614
Period size: 180 Copynumber: 2.1 Consensus size: 179
173537 ACATTTTCAA
* *
173547 AAAGTGTCGAACCCAAAACATCGAAACCCATTATTATAATATAATAGGTAAATTTACAATGTAAC
1 AAAGTGTCGATCCCAAAACATCGAAACCCATAATTATAATATAATAGGTAAATTTACAATGTAAC
173612 CGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTAATTT
66 CGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTAATTT
*
173677 TGTATCGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAATGCAT
131 TGTATCGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCAT
* * * *
173726 AAAGTGTCGATCCCAAAAATATCGAAACCCATAATTATAATGTAATAGGTATATTTTCAATGTAA
1 AAAGTGTCGATCCC-AAAACATCGAAACCCATAATTATAATATAATAGGTAAATTTACAATGTAA
* * *
173791 CCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAATATGTATCGATACTTTTTTAATT
65 CCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTAATT
* *
173856 TTGTGTCTATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCAT
130 TTGTATCGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCAT
173906 AAA-TGTCGAT
1 AAAGTGTCGAT
173916 ACATTTTCAA
Statistics
Matches: 177, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
179 20 0.11
180 157 0.89
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.32
Consensus pattern (179 bp):
AAAGTGTCGATCCCAAAACATCGAAACCCATAATTATAATATAATAGGTAAATTTACAATGTAAC
CGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTAATTT
TGTATCGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCAT
Found at i:174778 original size:13 final size:13
Alignment explanation
Indices: 174752--174784 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
174742 AGCGCGGTCT
174752 TTCTCAA-AGCTC
1 TTCTCAACAGCTC
*
174764 TTCTCAACAGTTC
1 TTCTCAACAGCTC
174777 TTCTCAAC
1 TTCTCAAC
174785 CACAACCTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.24, C:0.33, G:0.06, T:0.36
Consensus pattern (13 bp):
TTCTCAACAGCTC
Found at i:177669 original size:249 final size:251
Alignment explanation
Indices: 177287--177738 Score: 709
Period size: 249 Copynumber: 1.8 Consensus size: 251
177277 TAACAACCCA
* *
177287 AAAAACATTGAAACCCATAATTATAATGTAATGGGTAATTTTTCAATATAACCGGTATAAATATA
1 AAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTTCAATATAACCGGTATAAATATA
* *
177352 CCGGTTTTATGAAAAATATGTCTACAACATTTATCAACACTTATTAGTATTGTGTCGATAATTTT
66 CCGGTTTTATGAAAAATATGTCTACAACATGTATCAACACTTATTAATATTGTGTCGATAATTTT
* *
177417 TGTCCAGAATGGATGCCAAAAAGGGTGAAC-C-TACAAGTGTCGATACATTTTCATAGAGTGTCG
131 TGTCCAGAATGGATGCCAAAAAGGGTGAACGCATA-AAGTGTCGATACATTTTCAAAAAGTGTCG
177480 AT-CCAAAAGGGTTGCACGTATAAAGTGTCGATACATTTATTAAAAGTGTCGATCCC
195 ATCCCAAAAGGGTTGCACGTATAAAGTGTCGATACATTTATTAAAAGTGTCGATCCC
* *
177536 AAAAATATCGAAACCCATAATTATAATGTAATAGGTAATTTTGT-AATATAACCGGTATACATAT
1 AAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTT-TCAATATAACCGGTATAAATAT
* * * *
177600 ACCGGTTTTATGAGAGAATA-GATCTATAATATGTATCGACACTTATTAATATTGTGTCGATAA-
65 ACCGGTTTTATGA-AAAATATG-TCTACAACATGTATCAACACTTATTAATATTGTGTCGATAAT
*
177663 TTTTGTCCATAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGT
128 TTTTGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGT
177728 CGATCCCAAAA
193 CGATCCCAAAA
177739 ACATCGAAAC
Statistics
Matches: 184, Mismatches: 13, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
249 104 0.57
