Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
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: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 9 of 66
Found at i:3007360 original size:69 final size:69
Alignment explanation
Indices: 3007287--3007434 Score: 242
Period size: 69 Copynumber: 2.1 Consensus size: 69
3007277 ATAAGCTAAT
* * * *
3007287 CATGGATTGTCACATATTTTTGTACATAGCGTGTAACATGCTAACCATGACTTGTCACAGGTTTT
1 CATGGAGTGTCACATATTTTTATACATAGCGTGTAACACGCTAACCATGACTTGTCACAAGTTTT
3007352 TGTA
66 TGTA
* *
3007356 CATGGCGTGTCACATATTTTTATACATAGCGTGTAACACGCTAACCATGGCTTGTCACAAGTTTT
1 CATGGAGTGTCACATATTTTTATACATAGCGTGTAACACGCTAACCATGACTTGTCACAAGTTTT
3007421 TGTA
66 TGTA
3007425 CATGGAGTGT
1 CATGGAGTGT
3007435 AACTTCATAA
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 72 1.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (69 bp):
CATGGAGTGTCACATATTTTTATACATAGCGTGTAACACGCTAACCATGACTTGTCACAAGTTTT
TGTA
Found at i:3007364 original size:45 final size:45
Alignment explanation
Indices: 3007242--3007370 Score: 161
Period size: 45 Copynumber: 2.9 Consensus size: 45
3007232 GATTTGTGTA
* * * * *
3007242 CATGGCTTGTCACATATTTTTGTACATGGCATGTAATAAGCTAAT
1 CATGACTTGTCACATATTTTTGTACATGGCGTGTAACATGCTAAC
*
3007287 CATGGA-TTGTCACATATTTTTGTACATAGCGTGTAACATGCTAAC
1 CAT-GACTTGTCACATATTTTTGTACATGGCGTGTAACATGCTAAC
** *
3007332 CATGACTTGTCACAGGTTTTTGTACATGGCGTGTCACAT
1 CATGACTTGTCACATATTTTTGTACATGGCGTGTAACAT
3007371 ATTTTTATAC
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
44 2 0.03
45 69 0.96
46 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.36
Consensus pattern (45 bp):
CATGACTTGTCACATATTTTTGTACATGGCGTGTAACATGCTAAC
Found at i:3007366 original size:24 final size:24
Alignment explanation
Indices: 3007339--3007389 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3007329 AACCATGACT
* * *
3007339 TGTCACAGGTTTTTGTACATGGCG
1 TGTCACAGATTTTTATACATAGCG
*
3007363 TGTCACATATTTTTATACATAGCG
1 TGTCACAGATTTTTATACATAGCG
3007387 TGT
1 TGT
3007390 AACACGCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.41
Consensus pattern (24 bp):
TGTCACAGATTTTTATACATAGCG
Found at i:3007437 original size:114 final size:112
Alignment explanation
Indices: 3006953--3007437 Score: 484
Period size: 114 Copynumber: 4.3 Consensus size: 112
3006943 GTATATGGTA
* *
3006953 TGTCACATATTTTTGTACATAACGTGTAACACGCTAACCAT-GACTTGTCACAGGTTTTTGTACA
1 TGTCACATATTTTTGTACATGA-GTGTAACATGCTAACCATAG-CTTGTCACAGGTTTTTGTACA
* ** * * * * *
3007017 TGGCGTGTAACA-A--GCTAACCATAAC-TGTCACAAGTTTTTGTACTA-GGCT
64 TGGCGTGTCACATATTTTTAA-CATAGCGTGTAACAAG---CT-AACCATGGCT
*
3007066 TGTCACATATTTTTGTACAT-AGCATGTAACATGCTAACCATAGCTTGTCACAAGTTTTTGTACA
1 TGTCACATATTTTTGTACATGAG--TGTAACATGCTAACCATAGCTTGTCACAGGTTTTTGTACA
* *
3007130 TGGCGTGTCACATATTTTTGAACATAGCGTGTAACACGCTAACCATGACT
64 TGGCGTGTCACATATTTTT-AACATAGCGTGTAACAAGCTAACCATGGCT
** * * ** * *
3007180 TGTCACAGGTTTTTATACATGACGTGTAAAAAACTAACCATAGCTTGTCACAGATTTGTGTACAT
1 TGTCACATATTTTTGTACATGA-GTGTAACATGCTAACCATAGCTTGTCACAGGTTTTTGTACAT
* * * * * * *
3007245 GGCTTGTCACATATTTTTGTACATGGCATGTAATAAGCTAATCATGGAT
65 GGCGTGTCACATATTTTT-AACATAGCGTGTAACAAGCTAACCATGGCT
*
3007294 TGTCACATATTTTTGTACATAGCGTGTAACATGCTAACCAT-GACTTGTCACAGGTTTTTGTACA
1 TGTCACATATTTTTGTACAT-GAGTGTAACATGCTAACCATAG-CTTGTCACAGGTTTTTGTACA
*
3007358 TGGCGTGTCACATATTTTTATACATAGCGTGTAACACGCTAACCATGGCT
64 TGGCGTGTCACATATTTTTA-ACATAGCGTGTAACAAGCTAACCATGGCT
3007408 TGTCACA-AGTTTTTGTACATGGAGTGTAAC
1 TGTCACATA-TTTTTGTACAT-GAGTGTAAC
3007438 TTCATAAAAG
Statistics
Matches: 308, Mismatches: 49, Indels: 29
0.80 0.13 0.08
Matches are distributed among these distances:
111 1 0.00
112 1 0.00
113 72 0.23
114 216 0.70
115 2 0.01
116 7 0.02
117 9 0.03
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (112 bp):
TGTCACATATTTTTGTACATGAGTGTAACATGCTAACCATAGCTTGTCACAGGTTTTTGTACATG
GCGTGTCACATATTTTTAACATAGCGTGTAACAAGCTAACCATGGCT
Found at i:3016460 original size:203 final size:203
Alignment explanation
Indices: 3016184--3016591 Score: 638
Period size: 203 Copynumber: 2.0 Consensus size: 203
3016174 AGGTCTTATT
* *
3016184 TATGGCTAAAAGTCATGGTAATTTGCAAGATAAGAATGTGTGATTTATTGATAGTGCGTACTTAA
1 TATGGCTAAAAGTCATGGTAATTTGCAAGAGAAGAATGTGTGATTTATTGATAGTGCGTACTCAA
* *
3016249 ATCATATCACCGAAAATGAAGATGTCTTTGCTTCATTGGATAAAACATTCAAGTCTCAAGTTGAA
66 ACCATATCACCGAAAATGAAGATGTCTTTGCTTCATTGGATAAAACATTCAAGTCTCAAGTAGAA
* *
3016314 ATAGGTAATGGTGAATGTTTGAAGGTTTGCAGAGCTAGTATTATCAAGGTTGAAACATCAT-CAG
131 ATAGGTAATGGTGAATGTTTGAAGGTTTACAGAGCTAGTACTATCAAGGTTGAAACATCATCCA-
3016378 GTATGAAGC
195 GTATGAAGC
* * * * *
3016387 TATGGTTAAAAGTCCTGGTAATTTGCAAGAGAAGAATGTGTGGTTTATTGATAGTGCTTGCTCAA
1 TATGGCTAAAAGTCATGGTAATTTGCAAGAGAAGAATGTGTGATTTATTGATAGTGCGTACTCAA
** * * *
3016452 ACCATATCATTGGAAATGAAGATGTCTTTGCTTCATTGGATAAATCATTCAAGTCTCAAGTAGAG
66 ACCATATCACCGAAAATGAAGATGTCTTTGCTTCATTGGATAAAACATTCAAGTCTCAAGTAGAA
* *
3016517 ATAGGTAATGGTGAATGTTTGAAGGTTTACAGAGCTAGTACTGTTAAGGTTGAAACATCATCCAG
131 ATAGGTAATGGTGAATGTTTGAAGGTTTACAGAGCTAGTACTATCAAGGTTGAAACATCATCCAG
3016582 TATGAAGC
196 TATGAAGC
3016590 TA
1 TA
3016592 ATACCAAATG
Statistics
Matches: 186, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
203 184 0.99
204 2 0.01
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (203 bp):
TATGGCTAAAAGTCATGGTAATTTGCAAGAGAAGAATGTGTGATTTATTGATAGTGCGTACTCAA
ACCATATCACCGAAAATGAAGATGTCTTTGCTTCATTGGATAAAACATTCAAGTCTCAAGTAGAA
ATAGGTAATGGTGAATGTTTGAAGGTTTACAGAGCTAGTACTATCAAGGTTGAAACATCATCCAG
TATGAAGC
Found at i:3032023 original size:22 final size:23
Alignment explanation
Indices: 3031998--3032043 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
3031988 AACCATCGAT
3031998 AGTCTTTCT-TTCAAGTTTTATA
1 AGTCTTTCTGTTCAAGTTTTATA
**
3032020 AGTCTTTCTGTTTTAGTTTTATA
1 AGTCTTTCTGTTCAAGTTTTATA
3032043 A
1 A
3032044 CAGAGTATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.57
Consensus pattern (23 bp):
AGTCTTTCTGTTCAAGTTTTATA
Found at i:3067046 original size:21 final size:22
Alignment explanation
Indices: 3067013--3067053 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3067003 TAATTAAAAA
* *
3067013 TTTAAACTTCTAAATCTTAAAT
1 TTTAAACTCCTAAACCTTAAAT
3067035 TTTAAAC-CCTAAACCTTAA
1 TTTAAACTCCTAAACCTTAA
3067054 TATGAGATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (22 bp):
TTTAAACTCCTAAACCTTAAAT
Found at i:3069715 original size:24 final size:24
Alignment explanation
Indices: 3069683--3069736 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
3069673 ATATTCACAC
*
3069683 TGAATATTCTAAAATGAAGTTATT
1 TGAATATTCTAAAATGAAGCTATT
* *
3069707 TGAATATTCTAGAATGAGGCTATT
1 TGAATATTCTAAAATGAAGCTATT
3069731 T-AATAT
1 TGAATAT
3069737 AAAAATTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.41
Consensus pattern (24 bp):
TGAATATTCTAAAATGAAGCTATT
Found at i:3073604 original size:60 final size:60
Alignment explanation
Indices: 3073511--3073691 Score: 283
Period size: 60 Copynumber: 3.0 Consensus size: 60
3073501 AGACATCATC
*
3073511 ACCTACTCGTGGGAACTGCCCATGCCACCATATATAAATCGGGGCTTCAGGTCCCCCTTT
1 ACCTACTCGTGGGAACTACCCATGCCACCATATATAAATCGGGGCTTCAGGTCCCCCTTT
* * *
3073571 ACCTACTCGTGGGAACTACCCATGCCACCATATACAAATCGGGGCTTTAGGTCCCCTTTT
1 ACCTACTCGTGGGAACTACCCATGCCACCATATATAAATCGGGGCTTCAGGTCCCCCTTT
* * *
3073631 ACTTACTCATGGGAACTACCCATGCCACCCA-ATATAAATCGAGGCTTCAGGTCCCCCTTT
1 ACCTACTCGTGGGAACTACCCATGCCA-CCATATATAAATCGGGGCTTCAGGTCCCCCTTT
3073691 A
1 A
3073692 TAAATCAAAT
Statistics
Matches: 110, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
60 107 0.97
61 3 0.03
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.25
Consensus pattern (60 bp):
ACCTACTCGTGGGAACTACCCATGCCACCATATATAAATCGGGGCTTCAGGTCCCCCTTT
Found at i:3074314 original size:21 final size:22
Alignment explanation
Indices: 3074280--3074321 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
3074270 TATCTAGCTA
*
3074280 TTCCGTTTTTCTTTCCTGTTTC
1 TTCCGTTTCTCTTTCCTGTTTC
*
3074302 TTCC-TTTCTCTTTCTTGTTT
1 TTCCGTTTCTCTTTCCTGTTT
3074322 TTATTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.00, C:0.26, G:0.07, T:0.67
Consensus pattern (22 bp):
TTCCGTTTCTCTTTCCTGTTTC
Found at i:3074475 original size:13 final size:13
Alignment explanation
Indices: 3074450--3074494 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
3074440 TCCCTCTCTC
3074450 TTTCTTC-TTCTT
1 TTTCTTCTTTCTT
*
3074462 TTTCTTTTTTCTT
1 TTTCTTCTTTCTT
**
3074475 TTTCCCCTTTCTT
1 TTTCTTCTTTCTT
3074488 TTTCTTC
1 TTTCTTC
3074495 CTCGACGCCA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
12 6 0.23
13 20 0.77
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTCTTCTTTCTT
Found at i:3074538 original size:16 final size:16
Alignment explanation
Indices: 3074517--3074563 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
3074507 GCTCCCTCTC
3074517 TCTTTCTTCTTCTTTT
1 TCTTTCTTCTTCTTTT
3074533 TCTTTCTTCTT-TTTT
1 TCTTTCTTCTTCTTTT
3074548 T-TTCTCTTTCTTCTTT
1 TCTT-TC-TTCTTCTTT
3074564 CTTGTCTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 2 0.07
15 7 0.25
16 16 0.57
17 3 0.11
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TCTTTCTTCTTCTTTT
Found at i:3074541 original size:13 final size:13
Alignment explanation
Indices: 3074519--3074566 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
3074509 TCCCTCTCTC
3074519 TTTC-TTCTTCTT
1 TTTCTTTCTTCTT
3074531 TTTCTTTCTTCTT
1 TTTCTTTCTTCTT
*
3074544 TTTTTTTC-TCTT
1 TTTCTTTCTTCTT
3074556 TCTTCTTTCTT
1 T-TTCTTTCTT
3074567 GTCTTTTCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 9 0.29
13 21 0.68
14 1 0.03
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTCTTTCTTCTT
Found at i:3074555 original size:19 final size:19
Alignment explanation
Indices: 3074515--3074563 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
