Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold14
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: 2879421
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 64274 characters in sequence are not A, C, G, or T
File 15 of 17
Found at i:2447211 original size:79 final size:77
Alignment explanation
Indices: 2447128--2447330 Score: 207
Period size: 77 Copynumber: 2.6 Consensus size: 77
2447118 TGAAAAATCG
* * *
2447128 ATATTTTAGAAATAAAAATGAGGTTTAAGTATC-CTCTCAGAAATAACGGAGTTGGAACATCTTC
1 ATATTTTAGAAATAAAAACGAGGTTGAAGTATCTC-CTCAGAAATAACGG-GTTGGAACATC-CC
* *
2447192 GAGATGAAAAGTTTA
63 GAGATAAAAAATTTA
* * * * * *
2447207 ATATTTCAAAAATAAGAACGGGGTTGAAGTATCTCCTTAGAAATAACGGGTTGGAATATCCCGAG
1 ATATTTTAGAAATAAAAACGAGGTTGAAGTATCTCCTCAGAAATAACGGGTTGGAACATCCCGAG
2447272 ATAAAAAATTTA
66 ATAAAAAATTTA
* *
2447284 ATATTTT-GAAAATAAAAACGGGGTTAGAA-TAT-TCCCTCAAAAATAAC
1 ATATTTTAG-AAATAAAAACGAGGTT-GAAGTATCT-CCTCAGAAATAAC
2447331 AAGGTTAGAG
Statistics
Matches: 104, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
76 1 0.01
77 49 0.47
78 13 0.12
79 40 0.38
80 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.29
Consensus pattern (77 bp):
ATATTTTAGAAATAAAAACGAGGTTGAAGTATCTCCTCAGAAATAACGGGTTGGAACATCCCGAG
ATAAAAAATTTA
Found at i:2447304 original size:77 final size:77
Alignment explanation
Indices: 2447017--2447330 Score: 226
Period size: 79 Copynumber: 4.0 Consensus size: 77
2447007 TAAAAATCAT
* * * * *
2447017 GGTTGGAGTATCTCCGAGATGAAAAAAATTTAATGTTTTGGAAATGAAAACGGGATTTG-AGTAT
1 GGTTGGAATATCTCCGAGAT--AAAAAATTTAATATTTTGAAAATAAAAACGGG-GTTGAAGTAT
* **
2447081 CCCTTCGAAAGTGATGG
63 CCCTTAGAAA-T-AACG
* * * * ** * * *
2447098 GGTTGGAGTCTGC-CCGATGGTGAAAAA-TCGATATTTT-AGAAATAAAAATGAGGTTTAAGTAT
1 GGTTGGAATAT-CTCCGA-GATAAAAAATTTAATATTTTGA-AAATAAAAACGGGGTTGAAGTAT
*
2447160 CCTCTCAGAAATAACG
63 CC-CTTAGAAATAACG
* * * * ** *
2447176 GAGTTGGAACATCTTCGAGATGAAAAGTTTAATATTTCAAAAATAAGAACGGGGTTGAAGTATCT
1 G-GTTGGAATATCTCCGAGATAAAAAATTTAATATTTTGAAAATAAAAACGGGGTTGAAGTATC-
2447241 CCTTAGAAATAACG
64 CCTTAGAAATAACG
2447255 GGTTGGAATATC-CCGAGATAAAAAATTTAATATTTTGAAAATAAAAACGGGGTTAGAA-TATTC
1 GGTTGGAATATCTCCGAGATAAAAAATTTAATATTTTGAAAATAAAAACGGGGTT-GAAGTA-TC
* *
2447318 CCTCAAAAATAAC
64 CCTTAGAAATAAC
2447331 AAGGTTAGAG
Statistics
Matches: 182, Mismatches: 39, Indels: 28
0.73 0.16 0.11
Matches are distributed among these distances:
77 49 0.27
78 28 0.15
79 75 0.41
80 13 0.07
81 14 0.08
82 3 0.02
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.28
Consensus pattern (77 bp):
GGTTGGAATATCTCCGAGATAAAAAATTTAATATTTTGAAAATAAAAACGGGGTTGAAGTATCCC
TTAGAAATAACG
Found at i:2448030 original size:8 final size:8
Alignment explanation
Indices: 2448017--2448046 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
2448007 AGGGTTGGTC
2448017 AAAAAATA
1 AAAAAATA
2448025 AAAAAATA
1 AAAAAATA
2448033 TAAAAAATA
1 -AAAAAATA
2448042 AAAAA
1 AAAAA
2448047 CATTACATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (8 bp):
AAAAAATA
Found at i:2451989 original size:11 final size:11
Alignment explanation
Indices: 2451973--2452038 Score: 69
Period size: 12 Copynumber: 5.6 Consensus size: 11
2451963 ATGTTCAACT
*
2451973 AAAAAAAGAGAA
1 AAAAAAA-AGAG
2451985 AAAAAAAAGAG
1 AAAAAAAAGAG
2451996 AGAAAAAAAGGAG
1 A-AAAAAAA-GAG
*
2452009 AAAGAAAAGAG
1 AAAAAAAAGAG
*
2452020 AGAAAAAAATAG
1 A-AAAAAAAGAG
2452032 AAAAAAA
1 AAAAAAA
2452039 TAGGTTGAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
11 14 0.30
12 29 0.62
13 4 0.09
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.02
Consensus pattern (11 bp):
AAAAAAAAGAG
Found at i:2451997 original size:15 final size:14
Alignment explanation
Indices: 2451973--2452004 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
2451963 ATGTTCAACT
2451973 AAAAAAAGAGAAAA
1 AAAAAAAGAGAAAA
2451987 AAAAAAGAGAGAAAA
1 AAAAAA-AGAGAAAA
2452002 AAA
1 AAA
2452005 GGAGAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAGAAAA
Found at i:2452016 original size:24 final size:25
Alignment explanation
Indices: 2451973--2452038 Score: 98
Period size: 24 Copynumber: 2.7 Consensus size: 25
2451963 ATGTTCAACT
2451973 AAAAAAAGAGAAAAAAAAAAGAGAG
1 AAAAAAAGAGAAAAAAAAAAGAGAG
* *
2451998 AAAAAAAG-GAGAAAGAAAAGAGAG
1 AAAAAAAGAGAAAAAAAAAAGAGAG
*
2452022 AAAAAAATAGAAAAAAA
1 AAAAAAAGAGAAAAAAA
2452039 TAGGTTGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 21 0.60
25 14 0.40
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.02
Consensus pattern (25 bp):
AAAAAAAGAGAAAAAAAAAAGAGAG
Found at i:2452038 original size:13 final size:13
Alignment explanation
Indices: 2451973--2452028 Score: 76
Period size: 13 Copynumber: 4.3 Consensus size: 13
2451963 ATGTTCAACT
2451973 AAAAAAAGAGAAA
1 AAAAAAAGAGAAA
*
2451986 AAAAAAAGAGAGA
1 AAAAAAAGAGAAA
*
2451999 AAAAAAGGAGAAA
1 AAAAAAAGAGAAA
* *
2452012 GAAAAGAGAGAAA
1 AAAAAAAGAGAAA
2452025 AAAA
1 AAAA
2452029 TAGAAAAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAGAAA
Found at i:2453873 original size:97 final size:97
Alignment explanation
Indices: 2453718--2453957 Score: 313
Period size: 97 Copynumber: 2.5 Consensus size: 97
2453708 AATTTTATTT
* * ** * * *
2453718 ATCGGGGATACTCCAACCTTATTCCTT-CGAGAGGATACTTTAACCTCGCTTTTAAACACATCAA
1 ATCGGGGATACTCCAACCCTATT-CTTCCGAGGGGATACTCCAACCCCACTCTTAAACACATCAA
* *
2453782 AGTTTAAATCTTATTCTTATTTAAATTATCATC
65 AGTTTAAATCTTATTCTCACTTAAATTATCATC
* *
2453815 ATCGGGGATACTCTAACCCTATTCTTCCGAGGGGATACTCCGACCCCACTCTTAAACACATCAAA
1 ATCGGGGATACTCCAACCCTATTCTTCCGAGGGGATACTCCAACCCCACTCTTAAACACATCAAA
*
2453880 GTTTAAATCTTATTCTCACTTAAATTGTCATC
66 GTTTAAATCTTATTCTCACTTAAATTATCATC
* * * *