250 72 0.39
251 8 0.04
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (251 bp):
AAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTTCAATATAACCGGTATAAATATA
CCGGTTTTATGAAAAATATGTCTACAACATGTATCAACACTTATTAATATTGTGTCGATAATTTT
TGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCGA
TCCCAAAAGGGTTGCACGTATAAAGTGTCGATACATTTATTAAAAGTGTCGATCCC
Found at i:180570 original size:200 final size:197
Alignment explanation
Indices: 180172--180878 Score: 698
Period size: 200 Copynumber: 3.5 Consensus size: 197
180162 CTAAATATGC
* * * *
180172 GTCGATACATTT-TATACAAGTATC-AACCCAAAAAACATCAAAACCAATAATTATAATGTAATA
1 GTCGATACATTTAT-TAAAAGTATCGATCCC-AAAAACATCGAAACCGATAATTATAATGTAATA
* * * * *
180235 GGTAAATTAACAATGTAACC-AGTATAAATATACC-GGTTAATTAGAAAACAGGTCAACATAATG
64 GGTAAATTTACAATGTAACCGA-TATAAATATACCAGTTTTATGAGAAAATAGGTCAACATAATG
** * * * *
180298 TATTGACACTTGTGTAATTTGTGTCGATACTTATTGTCCAGGATGAATGCTC-AAACGAGGTGC-
128 TATCAACA-TT-TGTAATTTGTGTCGATACTT-TTGTCCAGAATAAATAC-CAAAAAG-GGTGCA
180361 ACGCATAAAGT
188 AC-CATAAAGT
* *
180372 GTCGATACATTTATTAAAAGTATCGATCTCAAAAACATCGAAACCGATAATTATAATGTATTAGG
1 GTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGG
* * *
180437 TAAATTTACAATGTAACCGATATAAATATACCAGTTTTATGATAAAATAGGTCAGCATAAAGTAT
66 TAAATTTACAATGTAACCGATATAAATATACCAGTTTTATGAGAAAATAGGTCAACATAATGTAT
180502 CAACATTTGATAAATTTGTGTCGATACTTTTGGTCCAGAATAAATACCAAAAAGGGTGCAACCAT
131 CAACATTTG-T-AATTTGTGTCGATACTTTT-GTCCAGAATAAATACCAAAAAGGGTGCAACCAT
180567 AAAGT
193 AAAGT
* ** * *
180572 GTCGATACATTTATAAAAAGTATCGATCCCGGAAACATCGAAACCCATAAGTATAATGTAATAGG
1 GTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGG
* * * * *
180637 TAAATTTTCAATGTAACCGATATAAATATACCAATTTTATGAGAGAATATGT-ATAAATAATGTA
66 TAAATTTACAATGTAACCGATATAAATATACCAGTTTTATGAGAAAATAGGTCA-ACATAATGTA
* * **
180701 TCGACACA-TTGTTAGTTTGTGTCGATACTTTTTTCCAGAATGAAATATGAATGCCCAACTA-GG
130 TC-A-ACATTTG-TAATTTGTGTCGATACTTTTGTCCAGAAT--AA-AT--A---CCAAAAAGGG
*
180764 TGCAAGCATAAAGT
184 TGCAACCATAAAGT
* ** * *
180778 GTCGATACATTTA--AAATTGTATCGATCTAAAAAACATCGTAACCGATAATAATAATGTAATAG
1 GTCGATACATTTATTAAA-AGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAG
* * * * * *
180841 GTAAATGTGCAATGTTACTGGTATAAATATACCGGTTT
65 GTAAATTTACAATGTAACCGATATAAATATACCAGTTT
180879 ACTTCGAAAA
Statistics
Matches: 429, Mismatches: 57, Indels: 37
0.82 0.11 0.07
Matches are distributed among these distances:
199 11 0.03
200 233 0.54
201 75 0.17
202 5 0.01
204 4 0.01
205 68 0.16
206 28 0.07
207 5 0.01
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.30
Consensus pattern (197 bp):
GTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGG
TAAATTTACAATGTAACCGATATAAATATACCAGTTTTATGAGAAAATAGGTCAACATAATGTAT
CAACATTTGTAATTTGTGTCGATACTTTTGTCCAGAATAAATACCAAAAAGGGTGCAACCATAAA
GT
Found at i:180943 original size:23 final size:23
Alignment explanation
Indices: 180887--180943 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
180877 TTACTTCGAA
*
180887 AATATGTTAATATAAGCGCTACAT
1 AATATGTT-ATATAAGAGCTACAT
* ** *
180911 ATTACATTATATAAGAGCTACCT
1 AATATGTTATATAAGAGCTACAT
180934 AATATGTTAT
1 AATATGTTAT
180944 TGTACTTGAT
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (23 bp):
AATATGTTATATAAGAGCTACAT