3074505 CTGCTCCCTC
3074515 TCTCTTTCTTC--TTCTTT
1 TCTCTTTCTTCTTTTCTTT
*
3074532 T-TCTTTCTTCTTTTTTTT
1 TCTCTTTCTTCTTTTCTTT
3074550 TCTCTTTCTTCTTT
1 TCTCTTTCTTCTTT
3074564 CTTGTCTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 9 0.32
17 1 0.04
18 6 0.21
19 12 0.43
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (19 bp):
TCTCTTTCTTCTTTTCTTT
Found at i:3074573 original size:23 final size:22
Alignment explanation
Indices: 3074517--3074574 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 22
3074507 GCTCCCTCTC
3074517 TCTTTCTTCTTCTTTT-TCTTTCT
1 TCTTTC-T-TTCTTTTCTCTTTCT
3074540 TC-TT-TTT-TTTTCTCTTTCT
1 TCTTTCTTTCTTTTCTCTTTCT
3074559 TCTTTCTTGTCTTTTC
1 TCTTTCTT-TCTTTTC
3074575 GCTCTTTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
18 4 0.13
19 11 0.37
20 3 0.10
21 2 0.07
22 3 0.10
23 7 0.23
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.74
Consensus pattern (22 bp):
TCTTTCTTTCTTTTCTCTTTCT
Found at i:3074730 original size:17 final size:18
Alignment explanation
Indices: 3074689--3074733 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
3074679 TTCTTCTTTC
* *
3074689 TTTCTCTTCTCTTCTCTT
1 TTTCTTTTCTCTTCTCCT
3074707 TTGTCTTTTC-CTTCTCCT
1 TT-TCTTTTCTCTTCTCCT
3074725 TTTCTTTTC
1 TTTCTTTTC
3074734 ACATGCTGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.29
18 11 0.46
19 6 0.25
ACGTcount: A:0.00, C:0.31, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTCTTTTCTCTTCTCCT
Found at i:3079806 original size:60 final size:60
Alignment explanation
Indices: 3079701--3079999 Score: 415
Period size: 60 Copynumber: 5.0 Consensus size: 60
3079691 AAATATCATC
* *
3079701 ACCTACTCGTGGGAACTGCCCATG-CACCATATATAAATC-AGGGCTTCAAGTCCCCCTTT
1 ACCTACTCGTGGGAACTGCCCACGCCACCATATATAAATCGA-GGCTTCAGGTCCCCCTTT
*
3079760 ACCTACTCGTGGGAACTGCTCACGCCACCATATATAAATCGAGGCTTCAGGTCCCCCTTT
1 ACCTACTCGTGGGAACTGCCCACGCCACCATATATAAATCGAGGCTTCAGGTCCCCCTTT
* * * **
3079820 ACCTACTCTTGAGAACTGCCCACGCCATCATATATAAATCGAGATTTCAGGTCCCCCTTT
1 ACCTACTCGTGGGAACTGCCCACGCCACCATATATAAATCGAGGCTTCAGGTCCCCCTTT
* * * *
3079880 ACCTACTCGTGGGAACTGTCCATGCCACCATATATAAATCGGGGCTTCAAGTCCCCCTTT
1 ACCTACTCGTGGGAACTGCCCACGCCACCATATATAAATCGAGGCTTCAGGTCCCCCTTT
* * * *
3079940 ACCTACACGTGGGAACTACCCACTCCACC-TAATATAAATCGGGGCTTCAGGTCCCCCTTT
1 ACCTACTCGTGGGAACTGCCCACGCCACCAT-ATATAAATCGAGGCTTCAGGTCCCCCTTT
3080000 TTAAATCAAA
Statistics
Matches: 213, Mismatches: 24, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
59 23 0.11
60 189 0.89
61 1 0.00
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.26
Consensus pattern (60 bp):
ACCTACTCGTGGGAACTGCCCACGCCACCATATATAAATCGAGGCTTCAGGTCCCCCTTT
Found at i:3080709 original size:15 final size:16
Alignment explanation
Indices: 3080682--3080713 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3080672 TCTCTTTTTC
3080682 CTTCTTCCTTTCTCTT
1 CTTCTTCCTTTCTCTT
3080698 CTTCTT-CTTTCTCTT
1 CTTCTTCCTTTCTCTT
3080713 C
1 C
3080714 CGGCACCGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (16 bp):
CTTCTTCCTTTCTCTT
Found at i:3080828 original size:31 final size:31
Alignment explanation
Indices: 3080793--3080886 Score: 122
Period size: 31 Copynumber: 3.1 Consensus size: 31
3080783 CTTGACGTCG
*
3080793 TTACTCCCTCTCTCTTTCGTTTTCTTTTTCT
1 TTACTCCCTCTCTCTTTCTTTTTCTTTTTCT
3080824 TTACTCCCTCTCTCTTTCTTTTTCTTTCTTCT
1 TTACTCCCTCTCTCTTTCTTTTTCTTT-TTCT
* *
3080856 TT-CT--TTTTCTCTTTCTTCTTTCTTTTTCT
1 TTACTCCCTCTCTCTTTCTT-TTTCTTTTTCT
3080885 TT
1 TT
3080887 CTTGTCTTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
29 17 0.29
30 7 0.12
31 28 0.48
32 6 0.10
ACGTcount: A:0.02, C:0.30, G:0.01, T:0.67
Consensus pattern (31 bp):
TTACTCCCTCTCTCTTTCTTTTTCTTTTTCT
Found at i:3080843 original size:4 final size:4
Alignment explanation
Indices: 3080836--3080895 Score: 53
Period size: 4 Copynumber: 16.2 Consensus size: 4
3080826 ACTCCCTCTC
3080836 TCTT TC-T T-TT TCTT TC-T TCTT TCTT T-TT CTCTT TC-T TCTT TC-T
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT -TCTT TCTT TCTT TCTT
3080879 T-TT TCTT TCTT GTCTT T
1 TCTT TCTT TCTT -TCTT T
3080896 TCTCTCTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 18
0.72 0.00 0.28
Matches are distributed among these distances:
3 16 0.34
4 25 0.53
5 6 0.13
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.75
Consensus pattern (4 bp):
TCTT
Found at i:3080857 original size:7 final size:7
Alignment explanation
Indices: 3080839--3080885 Score: 66
Period size: 6 Copynumber: 7.3 Consensus size: 7
3080829 CCCTCTCTCT
3080839 TTCTTT-
1 TTCTTTC
3080845 TTCTTTC
1 TTCTTTC
3080852 TTCTTTC
1 TTCTTTC
3080859 TT-TTTC
1 TTCTTTC
3080865 -TCTTTC
1 TTCTTTC
3080871 TTCTTTC
1 TTCTTTC
3080878 TT-TTTC
1 TTCTTTC
3080884 TT
1 TT
3080886 TCTTGTCTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
5 1 0.03
6 20 0.53
7 17 0.45
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (7 bp):
TTCTTTC
Found at i:3080870 original size:19 final size:19
Alignment explanation
Indices: 3080836--3080884 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
3080826 ACTCCCTCTC
3080836 TCTTTC-TTTT-TCTTTCT
1 TCTTTCTTTTTCTCTTTCT
3080853 TCTTTCTTTTTCTCTTTCT
1 TCTTTCTTTTTCTCTTTCT
3080872 TCTTTCTTTTTCT
1 TCTTTCTTTTTCT
3080885 TTCTTGTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.20
18 4 0.13
19 20 0.67
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (19 bp):
TCTTTCTTTTTCTCTTTCT
Found at i:3080887 original size:29 final size:28
Alignment explanation
Indices: 3080801--3080907 Score: 106
Period size: 31 Copynumber: 3.6 Consensus size: 28
3080791 CGTTACTCCC
* *
3080801 TCTCTCTTTCGTTTTCTTTTTCTTTACTCCC
1 TCTCTCTTTCTTTTTCTTTTTCTTT-CT--T
3080832 TCTCTCTTTCTTTTTCTTTCTTCTTTCTT
1 TCTCTCTTTCTTTTTCTTT-TTCTTTCTT
*
3080861 TTTCTCTTTCTTCTTTCTTTTTCTTTCTT
1 TCTCTCTTTCTT-TTTCTTTTTCTTTCTT
* *
3080890 GTCTTTTCTCTCTTTTTC
1 -TC-TCTCTTTCTTTTTC
3080908 CTTCCCTTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
29 20 0.30
30 12 0.18
31 28 0.42
32 6 0.09
ACGTcount: A:0.01, C:0.28, G:0.02, T:0.69
Consensus pattern (28 bp):
TCTCTCTTTCTTTTTCTTTTTCTTTCTT
Found at i:3080894 original size:19 final size:18
Alignment explanation
Indices: 3080836--3080895 Score: 79
Period size: 19 Copynumber: 3.3 Consensus size: 18
3080826 ACTCCCTCTC
3080836 TCTTTCTTTTTCTTTC-T
1 TCTTTCTTTTTCTTTCTT
3080853 TCTTTCTTTTTCTCTT-TCT
1 TCTTTCTTTTTCT-TTCT-T
3080872 TCTTTCTTTTTCTTTCTT
1 TCTTTCTTTTTCTTTCTT
3080890 GTCTTT
1 -TCTTT
3080896 TCTCTCTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
17 13 0.34
18 5 0.13
19 20 0.53
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.75
Consensus pattern (18 bp):
TCTTTCTTTTTCTTTCTT
Found at i:3080917 original size:36 final size:36
Alignment explanation
Indices: 3080836--3080918 Score: 91
Period size: 36 Copynumber: 2.3 Consensus size: 36
3080826 ACTCCCTCTC
* *
3080836 TCTTTCTTTTTCTTTCTTCTTTCTTTTTCTCTTTCT
1 TCTTCCTTTTTCTTTCTTCTGTCTTTTTCTCTTTCT
*
3080872 TCTTTCTTTTTCTTTC-T-TGTCTTTTCTCTCTTT-T
1 TCTTCCTTTTTCTTTCTTCTGTCTTTT-TCTCTTTCT
3080906 TCCTTCCCTTTTT
1 T-CTT-CCTTTTT
3080919 GTCGGCTTGA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
34 9 0.21
35 11 0.26
36 22 0.52
ACGTcount: A:0.00, C:0.27, G:0.01, T:0.72
Consensus pattern (36 bp):
TCTTCCTTTTTCTTTCTTCTGTCTTTTTCTCTTTCT
Found at i:3081005 original size:12 final size:13
Alignment explanation
Indices: 3080991--3081032 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
3080981 CACCCTCTTT
3080991 TCTTCTTCTTTT-
1 TCTTCTTCTTTTC
3081003 TCTTCTTTCTTTTC
1 TCTTC-TTCTTTTC
*
3081017 TCTTC-TCTTTTG
1 TCTTCTTCTTTTC
3081029 TCTT
1 TCTT
3081033 TTTCGTTCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 15 0.56
13 7 0.26
14 5 0.19
ACGTcount: A:0.00, C:0.26, G:0.02, T:0.71
Consensus pattern (13 bp):
TCTTCTTCTTTTC
Found at i:3081025 original size:19 final size:18
Alignment explanation
Indices: 3080988--3081049 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 18
3080978 GAGCACCCTC
*
3080988 TTTTCTTCTTCT-TTTTCT
1 TTTTCTT-TTCTCTTCTCT
3081006 TCTTTCTTTTCTCTTCTCT
1 T-TTTCTTTTCTCTTCTCT
3081025 TTTGTCTTTT-TCGTTCTCT
1 TTT-TCTTTTCTC-TTCTCT
3081044 TTTTCT
1 TTTTCT
3081050 CTTCACATGC
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
18 12 0.31
19 27 0.69
ACGTcount: A:0.00, C:0.24, G:0.03, T:0.73
Consensus pattern (18 bp):
TTTTCTTTTCTCTTCTCT
Found at i:3081032 original size:23 final size:24
Alignment explanation
Indices: 3080986--3081033 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
3080976 TCGAGCACCC
*
3080986 TCTTTTCTTCTTCTTTTTCTTCTT
1 TCTTTTCTTCTTCTTTTTCGTCTT
3081010 TCTTTTC-TCTTCTCTTTT-GTCTT
1 TCTTTTCTTCTTCT-TTTTCGTCTT
3081033 T
1 T
3081034 TTCGTTCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.00, C:0.25, G:0.02, T:0.73
Consensus pattern (24 bp):
TCTTTTCTTCTTCTTTTTCGTCTT
Found at i:3081032 original size:26 final size:24
Alignment explanation
Indices: 3080991--3081049 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
3080981 CACCCTCTTT
*
3080991 TCTTCTTCTTTTTCTTCTTTCTTTTC
1 TCTTCTTCTTTTTCTT-TTTC-GTTC
3081017 TCTTC-TCTTTTGTCTTTTTCGTTC
1 TCTTCTTCTTTT-TCTTTTTCGTTC
*
3081041 TCTTTTTCT
1 TCTTCTTCT
3081050 CTTCACATGC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
24 7 0.24
25 13 0.45
26 9 0.31
ACGTcount: A:0.00, C:0.25, G:0.03, T:0.71
Consensus pattern (24 bp):
TCTTCTTCTTTTTCTTTTTCGTTC
Found at i:3082445 original size:17 final size:17
Alignment explanation
Indices: 3082423--3082456 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3082413 AAAGTCAAGT
3082423 CTTAATATGAATAATCA
1 CTTAATATGAATAATCA
* *
3082440 CTTAATTTGTATAATCA
1 CTTAATATGAATAATCA
3082457 TATTTGAACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (17 bp):
CTTAATATGAATAATCA
Found at i:3087652 original size:20 final size:20
Alignment explanation