2453912 ATCGAGGACACTCCAACCC-ATTCCTCCGAGGGGATACTCTAACCCC
1 ATCGGGGATACTCCAACCCTATTCTTCCGAGGGGATACTCCAACCCC
2453958 GTTTTTCAAT
Statistics
Matches: 124, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
96 27 0.22
97 97 0.78
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (97 bp):
ATCGGGGATACTCCAACCCTATTCTTCCGAGGGGATACTCCAACCCCACTCTTAAACACATCAAA
GTTTAAATCTTATTCTCACTTAAATTATCATC
Found at i:2456188 original size:20 final size:20
Alignment explanation
Indices: 2456144--2456213 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
2456134 AAATAGTCTA
***
2456144 GTATCGATACATTGCAAGCAT
1 GTATCGATACATT-CACTAAT
2456165 GTATCGATACATTCACTAAT
1 GTATCGATACATTCACTAAT
* * *
2456185 GTATCAATACATTAACGTATT
1 GTATCGATACATTCAC-TAAT
2456206 GTATCGAT
1 GTATCGAT
2456214 GCAAATTGTA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 18 0.44
21 23 0.56
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (20 bp):
GTATCGATACATTCACTAAT
Found at i:2456819 original size:166 final size:167
Alignment explanation
Indices: 2456508--2456830 Score: 400
Period size: 166 Copynumber: 1.9 Consensus size: 167
2456498 AGGTGTTTAC
* * *
2456508 AAATATGACAAATGCATAGATTCTTAATGAAAATTAGATTTTTTTCTGATATGAAAGAAATTGAT
1 AAATATGACAAATACATAGATTCTTAATGAAAATCAGATTCTTTTCTGATATGAAAGAAATTGAT
* * * * * * *
2456573 GAGACTAATACATGGATTGTAATTGTCAAACTGCAAGGAATAGATTAATACATGGCTTAGAGTTC
66 AAGACTAATACATGGATTGTAAATGTCAAACTGCAAGGAATAGACTAATACATAGATTAAAATTC
*
2456638 GAAAGATGAGACTAATGCATGGATTCTGTTTTTGAAT
131 AAAAGATGAGACTAATGCATGGATTCTGTTTTTGAAT
* * * * * *
2456675 AAATATGATAAATATATAGATTTTTAAT-AGGAATCAGATTCTTTT-TGATATGAAGGAAGTTGA
1 AAATATGACAAATACATAGATTCTTAATGA-AAATCAGATTCTTTTCTGATATGAAAGAAATTGA
* * * * **
2456738 TAAGACTAATGCATGGATTGTAAATGTCAGATTGTAAGGAATAGACTAATTTATAGATTAAAATT
65 TAAGACTAATACATGGATTGTAAATGTCAAACTGCAAGGAATAGACTAATACATAGATTAAAATT
2456803 CAAAAGAT-AGGACTAATGCATGGATTCT
130 CAAAAGATGA-GACTAATGCATGGATTCT
2456831 ATCTTGAAAT
Statistics
Matches: 131, Mismatches: 23, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
165 1 0.01
166 94 0.72
167 36 0.27
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.34
Consensus pattern (167 bp):
AAATATGACAAATACATAGATTCTTAATGAAAATCAGATTCTTTTCTGATATGAAAGAAATTGAT
AAGACTAATACATGGATTGTAAATGTCAAACTGCAAGGAATAGACTAATACATAGATTAAAATTC
AAAAGATGAGACTAATGCATGGATTCTGTTTTTGAAT
Found at i:2458884 original size:31 final size:31
Alignment explanation
Indices: 2458846--2458911 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
2458836 AAACTCATTG
2458846 TAAAAATAGATGGTACACTCTTATGGAAAAA
1 TAAAAATAGATGGTACACTCTTATGGAAAAA
*
2458877 TAAAAATAGATGGTACACTCTTATTGAAAAA
1 TAAAAATAGATGGTACACTCTTATGGAAAAA
2458908 TAAA
1 TAAA
2458912 GGAACATTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.50, C:0.09, G:0.14, T:0.27
Consensus pattern (31 bp):
TAAAAATAGATGGTACACTCTTATGGAAAAA
Found at i:2460661 original size:21 final size:20
Alignment explanation
Indices: 2460634--2460681 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 20
2460624 GTTCTATCAA
2460634 TTATTAATTTAATTTAATT-T
1 TTATTAATTT-ATTTAATTAT
2460654 TATATTAAATTTATTTAATTAT
1 T-TATT-AATTTATTTAATTAT
2460676 TTATTA
1 TTATTA
2460682 TGTGTTGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 2 0.08
21 16 0.64
22 7 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTAATTTATTTAATTAT
Found at i:2463690 original size:19 final size:20
Alignment explanation
Indices: 2463668--2463707 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
2463658 GATTCTTAAT
2463668 TTTATTATATA-AATATAGA
1 TTTATTATATAGAATATAGA
2463687 TTTATTATATAGAATATAGA
1 TTTATTATATAGAATATAGA
2463707 T
1 T
2463708 ATATACAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (20 bp):
TTTATTATATAGAATATAGA
Found at i:2464489 original size:18 final size:17
Alignment explanation
Indices: 2464460--2464528 Score: 56
Period size: 16 Copynumber: 4.1 Consensus size: 17
2464450 CAGCAACCCC
2464460 TTTTCT-CTTTCTTTCT
1 TTTTCTCCTTTCTTTCT
2464476 TTTTCTCCCTTTCTTT-T
1 TTTTCT-CCTTTCTTTCT
*
2464493 TCTT-TCCTTT-TTTCT
1 TTTTCTCCTTTCTTTCT
*
2464508 TCTTTCCTTCCTTTTTTTCT
1 T-TTT-C-TCCTTTCTTTCT
2464528 T
1 T
2464529 CAAAATTTAC
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
14 3 0.07
15 7 0.16
16 9 0.21
17 4 0.09
18 8 0.19
19 6 0.14
20 6 0.14
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTCTCCTTTCTTTCT
Found at i:2464501 original size:15 final size:15
Alignment explanation
Indices: 2464459--2464523 Score: 73
Period size: 15 Copynumber: 4.4 Consensus size: 15
2464449 GCAGCAACCC
2464459 CTTTTCTCTTT-CTTT
1 CTTTT-TCTTTCCTTT
*
2464474 CTTTTTC-TCCCTTT
1 CTTTTTCTTTCCTTT
2464488 CTTTTTCTTTCCTTT
1 CTTTTTCTTTCCTTT
*
2464503 -TTTCTTCTTTCCTTC
1 CTTT-TTCTTTCCTTT
2464518 CTTTTT
1 CTTTTT
2464524 TTCTTCAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
13 1 0.02
14 16 0.37
15 23 0.53
16 3 0.07
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (15 bp):
CTTTTTCTTTCCTTT
Found at i:2464518 original size:19 final size:20
Alignment explanation
Indices: 2464485--2464529 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2464475 TTTTTCTCCC
*
2464485 TTTCTT-TTTCTTTCC-TTT
1 TTTCTTCTTTCCTTCCTTTT
2464503 TTTCTTCTTTCCTTCCTTTT
1 TTTCTTCTTTCCTTCCTTTT
2464523 TTTCTTC
1 TTTCTTC
2464530 AAAATTTACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 6 0.25
19 8 0.33
20 10 0.42
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTCTTCTTTCCTTCCTTTT
Found at i:2464755 original size:70 final size:67
Alignment explanation
Indices: 2464587--2464778 Score: 213
Period size: 70 Copynumber: 2.8 Consensus size: 67
2464577 GAGTTCTATA
* * *
2464587 ATCAAATTAAAAAATAAATCTTAAATTTTTATAAATAAAAATAAATTAAATCATCAAAAATTTAA