Found at i:181030 original size:23 final size:23
Alignment explanation
Indices: 180980--181024 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
180970 TGCCTATTTT
*
180980 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
* *
181003 ATTATATAAGTGCTACTTAATA
1 ATTATATAAGCGCTACCTAATA
181025 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:181952 original size:157 final size:157
Alignment explanation
Indices: 181624--182006 Score: 445
Period size: 157 Copynumber: 2.5 Consensus size: 157
181614 TTCCTCCTTC
*
181624 ATTTTAAGTACA--TTTTTAATAAATTTGAACCACATGCTCCTAAACCATAGTAGAATACATGTG
1 ATTTTAAGTACATTTTTTTACTAAATTTGAACCACATGCTCCTAAACCATAGTAGAATACATGTG
* *
181687 TACTTTCAATCTCTTTTTGATAACAAATTTTTTCTTTTTCAATTCAGTCCTTCAATTTTTCATAA
66 TACTTTCAATCTCTTTTTGATAACAAATTTTTTATTTTTCAATTCAGTCATTCAATTTTTCATAA
** ** *
181752 TCTTTTTATTTTTTCAATTCATTATTT
131 TCTCCTTATTCCTTCAATTCATGATTT
* * *
181779 A-TTTAAGTCCATTTTTTTTACTAAATTTGAGCCACATGCTCCTAAACTATAGTAGAATACATGT
1 ATTTTAAGTACA-TTTTTTTACTAAATTTGAACCACATGCTCCTAAACCATAGTAGAATACATGT
*** * * *
181843 GTACTTTCAACTCCTCTTTTTGATAA-TTTTTTTTTATTTTTGAATTTAGTCATTCAATTTTTTA
65 GTACTTTCAA-T-CTCTTTTTGATAACAAATTTTTTATTTTTCAATTCAGTCATTCAATTTTTCA
* * **
181907 TAATCTCCTTGTTCCTTCACTTTGTGATTT
128 TAATCTCCTTATTCCTTCAATTCATGATTT
* * * * * *
181937 ATTTTAAGT-CATTTTTTTACCAAATTTGAATCACATGCTCATATACCAAAAT-GAATACATGTG
1 ATTTTAAGTACATTTTTTTACTAAATTTGAACCACATGCTCCTAAACCATAGTAGAATACATGTG
182000 TAACTTT
66 T-ACTTT
182007 GATTGTTATT
Statistics
Matches: 192, Mismatches: 29, Indels: 12
0.82 0.12 0.05
Matches are distributed among these distances:
154 9 0.05
155 1 0.01
156 12 0.06
157 95 0.49
158 55 0.29
159 20 0.10
ACGTcount: A:0.29, C:0.16, G:0.08, T:0.48
Consensus pattern (157 bp):
ATTTTAAGTACATTTTTTTACTAAATTTGAACCACATGCTCCTAAACCATAGTAGAATACATGTG
TACTTTCAATCTCTTTTTGATAACAAATTTTTTATTTTTCAATTCAGTCATTCAATTTTTCATAA
TCTCCTTATTCCTTCAATTCATGATTT
Found at i:193310 original size:31 final size:31
Alignment explanation
Indices: 193272--193367 Score: 126
Period size: 31 Copynumber: 3.2 Consensus size: 31
193262 ATCCGAGAAA
*
193272 AACATGTGCTACAGAGTCTAATTCATGGACC
1 AACATGTGCTACAGAGTCTAATTCATAGACC
**
193303 AACATGTGCTACAGAGTCTAAATTCA-AGAAA
1 AACATGTGCTACAGAGTCT-AATTCATAGACC
*
193334 AACATGTGCTACAGAG--TAATTCATCGACC
1 AACATGTGCTACAGAGTCTAATTCATAGACC
193363 AACAT
1 AACAT
193368 TGTTGATTGA
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
28 6 0.11
29 8 0.14
31 37 0.65
32 6 0.11
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.24
Consensus pattern (31 bp):
AACATGTGCTACAGAGTCTAATTCATAGACC
Found at i:195346 original size:14 final size:14
Alignment explanation
Indices: 195327--195356 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
195317 TTTAGATTTT
*
195327 TTAAAATTACATTA
1 TTAAAAATACATTA
195341 TTAAAAATACATTA
1 TTAAAAATACATTA
195355 TT
1 TT
195357 GATAAATATA
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:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:195455 original size:21 final size:21
Alignment explanation
Indices: 195431--195470 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
195421 ATGTGATATG
*
195431 ATTTATGGTTTAGGGTTTAGA
1 ATTTATGATTTAGGGTTTAGA
195452 ATTTATGATTTAGGGTTTA
1 ATTTATGATTTAGGGTTTA