Indices: 3087607--3087644 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3087597 TTTTGGCCCC
3087607 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
3087627 ATTTGACTTATTGGAGTA
1 ATTTGACTTATTGGAGTA
3087645 AGATTTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:3087728 original size:27 final size:27
Alignment explanation
Indices: 3087698--3087755 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
3087688 TTGGAGTAAA
* *
3087698 AGGGTAAAATGGTAATTTTGCCACC-CC
1 AGGGCAAAATGATAATTTT-CCACCACC
*
3087725 AGGGGCAAAATTATAATTTTCCACCACC
1 A-GGGCAAAATGATAATTTTCCACCACC
3087753 AGG
1 AGG
3087756 ACATTTTTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
27 8 0.31
28 18 0.69
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (27 bp):
AGGGCAAAATGATAATTTTCCACCACC
Found at i:3092680 original size:17 final size:17
Alignment explanation
Indices: 3092635--3092680 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
3092625 ACCTTAATTA
3092635 ATTTAATTAATTTTAAC
1 ATTTAATTAATTTTAAC
* *
3092652 -TTTTATTAAATTTTCAC
1 ATTTAATT-AATTTTAAC
3092669 ATTTAATTAATT
1 ATTTAATTAATT
3092681 GCTTACCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 6 0.25
17 12 0.50
18 6 0.25
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTAATTAATTTTAAC
Found at i:3093752 original size:2 final size:2
Alignment explanation
Indices: 3093745--3093775 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3093735 CTAGCAAACC
*
3093745 TA TA TA TA TA TC TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3093776 GAATAACATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3097098 original size:98 final size:99
Alignment explanation
Indices: 3096937--3097117 Score: 222
Period size: 97 Copynumber: 1.8 Consensus size: 99
3096927 GTTTAGTTTT
* * * ** * * *
3096937 AAGAGTTTATGTTCTAGTGAAATACAAAAAATATAGACCAAGTTACATGCCCTGTTGA-TAAAAA
1 AAGAGTTTATGTCCTAGTGAAACACAAAAAATAGAGACCAAGTTACACACCATGTTAACAAAAAA
*
3097001 ATTATAACATGTCATATTTAAGGTGTTTAACTTC
66 ATTATAACACGTCATATTTAAGGTGTTTAACTTC
* *
3097035 AAGAGTTTATGTCCTAGTGAAACAC-AAAAATAGAGATCAAGTTATACACCATGTTAAACAAAAA
1 AAGAGTTTATGTCCTAGTGAAACACAAAAAATAGAGACCAAGTTACACACCATGTT-AACAAAAA
* *
3097099 AATTGTTACACGTCATATT
65 AATTATAACACGTCATATT
3097118 AAAAAAAAAA
Statistics
Matches: 68, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
97 24 0.35
98 24 0.35
99 20 0.29
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (99 bp):
AAGAGTTTATGTCCTAGTGAAACACAAAAAATAGAGACCAAGTTACACACCATGTTAACAAAAAA
ATTATAACACGTCATATTTAAGGTGTTTAACTTC
Found at i:3097119 original size:28 final size:28
Alignment explanation
Indices: 3097088--3097142 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
3097078 ATACACCATG
* **
3097088 TTAAACAAAAAAATTGTTACACGTCATA
1 TTAAAAAAAAAAATTAATACACGTCATA
3097116 TTAAAAAAAAAAATTAATACACGTCAT
1 TTAAAAAAAAAAATTAATACACGTCAT
3097143 GTTTAATGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.55, C:0.13, G:0.05, T:0.27
Consensus pattern (28 bp):
TTAAAAAAAAAAATTAATACACGTCATA
Found at i:3097148 original size:127 final size:125
Alignment explanation
Indices: 3096996--3097314 Score: 313
Period size: 125 Copynumber: 2.5 Consensus size: 125
3096986 CCCTGTTGAT
* * * *
3096996 AAAAAATT-ATAACATGTCATATTTAAGGTGTTTAACTTCAAGAGTTTATGTCCTAGTGAAACAC
1 AAAAAATTAAT-ACACGTCATGTTTAAGGTGTTTAACTTCAAGAGTTTATGTTCTAGTGAAATAC
* * * * *
3097060 AAAAATAGAGATCAAGTTATA-CACCATGTTAAACAAAAAAATTGTTACACGTCATATTAAAAA
65 AAAAATAGACACCAAGTTACATCA-CATATT-AA-AAAAAAATTATTACACGTCATATTAAAAA
* * * * * *
3097123 AAAAAATTAATACACGTCATGTTTAATGTGTTTAAC-TCTAATAATTTATATTCTACTAAAATAC
1 AAAAAATTAATACACGTCATGTTTAAGGTGTTTAACTTC-AAGAGTTTATGTTCTAGTGAAATAC
* * * * * *
3097187 AAAGATAGACACCAAGTTACATGACATATTGAAAAAAAATTATTACAGGTCATGTTGAAAA
65 AAAAATAGACACCAAGTTACATCACATATTAAAAAAAAATTATTACACGTCATATTAAAAA
* * ** * *
3097248 AAAAAGTTATTACACACCATGTTTAAGGTGTTTAA-TGCCAAGAGTTTATGTTTTAGTGAAATAC
1 AAAAAATTAATACACGTCATGTTTAAGGTGTTTAACT-TCAAGAGTTTATGTTCTAGTGAAATAC
3097312 AAA
65 AAA
3097315 GAAAAAGATT
Statistics
Matches: 154, Mismatches: 33, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
125 77 0.50
126 4 0.03
127 70 0.45
128 3 0.02
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (125 bp):
AAAAAATTAATACACGTCATGTTTAAGGTGTTTAACTTCAAGAGTTTATGTTCTAGTGAAATACA
AAAATAGACACCAAGTTACATCACATATTAAAAAAAAATTATTACACGTCATATTAAAAA
Found at i:3097268 original size:28 final size:27
Alignment explanation
Indices: 3097218--3097270 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
3097208 TGACATATTG
***
3097218 AAAAAAAATTATTACAGGTCATGTTGA
1 AAAAAAAATTATTACACACCATGTTGA
3097245 AAAAAAAAGTTATTACACACCATGTT
1 AAAAAAAA-TTATTACACACCATGTT
3097271 TAAGGTGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 8 0.36
28 14 0.64
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.28
Consensus pattern (27 bp):
AAAAAAAATTATTACACACCATGTTGA
Found at i:3101064 original size:17 final size:17
Alignment explanation
Indices: 3101033--3101066 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3101023 TTCTCTCTCC
* *
3101033 TTCTTTTTCTTTTTTAT
1 TTCTTTTTATCTTTTAT
3101050 TTCTTTTTATCTTTTAT
1 TTCTTTTTATCTTTTAT
3101067 CCTTTCATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (17 bp):
TTCTTTTTATCTTTTAT
Found at i:3101948 original size:28 final size:28
Alignment explanation
Indices: 3101881--3101955 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 28
3101871 AGGCATTAAA
* ** *
3101881 GTGTAAC-AAATA-TTTTTGAATTTGTC
1 GTGTAACAAAATATTTTTTAAACATGGC
3101907 GTGTAACAATAATATTTTTTAAACATGGC
1 GTGTAACAA-AATATTTTTTAAACATGGC
3101936 GTGTAACAAAATATTGTTTT
1 GTGTAACAAAATATT-TTTT
3101956 TTCAACATAG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
26 7 0.17
27 1 0.02
28 10 0.24
29 23 0.56
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.43
Consensus pattern (28 bp):
GTGTAACAAAATATTTTTTAAACATGGC
Found at i:3101963 original size:31 final size:29
Alignment explanation
Indices: 3101906--3101975 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 29
3101896 TTGAATTTGT
*
3101906 CGTGTAACAATAATATTTTTTAAACATGG
1 CGTGTAACAATAATATTTTTTAAACATAG
*
3101935 CGTGTAACAA-AATATTGTTTTTTCAACATAG
1 CGTGTAACAATAATA---TTTTTTAAACATAG
*
3101966 TGTGTAACAA
1 CGTGTAACAA
3101976 CCTTTTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.11
29 10 0.29
31 21 0.60
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.37
Consensus pattern (29 bp):
CGTGTAACAATAATATTTTTTAAACATAG
Found at i:3102073 original size:51 final size:52
Alignment explanation
Indices: 3102011--3102119 Score: 175
Period size: 51 Copynumber: 2.1 Consensus size: 52
3102001 TGTTTTTGTA
* *
3102011 CATGGCATGTAACAACAGTATTTTTTTTCAAC-TGACGTGTAACAACCTAAC
1 CATGGCATGTAACAACAATATTTTTTTTCAACATGACGTGCAACAACCTAAC
* *
3102062 CATGGCGTGTAACAACAATATTTTTTTTCAACATGGCGTGCAACAACCTAAC
1 CATGGCATGTAACAACAATATTTTTTTTCAACATGACGTGCAACAACCTAAC
3102114 CATGGC
1 CATGGC
3102120 TTGTCATATG
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
51 30 0.57
52 23 0.43
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (52 bp):
CATGGCATGTAACAACAATATTTTTTTTCAACATGACGTGCAACAACCTAAC
Found at i:3102152 original size:45 final size:45
Alignment explanation
Indices: 3102092--3102206 Score: 158
Period size: 45 Copynumber: 2.6 Consensus size: 45
3102082 TTTTTTTTCA
* * *
3102092 ACATGGCGTGCAACAACCTAACCATGGCTTGTCATATGTTTTTAT
1 ACATGGCGTGTAACAACCTAACCATGGCTTGTCACATATTTTTAT
* *
3102137 ACATGGCGTGTAACAACCTAACCATGGCTTGTTACATATTTTTGT
1 ACATGGCGTGTAACAACCTAACCATGGCTTGTCACATATTTTTAT
* * *
3102182 ATATAGCATGTAACAACCTAACCAT
1 ACATGGCGTGTAACAACCTAACCAT
3102207 AACGTATAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 62 1.00
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (45 bp):
ACATGGCGTGTAACAACCTAACCATGGCTTGTCACATATTTTTAT
Found at i:3102263 original size:24 final size:24
Alignment explanation
Indices: 3102236--3102287 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
3102226 ATGACTTGTC
*
3102236 ACATATTTTTGTACATGGCGTGTA
1 ACATATTTTTGTACATGGCATGTA
*
3102260 ACATGTTTTTGTACATGGCATGTA
1 ACATATTTTTGTACATGGCATGTA
3102284 ACAT
1 ACAT
3102288 CATAGCGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.40
Consensus pattern (24 bp):
ACATATTTTTGTACATGGCATGTA
Found at i:3105569 original size:2 final size:2
Alignment explanation
Indices: 3105562--3105606 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3105552 AGGCATCCAG
3105562 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3105604 TA T
1 TA T
3105607 CTTTGAGTCG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3105994 original size:219 final size:218
Alignment explanation
Indices: 3105612--3106051 Score: 871
Period size: 219 Copynumber: 2.0 Consensus size: 218
3105602 TATATCTTTG
3105612 AGTCGCGTCACTTCGTTGATCTTGTCATCCTTTGCTTTGAATTATTTTTATATTTACTAAAACAT
1 AGTCGCGTCACTTCGTTGATCTTGTCATCCTTTGCTTTGAATTATTTTTATATTTACTAAAACAT
3105677 GTTTATATTTGGCCATTGAATGGCAATAATAGATGATTAATGGATTGTAATTATGATTCCACTTA
66 GTTTATATTTGGCCATTGAATGGCAATAATAGATGATTAATGGATTGTAATTATGATTCCACTTA
3105742 TGTTTACAAATTACAAACTTATAGGTTTGTTTAAGATGAAATTGAAAATGCAAACCCACTTTAAT
131 TGTTTACAAATTACAAACTTATAGGTTTGTTTAAGATGAAATTGAAAATGCAAACCCACTTTAAT
3105807 ACGAGTGGCTTAAGGAATTCTTC
196 ACGAGTGGCTTAAGGAATTCTTC
3105830 AGTNCGCGTCACTTCGTTGATCTTGTCATCCTTTGCTTTGAATTATTTTTATATTTACTAAAACA
1 AGT-CGCGTCACTTCGTTGATCTTGTCATCCTTTGCTTTGAATTATTTTTATATTTACTAAAACA
3105895 TGTTTATATTTGGCCATTGAATGGCAATAATAGATGATTAATGGATTGTAATTATGATTCCACTT
65 TGTTTATATTTGGCCATTGAATGGCAATAATAGATGATTAATGGATTGTAATTATGATTCCACTT
3105960 ATGTTTACAAATTACAAACTTATAGGTTTGTTTAAGATGAAATTGAAAATGCAAACCCACTTTAA
130 ATGTTTACAAATTACAAACTTATAGGTTTGTTTAAGATGAAATTGAAAATGCAAACCCACTTTAA
3106025 TACGAGTGGCTTAAGGAATTCTTC
195 TACGAGTGGCTTAAGGAATTCTTC
3106049 AGT
1 AGT
3106052 TGAACATACA
Statistics