1 ATCAAA-T-AAAAATAAAT-TTAAATTTCTATAAATAAAAATAAATTATA-CCTCAAAAATTTAA
2464652 ACTCAT
62 ACTCAT
* * * * *
2464658 ATCATATAAAAATATATTTAAATTTCTACAAATCAAAATAAATTATACCTTAAAAATTTAAACTC
1 ATCAAATAAAAATAAATTTAAATTTCTATAAATAAAAATAAATTATACCTCAAAAATTTAAACTC
*
2464723 GTGT
66 --AT
* * *
2464727 AGTCAAATAAAAATAAATTTAAACTTCTATAAATTAAAATAAATAATACCTC
1 A-TCAAATAAAAATAAATTTAAATTTCTATAAATAAAAATAAATTATACCTC
2464779 TAATCAAAAT
Statistics
Matches: 102, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
67 16 0.16
68 26 0.25
69 11 0.11
70 44 0.43
71 5 0.05
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (67 bp):
ATCAAATAAAAATAAATTTAAATTTCTATAAATAAAAATAAATTATACCTCAAAAATTTAAACTC
AT
Found at i:2465116 original size:24 final size:22
Alignment explanation
Indices: 2465084--2465129 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
2465074 ATGGGTGTAT
2465084 CACCCGTGACCCTTTTTTATTTTA
1 CACCCGTGA--CTTTTTTATTTTA
*
2465108 CACCCGTGATTTTTTTATTTTA
1 CACCCGTGACTTTTTTATTTTA
2465130 TTTTTTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 12 0.57
24 9 0.43
ACGTcount: A:0.17, C:0.24, G:0.09, T:0.50
Consensus pattern (22 bp):
CACCCGTGACTTTTTTATTTTA
Found at i:2465209 original size:23 final size:24
Alignment explanation
Indices: 2465179--2465245 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 24
2465169 ATAATTAATA
*
2465179 TTTTAATTT-GTT-AATATAATTT
1 TTTTAATTTAATTAAATATAATTT
*
2465201 TTTTAAATTTAATTAAATATTA-TT
1 TTTT-AATTTAATTAAATATAATTT
* *
2465225 TTTT-ATTTTATTAAAAATAAT
1 TTTTAATTTAATTAAATATAAT
2465246 AATTAATACA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
22 17 0.47
23 5 0.14
24 8 0.22
25 6 0.17
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (24 bp):
TTTTAATTTAATTAAATATAATTT
Found at i:2465480 original size:3 final size:3
Alignment explanation
Indices: 2465472--2465515 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
2465462 ATTTTAAAAA
* *
2465472 ATT ATT ATT ATT ATT CTT ATT ATT AAT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2465516 AATAAAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:2465762 original size:27 final size:27
Alignment explanation
Indices: 2465705--2465781 Score: 68
Period size: 27 Copynumber: 2.9 Consensus size: 27
2465695 TTTTTTAATA
* *
2465705 TTAAATATGA-TTTGTAAAATATACTT
1 TTAAATATTATTTTGCAAAATATACTT
* * *
2465731 ATAAATATTATTTTGCAAATTATATTT
1 TTAAATATTATTTTGCAAAATATACTT
* *
2465758 TTAAA-ATTTTTTTACATAAATATA
1 TTAAATATTATTTTGCA-AAATATA
2465782 ATTTATTTAA
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
26 17 0.43
27 23 0.57
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (27 bp):
TTAAATATTATTTTGCAAAATATACTT
Found at i:2465850 original size:35 final size:35
Alignment explanation
Indices: 2465770--2465854 Score: 100
Period size: 36 Copynumber: 2.4 Consensus size: 35
2465760 AAAATTTTTT
* * *
2465770 TACA-TAAATATAATTTATTTAAATTTTAGTAATA
1 TACATTAAATATAATTTATTAAAAATTTAATAATA
* *
2465804 TGCATTAAAATATAATTTATTAAAAATTTAATTATA
1 TACATT-AAATATAATTTATTAAAAATTTAATAATA
*
2465840 TATATTAAATATAAT
1 TACATTAAATATAAT
2465855 ATAAATAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
34 3 0.07
35 10 0.24
36 29 0.69
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (35 bp):
TACATTAAATATAATTTATTAAAAATTTAATAATA
Found at i:2467740 original size:198 final size:198
Alignment explanation
Indices: 2467393--2467807 Score: 722
Period size: 198 Copynumber: 2.1 Consensus size: 198
2467383 CATCATCAGA
* *
2467393 AACTTGAGGAGCCTCCACGAAAGAATGATCAGCATTATTAGTCATTTGACCTGTGTCATTTGTAA
1 AACTTGAGGAGCCTCCACGAAAGAATGATCAGCATTATCAGTCATTTGACCTATGTCATTTGTAA
*
2467458 TGAATGCAACATCTTCAGTGAATATCTCAAACATCGATAAAACATTATCCTCTGATTCTTGAACT
66 TGAATGCAACATCTTCAGTGAATATATCAAACATCGATAAAACATTATCCTCTGATTCTTGAACT
* * **
2467523 TGAGGACCCATATCAACTTGGGGAGACCCCCTGACTGCAGGAGTAGCCTCCGCATCAGCAACCAC
131 TGAGGAACCATAGCAACTTGGGGAGACCCCCTGACTGCAGGAACAGCCTCCGCATCAGCAACCAC
2467588 TGG
196 TGG
*
2467591 AACTTGAGGAGCCTCGACGAAAGAATGATCAGCATTATCAGTCATTTGACCTATGTCATTTGTAA
1 AACTTGAGGAGCCTCCACGAAAGAATGATCAGCATTATCAGTCATTTGACCTATGTCATTTGTAA
* * *
2467656 TGAATGCATCATCTTCAGTGAATATATCCAACATCGATAAAACGTTATCCTCTGATTCTTGAACT
66 TGAATGCAACATCTTCAGTGAATATATCAAACATCGATAAAACATTATCCTCTGATTCTTGAACT
2467721 TGAGGAACCATAGCAACTTGGGGAGACCCCCTGACTGCAGGAACAGCCTCCGCATCAGCAACCAC
131 TGAGGAACCATAGCAACTTGGGGAGACCCCCTGACTGCAGGAACAGCCTCCGCATCAGCAACCAC
2467786 TGG
196 TGG
*
2467789 AACTTGAGGAGCATCCACG
1 AACTTGAGGAGCCTCCACG
2467808 CATGTAGGGG
Statistics
Matches: 204, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
198 204 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (198 bp):
AACTTGAGGAGCCTCCACGAAAGAATGATCAGCATTATCAGTCATTTGACCTATGTCATTTGTAA
TGAATGCAACATCTTCAGTGAATATATCAAACATCGATAAAACATTATCCTCTGATTCTTGAACT
TGAGGAACCATAGCAACTTGGGGAGACCCCCTGACTGCAGGAACAGCCTCCGCATCAGCAACCAC
TGG
Found at i:2468995 original size:27 final size:27
Alignment explanation
Indices: 2468940--2469027 Score: 64
Period size: 27 Copynumber: 3.4 Consensus size: 27
2468930 ATAAAAAGAT
* *
2468940 AAGCTAAATC-AATGAAAA-AAATACTAA
1 AAGCAAAATCAAAAGAAAACAAA-AC-AA
*
2468967 AAGCAAAATCAAAGGAAAACAAAACAA
1 AAGCAAAATCAAAAGAAAACAAAACAA
* *
2468994 AA--AAAA--AAAAG-CAACAAATCAA
1 AAGCAAAATCAAAAGAAAACAAAACAA
2469016 AAGCAAAATCAA
1 AAGCAAAATCAA
2469028 TGGGTATTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
22 11 0.22
23 4 0.08
24 4 0.08
25 4 0.08
26 2 0.04
27 13 0.26
28 9 0.18
29 3 0.06
ACGTcount: A:0.69, C:0.14, G:0.08, T:0.09
Consensus pattern (27 bp):
AAGCAAAATCAAAAGAAAACAAAACAA
Found at i:2469326 original size:26 final size:25
Alignment explanation