195471 AGGTTTTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (21 bp):
ATTTATGATTTAGGGTTTAGA
Found at i:197473 original size:12 final size:12
Alignment explanation
Indices: 197458--197492 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
197448 TAGGTTTAAA
197458 TTCGAGTTTGAG
1 TTCGAGTTTGAG
197470 TTCGAGTTTGAG
1 TTCGAGTTTGAG
*
197482 TTCGAGCTTGA
1 TTCGAGTTTGA
197493 ATCGAGCTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.17, C:0.11, G:0.31, T:0.40
Consensus pattern (12 bp):
TTCGAGTTTGAG
Found at i:197499 original size:11 final size:11
Alignment explanation
Indices: 197483--197509 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
197473 GAGTTTGAGT
197483 TCGAGCTTGAA
1 TCGAGCTTGAA
197494 TCGAGCTTGAA
1 TCGAGCTTGAA
197505 TCGAG
1 TCGAG
197510 ATCGAGTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:201582 original size:38 final size:38
Alignment explanation
Indices: 201540--201785 Score: 367
Period size: 38 Copynumber: 6.5 Consensus size: 38
201530 TTCAAAACCA
* *
201540 TATATAATATATTTCCAAAATATTTT-AAAACTATATAT
1 TATAT-ATATATTTTCAAAATGTTTTAAAAACTATATAT
*
201578 TATATATATTTTTTCAAAATGTTTTAAAAACTATATAT
1 TATATATATATTTTCAAAATGTTTTAAAAACTATATAT
*
201616 TATATATATTTTTTCAAAATGTTTTAAAAACTCA-ATA-
1 TATATATATATTTTCAAAATGTTTTAAAAACT-ATATAT
*
201653 T-TATATATATTTTCAAAATGTTTTAAAAATTATATAT
1 TATATATATATTTTCAAAATGTTTTAAAAACTATATAT
*
201690 TATATATATATGTTCAAAATGTTTTAAAAACTATATTAT
1 TATATATATATTTTCAAAATGTTTTAAAAACTATA-TAT
201729 ATATATATATATTTTCAAAATGTTTTAAAAACTATATAT
1 -TATATATATATTTTCAAAATGTTTTAAAAACTATATAT
201768 TATATATATA-TTTCAAAA
1 TATATATATATTTTCAAAA
201786 ATCATTTGCA
Statistics
Matches: 193, Mismatches: 8, Indels: 15
0.89 0.04 0.07
Matches are distributed among these distances:
35 1 0.01
36 31 0.16
37 27 0.14
38 93 0.48
39 7 0.04
40 34 0.18
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (38 bp):
TATATATATATTTTCAAAATGTTTTAAAAACTATATAT
Found at i:202767 original size:86 final size:86
Alignment explanation
Indices: 202512--203270 Score: 929
Period size: 86 Copynumber: 8.9 Consensus size: 86
202502 GTAATCTAAA
* * * * * *
202512 ATGCCCTTGAGCTTAATAG-AATCAAACTCGAAAGT-ATTTGTTGACAGATAGCCCTTCTCGCCT
1 ATGCCTTTGAGCTGAAT-GTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCT
*
202575 TGAGCTATGCTATAAATTTGAT
65 TGAGCTATGCTGTAAATTTGAT
* * * * * * * * *
202597 ATACCTTTGAGGTGAACGTAATCGAACTCTAAGGTC-TTTGCTAATAGATAACTCTTCTTGCCTT
1 ATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTT
* * *
202661 AAGTTATGCTGTAAGTTTGAT
66 GAGCTATGCTGTAAATTTGAT
* *
202682 ACT-CCTTTTAGATGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCT
1 A-TGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCT
202746 TGAGCTATGCTGTAAATTTGAT
65 TGAGCTATGCTGTAAATTTGAT
* * *
202768 GTGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCACCTT
1 ATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTT
*
202833 AAGCTATGCTGTAAATTTGAT
66 GAGCTATGCTGTAAATTTGAT
* * * * *
202854 ATTCCTTTAAGCTGAATGTAATCGAATTCGAAGGTC-TTTGTTGAAAGATAGCCCTTCTCGCCTT
1 ATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTT
*
202918 GAGCTATCCTGTAAATTTGAT
66 GAGCTATGCTGTAAATTTGAT
* *
202939 ATGCCTTTGAGCTGAATGTAATAGAACTCAAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTT
1 ATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTT
*
203004 GGGCTATGCTGTAAATTTGAT
66 GAGCTATGCTGTAAATTTGAT
* * * *
203025 GTGCCTTTGAGCTTAATGTAATCGAACTCGAAGGTC-TTTGCTGACAGATAACCCTTCTCACCTT
1 ATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTT
* ** * *
203089 GAGTTATATTGTAAGTTTAAT
66 GAGCTATGCTGTAAATTTGAT
* * * * *
203110 ATGCCTTTGAACTGAATGTAATTGAACTCGAAGGTCTTTTGGTGACATATAACCCTTCTCACCTT
1 ATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTT
** *
203175 GAGCTATATTGTAAATTTAAT
66 GAGCTATGCTGTAAATTTGAT
* * * * * *
203196 ATTCCTTTGAGCTGAATGTAATCGAACTTGAAGGT-ATTGGTTGATAGATAACCCTTATCGCCTT
1 ATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTT
*
203260 GAGTTATGCTG
66 GAGCTATGCTG
203271 CCAATAATTC
Statistics
Matches: 580, Mismatches: 87, Indels: 14
0.85 0.13 0.02
Matches are distributed among these distances:
84 1 0.00
85 274 0.47
86 305 0.53
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.36
Consensus pattern (86 bp):
ATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTT
GAGCTATGCTGTAAATTTGAT
Found at i:202896 original size:171 final size:171
Alignment explanation
Indices: 202518--203270 Score: 961
Period size: 171 Copynumber: 4.4 Consensus size: 171
202508 TAAAATGCCC
* * * * *
202518 TTGAGCTTAATAG-AATCAAACTCGAAAGTATTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTA
1 TTGAGCTGAAT-GTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTA
* * * * * * * *
202582 TGCTATAAATTTGATATACCTTTGAGGTGAACGTAATCGAACTCTAAGGTC-TTTGCTAATAGAT
65 TGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGAT
* ** * * *
202646 AACTCTTCTTGCCTTAAGTTATGCTGTAAGTTTGATACTCCT
130 AACCCTTCTCACCTTAAGCTATGCTGTAAATTTGATATTCCT
* *
202688 TTTAGATGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTA
1 TTGAGCTGAATGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTA
*
202753 TGCTGTAAATTTGATGTGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGAT
65 TGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGAT
*
202818 AGCCCTTCTCACCTTAAGCTATGCTGTAAATTTGATATTCCT
130 AACCCTTCTCACCTTAAGCTATGCTGTAAATTTGATATTCCT
* * * *
202860 TTAAGCTGAATGTAATCGAATTCGAAGGTCTTTGTTGAAAGATAGCCCTTCTCGCCTTGAGCTAT
1 TTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTAT
* * *
202925 CCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATAGAACTCAAAGGTCTTTTGTTGACAGATA
66 GCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATA
* ** * *
202990 ACCCTTCTCGCCTTGGGCTATGCTGTAAATTTGATGTGCCT
131 ACCCTTCTCACCTTAAGCTATGCTGTAAATTTGATATTCCT
* * * *
203031 TTGAGCTTAATGTAATCGAACTCGAAGGTCTTTGCTGACAGATAACCCTTCTCACCTTGAGTTAT
1 TTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTAT
** * * * * * *
203096 ATTGTAAGTTTAATATGCCTTTGAACTGAATGTAATTGAACTCGAAGGTCTTTTGGTGACATATA
66 GCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATA
* ** *
203161 ACCCTTCTCACCTTGAGCTATATTGTAAATTTAATATTCCT
131 ACCCTTCTCACCTTAAGCTATGCTGTAAATTTGATATTCCT
* * * * * *
203202 TTGAGCTGAATGTAATCGAACTTGAAGGTATTGGTTGATAGATAACCCTTATCGCCTTGAGTTAT
1 TTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTAT
203267 GCTG
66 GCTG
203271 CCAATAATTC
Statistics
Matches: 508, Mismatches: 72, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
169 1 0.00
170 22 0.04
171 413 0.81