Matches: 221, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
218 3 0.01
219 218 0.99
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (218 bp):
AGTCGCGTCACTTCGTTGATCTTGTCATCCTTTGCTTTGAATTATTTTTATATTTACTAAAACAT
GTTTATATTTGGCCATTGAATGGCAATAATAGATGATTAATGGATTGTAATTATGATTCCACTTA
TGTTTACAAATTACAAACTTATAGGTTTGTTTAAGATGAAATTGAAAATGCAAACCCACTTTAAT
ACGAGTGGCTTAAGGAATTCTTC
Found at i:3106358 original size:20 final size:20
Alignment explanation
Indices: 3106324--3106367 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3106314 AGAGCTATAT
* * *
3106324 TAGATATCTTGTATCTTCAA
1 TAGATATCATATATCCTCAA
3106344 TAGATATCATATATCCTCAA
1 TAGATATCATATATCCTCAA
3106364 -AGAT
1 TAGAT
3106368 TAATTTTCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (20 bp):
TAGATATCATATATCCTCAA
Found at i:3107437 original size:12 final size:12
Alignment explanation
Indices: 3107422--3107446 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3107412 TTGATAATAA
3107422 AAATATAAAACT
1 AAATATAAAACT
3107434 AAATATAAAACT
1 AAATATAAAACT
3107446 A
1 A
3107447 TAATTTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATATAAAACT
Found at i:3107933 original size:28 final size:28
Alignment explanation
Indices: 3107872--3107934 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
3107862 AACTTATAAC
*
3107872 ATATGAACAAATAGAATAAAAATGAAAA
1 ATATAAACAAATAGAATAAAAATGAAAA
* * *
3107900 AAATAAACAAATATAATTAAAAAT-AATA
1 ATATAAACAAATAGAA-TAAAAATGAAAA
3107928 ATATAAA
1 ATATAAA
3107935 TTAAAAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
28 22 0.76
29 7 0.24
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.22
Consensus pattern (28 bp):
ATATAAACAAATAGAATAAAAATGAAAA
Found at i:3108872 original size:2 final size:2
Alignment explanation
Indices: 3108865--3108905 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3108855 TAATATTTTC
3108865 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3108906 CAATTAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3123172 original size:15 final size:15
Alignment explanation
Indices: 3123152--3123197 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
3123142 TTCTTAAAAC
3123152 AACTTTAAAACCAAA
1 AACTTTAAAACCAAA
3123167 AACTTTAAAATCC-AA
1 AACTTTAAAA-CCAAA
*
3123182 AGCTTTAAAACCAAA
1 AACTTTAAAACCAAA
3123197 A
1 A
3123198 TCTCTGATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 2 0.07
15 24 0.86
16 2 0.07
ACGTcount: A:0.57, C:0.20, G:0.02, T:0.22
Consensus pattern (15 bp):
AACTTTAAAACCAAA
Found at i:3127015 original size:18 final size:19
Alignment explanation
Indices: 3126992--3127031 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
3126982 ATGATTAGTA
*
3126992 AAGAC-TTTCCATACATGG
1 AAGACGTTTCCATACACGG
3127010 AAGACTGTTTCCATACACGG
1 AAGAC-GTTTCCATACACGG
3127030 AA
1 AA
3127032 TTAAAAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
20 14 0.74
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (19 bp):
AAGACGTTTCCATACACGG
Found at i:3130704 original size:214 final size:215
Alignment explanation
Indices: 3130333--3130759 Score: 795
Period size: 214 Copynumber: 2.0 Consensus size: 215
3130323 CTCGGAGTTG
3130333 GAACATCCGTTTTGATGAAGCTATAAAAGGGTTTGACTTTCATCAAAAAATGAGGATGAACCATG
1 GAACATCCGTTTTGATGAAGCTATAAAAGGGTTTGACTTTCATCAAAAAATGAGGATGAACCATG
*
3130398 TGTCTATAAAAAGGTTAGTGGAAGTGCCATAATTTTCCTAGTGTTATATATTGATGACATATTGC
66 TGTCTATAAAAAGGTTAGTGGAAGTGCCATAATTTTCCTAGTGTTATATATTAATGACATATTGC
3130463 TCATAGGAAATGATATACCATTGCTGCAATCTACAAAAATTTGGTTGTCCAAACAATTCTCCATG
131 TCATAGGAAATGATATACCATTGCTGCAATCTACAAAAATTTGGTTGTCCAAACAATTCTCCATG
3130528 AAAGATTTGGGAGAAGCAAC
196 AAAGATTTGGGAGAAGCAAC
3130548 NGAACATCCGTTTTGATGAAGCTATAAAAGGGTTTGAC-TTCAT-AAAAAATGAGGATGAACCAT
1 -GAACATCCGTTTTGATGAAGCTATAAAAGGGTTTGACTTTCATCAAAAAATGAGGATGAACCAT
*
3130611 GTGTCTATAAAAAGGTTAGTGGAAGTGCCATAATTTTCCTAGTGTTATATGTTAATGACATATTG
65 GTGTCTATAAAAAGGTTAGTGGAAGTGCCATAATTTTCCTAGTGTTATATATTAATGACATATTG
*
3130676 CTCATAGGAAATGATATACCATTGCTGCAATCTACAAAGATTTGGTTGTCCAAACAATTCTCCAT
130 CTCATAGGAAATGATATACCATTGCTGCAATCTACAAAAATTTGGTTGTCCAAACAATTCTCCAT
*
3130741 GAAGGATTTGGGAGAAGCA
195 GAAAGATTTGGGAGAAGCA
3130760 GCTTACATTC
Statistics
Matches: 207, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
214 165 0.80
215 5 0.02
216 37 0.18
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (215 bp):
GAACATCCGTTTTGATGAAGCTATAAAAGGGTTTGACTTTCATCAAAAAATGAGGATGAACCATG
TGTCTATAAAAAGGTTAGTGGAAGTGCCATAATTTTCCTAGTGTTATATATTAATGACATATTGC
TCATAGGAAATGATATACCATTGCTGCAATCTACAAAAATTTGGTTGTCCAAACAATTCTCCATG
AAAGATTTGGGAGAAGCAAC
Found at i:3139753 original size:64 final size:63
Alignment explanation
Indices: 3139677--3139800 Score: 178
Period size: 64 Copynumber: 2.0 Consensus size: 63
3139667 CCCTTAACAA
* *
3139677 TTTTAAATTTTTTATAACT-TATTTTTATTTTTTCTGAAATCTTATAATTTCGTCTTTACAAAAC
1 TTTTAAAATTTTTATAA-TATATTTTTATTTTTTC-AAAATCTTATAATTTCGTCTTTACAAAAC
* * *
3139741 TTTTAAAATTTTTCTAATATATTTTTATTTTTTCAAAATTTTATAATTTTGTCTTTACAA
1 TTTTAAAATTTTTATAATATATTTTTATTTTTTCAAAATCTTATAATTTCGTCTTTACAA
3139801 TAATTTTTTA
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
63 24 0.44
64 30 0.56
ACGTcount: A:0.31, C:0.09, G:0.02, T:0.58
Consensus pattern (63 bp):
TTTTAAAATTTTTATAATATATTTTTATTTTTTCAAAATCTTATAATTTCGTCTTTACAAAAC
Found at i:3141142 original size:34 final size:34
Alignment explanation
Indices: 3141103--3141171 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
3141093 AAGAGTGACT
3141103 AAAGAGTAGTCATACAAGATCATGGATTGAATCA
1 AAAGAGTAGTCATACAAGATCATGGATTGAATCA
*
3141137 AAAGAGTAGTCATACAAGATTATGGATTGAATCA
1 AAAGAGTAGTCATACAAGATCATGGATTGAATCA
3141171 A
1 A
3141172 TAATTCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (34 bp):
AAAGAGTAGTCATACAAGATCATGGATTGAATCA
Found at i:3144721 original size:31 final size:29
Alignment explanation
Indices: 3144685--3144757 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
3144675 ATTTTATAAA
* *
3144685 AAATTAAATAAATATT-TATTTTTATTAT
1 AAATTAAATAAATTTTATATTTTTATTTT
* *
3144713 -ATTTAATTAAATTTTTATATTTTTATTTT
1 AAATTAAATAAA-TTTTATATTTTTATTTT
3144742 AAATTAAATAAATTTT
1 AAATTAAATAAATTTT
3144758 TATAATTAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
27 9 0.25
28 3 0.08
29 15 0.42
30 9 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
AAATTAAATAAATTTTATATTTTTATTTT
Found at i:3144746 original size:26 final size:28
Alignment explanation
Indices: 3144688--3144751 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
3144678 TTATAAAAAA
*
3144688 TTAAA-TAAATATTTATTTTTATTATAT
1 TTAAATTAAATATTTATATTTATTATAT
*
3144715 TT-AATTAAATTTTTATATTT-TTAT-T
1 TTAAATTAAATATTTATATTTATTATAT
3144740 TTAAATTAAATA
1 TTAAATTAAATA
3144752 AATTTTTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
25 3 0.09
26 14 0.44
27 15 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
TTAAATTAAATATTTATATTTATTATAT
Found at i:3144879 original size:14 final size:15
Alignment explanation
Indices: 3144860--3144891 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
3144850 AAATGATATT
3144860 TTAATTAATTA-TAA
1 TTAATTAATTATTAA
3144874 TTAATTAATTATTAA
1 TTAATTAATTATTAA
3144889 TTA
1 TTA
3144892 TAAAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAATTAATTATTAA
Found at i:3164402 original size:22 final size:24
Alignment explanation
Indices: 3164358--3164427 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 24
3164348 TTGTCTTCTT
*
3164358 TTTTCTTTTTTTTCTTCCCTTT-C
1 TTTTCCTTTTTTTCTTCCCTTTCC
*
3164381 -TTTCCTTTTTTTC-TCTCTTTTCC
1 TTTTCCTTTTTTTCTTC-CCTTTCC
3164404 TTTTCTCTTTCTTTTCTTCTCCTT
1 TTTTC-CTTT-TTTTCTTC-CCTT
3164428 CCCTGCGGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
21 2 0.05
22 16 0.42
23 1 0.03
24 4 0.11
25 4 0.11
26 5 0.13
27 6 0.16
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (24 bp):
TTTTCCTTTTTTTCTTCCCTTTCC
Found at i:3164407 original size:17 final size:18
Alignment explanation
Indices: 3164381--3164419 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
3164371 CTTCCCTTTC
*
3164381 TTTCCTTTTTTTCTCTCT
1 TTTCCTTTTTCTCTCTCT
*
3164399 TTTCC-TTTTCTCTTTCT
1 TTTCCTTTTTCTCTCTCT
3164416 TTTC
1 TTTC
3164420 TTCTCCTTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTCCTTTTTCTCTCTCT
Found at i:3164472 original size:16 final size:15
Alignment explanation
Indices: 3164446--3164479 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
3164436 GTCTCCCTTC
*
3164446 TCTTTTTCTTTTTCT
1 TCTTTTTCTTTTCCT
3164461 TCTTTCTTCTTTTCCT
1 TCTTT-TTCTTTTCCT
3164477 TCT
1 TCT
3164480 CTTTGTCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (15 bp):
TCTTTTTCTTTTCCT
Found at i:3165298 original size:2 final size:2
Alignment explanation
Indices: 3165291--3165340 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
3165281 GATACACAAC
3165291 AT AT AT AT AT AT AT 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
3165333 AT AT AT AT
1 AT AT AT AT
3165341 CAGCATCCTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3166401 original size:15 final size:15
Alignment explanation
Indices: 3166381--3166413 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3166371 CCCTGATAAT
*
3166381 TTTAAAGGTGAAATA
1 TTTAAAGGTAAAATA
3166396 TTTAAAGGTAAAATA
1 TTTAAAGGTAAAATA
3166411 TTT
1 TTT
3166414 TGACTTTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.39
Consensus pattern (15 bp):
TTTAAAGGTAAAATA
Found at i:3168219 original size:37 final size:37
Alignment explanation
Indices: 3168169--3168243 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
3168159 TAAAAAAGTA
3168169 TAAAAACTAATTATATAATTGGACAGTTTATAAGAAT
1 TAAAAACTAATTATATAATTGGACAGTTTATAAGAAT
3168206 TAAAAACTAATTATATAATTGGACAGTTTATAAGAAT
1 TAAAAACTAATTATATAATTGGACAGTTTATAAGAAT
3168243 T
1 T