Indices: 2469279--2469329 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
2469269 TTAAAAATTA
* *
2469279 AAAATTAAATTTTAGTTTTTTTTAT
1 AAAATAAAATTTTAGTTCTTTTTAT
*
2469304 AAAATAAAATTTTTGTTACTTTTTAT
1 AAAATAAAATTTTAGTT-CTTTTTAT
2469330 TTTTAATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (25 bp):
AAAATAAAATTTTAGTTCTTTTTAT
Found at i:2469558 original size:31 final size:28
Alignment explanation
Indices: 2469523--2469591 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
2469513 CTTGCTAGTG
*
2469523 TAATTTTTAAATTTTAAAAAATATTTTAAAT
1 TAATTTTTAAA-TTT-AAAAATATATT-AAT
2469554 TAATTTTTAAATTTAAAAATATATTAAT
1 TAATTTTTAAATTTAAAAATATATTAAT
*
2469582 AAATTTTTAA
1 TAATTTTTAA
2469592 TTTCAAGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 12 0.33
29 10 0.28
30 3 0.08
31 11 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
TAATTTTTAAATTTAAAAATATATTAAT
Found at i:2470098 original size:20 final size:20
Alignment explanation
Indices: 2470070--2470108 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2470060 AAATTAATTT
*
2470070 AATAAAAAATAATTTATTAA
1 AATAAAAAATAAATTATTAA
*
2470090 AATATAAAATAAATTATTA
1 AATAAAAAATAAATTATTA
2470109 TTTACTTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AATAAAAAATAAATTATTAA
Found at i:2470364 original size:18 final size:18
Alignment explanation
Indices: 2470341--2470381 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2470331 ATTAAATAAA
*
2470341 ATAAA-TATTTTATATTTT
1 ATAAATTATTTAATA-TTT
2470359 ATAAATTATTTAATATTT
1 ATAAATTATTTAATATTT
2470377 ATAAA
1 ATAAA
2470382 ATAAATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATAAATTATTTAATATTT
Found at i:2470383 original size:19 final size:19
Alignment explanation
Indices: 2470346--2470406 Score: 52
Period size: 19 Copynumber: 3.1 Consensus size: 19
2470336 ATAAAATAAA
*
2470346 TATTTTATATTT-TATAAAT
1 TATTTAATATTTATA-AAAT
2470365 TATTTAATATTTATAAAAT
1 TATTTAATATTTATAAAAT
* *
2470384 AAATTAAATCATATTATAAAAT
1 -TATTTAAT-AT-TTATAAAAT
2470406 T
1 T
2470407 TTAAATCTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 15 0.44
20 8 0.24
21 2 0.06
22 9 0.26
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTTAATATTTATAAAAT
Found at i:2470385 original size:23 final size:23
Alignment explanation
Indices: 2470336--2470389 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 23
2470326 CAAAAATTAA
*
2470336 ATAAAATAAA-TATTTTATATTT
1 ATAAAATAAATTATTTAATATTT
2470358 -T---ATAAATTATTTAATATTT
1 ATAAAATAAATTATTTAATATTT
2470377 ATAAAATAAATTA
1 ATAAAATAAATTA
2470390 AATCATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 9
0.72 0.03 0.25
Matches are distributed among these distances:
18 5 0.19
19 11 0.42
20 1 0.04
21 1 0.04
23 8 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATAAAATAAATTATTTAATATTT
Found at i:2475867 original size:13 final size:13
Alignment explanation
Indices: 2475849--2475876 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2475839 ATACAAAGAT
2475849 CAATGTATCGATA
1 CAATGTATCGATA
2475862 CAATGTATCGATA
1 CAATGTATCGATA
2475875 CA
1 CA
2475877 TTGAATAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:2475873 original size:33 final size:33
Alignment explanation
Indices: 2475831--2475896 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2475821 AAATTCCCAG
2475831 ATGTATCGATACAAAG-ATCAATGTATCGATACA
1 ATGTATCGATACAAAGAAT-AATGTATCGATACA
**
2475864 ATGTATCGATACATTGAATAATGTATCGATACA
1 ATGTATCGATACAAAGAATAATGTATCGATACA
2475897 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (33 bp):
ATGTATCGATACAAAGAATAATGTATCGATACA
Found at i:2475952 original size:19 final size:19
Alignment explanation
Indices: 2475928--2476022 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
2475918 AGCGATATAT
2475928 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
2475947 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
2475960 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
2475979 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
*
2475992 TGTATCGATACAATACTTA
1 TGTATCGATACAACACTTA
2476011 TGTATCGATACA
1 TGTATCGATACA
2476023 TTTACTATTT
Statistics
Matches: 63, Mismatches: 1, Indels: 24
0.72 0.01 0.27
Matches are distributed among these distances:
13 18 0.29
14 2 0.03
16 11 0.17
18 2 0.03
19 30 0.48
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:2475962 original size:32 final size:32
Alignment explanation
Indices: 2475920--2476024 Score: 192
Period size: 32 Copynumber: 3.3 Consensus size: 32
2475910 AGCTTTGGAG
*
2475920 CGATATATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
2475952 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
*
2475984 CGATACATTGTATCGATACAATACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
2476016 CGATACATT
1 CGATACATT
2476025 TACTATTTGT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 71 1.00
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.36
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:2475965 original size:13 final size:13
Alignment explanation
Indices: 2475947--2476003 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
2475937 ACAACACTTA
2475947 TGTATCGATACAT
1 TGTATCGATACAT
2475960 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
2475978 ATGTATCGATACAT
1 -TGTATCGATACAT
2475992 TGTATCGATACA
1 TGTATCGATACA
2476004 ATACTTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2476037 original size:21 final size:19
Alignment explanation
Indices: 2475927--2476044 Score: 80
Period size: 19 Copynumber: 6.7 Consensus size: 19
2475917 GAGCGATATA
*
2475927 TTGTATCGATACAACACTT
1 TTGTATCGATACAATACTT
*
2475946 ATGTATCGATAC---A---
1 TTGTATCGATACAATACTT
*
2475959 TTGTATCGATACAACACTT