172 72 0.14
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (171 bp):
TTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTAT
GCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATA
ACCCTTCTCACCTTAAGCTATGCTGTAAATTTGATATTCCT
Found at i:203004 original size:257 final size:255
Alignment explanation
Indices: 202513--203270 Score: 975
Period size: 257 Copynumber: 3.0 Consensus size: 255
202503 TAATCTAAAA
* * * * *
202513 TGCCCTTGAGCTTAATAG-AATCAAACTCGAAAGTATTTGTTGACAGATAGCCCTTCTCGCCTTG
1 TGCCTTTGAGCTTAAT-GTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCACCTTG
* * * * *
202577 AGCTATGCTATAAATTTGATATACCTTTGAGGTGAACGTAATCGAACTCTAAGGTCTTTGCT-AA
65 AGCTATGCTGTAAATTTGATATACCTTTAAGCTGAATGTAATCGAACTCGAAGGTCTTTGCTGAA
* * * * * * * *
202641 TAGATAACTCTTCTTGCCTTAAGTTATGCTGTAAGTTTGATACTCCTTTTAGATGAATGTAATCG
130 -AGATAACCCTTCTCGCCTTGAGCTATACTGTAAATTTGATA-TCCTTTGAGCTGAATGTAATCG
202706 AACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATG
193 AACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATG
* *
202769 TGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCACCTTA
1 TGCCTTTGAGCTTAATGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAGCCCTTCTCACCTTG
* * *
202834 AGCTATGCTGTAAATTTGATATTCCTTTAAGCTGAATGTAATCGAATTCGAAGGTCTTTGTTGAA
65 AGCTATGCTGTAAATTTGATATACCTTTAAGCTGAATGTAATCGAACTCGAAGGTCTTTGCTGAA
* * *
202899 AGATAGCCCTTCTCGCCTTGAGCTATCCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATAGA
130 AGATAACCCTTCTCGCCTTGAGCTATACTGTAAATTTGATAT-CCTTTGAGCTGAATGTAATCGA
* *
202964 ACTCAAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGGGCTATGCTGTAAATTTGATG
194 ACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATG
* *
203026 TGCCTTTGAGCTTAATGTAATCGAACTCGAAGGTCTTTGCTGACAGATAACCCTTCTCACCTTGA
1 TGCCTTTGAGCTTAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCACCTTGA
* ** * * * * *
203091 GTTATATTGTAAGTTTAATATGCCTTTGAA-CTGAATGTAATTGAACTCGAAGGTCTTTTGGTGA
66 GCTATGCTGTAAATTTGATATACCTTT-AAGCTGAATGTAATCGAACTCGAAGGTC-TTTGCTGA
* * * * *
203155 CATATAACCCTTCTCACCTTGAGCTATATTGTAAATTTAATATTCCTTTGAGCTGAATGTAATCG
129 AAGATAACCCTTCTCGCCTTGAGCTATACTGTAAATTTGATA-TCCTTTGAGCTGAATGTAATCG
* * * * * *
203220 AACTTGAAGGT-ATTGGTTGATAGATAACCCTTATCGCCTTGAGTTATGCTG
193 AACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTG
203271 CCAATAATTC
Statistics
Matches: 439, Mismatches: 56, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
255 1 0.00
256 134 0.31
257 301 0.69
258 3 0.01
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.36
Consensus pattern (255 bp):
TGCCTTTGAGCTTAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCACCTTGA
GCTATGCTGTAAATTTGATATACCTTTAAGCTGAATGTAATCGAACTCGAAGGTCTTTGCTGAAA
GATAACCCTTCTCGCCTTGAGCTATACTGTAAATTTGATATCCTTTGAGCTGAATGTAATCGAAC
TCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATG
Found at i:204832 original size:20 final size:20
Alignment explanation
Indices: 204807--204844 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
204797 TTTCAAAGTG
*
204807 ATGCATTGATGCACCAATCC
1 ATGCATCGATGCACCAATCC
204827 ATGCATCGATGCACCAAT
1 ATGCATCGATGCACCAAT
204845 TATTTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.24
Consensus pattern (20 bp):
ATGCATCGATGCACCAATCC
Done.