3168244 TCATGTGAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.48, C:0.05, G:0.11, T:0.36
Consensus pattern (37 bp):
TAAAAACTAATTATATAATTGGACAGTTTATAAGAAT
Found at i:3172517 original size:31 final size:31
Alignment explanation
Indices: 3172479--3172557 Score: 158
Period size: 31 Copynumber: 2.5 Consensus size: 31
3172469 AGTAAAATGA
3172479 TTAAAATATTAAAATGAAGCTACAATAAAGT
1 TTAAAATATTAAAATGAAGCTACAATAAAGT
3172510 TTAAAATATTAAAATGAAGCTACAATAAAGT
1 TTAAAATATTAAAATGAAGCTACAATAAAGT
3172541 TTAAAATATTAAAATGA
1 TTAAAATATTAAAATGA
3172558 TTAAAATACC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.56, C:0.05, G:0.09, T:0.30
Consensus pattern (31 bp):
TTAAAATATTAAAATGAAGCTACAATAAAGT
Found at i:3172969 original size:12 final size:12
Alignment explanation
Indices: 3172952--3172978 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3172942 CTCTCAACCC
3172952 TCACCACCATCA
1 TCACCACCATCA
3172964 TCACCACCATCA
1 TCACCACCATCA
3172976 TCA
1 TCA
3172979 TCAAGATGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.48, G:0.00, T:0.19
Consensus pattern (12 bp):
TCACCACCATCA
Found at i:3180970 original size:21 final size:21
Alignment explanation
Indices: 3180944--3180987 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3180934 TTACACAAAT
*
3180944 CTCTATATGGCTTGAAGCAAG
1 CTCTATATGGCTTAAAGCAAG
**
3180965 CTCTATATTTCTTAAAGCAAG
1 CTCTATATGGCTTAAAGCAAG
3180986 CT
1 CT
3180988 TCCAGACAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (21 bp):
CTCTATATGGCTTAAAGCAAG
Found at i:3187532 original size:136 final size:135
Alignment explanation
Indices: 3187391--3187662 Score: 483
Period size: 136 Copynumber: 2.0 Consensus size: 135
3187381 TTTTGAGATC
3187391 TCTTTATTTTCAATGATTTCAAGTACTTGAATTTTTTCTGAAATTTTTATCAATTATGTCAAAGG
1 TCTTTATTTTCAATGATTTCAAGTACTTGAATTTTTTCTGAAATTTTTATCAATTATGTCAAAGG
*
3187456 TCTCTTCTAGAGTTTCTACTT-CCTCTTTCTGACCATCTTAAATATTTACTCATTTTCTTTTTTT
66 TCTCTTCTAGAGTTTCTA-TTACCTCTTTCTGACCATCTTAAATATTTACTCATTTTCTTTTTTG
3187520 AAAATT
130 AAAATT
*
3187526 TNCTTTATTTTCAATGATTTCAAGTACTTGAATTTTTTCTGAAATTTTTATCAATTATGTCAAGG
1 T-CTTTATTTTCAATGATTTCAAGTACTTGAATTTTTTCTGAAATTTTTATCAATTATGTCAAAG
* *
3187591 GTCTCTTCTAGAGTTTCTATTACCTCTTTCTGACCATTTTGAATATTTACTCATTTTCTTTTTTG
65 GTCTCTTCTAGAGTTTCTATTACCTCTTTCTGACCATCTTAAATATTTACTCATTTTCTTTTTTG
3187656 AAAATT
130 AAAATT
3187662 T
1 T
3187663 TATCTTTGGA
Statistics
Matches: 131, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
135 3 0.02
136 128 0.98
ACGTcount: A:0.25, C:0.15, G:0.08, T:0.51
Consensus pattern (135 bp):
TCTTTATTTTCAATGATTTCAAGTACTTGAATTTTTTCTGAAATTTTTATCAATTATGTCAAAGG
TCTCTTCTAGAGTTTCTATTACCTCTTTCTGACCATCTTAAATATTTACTCATTTTCTTTTTTGA
AAATT
Found at i:3189547 original size:20 final size:20
Alignment explanation
Indices: 3189522--3189567 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
3189512 TTTTTACCCC
*
3189522 ATTTGACTTATTTGAGTATA
1 ATTTGACTTATTGGAGTATA
*
3189542 ATTTGACTTATTGGAGTATG
1 ATTTGACTTATTGGAGTATA
3189562 ATTTGA
1 ATTTGA
3189568 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.04, G:0.20, T:0.48
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:3192910 original size:28 final size:28
Alignment explanation
Indices: 3192812--3192919 Score: 164
Period size: 28 Copynumber: 3.8 Consensus size: 28
3192802 ATCTTTTCGT
*
3192812 TATTCATCCACTTCT-AGTGGGTTGAAAG
1 TATTCATCCACTTTTGA-TGGGTTGAAAG
*
3192840 TATTCATCCACTTTTGGTGGGTTGAAAG
1 TATTCATCCACTTTTGATGGGTTGAAAG
3192868 TATTCATCCACTTTTGATGGGTTGAAAG
1 TATTCATCCACTTTTGATGGGTTGAAAG
*
3192896 TATTCATTCACTTTTTGATGGGTT
1 TATTCATCCAC-TTTTGATGGGTT
3192920 ATCCACTTCT
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
28 62 0.84
29 12 0.16
ACGTcount: A:0.22, C:0.15, G:0.21, T:0.42
Consensus pattern (28 bp):
TATTCATCCACTTTTGATGGGTTGAAAG
Found at i:3192959 original size:8 final size:8
Alignment explanation
Indices: 3192946--3192972 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
3192936 TTATCAATTT
3192946 TTAGTGGG
1 TTAGTGGG
3192954 TTAGTGGG
1 TTAGTGGG
3192962 TTAGTGGG
1 TTAGTGGG
3192970 TTA
1 TTA
3192973 AGGCATTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.44, T:0.41
Consensus pattern (8 bp):
TTAGTGGG
Found at i:3193051 original size:25 final size:26
Alignment explanation
Indices: 3193023--3193084 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
3193013 TAGATTTTGA
* *
3193023 TGGTAAAATTAT-TATCCACTTATGG
1 TGGTAAAATTATCCATCCACTTATGC
*
3193048 TGGTAAAATTATCCATTCACTTATGC
1 TGGTAAAATTATCCATCCACTTATGC
*
3193074 TGATAAAATTA
1 TGGTAAAATTA
3193085 GAGGAAATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 12 0.38
26 20 0.62
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (26 bp):
TGGTAAAATTATCCATCCACTTATGC
Found at i:3193887 original size:22 final size:22
Alignment explanation
Indices: 3193862--3193903 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3193852 TAGTTTTAGG
*
3193862 CATTATGTGACTAATTTTTATA
1 CATTACGTGACTAATTTTTATA
* *
3193884 CATTGCGTGACTGATTTTTA
1 CATTACGTGACTAATTTTTA
3193904 AGCAATGCCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (22 bp):
CATTACGTGACTAATTTTTATA
Found at i:3193941 original size:23 final size:23
Alignment explanation
Indices: 3193914--3193974 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
3193904 AGCAATGCCT
*
3193914 AAGTCACACAATGCTTTACTAAC
1 AAGTCACACAATGCCTTACTAAC
*
3193937 TAGTCACACAATGCCTTACTAAC
1 AAGTCACACAATGCCTTACTAAC
*
3193960 AAGTCACGCAATGCC
1 AAGTCACACAATGCC
3193975 CATCAACTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.36, C:0.30, G:0.11, T:0.23
Consensus pattern (23 bp):
AAGTCACACAATGCCTTACTAAC
Found at i:3194049 original size:69 final size:69
Alignment explanation
Indices: 3193934--3194127 Score: 255
Period size: 69 Copynumber: 2.8 Consensus size: 69
3193924 ATGCTTTACT
* * * * *
3193934 AACTAGTCACACAATGCCTTACTAACAAGTCACGCAATGCCCATCAACTAGTCATGTAATGCCTT
1 AACTAGTCACACAATGCC-CA-TAACTAGTCACGCAATGCCTATCAACTAGTCACGCAATGCCTT
3193999 ATCAAA
64 ATCAAA
* *
3194005 AACTAGTCACGCAATGCCCA-AAGTTAGTCACGCAATGCCTATCAACTAGTCACGCAATGCCTTA
1 AACTAGTCACACAATGCCCATAA-CTAGTCACGCAATGCCTATCAACTAGTCACGCAATGCCTTA
3194069 TCAAA
65 TCAAA
* **
3194074 AACTAGTCACACAATGCCTATTAACTAGTCACGCAATGCCTAAAAACTAGTCAC
1 AACTAGTCACACAATGCCCA-TAACTAGTCACGCAATGCCTATCAACTAGTCAC
3194128 ATAATTTTCA
Statistics
Matches: 108, Mismatches: 12, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
68 2 0.02
69 59 0.55
70 28 0.26
71 19 0.18
ACGTcount: A:0.37, C:0.28, G:0.12, T:0.23
Consensus pattern (69 bp):
AACTAGTCACACAATGCCCATAACTAGTCACGCAATGCCTATCAACTAGTCACGCAATGCCTTAT
CAAA
Found at i:3194057 original size:22 final size:22
Alignment explanation
Indices: 3193934--3194127 Score: 169
Period size: 22 Copynumber: 8.5 Consensus size: 22
3193924 ATGCTTTACT
*
3193934 AACTAGTCACACAATGCCT-TAC
1 AACTAGTCACGCAATGCCTAT-C
* *
3193956 TAACAAGTCACGCAATGCCCATC
1 -AACTAGTCACGCAATGCCTATC
* *
3193979 AACTAGTCATGTAATGCCTTATC
1 AACTAGTCACGCAATGCC-TATC
*
3194002 AAAAACTAGTCACGCAATGCCCA--
1 ---AACTAGTCACGCAATGCCTATC
*
3194025 AAGTTAGTCACGCAATGCCTATC
1 AA-CTAGTCACGCAATGCCTATC
3194048 AACTAGTCACGCAATGCCTTATC
1 AACTAGTCACGCAATGCC-TATC
* *
3194071 AAAAACTAGTCACACAATGCCTATT
1 ---AACTAGTCACGCAATGCCTATC
**
3194096 AACTAGTCACGCAATGCCTAAA
1 AACTAGTCACGCAATGCCTATC
3194118 AACTAGTCAC
1 AACTAGTCAC
3194128 ATAATTTTCA
Statistics
Matches: 141, Mismatches: 18, Indels: 25
0.77 0.10 0.14
Matches are distributed among these distances:
20 2 0.01
21 16 0.11
22 59 0.42
23 26 0.18
24 1 0.01
25 4 0.03
26 33 0.23
ACGTcount: A:0.37, C:0.28, G:0.12, T:0.23
Consensus pattern (22 bp):
AACTAGTCACGCAATGCCTATC
Found at i:3194100 original size:48 final size:45
Alignment explanation
Indices: 3193934--3194128 Score: 182
Period size: 48 Copynumber: 4.2 Consensus size: 45
3193924 ATGCTTTACT
* * *
3193934 AACTAGTCACACAATGCCTTACTAACAAGTCACGCAATGCC-CATC
1 AACTAGTCACACAATGCCTTATTAACTAGTCACGCAATGCCTCA-A
*** *
3193979 AACTAGTCATGTAATGCCTTATCAAAAACTAGTCACGCAATGCC-CAA
1 AACTAGTCACACAATGCCTTAT---TAACTAGTCACGCAATGCCTCAA
** * *
3194026 AGTTAGTCACGCAATGCC-TATCAACTAGTCACGCAATGCCTTATCAAA
1 AACTAGTCACACAATGCCTTATTAACTAGTCACGCAATGCC---TC-AA
*
3194074 AACTAGTCACACAATGCC-TATTAACTAGTCACGCAATGCCTAAA
1 AACTAGTCACACAATGCCTTATTAACTAGTCACGCAATGCCTCAA
3194118 AACTAGTCACA
1 AACTAGTCACA
3194129 TAATTTTCAA
Statistics
Matches: 125, Mismatches: 17, Indels: 17
0.79 0.11 0.11
Matches are distributed among these distances:
43 18 0.14
44 13 0.10
45 19 0.15
46 3 0.02
47 15 0.12
48 57 0.46
ACGTcount: A:0.37, C:0.28, G:0.12, T:0.23
Consensus pattern (45 bp):
AACTAGTCACACAATGCCTTATTAACTAGTCACGCAATGCCTCAA
Found at i:3194829 original size:59 final size:59
Alignment explanation
Indices: 3194718--3194834 Score: 135
Period size: 59 Copynumber: 2.0 Consensus size: 59
3194708 CTTCCATGTT
* * ** * * * ** *
3194718 CATGATCATAATTATTAAATGATGTTGCATTTATTTTAGGGAATGGATGGATTCATGAC
1 CATGACCATAATTATTAAATGATATCACATTCACTTCAGGGAATCAACGGATTCATGAC
*
3194777 CATGACCATAATTATTAAATGATATCACATTCACTTCAGGGAATCAACGGATTTATGA
1 CATGACCATAATTATTAAATGATATCACATTCACTTCAGGGAATCAACGGATTCATGA
3194835 TTTTTTTATT
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
59 47 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (59 bp):
CATGACCATAATTATTAAATGATATCACATTCACTTCAGGGAATCAACGGATTCATGAC
Found at i:3204659 original size:16 final size:16
Alignment explanation
Indices: 3204634--3204664 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3204624 AATTTTTTAT
*
3204634 ATATTTATATATATTA
1 ATATTAATATATATTA
3204650 ATATTAATATATATT
1 ATATTAATATATATT
3204665 TTTTATATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATATTAATATATATTA
Found at i:3204973 original size:21 final size:21
Alignment explanation
Indices: 3204949--3204989 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3204939 TTATGAATAT