1 TTGTATCGATACAATACTT
*
2475978 ATGTATCGATAC---A---
1 TTGTATCGATACAATACTT
2475991 TTGTATCGATACAATACTT
1 TTGTATCGATACAATACTT
* *
2476010 ATGTATCGATACATTTACTAT
1 TTGTATCGATACA-ATACT-T
2476031 TTGTATCGATACAA
1 TTGTATCGATACAA
2476045 ATTGTTGAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 27
0.69 0.07 0.24
Matches are distributed among these distances:
13 22 0.29
16 4 0.05
19 34 0.44
20 4 0.05
21 13 0.17
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACAATACTT
Found at i:2476826 original size:49 final size:49
Alignment explanation
Indices: 2476764--2477001 Score: 300
Period size: 49 Copynumber: 4.8 Consensus size: 49
2476754 TGAGAAAGAC
** * *
2476764 GCCAATAAACTGATTCAAGGCTAGCAATATTGGACTTAAAGATGAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATGAAGGT
* *
2476813 GCCAATATACTGATTCAAGGCCAGCAACATT-GATCTTAAAGGTGAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCAACATTGGA-CTTAAAGATGAAGGT
* * *
2476862 GCTAATGTGCTGATTCAAAGCCAGCAACATTGGACTTAAAGATGACAAAGG-
1 GCCAATATGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATG---AAGGT
* * *
2476913 GCCAATATGCTGATTCAAAGCCAGCGATATTGGACTTAAAGATGAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATGAAGGT
* *
2476962 GCCAATGTGCTGATTCAAGGCCAACAACATTGGACTTAAA
1 GCCAATATGCTGATTCAAGGCCAGCAACATTGGACTTAAA
2477002 AGTGCAAATA
Statistics
Matches: 165, Mismatches: 18, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
48 6 0.04
49 113 0.68
50 2 0.01
51 40 0.24
52 4 0.02
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.24
Consensus pattern (49 bp):
GCCAATATGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATGAAGGT
Found at i:2476959 original size:100 final size:98
Alignment explanation
Indices: 2476773--2477047 Score: 334
Period size: 100 Copynumber: 2.8 Consensus size: 98
2476763 CGCCAATAAA
* * * *
2476773 CTGATTCAAGGCTAGCAATATTGGACTTAAAGATG-AAGGTGCCAATATACTGATTCAAGGCCAG
1 CTGATTCAAGGCCAGCAACATTGGACTTAAAGATGCAAGG-GCCAATATGCTGATTCAAAGCCAG
* * * *
2476837 CAACATT-GATCTTAAAGGTGAAGGTGCTAATGTG
65 CGATATTGGA-CTTAAAGATGAAGGTGCCAATGTG
*
2476871 CTGATTCAAAGCCAGCAACATTGGACTTAAAGATGACAAAGGGCCAATATGCTGATTCAAAGCCA
1 CTGATTCAAGGCCAGCAACATTGGACTTAAAGATG-C-AAGGGCCAATATGCTGATTCAAAGCCA
2476936 GCGATATTGGACTTAAAGATGAAGGTGCCAATGTG
64 GCGATATTGGACTTAAAGATGAAGGTGCCAATGTG
* *
2476971 CTGATTCAAGGCCAACAACATTGGACTTAAA-AGTGC-A-----AATATGCTGATTTAAAGCCAG
1 CTGATTCAAGGCCAGCAACATTGGACTTAAAGA-TGCAAGGGCCAATATGCTGATTCAAAGCCAG
2477029 CGATATTGGACTTAGAAGA
65 CGATATTGGACTTA-AAGA
2477048 AGATGCCACC
Statistics
Matches: 159, Mismatches: 12, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
92 34 0.21
93 4 0.03
97 1 0.01
98 32 0.20
99 2 0.01
100 80 0.50
101 6 0.04
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (98 bp):
CTGATTCAAGGCCAGCAACATTGGACTTAAAGATGCAAGGGCCAATATGCTGATTCAAAGCCAGC
GATATTGGACTTAAAGATGAAGGTGCCAATGTG
Found at i:2477037 original size:43 final size:46
Alignment explanation
Indices: 2476773--2477049 Score: 177
Period size: 49 Copynumber: 5.8 Consensus size: 46
2476763 CGCCAATAAA
* * * * *
2476773 CTGATTCAAGGCTAGCAATATTGGACTTAAAGATGAAGGTGCCAATATA
1 CTGATTCAAAGCCAGCGATATTGGACTT--AGA-GAAGGTGCAAATATG
* * * * * *
2476822 CTGATTCAAGGCCAGCAACATT-GATCTTAAAGGTGAAGGTGCTAATGTG
1 CTGATTCAAAGCCAGCGATATTGGA-CTT--A-GAGAAGGTGCAAATATG
* * *
2476871 CTGATTCAAAGCCAGCAACATTGGACTTAAAGATGACAAAGG-GCCAATATG
1 CTGATTCAAAGCCAGCGATATTGGACTT--AGA-G---AAGGTGCAAATATG
* *
2476922 CTGATTCAAAGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTG
1 CTGATTCAAAGCCAGCGATATTGGACTT--AGA-GAAGGTGCAAATATG
* * * *
2476971 CTGATTCAAGGCCAACAACATTGGACTTA-A-AA-GTGCAAATATG
1 CTGATTCAAAGCCAGCGATATTGGACTTAGAGAAGGTGCAAATATG
*
2477014 CTGATTTAAAGCCAGCGATATTGGACTTAGAAGAAG
1 CTGATTCAAAGCCAGCGATATTGGACTTAG-AGAAG
2477050 ATGCCACCAA
Statistics
Matches: 192, Mismatches: 24, Indels: 26
0.79 0.10 0.11
Matches are distributed among these distances:
43 33 0.17
44 2 0.01
45 1 0.01
46 3 0.02
47 1 0.01
48 7 0.04
49 98 0.51
50 3 0.02
51 40 0.21
52 4 0.02
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (46 bp):
CTGATTCAAAGCCAGCGATATTGGACTTAGAGAAGGTGCAAATATG
Found at i:2477227 original size:57 final size:57
Alignment explanation
Indices: 2477119--2477437 Score: 443
Period size: 57 Copynumber: 5.6 Consensus size: 57
2477109 TTGCCATTAC
* *
2477119 CTTGTGGGCTTTG--AAGGTTGCCACTGACTTATGGGC-TTTGAAAAGGTTGCCACTGA
1 CTTGTGGGCTTTGAAAAGG-TGCCACTGACTTGTGGGCTTTTGAAAA-GATGCCACTGA
* *
2477175 CTTATGGGCTTTGAAAATGTGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTGA
1 CTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTGA
* *
2477232 CTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTTGAAAAGATGTCACTAA
1 CTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTGA
2477289 CTTGTGGGCTTTTG--AAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTGA
1 CTTGTGGGC-TTTGAAAAGG-TGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTGA
* * *
2477346 CTTGTGGGCTTTGAAAAGGTGCCACTGACTTCTGAGC-TTTGAAAAGGGTGCCACTGA
1 CTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTTGAAAA-GATGCCACTGA
* *
2477403 CTTGTGAGCTTTGAAAAGGGTGCCACTGTCTTGTG
1 CTTGTGGGCTTTGAAAA-GGTGCCACTGACTTGTG
2477438 AGAATGTCTA
Statistics
Matches: 238, Mismatches: 16, Indels: 16
0.88 0.06 0.06
Matches are distributed among these distances:
56 28 0.12
57 176 0.74
58 34 0.14
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.32
Consensus pattern (57 bp):
CTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTGA
Found at i:2477439 original size:29 final size:28
Alignment explanation
Indices: 2477119--2477437 Score: 421
Period size: 29 Copynumber: 11.2 Consensus size: 28