3204949 ATATAATT-ATATTATATATAC
1 ATATAATTAAT-TTATATATAC
*
3204970 ATATATTTAATTTATATATA
1 ATATAATTAATTTATATATA
3204990 AACATTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
ATATAATTAATTTATATATAC
Found at i:3205008 original size:21 final size:21
Alignment explanation
Indices: 3204960--3205022 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
3204950 TATAATTATA
*
3204960 TTATATATACATATATTTAATT
1 TTATATAAACAT-TATTTAATT
3204982 TATATATAAACATTATTATAA-T
1 T-TATATAAACATTATT-TAATT
*
3205004 TTATAATAAACTTTATTTA
1 TTAT-ATAAACATTATTTA
3205023 TATGATTACA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
21 5 0.14
22 18 0.50
23 13 0.36
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (21 bp):
TTATATAAACATTATTTAATT
Found at i:3205024 original size:23 final size:23
Alignment explanation
Indices: 3204950--3205020 Score: 83
Period size: 23 Copynumber: 3.0 Consensus size: 23
3204940 TATGAATATA
*
3204950 TATAATTATATTATATATACATATAT
1 TATAATT-TA-TATATAAACAT-TAT
3204976 T-TAATTTATATATAAACATTAT
1 TATAATTTATATATAAACATTAT
*
3204998 TATAATTTATA-ATAAACTTTAT
1 TATAATTTATATATAAACATTAT
3205020 T
1 T
3205021 TATATGATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
22 15 0.36
23 19 0.45
24 2 0.05
25 5 0.12
26 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (23 bp):
TATAATTTATATATAAACATTAT
Found at i:3205232 original size:202 final size:191
Alignment explanation
Indices: 3204954--3205406 Score: 506
Period size: 202 Copynumber: 2.3 Consensus size: 191
3204944 AATATATATA
** * * *
3204954 ATTATAT-TATATATACATATATTTAATTTA-TATATAAACAT-TATTATAATTTATA-ATAAAC
1 ATTATATATATATATA-ATA-AAATAATATATTATATATACATATATT-TAATTTATACATAAAA
* * * ** *
3205015 T-TTATTTATATGATTACACTTAATAACTTTACTAGCTATCACTTTAGATTTTATAATGTATTGT
63 TACTA-CTATATGATTACACTTAATAACTTTACTAGCTATCACCTTAGATTTTATAACATATTAT
*
3205079 TTATTA-TTAGTTATTATTGTATA-AACTTTGATAAAAAACATTATAACATATAAGTTATGTCAT
127 TTA-TACTTAGTTATTATT-TATAGAACTTCGATAAAAAACATTATAACATATAA-TT-TGT-A-
*
3205142 TGATTTCGTGT
186 TCA--T--T-T
* *
3205153 ATATATATATATATATAATAAAGTCATATATTATATATACATATATTTAATTTATACATAAAATA
1 AT-TATATATATATATAATAAAATAATATATTATATATACATATATTTAATTTATACATAAAATA
* *
3205218 CTACTANTATGATTACACTTAATAACTTTATTAGTTATCACCTTAGATTTTATAACATATTATTT
65 CTACTA-TATGATTACACTTAATAACTTTACTAGCTATCACCTTAGATTTTATAACATATTATTT
* * *
3205283 ATACTTAGTTATTATTTATATGAACTTCGATATAAAACATTTTAATATATAATTTGTATCATTT
129 ATACTTAGTTATTATTTATA-GAACTTCGATAAAAAACATTATAACATATAATTTGTATCATTT
*
3205347 ATTTTATATATATATAATAAAATAATATATTATATATACATATATTTAATTTATACATAA
1 ATTATATATATATATAATAAAATAATATATTATATATACATATATTTAATTTATACATAA
3205407 GCATTACTAT
Statistics
Matches: 222, Mismatches: 22, Indels: 26
0.82 0.08 0.10
Matches are distributed among these distances:
193 55 0.25
194 3 0.01
195 1 0.00
197 1 0.00
199 10 0.05
200 28 0.13
201 29 0.13
202 69 0.31
203 26 0.12
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.47
Consensus pattern (191 bp):
ATTATATATATATATAATAAAATAATATATTATATATACATATATTTAATTTATACATAAAATAC
TACTATATGATTACACTTAATAACTTTACTAGCTATCACCTTAGATTTTATAACATATTATTTAT
ACTTAGTTATTATTTATAGAACTTCGATAAAAAACATTATAACATATAATTTGTATCATTT
Found at i:3205401 original size:193 final size:199
Alignment explanation
Indices: 3205021--3205406 Score: 522
Period size: 202 Copynumber: 2.0 Consensus size: 199
3205011 AAACTTTATT
* ** *
3205021 TATATGATTACACTTAATAACTTTACTAGCTATCACTTTAGATTTTATAATGTATTGTTTATTAT
1 TATATGATTACACTTAATAACTTTACTAGCTATCACCTTAGATTTTATAACATATTATTTATTAT
* *
3205086 TAGTTATTATTGTATAAACTTTGATAAAAAACATTATAACATATAAGTTATGTCATTGATTTCGT
66 TAGTTATTATTGTATAAACTTCGATAAAAAACATTATAACATATAAGTTATGTCATTCA-TTC-T
* *
3205151 GTATATATATATATATATAATAAAGTCATATATTATATATACATATATTTAATTTATACATAAAA
129 GTATATATATATATATATAATAAAATAATATATTATATATACATATATTTAATTTATACATAAAA
3205216 TACTAC
194 TACTAC
* *
3205222 TANTATGATTACACTTAATAACTTTATTAGTTATCACCTTAGATTTTATAACATATTATTTA-TA
1 TA-TATGATTACACTTAATAACTTTACTAGCTATCACCTTAGATTTTATAACATATTATTTATTA
* * *
3205286 CTTAGTTATTATT-TATATGAACTTCGATATAAAACATTTTAATATATAA-TT-TGT-A-TCA-T
65 -TTAGTTATTATTGTATA--AACTTCGATAAAAAACATTATAACATATAAGTTATGTCATTCATT
*
3205345 -T-TAT-TTTATATATATATAATAAAATAATATATTATATATACATATATTTAATTTATACATAA
127 CTGTATATATATATATATATAATAAAATAATATATTATATATACATATATTTAATTTATACATAA
3205407 GCATTACTAT
Statistics
Matches: 167, Mismatches: 14, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
193 55 0.33
194 3 0.02
195 1 0.01
197 1 0.01
199 2 0.01
200 1 0.01
201 11 0.07
202 67 0.40
203 26 0.16
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.46
Consensus pattern (199 bp):
TATATGATTACACTTAATAACTTTACTAGCTATCACCTTAGATTTTATAACATATTATTTATTAT
TAGTTATTATTGTATAAACTTCGATAAAAAACATTATAACATATAAGTTATGTCATTCATTCTGT
ATATATATATATATATAATAAAATAATATATTATATATACATATATTTAATTTATACATAAAATA
CTAC
Found at i:3220196 original size:20 final size:21
Alignment explanation
Indices: 3220153--3220197 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
3220143 ATGTCTAAAG
* *
3220153 TAATTATTTGAAATGAAATTA
1 TAATTATTTGAAATAAAATAA
*
3220174 TAATTGTTTG-AATAAAATAA
1 TAATTATTTGAAATAAAATAA
3220194 TAAT
1 TAAT
3220198 ATTCAATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (21 bp):
TAATTATTTGAAATAAAATAA
Found at i:3222471 original size:19 final size:19
Alignment explanation
Indices: 3222447--3222484 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3222437 ACTTCTAAAC
*
3222447 CTCAAATCATACTGCAATA
1 CTCAAATCATACTCCAATA
3222466 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
3222485 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.03, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:3228590 original size:19 final size:19
Alignment explanation
Indices: 3228563--3228608 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
3228553 AGGAGACAAG
*
3228563 ATAAAATTTT-TAGAATAAA
1 ATAATATTTTATA-AATAAA
3228582 ATAATATTTTATAAATAAA
1 ATAATATTTTATAAATAAA
3228601 ATAATATT
1 ATAATATT
3228609 AAAATATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 23 0.92
20 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
ATAATATTTTATAAATAAA
Found at i:3229057 original size:20 final size:20
Alignment explanation
Indices: 3229012--3229049 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3229002 TTTTGGCCTC
*
3229012 ATTTGACTTATTGGAGTATA
1 ATTTGACTCATTGGAGTATA
3229032 ATTTGACTCATTGGAGTA
1 ATTTGACTCATTGGAGTA
3229050 AGATTTGAGG
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:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (20 bp):
ATTTGACTCATTGGAGTATA
Found at i:3230288 original size:13 final size:13
Alignment explanation
Indices: 3230270--3230294 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3230260 AAAAAAATTG
3230270 TGATTTTATAAAA
1 TGATTTTATAAAA
3230283 TGATTTTATAAA
1 TGATTTTATAAA
3230295 TTTTCTGGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:3237426 original size:21 final size:21
Alignment explanation
Indices: 3237396--3237463 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
3237386 GGACATGTTC
3237396 ATGCAATTCATGAAAAAGACTG
1 ATGC-ATTCATGAAAAAGACTG
* *
3237418 ATGCATTCATTACAAAGACTG
1 ATGCATTCATGAAAAAGACTG
* *
3237439 ATGCATTTATGATAAAGACTG
1 ATGCATTCATGAAAAAGACTG
3237460 ATGC
1 ATGC
3237464 CTCCATTCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
21 37 0.90
22 4 0.10
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.28
Consensus pattern (21 bp):
ATGCATTCATGAAAAAGACTG
Found at i:3238843 original size:6 final size:6
Alignment explanation
Indices: 3238827--3238859 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
3238817 AACTTACTTT
3238827 TTTTTA TTTTT- TATTTTA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA T-TTTTA TTTTTA TTTTTA TTT
3238860 AATTATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 1 0.04
6 23 0.92
7 1 0.04
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:3238923 original size:12 final size:11
Alignment explanation
Indices: 3238906--3238936 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
3238896 AAGTTCATGT
3238906 AAAAAAAATTTC
1 AAAAAAAA-TTC
3238918 AAAAAAAATTC
1 AAAAAAAATTC
3238929 AAAAAAAA
1 AAAAAAAA
3238937 GTAGTAAGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:3239139 original size:22 final size:22
Alignment explanation
Indices: 3239113--3239163 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
3239103 AGGGCTACCA
3239113 ATTGGGCAACCCACTACCCTCC
1 ATTGGGCAACCCACTACCCTCC
* *
3239135 ATTGGGCAGCCCACTACCTTCC
1 ATTGGGCAACCCACTACCCTCC
3239157 ATTGGGC
1 ATTGGGC
3239164 TGCCAACATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.39, G:0.20, T:0.22
Consensus pattern (22 bp):
ATTGGGCAACCCACTACCCTCC
Found at i:3239244 original size:8 final size:7
Alignment explanation
Indices: 3239218--3239276 Score: 73
Period size: 8 Copynumber: 7.9 Consensus size: 7
3239208 TTATTTGGAC
3239218 TACCCAT
1 TACCCAT
3239225 TACCCAT
1 TACCCAT
3239232 TACCCATT
1 TACCCA-T
*
3239240 TACCCAC
1 TACCCAT
3239247 TAGCCCATT
1 TA-CCCA-T
3239256 TACCCATT
1 TACCCA-T
3239264 TACCCAT
1 TACCCAT
3239271 TACCCA
1 TACCCA
3239277 ACAAAAACCT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
7 22 0.47
8 23 0.49
9 2 0.04
ACGTcount: A:0.27, C:0.42, G:0.02, T:0.29
Consensus pattern (7 bp):
TACCCAT
Found at i:3239255 original size:16 final size:15
Alignment explanation
Indices: 3239216--3239276 Score: 72
Period size: 15 Copynumber: 4.1 Consensus size: 15
3239206 TCTTATTTGG
3239216 ACTACCCA-TTACCC
1 ACTACCCATTTACCC
*
3239230 ATTACCCATTTACCC
1 ACTACCCATTTACCC
3239245 ACTAGCCCATTTACCC
1 ACTA-CCCATTTACCC
*
3239261 ATTTACCCA-TTACCC
1 A-CTACCCATTTACCC
3239276 A
1 A
3239277 ACAAAAACCT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
14 7 0.17
15 16 0.39
16 16 0.39
17 2 0.05
ACGTcount: A:0.28, C:0.43, G:0.02, T:0.28