2477109 TTGCCATTAC
2477119 CTTGTGGGCTTTG--AAGGTTGCCACTGA
1 CTTGTGGGCTTTGAAAAGG-TGCCACTGA
*
2477146 CTTATGGGCTTTGAAAAGGTTGCCACTGA
1 CTTGTGGGCTTTGAAAAGG-TGCCACTGA
* *
2477175 CTTATGGGCTTTGAAAATGTGCCACTGA
1 CTTGTGGGCTTTGAAAAGGTGCCACTGA
*
2477203 CTTGTGGGCTTTTGAAAAGATGCCACTGA
1 CTTGTGGGC-TTTGAAAAGGTGCCACTGA
2477232 CTTGTGGGCTTTGAAAAGGTGCCACTGA
1 CTTGTGGGCTTTGAAAAGGTGCCACTGA
* * *
2477260 CTTGTGGGCTTTTGAAAAGATGTCACTAA
1 CTTGTGGGC-TTTGAAAAGGTGCCACTGA
2477289 CTTGTGGGCTTTTG--AAGGTTGCCACTGA
1 CTTGTGGGC-TTTGAAAAGG-TGCCACTGA
*
2477317 CTTGTGGGCTTTTGAAAAGATGCCACTGA
1 CTTGTGGGC-TTTGAAAAGGTGCCACTGA
2477346 CTTGTGGGCTTTGAAAAGGTGCCACTGA
1 CTTGTGGGCTTTGAAAAGGTGCCACTGA
* *
2477374 CTTCTGAGCTTTGAAAAGGGTGCCACTGA
1 CTTGTGGGCTTTGAAAA-GGTGCCACTGA
* *
2477403 CTTGTGAGCTTTGAAAAGGGTGCCACTGT
1 CTTGTGGGCTTTGAAAA-GGTGCCACTGA
2477432 CTTGTG
1 CTTGTG
2477438 AGAATGTCTA
Statistics
Matches: 266, Mismatches: 18, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
27 15 0.06
28 98 0.37
29 150 0.56
30 3 0.01
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.32
Consensus pattern (28 bp):
CTTGTGGGCTTTGAAAAGGTGCCACTGA
Found at i:2477835 original size:37 final size:37
Alignment explanation
Indices: 2477794--2477878 Score: 125
Period size: 37 Copynumber: 2.3 Consensus size: 37
2477784 CAAGATGAAG
* * *
2477794 CACAAATGCCTCATGTAAAATGAAATGTTATGAATGT
1 CACAAATGCATCATGCAAAATGAAATATTATGAATGT
* *
2477831 CACAAATACATCATGCAAAATGAAATATTGTGAATGT
1 CACAAATGCATCATGCAAAATGAAATATTATGAATGT
2477868 CACAAATGCAT
1 CACAAATGCAT
2477879 GATTGTGGCA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.27
Consensus pattern (37 bp):
CACAAATGCATCATGCAAAATGAAATATTATGAATGT
Found at i:2478922 original size:15 final size:15
Alignment explanation
Indices: 2478904--2478934 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2478894 CCGGACCCTT
2478904 TTTGTTTTTTTGTTG
1 TTTGTTTTTTTGTTG
*
2478919 TTTGTTTTTTTTTTG
1 TTTGTTTTTTTGTTG
2478934 T
1 T
2478935 AGAGGACGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (15 bp):
TTTGTTTTTTTGTTG
Found at i:2485760 original size:15 final size:15
Alignment explanation
Indices: 2485726--2485760 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2485716 TCATGGCAAA
2485726 CTTTTGACCTTCTAC
1 CTTTTGACCTTCTAC
* *
2485741 TTTTTGACCTTCTGC
1 CTTTTGACCTTCTAC
2485756 CTTTT
1 CTTTT
2485761 CTACTTCTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.29, G:0.09, T:0.54
Consensus pattern (15 bp):
CTTTTGACCTTCTAC
Found at i:2490764 original size:112 final size:112
Alignment explanation
Indices: 2490567--2490832 Score: 480
Period size: 112 Copynumber: 2.4 Consensus size: 112
2490557 TTTTAGTTGA
* *
2490567 AAACGAGGTTGGAGTGTCCCCTC-AGAGGAATGGGGTTGGAGTGTCCTTGATAATGATATTTTGG
1 AAACGAGGTTGGAGTATCCCCTCGA-AGGAATAGGGTTGGAGTGTCCTTGATAATGATATTTTGG
2490631 GATATTTAGGGTAAAAACAAGATTTGAATCATGATAAGATTAAAAAAC
65 GATATTTAGGGTAAAAACAAGATTTGAATCATGATAAGATTAAAAAAC
2490679 AAACGAGGTTGGAGTATCCCCTCGAAGGAATAGGGTTGGAGTGTCCTTGATAATGATATTTTGGG
1 AAACGAGGTTGGAGTATCCCCTCGAAGGAATAGGGTTGGAGTGTCCTTGATAATGATATTTTGGG
*
2490744 ATATTTGGGGTAAAAACAAGATTTGAATCATGATAAGATTAAAAAAC
66 ATATTTAGGGTAAAAACAAGATTTGAATCATGATAAGATTAAAAAAC
*
2490791 AAACGGGGTTGGAGTATCCCCTCGAAGGAATAGGGTTGGAGT
1 AAACGAGGTTGGAGTATCCCCTCGAAGGAATAGGGTTGGAGT
2490833 ATTCCCGAAA
Statistics
Matches: 149, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
112 148 0.99
113 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.28, T:0.27
Consensus pattern (112 bp):
AAACGAGGTTGGAGTATCCCCTCGAAGGAATAGGGTTGGAGTGTCCTTGATAATGATATTTTGGG
ATATTTAGGGTAAAAACAAGATTTGAATCATGATAAGATTAAAAAAC
Found at i:2493118 original size:16 final size:16
Alignment explanation
Indices: 2493093--2493134 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
2493083 GTATCGATAC
*
2493093 AAATTGTTGAAATTTA
1 AAATTTTTGAAATTTA
2493109 AAATTTTTGAAATTTA
1 AAATTTTTGAAATTTA
2493125 AAATTTTTGA
1 AAATTTTTGA
2493135 CCGTTGGGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.48
Consensus pattern (16 bp):
AAATTTTTGAAATTTA
Found at i:2495182 original size:2 final size:2
Alignment explanation
Indices: 2495177--2495210 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2495167 ATTTTATCTC
2495177 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
2495211 GAGGTTTACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2496644 original size:18 final size:19
Alignment explanation
Indices: 2496618--2496664 Score: 62
Period size: 17 Copynumber: 2.5 Consensus size: 19
2496608 AAAGATTTAA
*
2496618 TAATCTTTTTCTTTT-TTT
1 TAATGTTTTTCTTTTATTT
2496636 TAATG-TTTTCTTTTATTT
1 TAATGTTTTTCTTTTATTT
2496654 TAAATGTTTTT
1 T-AATGTTTTT
2496665 ATTCAGTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 9 0.36
18 8 0.32
19 4 0.16
20 4 0.16
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.72
Consensus pattern (19 bp):
TAATGTTTTTCTTTTATTT
Found at i:2496935 original size:7 final size:7
Alignment explanation
Indices: 2496925--2496951 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2496915 TTATTTTTCC
2496925 TTTTCTT
1 TTTTCTT
2496932 TTTTCTT
1 TTTTCTT
2496939 TTTTCTT
1 TTTTCTT
2496946 TTTTCT
1 TTTTCT
2496952 CTCTCTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTCTT
Found at i:2496936 original size:13 final size:14
Alignment explanation
Indices: 2496918--2496976 Score: 59
Period size: 14 Copynumber: 4.1 Consensus size: 14
2496908 CTAGAAATTA
2496918 TTTTTC-CTTTTCT
1 TTTTTCTCTTTTCT
*
2496931 TTTTTCTTTTTTCT
1 TTTTTCTCTTTTCT
*
2496945 TTTTTCTCTCTCTTAT
1 TTTTTCTCT-T-TTCT
2496961 TCTTTTCT-TTTTCT
1 T-TTTTCTCTTTTCT
2496975 TT
1 TT
2496977 CCAGTTAGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
13 7 0.18
14 18 0.47
15 2 0.05
16 5 0.13
17 6 0.16
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTCTCTTTTCT
Found at i:2498845 original size:16 final size:16
Alignment explanation
Indices: 2498801--2498846 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
2498791 TAATCTTGAA
2498801 AAATA-ATATATATAT
1 AAATACATATATATAT
* *
2498816 AAATACACAAATATATT
1 AAATACATATATATA-T
2498833 AAA-ACATATATATA
1 AAATACATATATATA
2498847 ATTTATATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
15 5 0.20
16 16 0.64
17 4 0.16
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATACATATATATAT
Found at i:2498951 original size:85 final size:87
Alignment explanation
Indices: 2498749--2498986 Score: 358
Period size: 87 Copynumber: 2.8 Consensus size: 87
2498739 ACACATATAT
*
2498749 ATATATATATAATTTATATGTTTAATACTTTTAATGCAATTATAATCTTGAAAAATAATATATAT
1 ATATATATATAATTTATATGTTTAATACTTTTAATGCAATTATAATATTGAAAAATAATATATAT
*
2498814 ATAAATACACAAATATATTAAAAC
66 AT-AATA-ACAAATATATCAAAAC
*
2498838 --ATATATATAATTTATATGTTTAATACTTTTAATGCAATTATAATATTGAAAATTAATATATAT
1 ATATATATATAATTTATATGTTTAATACTTTTAATGCAATTATAATATTGAAAAATAATATATAT
* *
2498901 AT-AT-ATATATATATCAAAAC
66 ATAATAACAAATATATCAAAAC
* * *
2498921 ATATATATATAATTTATATATTTAATACTTTTAACGTAATTATAATATTGAAAAATAATATATAT
1 ATATATATATAATTTATATGTTTAATACTTTTAATGCAATTATAATATTGAAAAATAATATATAT
2498986 A
66 A
2498987 GCACATAGTA
Statistics
Matches: 138, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
83 13 0.09
85 62 0.45
87 63 0.46
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.43
Consensus pattern (87 bp):
ATATATATATAATTTATATGTTTAATACTTTTAATGCAATTATAATATTGAAAAATAATATATAT
ATAATAACAAATATATCAAAAC
Found at i:2499758 original size:2 final size:2
Alignment explanation
Indices: 2499753--2499782 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2499743 AATTTTTTTA
2499753 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
2499783 GACTAAACTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2500033 original size:17 final size:17
Alignment explanation
Indices: 2499984--2500037 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
2499974 CTATTAGGAG
2499984 ATATTAATTTGAAAAAA
1 ATATTAATTTGAAAAAA
* * *
2500001 AAATTGA-TT-AAGAAA
1 ATATTAATTTGAAAAAA
*
2500016 ATTTTAATTTGAAAAAA
1 ATATTAATTTGAAAAAA
2500033 ATATT
1 ATATT
2500038 TGAAAAAAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
15 9 0.33
16 4 0.15
17 14 0.52
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (17 bp):
ATATTAATTTGAAAAAA
Found at i:2500047 original size:14 final size:13
Alignment explanation
Indices: 2500022--2500046 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2500012 GAAAATTTTA
2500022 ATTTGAAAAAAAT
1 ATTTGAAAAAAAT
2500035 ATTTGAAAAAAA
1 ATTTGAAAAAAA
2500047 AAACAAATAT
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:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (13 bp):
ATTTGAAAAAAAT
Found at i:2503535 original size:20 final size:22
Alignment explanation
Indices: 2503492--2503538 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
2503482 TGTGAATGGA
2503492 TAAAAAAAATATGAAATTATTT
1 TAAAAAAAATATGAAATTATTT
2503514 TAAAAATAAA-AT-AAATTA-TT
1 TAAAAA-AAATATGAAATTATTT
2503534 TAAAA
1 TAAAA
2503539 TTTGAGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.29
21 6 0.25
22 8 0.33
23 3 0.12
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (22 bp):
TAAAAAAAATATGAAATTATTT
Found at i:2510660 original size:22 final size:23
Alignment explanation
Indices: 2510621--2510666 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
2510611 ATTTTCTATT
2510621 TAAAAGAATCTATAATATTAAAA
1 TAAAAGAATCTATAATATTAAAA
*
2510644 TAAAA-AAT-TATAAATATTCAAA
1 TAAAAGAATCTAT-AATATTAAAA
2510666 T
1 T
2510667 TCAAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 3 0.14
22 13 0.62
23 5 0.24
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (23 bp):
TAAAAGAATCTATAATATTAAAA
Found at i:2511981 original size:11 final size:10
Alignment explanation
Indices: 2511962--2512004 Score: 52
Period size: 11 Copynumber: 4.2 Consensus size: 10
2511952 ATTAAATGGG
2511962 TTTTTAAATA
1 TTTTTAAATA
2511972 TTTATTAAATAA
1 TTT-TTAAAT-A
*
2511984 ATTTTAAAT-
1 TTTTTAAATA
2511993 TTTTTAAATA
1 TTTTTAAATA
2512003 TT
1 TT
2512005 AATTCAGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
9 8 0.29
10 5 0.18
11 12 0.43
12 3 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TTTTTAAATA
Found at i:2512008 original size:22 final size:22
Alignment explanation
Indices: 2511963--2512002 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2511953 TTAAATGGGT
2511963 TTTTAAATATTTATTAAATAAA
1 TTTTAAATATTTATTAAATAAA
2511985 TTTTAAAT-TTT-TTAAATA
1 TTTTAAATATTTATTAAATA
2512003 TTAATTCAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 8 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTTAAATATTTATTAAATAAA
Found at i:2513711 original size:13 final size:14
Alignment explanation
Indices: 2513687--2513719 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
2513677 ATAGAAAATT
2513687 TTTTTTCTTTTCAA
1 TTTTTTCTTTTCAA
2513701 TTTTTTC-TTTCAA
1 TTTTTTCTTTTCAA
2513714 TTTTTT
1 TTTTTT
2513720 TTCACTCTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTTTCTTTTCAA
Found at i:2513720 original size:14 final size:15
Alignment explanation
Indices: 2513686--2513720 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
2513676 AATAGAAAAT
2513686 TTTTTTTCTTTTCAA
1 TTTTTTTCTTTTCAA
2513701 -TTTTTTC-TTTCAA
1 TTTTTTTCTTTTCAA
2513714 TTTTTTT
1 TTTTTTT
2513721 TCACTCTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTTTCTTTTCAA
Found at i:2514364 original size:22 final size:22