Consensus pattern (15 bp):
ACTACCCATTTACCC
Found at i:3246273 original size:22 final size:22
Alignment explanation
Indices: 3246248--3246468 Score: 86
Period size: 22 Copynumber: 10.0 Consensus size: 22
3246238 TGTGTAATCG
*
3246248 GTTTTTGGGCATTATGTGACTA
1 GTTTTTAGGCATTATGTGACTA
*
3246270 GTTTTTAGGCATTATGTTACTA
1 GTTTTTAGGCATTATGTGACTA
* * *
3246292 ATTTTTAGGCACTGTGTGACT-
1 GTTTTTAGGCATTATGTGACTA
** * **
3246313 GACTGTAGATATTGA-GTGACTA
1 GTTTTTAGGCATT-ATGTGACTA
* * **
3246335 GTTTTAAAGCATTGCGTGACTA
1 GTTTTTAGGCATTATGTGACTA
* * * *
3246357 ATTTTTAGGTATTACGTGACTG
1 GTTTTTAGGCATTATGTGACTA
** * **
3246379 GTTGATATGGTATTGCGTGACTA
1 GTTTTTA-GGCATTATGTGACTA
** ** *
3246402 GTTGATAGGCATTGCGTGACTT
1 GTTTTTAGGCATTATGTGACTA
* * *
3246424 GTTAGTAAGGCATTGTGTGACTA
1 GTT-TTTAGGCATTATGTGACTA
* * *
3246447 GTTAGTAAGGCATTGTGTGACT
1 GTT-TTTAGGCATTATGTGACT
3246469 TAGACATTGC
Statistics
Matches: 155, Mismatches: 39, Indels: 9
0.76 0.19 0.04
Matches are distributed among these distances:
21 12 0.08
22 86 0.55
23 57 0.37
ACGTcount: A:0.23, C:0.10, G:0.27, T:0.40
Consensus pattern (22 bp):
GTTTTTAGGCATTATGTGACTA
Found at i:3246376 original size:65 final size:67
Alignment explanation
Indices: 3246263--3246422 Score: 164
Period size: 65 Copynumber: 2.4 Consensus size: 67
3246253 TGGGCATTAT
* ** * **
3246263 GTGACTAGTTTTTAGGCATTATGTTACTAATTTTTAGGCACTGTGTGACTGACTG-TA-GATATT
1 GTGACTAGTTTTAAGGCATTGCGTGACTAATTTTTAGGCACTACGTGACTGACTGATATGATATT
3246326 GA
66 GA
* * * ** *
3246328 GTGACTAGTTTTAAAGCATTGCGTGACTAATTTTTAGGTATTACGTGACTGGTTGATATGGTATT
1 GTGACTAGTTTTAAGGCATTGCGTGACTAATTTTTAGGCACTACGTGACTGACTGATATGATATT
*
3246393 GC
66 GA
*
3246395 GTGACTAG-TTGATAGGCATTGCGTGACT
1 GTGACTAGTTTTA-AGGCATTGCGTGACT
3246423 TGTTAGTAAG
Statistics
Matches: 77, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
65 44 0.57
66 5 0.06
67 28 0.36
ACGTcount: A:0.24, C:0.11, G:0.26, T:0.39
Consensus pattern (67 bp):
GTGACTAGTTTTAAGGCATTGCGTGACTAATTTTTAGGCACTACGTGACTGACTGATATGATATT
GA
Found at i:3246420 original size:45 final size:44
Alignment explanation
Indices: 3246343--3246468 Score: 119
Period size: 45 Copynumber: 2.8 Consensus size: 44
3246333 TAGTTTTAAA
* * * * *
3246343 GCATTGCGTGACTAATTTTTAGGTATTACGTGACTGGTT-GATATG
1 GCATTGCGTGACT-AGTTATAGGCATTGCGTGACTGGTTAG-TAAG
* *
3246388 GTATTGCGTGACTAGTTGATAGGCATTGCGTGACTTGTTAGTAAG
1 GCATTGCGTGACTAGTT-ATAGGCATTGCGTGACTGGTTAGTAAG
* *
3246433 GCATTGTGTGACTAGTTAGTAAGGCATTGTGTGACT
1 GCATTGCGTGACTAGTTA-T-AGGCATTGCGTGACT
3246469 TAGACATTGC
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
44 4 0.06
45 48 0.72
46 15 0.22
ACGTcount: A:0.22, C:0.11, G:0.29, T:0.37
Consensus pattern (44 bp):
GCATTGCGTGACTAGTTATAGGCATTGCGTGACTGGTTAGTAAG
Found at i:3246450 original size:23 final size:23
Alignment explanation
Indices: 3246323--3246468 Score: 113
Period size: 23 Copynumber: 6.5 Consensus size: 23
3246313 GACTGTAGAT
* * *
3246323 ATTGAGTGACTAGTT-TTAAAGC
1 ATTGCGTGACTAGTTAGTAAGGC
* * * *
3246345 ATTGCGTGACTAATT-TTTAGGT
1 ATTGCGTGACTAGTTAGTAAGGC
* * * *
3246367 ATTACGTGACTGGTT-GATATGGT
1 ATTGCGTGACTAGTTAG-TAAGGC
3246390 ATTGCGTGACTAGTT-G-ATAGGC
1 ATTGCGTGACTAGTTAGTA-AGGC
*
3246412 ATTGCGTGACTTGTTAGTAAGGC
1 ATTGCGTGACTAGTTAGTAAGGC
*
3246435 ATTGTGTGACTAGTTAGTAAGGC
1 ATTGCGTGACTAGTTAGTAAGGC
*
3246458 ATTGTGTGACT
1 ATTGCGTGACT
3246469 TAGACATTGC
Statistics
Matches: 102, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
21 1 0.01
22 45 0.44
23 55 0.54
24 1 0.01
ACGTcount: A:0.24, C:0.10, G:0.28, T:0.38
Consensus pattern (23 bp):
ATTGCGTGACTAGTTAGTAAGGC
Found at i:3246504 original size:22 final size:22
Alignment explanation
Indices: 3246476--3246548 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
3246466 ACTTAGACAT
*
3246476 TGCTTAAAAATTAGTTACGCAA
1 TGCTTAAAAATTAGTTACGTAA
** *
3246498 TGCTTAAAAACCAGTCACGTAA
1 TGCTTAAAAATTAGTTACGTAA
** *
3246520 TGCCCAAAAATTAATTACGTAA
1 TGCTTAAAAATTAGTTACGTAA
*
3246542 TGATTAA
1 TGCTTAA
3246549 GTCACATAAT
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.29
Consensus pattern (22 bp):
TGCTTAAAAATTAGTTACGTAA
Found at i:3250813 original size:73 final size:73
Alignment explanation
Indices: 3250726--3250872 Score: 285
Period size: 73 Copynumber: 2.0 Consensus size: 73
3250716 GATGCATACA
3250726 CCAGCAAAAACATACGGATCCTTTTGAGTCCATTCCATCTCCATCCTAACTGCCAAGCACTTAAA
1 CCAGCAAAAACATACGGATCCTTTTGAGTCCATTCCATCTCCATCCTAACTGCCAAGCACTTAAA
3250791 ACGCTGCT
66 ACGCTGCT
*
3250799 CCAGCAAAAACATACGGATCCTTTTGAGTCCATTCCATCTCCATCCTAACTGCCATGCACTTAAA
1 CCAGCAAAAACATACGGATCCTTTTGAGTCCATTCCATCTCCATCCTAACTGCCAAGCACTTAAA
3250864 ACGCTGCT
66 ACGCTGCT
3250872 C
1 C
3250873 GGGCTCAAAG
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.29, C:0.33, G:0.12, T:0.25
Consensus pattern (73 bp):
CCAGCAAAAACATACGGATCCTTTTGAGTCCATTCCATCTCCATCCTAACTGCCAAGCACTTAAA
ACGCTGCT
Found at i:3251213 original size:22 final size:24
Alignment explanation
Indices: 3251185--3251245 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 24
3251175 TCAAATCTTA
3251185 ATCTTGATCAC-AA-ACACTTGAT
1 ATCTTGATCACGAACACACTTGAT
* *
3251207 ATTTTGATCACGAACTTCACTTGAT
1 ATCTTGATCACGAAC-ACACTTGAT
3251232 ATCTTGATCACGAA
1 ATCTTGATCACGAA
3251246 TTTCGTTGCC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 10 0.30
23 2 0.06
25 21 0.64
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.34
Consensus pattern (24 bp):
ATCTTGATCACGAACACACTTGAT
Found at i:3251292 original size:29 final size:29
Alignment explanation
Indices: 3251210--3251283 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 29
3251200 ACTTGATATT
3251210 TTGATCACGAACTTCACTTG--A--T-ATC
1 TTGATCACGAACTTCA-TTGCCACCTGATC
* *
3251235 TTGATCACGAATTTCGTTGCCACCTGATC
1 TTGATCACGAACTTCATTGCCACCTGATC
*
3251264 TTGATCATGAACTTCATTGC
1 TTGATCACGAACTTCATTGC
3251284 TGCTTGATCA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
24 3 0.08
25 14 0.36
26 1 0.03
28 1 0.03
29 20 0.51
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.36
Consensus pattern (29 bp):
TTGATCACGAACTTCATTGCCACCTGATC
Found at i:3251791 original size:82 final size:79
Alignment explanation
Indices: 3251685--3251837 Score: 180
Period size: 82 Copynumber: 1.9 Consensus size: 79
3251675 AGCATAATTA
* * * * * *
3251685 TTAGAGATAAATTAAATGATCAATAATTAAATTTTGATTGGTCAAAAAATAAGAATATTATCTTT
1 TTAGAGACAAATTAAATGACCAATAACTAAATTTTAATTGATC--AAAATAA-AATATTATCTTC
3251750 AAATTATCTTGATTTAT
63 AAATTATCTTGATTTAT
** * * *
3251767 TTAGAGACAAATTTGATGACCAATAACTGAATTTTAATTGATCCAAATTAAATATTATCTTCAAA
1 TTAGAGACAAATTAAATGACCAATAACTAAATTTTAATTGATCAAAATAAAATATTATCTTCAAA
3251832 TTATCT
66 TTATCT
3251838 CAAGGGATAA
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
79 20 0.33
80 5 0.08
82 35 0.58
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.40
Consensus pattern (79 bp):
TTAGAGACAAATTAAATGACCAATAACTAAATTTTAATTGATCAAAATAAAATATTATCTTCAAA
TTATCTTGATTTAT
Found at i:3252238 original size:33 final size:32
Alignment explanation
Indices: 3252171--3252282 Score: 115
Period size: 33 Copynumber: 3.6 Consensus size: 32
3252161 TATGACCTTA
* *
3252171 GAAGATGTATATTGCAA-AAAA-ACT-A-TTT
1 GAAGAAGTATATTGCAATAAAACAATAACTTT
* * *
3252199 GAAGAAGTATATTGCAATAAGACTATAATTTT
1 GAAGAAGTATATTGCAATAAAACAATAACTTT
*
3252231 GAAAGAAGTATATTGCAATAAAACAATAACCTTG
1 G-AAGAAGTATATTGCAATAAAACAATAA-CTTT
*
3252265 GAATAAGTATATTGCAAT
1 GAAGAAGTATATTGCAAT
3252283 TGGTATTGTA
Statistics
Matches: 69, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
28 16 0.23
29 3 0.04
30 1 0.01
31 1 0.01
32 4 0.06
33 41 0.59
34 3 0.04
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.30
Consensus pattern (32 bp):
GAAGAAGTATATTGCAATAAAACAATAACTTT
Found at i:3252980 original size:41 final size:38
Alignment explanation
Indices: 3252881--3252983 Score: 102
Period size: 41 Copynumber: 2.7 Consensus size: 38
3252871 TGATAGCAAT
* *
3252881 TTGAAAGGTGCTCTTTATAATAG--CACTTGTCAATCC
1 TTGAAAGGTGCTCTTTATAATAGCACACTTGTCAAACA
* * * *
3252917 GTGAAGGGTGCTATTTAAAATAGCACACAATTTGTCAAACA
1 TTGAAAGGTGCTCTTTATAATAGCACAC---TTGTCAAACA
*
3252958 TTGAAAGGTACTCTTTATAATAGCAC
1 TTGAAAGGTGCTCTTTATAATAGCAC
3252984 TTGTTGGTCT
Statistics
Matches: 51, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
36 19 0.37
38 3 0.06
41 29 0.57
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (38 bp):
TTGAAAGGTGCTCTTTATAATAGCACACTTGTCAAACA
Found at i:3254280 original size:69 final size:66
Alignment explanation
Indices: 3254085--3254286 Score: 230
Period size: 69 Copynumber: 3.1 Consensus size: 66
3254075 TGTAGTTCAA
* * * *
3254085 TTTTTTTTTTTTGCCTTAACTTTTGCCTAAGTCGTCCTGTTACATATTTTCAACTTAAC-AG-GC
1 TTTTTTTTTTTTGCCTTAACTTTTGCCTAAGTTGTCCTGTTAAAGATTTTCAATTTAACAAGCGC
3254148 T
66 T
* * * * * * *
3254149 TTTTTTTTTTTTGCCCTAACTTTTGCCTTAGTTGTCCTGTTAAGGATTTTTAGTTTATCAAGCTT
1 TTTTTTTTTTTTGCCTTAACTTTTGCCTAAGTTGTCCTGTTAAAGATTTTCAATTTAACAAGC-G
3254214 CTTT
65 C--T
* * *
3254218 TTTTTTTTTTTTGCCTTAAATTTTGCCTAAGTTGTCATGTTAAAGATTTTCAATTTAGCAAGC-C
1 TTTTTTTTTTTTGCCTTAACTTTTGCCTAAGTTGTCCTGTTAAAGATTTTCAATTTAACAAGCGC
3254282 T
66 T
3254283 TTTT
1 TTTT
3254287 ATGTGCAGTT
Statistics
Matches: 114, Mismatches: 19, Indels: 9
0.80 0.13 0.06
Matches are distributed among these distances:
64 49 0.43
65 7 0.06
67 2 0.02
69 56 0.49
ACGTcount: A:0.18, C:0.16, G:0.12, T:0.53
Consensus pattern (66 bp):
TTTTTTTTTTTTGCCTTAACTTTTGCCTAAGTTGTCCTGTTAAAGATTTTCAATTTAACAAGCGC
T
Found at i:3261147 original size:438 final size:438
Alignment explanation
Indices: 3260332--3261208 Score: 1524
Period size: 438 Copynumber: 2.0 Consensus size: 438
3260322 TTGCTTATCC
*
3260332 TCTCTTTGTAACAATCACACTGAATATTATAGAATAGAGGCTATTTAATATAAAATTCAGTGCAT
1 TCTCTTTGTAACAATCACACTAAATATTATAGAATAGAGGCTATTTAATATAAAATTCAGTGCAT
**
3260397 AATGATAGCATATAGTAACTTGTTATTACCCACTGAACTTTTATTGTTAGTTTTGCTAACTCAAA
66 AAAAATAGCATATAGTAACTTGTTATTACCCACTGAACTTTTATTGTTAGTTTTGCTAACTCAAA
* *
3260462 GTTGGGTTTCCAGTACTAATGCATTTAAGTCAAGGGCTTTAGCTTTATTCTACTAGATATTGATT
131 GTTGGATTTCCAATACTAATGCATTTAAGTCAAGGGCTTTAGCTTTATTCTACTAGATATTGATT
*
3260527 TTACAGTCTTTTTTGGCAATGCTTTGGTAAATGGATCAACCAAATTCTTACAAGATTTAACATAA
196 TTACAGTCTTTTTTGGCAATGCTTTGGTAAACGGATCAACCAAATTCTTACAAGATTTAACATAA
3260592 ACTATTGTTATAACATCATTTGATATTGATTCTCTTATGTAGGCATGTCACAGACTTATGTGTCT
261 ACTATTGTTATAACATCATTTGATATTGATTCTCTTATGTAGGCATGTCACAGACTTATGTGTCT
*
3260657 AGACTTTCCATTATAAATCTTATTGTGGGCCACACACCTTGTAGCCTTACTATCACAATATATGG
326 AGACTTTCCATTATAAATCTTATTCTGGGCCACACACCTTGTAGCCTTACTATCACAATATATGG
3260722 AAATGGTTGACATCTATTGTGGCCACAACTTTATAACTAATTACAAAT
391 AAATGGTTGACATCTATTGTGGCCACAACTTTATAACTAATTACAAAT
* *
3260770 TCTCTTTGTAACAATCACATTAAATATTATAGAAT-GAGGCTATTTAATGTTAAAATTCAGTGCA
1 TCTCTTTGTAACAATCACACTAAATATTATAGAATAGAGGCTATTTAAT-ATAAAATTCAGTGCA
* ** * *
3260834 TAAAAATAGCATATATTAACTTGTTATTAGGCATTGAATTTTTATTGTTAGTTTTGCTAACTCAA
65 TAAAAATAGCATATAGTAACTTGTTATTACCCACTGAACTTTTATTGTTAGTTTTGCTAACTCAA
*
3260899 AGTTGGATTTTCAATACTAATGCATTTAAGTCAAGGGCTTTAGCTTTATTCTACTAGATATTGAT
130 AGTTGGATTTCCAATACTAATGCATTTAAGTCAAGGGCTTTAGCTTTATTCTACTAGATATTGAT
* * *
3260964 TTTACAGTCTTTTTTGGCAATGCTTTGGTAAGCGGATCAGCCAAATTCTTGCAAGATTTAACATA
195 TTTACAGTCTTTTTTGGCAATGCTTTGGTAAACGGATCAACCAAATTCTTACAAGATTTAACATA
3261029 AACTATTGTTATAACATCATTTGATATTGATTCTCTTATGTAGGCATGTCACAGACTTATGTG-C
260 AACTATTGTTATAACATCATTTGATATTGATTCTCTTATGTAGGCATGTCACAGACTTATGTGTC
* * *
3261093 TTAGACTTTTCATTATAAATCTTATTCTGGGCTACACACCTTGTAGCCTTACTATTACAATATAT
325 -TAGACTTTCCATTATAAATCTTATTCTGGGCCACACACCTTGTAGCCTTACTATCACAATATAT
*
3261158 GGAAATGGTTGACATCTGTTGTGGCCACAACTTTATAACTAATTACAAAT
389 GGAAATGGTTGACATCTATTGTGGCCACAACTTTATAACTAATTACAAAT
3261208 T
1 T
3261209 TCTCAACCAT
Statistics
Matches: 415, Mismatches: 22, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
437 14 0.03
438 401 0.97
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (438 bp):
TCTCTTTGTAACAATCACACTAAATATTATAGAATAGAGGCTATTTAATATAAAATTCAGTGCAT
AAAAATAGCATATAGTAACTTGTTATTACCCACTGAACTTTTATTGTTAGTTTTGCTAACTCAAA
GTTGGATTTCCAATACTAATGCATTTAAGTCAAGGGCTTTAGCTTTATTCTACTAGATATTGATT
TTACAGTCTTTTTTGGCAATGCTTTGGTAAACGGATCAACCAAATTCTTACAAGATTTAACATAA
ACTATTGTTATAACATCATTTGATATTGATTCTCTTATGTAGGCATGTCACAGACTTATGTGTCT
AGACTTTCCATTATAAATCTTATTCTGGGCCACACACCTTGTAGCCTTACTATCACAATATATGG
AAATGGTTGACATCTATTGTGGCCACAACTTTATAACTAATTACAAAT
Found at i:3276471 original size:113 final size:114
Alignment explanation
Indices: 3276280--3276485 Score: 308
Period size: 113 Copynumber: 1.8 Consensus size: 114
3276270 AAAGTACGTT
* *
3276280 CTTTTTGGAATGGTAGCGCAGACTGTGATTTCTGAGAAGATGGAGAGAATTTGTGAAATATTAGT
1 CTTTTTGGAATGGTAGCGCACACTGTGATTTCT-AGAAGATGGAGAGAATTTGTGAAATACTAGT
3276345 CTATATTTGGGGTGTAAGCACCATTTTTGGTCCAATATTCAAAGGGATATA
65 CTATATTTGGGGTGTAAGCACC-TTTTTGGTCCAATATTCAAAGGGATATA
* * * *
3276396 CTTTTTGGAGTGGTAGTGCACACTGTGATTTCT-G-AGATGGAGAGAATTTTTGAAATGCTAGTC
1 CTTTTTGGAATGGTAGCGCACACTGTGATTTCTAGAAGATGGAGAGAATTTGTGAAATACTAGTC
* *
3276459 TATGTTTTGGGTGTAAGCACCTTTTTG
66 TATATTTGGGGTGTAAGCACCTTTTTG
3276486 TGTTTTCTCT
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
112 6 0.07
113 45 0.55
114 1 0.01
116 30 0.37
ACGTcount: A:0.26, C:0.11, G:0.27, T:0.37
Consensus pattern (114 bp):
CTTTTTGGAATGGTAGCGCACACTGTGATTTCTAGAAGATGGAGAGAATTTGTGAAATACTAGTC
TATATTTGGGGTGTAAGCACCTTTTTGGTCCAATATTCAAAGGGATATA
Found at i:3277282 original size:2 final size:2
Alignment explanation
Indices: 3277273--3277320 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
3277263 CAATTTTTTA
*
3277273 AT AT -T AT AT AT AT AT AT AT AT AT AC AT AT AT A- 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
3277313 AT AT AT AT
1 AT AT AT AT
3277321 TCTTTCTCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3281142 original size:28 final size:28
Alignment explanation
Indices: 3281088--3281142 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
3281078 TACTAGGTAA
*
3281088 ATAACATAATTAATTTATAATCGTATCC
1 ATAACATAATTAATTTATAAACGTATCC
*
3281116 ATAACATAATTAATTTATAAACTTATC
1 ATAACATAATTAATTTATAAACGTATC
3281143 TATTTTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.45, C:0.13, G:0.02, T:0.40
Consensus pattern (28 bp):
ATAACATAATTAATTTATAAACGTATCC
Found at i:3281192 original size:21 final size:23
Alignment explanation
Indices: 3281167--3281214 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 23
3281157 ATCATAAGTA
3281167 ATTTTTAATCTTATTT-A-TTTT
1 ATTTTTAATCTTATTTAATTTTT
*
3281188 ATTTTTAATGTTATTTAATTTTT
1 ATTTTTAATCTTATTTAATTTTT
3281211 ATTT
1 ATTT
3281215 ATTTTTTACC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 15 0.62
22 1 0.04
23 8 0.33
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (23 bp):
ATTTTTAATCTTATTTAATTTTT
Found at i:3281203 original size:17 final size:15
Alignment explanation
Indices: 3281177--3281219 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 15
3281167 ATTTTTAATC
3281177 TTATTTATTTTATTT
1 TTATTTATTTTATTT
*
3281192 TTAATGTTATTTAATTT
1 TT-AT-TTATTTTATTT
3281209 TTATTTATTTT
1 TTATTTATTTT
3281220 TTACCTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 8 0.33
16 4 0.17
17 12 0.50
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (15 bp):
TTATTTATTTTATTT
Found at i:3281707 original size:16 final size:15
Alignment explanation
Indices: 3281682--3281711 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3281672 ATGTGAAATT
3281682 TAATATTTATAATAA
1 TAATATTTATAATAA
3281697 TAATAATTTATAATA
1 TAAT-ATTTATAATA
3281712 TACAGTACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATATTTATAATAA
Found at i:3282492 original size:56 final size:57
Alignment explanation
Indices: 3282431--3282544 Score: 194
Period size: 57 Copynumber: 2.0 Consensus size: 57
3282421 CATGGTACAC
3282431 TAATTAATGAAGGATGAACAAGCCACG-TTGCCAACAGCTTTGAAAATGAAGGAGAT
1 TAATTAATGAAGGATGAACAAGCCACGTTTGCCAACAGCTTTGAAAATGAAGGAGAT
* * *
3282487 TAATTAATGAAGGATGAACAAGTCACGTTTGCCAGCGGCTTTGAAAATGAAGGAGAT
1 TAATTAATGAAGGATGAACAAGCCACGTTTGCCAACAGCTTTGAAAATGAAGGAGAT
3282544 T
1 T
3282545 CGATGAAGTA
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
56 26 0.48
57 28 0.52
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.24
Consensus pattern (57 bp):
TAATTAATGAAGGATGAACAAGCCACGTTTGCCAACAGCTTTGAAAATGAAGGAGAT
Found at i:3283207 original size:6 final size:6
Alignment explanation
Indices: 3283196--3283220 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3283186 TCAATTAAGA
3283196 ATTTAT ATTTAT ATTTAT ATTTAT A
1 ATTTAT ATTTAT ATTTAT ATTTAT A
3283221 GATCATGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
ATTTAT
Found at i:3286240 original size:50 final size:50
Alignment explanation
Indices: 3286165--3286262 Score: 187
Period size: 50 Copynumber: 2.0 Consensus size: 50
3286155 TCAAGGTGGT
*
3286165 GAGTCCTCCGATAAAGACAAGGAAATTGCATCCGAGGACCAGTAGACAAA
1 GAGTCCTCCGATAAAGACAAGGAAATTGCATCCGAAGACCAGTAGACAAA
3286215 GAGTCCTCCGATAAAGACAAGGAAATTGCATCCGAAGACCAGTAGACA
1 GAGTCCTCCGATAAAGACAAGGAAATTGCATCCGAAGACCAGTAGACA
3286263 GAGTACTTCG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.40, C:0.22, G:0.23, T:0.14
Consensus pattern (50 bp):
GAGTCCTCCGATAAAGACAAGGAAATTGCATCCGAAGACCAGTAGACAAA
Found at i:3288628 original size:22 final size:23
Alignment explanation
Indices: 3288603--3288646 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3288593 AAGTCACTCA
*
3288603 ATGCCTA-ATATCCACTCACATT
1 ATGCCTACATAACCACTCACATT
*
3288625 ATGCCTACATAACCAGTCACAT
1 ATGCCTACATAACCACTCACAT
3288647 ACTGGCCCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.34, C:0.32, G:0.07, T:0.27
Consensus pattern (23 bp):
ATGCCTACATAACCACTCACATT
Found at i:3288899 original size:22 final size:22
Alignment explanation
Indices: 3288834--3288882 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
3288824 CATTATGCCA
3288834 ACATAACAACAGGTCACGCAAT
1 ACATAACAACAGGTCACGCAAT
3288856 ACATAACAACAGGTCACGCAAT
1 ACATAACAACAGGTCACGCAAT
3288878 ACATA
1 ACATA
3288883 GAAATCAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.47, C:0.27, G:0.12, T:0.14
Consensus pattern (22 bp):
ACATAACAACAGGTCACGCAAT
Found at i:3288983 original size:188 final size:188
Alignment explanation
Indices: 3288658--3289026 Score: 540
Period size: 188 Copynumber: 2.0 Consensus size: 188
3288648 CTGGCCCAAT
* * * *
3288658 GTCATGCAATACATAACAACAGGTCATGTAATACATAAAAACCAGGCACATAATGCCTAAAAACT
1 GTCACGCAATACATAACAACAGGTCACGCAATACATAAAAACCAGGCACACAATGCCTAAAAACT
* * **
3288723 AGTGAACAAAAGCCTCAAAACAAGAGATGAATTGCATAAGTCATGCATCGCCAATCTCGTAATAC
66 AGTGAACAAAAGCCTCAAAACAAGAGATGAATTGCACAAGTCATGCACCGCCAATCTCACAATAC
* *
3288788 TTAATAATAAGTCACTCAATGCCTAATATCCACTCACATTATGCCAACATAACAACAG
131 CTAATAATAAGTCACTCAATACCTAATATCCACTCACATTATGCCAACATAACAACAG
* * ** *
3288846 GTCACGCAATACATAACAACAGGTCACGCAATACATAGAAATCAGTTACGCAATGCCTAAAAACT
1 GTCACGCAATACATAACAACAGGTCACGCAATACATAAAAACCAGGCACACAATGCCTAAAAACT
* * *
3288911 AGTGAATAAAAGCCTCAAAACAAGAGATGAATTGCACAAGTCATGCACCGTCAGTCTCACAATAC
66 AGTGAACAAAAGCCTCAAAACAAGAGATGAATTGCACAAGTCATGCACCGCCAATCTCACAATAC
** * *
3288976 CTAATAATAAGTCACTTGATACCTAATATCCACTCACGTTATGCCACCATA
131 CTAATAATAAGTCACTCAATACCTAATATCCACTCACATTATGCCAACATA
3289027 TGTAGTCACG
Statistics
Matches: 159, Mismatches: 22, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
188 159 1.00
ACGTcount: A:0.42, C:0.24, G:0.13, T:0.22
Consensus pattern (188 bp):
GTCACGCAATACATAACAACAGGTCACGCAATACATAAAAACCAGGCACACAATGCCTAAAAACT
AGTGAACAAAAGCCTCAAAACAAGAGATGAATTGCACAAGTCATGCACCGCCAATCTCACAATAC
CTAATAATAAGTCACTCAATACCTAATATCCACTCACATTATGCCAACATAACAACAG
Done.