Alignment explanation
Indices: 2514339--2514381 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2514329 TACTTTTGAC
2514339 AAAAAATGATTTTAA-ATTATAT
1 AAAAAA-GATTTTAACATTATAT
*
2514361 AAAAAAGTTTTTAACATTATA
1 AAAAAAGATTTTAACATTATA
2514382 ACCATTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (22 bp):
AAAAAAGATTTTAACATTATAT
Found at i:2514548 original size:13 final size:14
Alignment explanation
Indices: 2514525--2514553 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2514515 AATACAAGAG
2514525 AAAAATGAAAATAA
1 AAAAATGAAAATAA
2514539 AAAAAT-AAAATAA
1 AAAAATGAAAATAA
2514552 AA
1 AA
2514554 GGTTAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (14 bp):
AAAAATGAAAATAA
Found at i:2514571 original size:262 final size:262
Alignment explanation
Indices: 2514085--2514591 Score: 695
Period size: 262 Copynumber: 1.9 Consensus size: 262
2514075 TGGTAAAAAA
* * * * *
2514085 ATTTTTAATTATATAGAAAATTTTTTAACATTATCATCATTTTTTCTCTTAAATTTTTTAAAGGA
1 ATTTTAAATTATATAAAAAAGTTTTTAACATTATAACCA-TTTTTCTCTTAAATTTTTTAAAGGA
*
2514150 TCTTCTAACAAAAAAAAGGTACAAATTATTATAACTTAAAAAATTATGAAGCACAAACTATTGAT
65 TCTTCTAACAAAAAAAAAGTACAAATTATTATAACTTAAAAAATTATGAAGCACAAACTATTGAT
* *
2514215 CTTTGACTTTTTTCTAAAAAAAAAAAAGCAAAAAAGAATAAAAGAGAAAATTGAAAATAAAAGAA
130 ATTTGACTTTTTTCTAAAAAAAAAAAAGCAAAAAAGAATAAAAGAGAAAAATGAAAATAAAAGAA
*
2514280 AATAAAATAAAAGGTTAAATTTTTTATCATCTTA-TTTTCTTCATTTTTTTACTTTTGACAAAAA
195 AATAAAATAAAAGGTTAAATTTCTTATCATCTTATTTTTCTTCATTTTTTTACTTTTGACAAAAA
2514344 ATG
260 ATG
*
2514347 ATTTTAAATTATATAAAAAAGTTTTTAACATTATAACCA-TTTTCTTTTAAATTTTTTCTTAAAA
1 ATTTTAAATTATATAAAAAAGTTTTTAACATTATAACCATTTTTCTCTTAAA--TTTT-TT-AAA
* * * * * *
2514411 GGGTTTTCTAACAAAAAAAAAAGTGCAAGTTATTATGA-TTGAAAAAATTATGAAGCACAAATTA
62 GGATCTTCTAAC-AAAAAAAAAGTACAAATTATTATAACTT-AAAAAATTATGAAGCACAAACTA
* * ** *
2514475 TTGATATTTGACATTTTTT-TTAACAAATTAAA-CAAAAAAGAATACAAGAGAAAAATGAAAAT-
125 TTGATATTTGAC-TTTTTTCTAAAAAAAAAAAAGCAAAAAAGAATAAAAGAGAAAAATGAAAATA
*
2514537 AAA-AAAATAAAATAAAAGGTTAAATTTCTTATCATCTTATTTTTGTTCATTTTTT
189 AAAGAAAATAAAATAAAAGGTTAAATTTCTTATCATCTTATTTTTCTTCATTTTTT
2514592 AAAACTTTTG
Statistics
Matches: 215, Mismatches: 22, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
260 11 0.05
262 73 0.34
263 19 0.09
264 43 0.20
265 63 0.29
266 6 0.03
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (262 bp):
ATTTTAAATTATATAAAAAAGTTTTTAACATTATAACCATTTTTCTCTTAAATTTTTTAAAGGAT
CTTCTAACAAAAAAAAAGTACAAATTATTATAACTTAAAAAATTATGAAGCACAAACTATTGATA
TTTGACTTTTTTCTAAAAAAAAAAAAGCAAAAAAGAATAAAAGAGAAAAATGAAAATAAAAGAAA
ATAAAATAAAAGGTTAAATTTCTTATCATCTTATTTTTCTTCATTTTTTTACTTTTGACAAAAAA
TG
Found at i:2521322 original size:2 final size:2
Alignment explanation
Indices: 2521315--2521346 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2521305 CTTAAGTTGA
2521315 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
2521347 TTTAGATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2522420 original size:19 final size:18
Alignment explanation
Indices: 2522396--2522445 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 18
2522386 TTTTATGCAC
*
2522396 TTTTATGATTTTATAAATA
1 TTTTAT-ATTTTACAAATA
2522415 TTTTATATTTTACAAATCGA
1 TTTTATATTTTACAAAT--A
2522435 TATTTATATTT
1 T-TTTATATTT
2522446 AGCAATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 10 0.37
19 6 0.22
20 2 0.07
21 9 0.33
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (18 bp):
TTTTATATTTTACAAATA
Found at i:2530504 original size:20 final size:20
Alignment explanation
Indices: 2530476--2530547 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 20
2530466 TTTTACCCAG
2530476 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
2530496 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
2530516 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
2530536 ATGTATCGATAC
1 ATGTATCGATAC
2530548 TTATGTCTTT
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:2534782 original size:2 final size:2
Alignment explanation
Indices: 2534775--2534802 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2534765 AGAGCACCTA
2534775 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
2534803 TCTTAACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2539888 original size:25 final size:25
Alignment explanation
Indices: 2539859--2539918 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
2539849 TTTTATATGT
2539859 TTAAAAATAAAACAAAATAATAAAA
1 TTAAAAATAAAACAAAATAATAAAA
* *
2539884 TTAAAAAT-AGATAAAATAATAAAA
1 TTAAAAATAAAACAAAATAATAAAA
*
2539908 TGTTAAAATAA
1 T-TAAAAATAA
2539919 TAATGTGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.50
25 14 0.47
26 1 0.03
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.25
Consensus pattern (25 bp):
TTAAAAATAAAACAAAATAATAAAA
Found at i:2539907 original size:8 final size:8
Alignment explanation
Indices: 2539872--2539921 Score: 57
Period size: 8 Copynumber: 6.2 Consensus size: 8
2539862 AAAATAAAAC
2539872 AAAATAAT
1 AAAATAAT
*
2539880 AAAATTA-
1 AAAATAAT
2539887 AAAATAGAT
1 AAAATA-AT
2539896 AAAATAAT
1 AAAATAAT
**
2539904 AAAATGTT
1 AAAATAAT
2539912 AAAATAAT
1 AAAATAAT
2539920 AA
1 AA
2539922 TGTGATTGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
7 5 0.15
8 23 0.68
9 6 0.18
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (8 bp):
AAAATAAT
Found at i:2540379 original size:22 final size:20
Alignment explanation
Indices: 2540334--2540410 Score: 84
Period size: 24 Copynumber: 3.5 Consensus size: 20
2540324 CAGAATTGCT
2540334 TTTTTTTCAATAGC-TTTTGA
1 TTTTTTTC-ATAGCTTTTTGA
2540354 TTTTTTTCATAGCTTTTTTGA
1 TTTTTTTCATAGC-TTTTTGA
2540375 CTTTTTTTTTCATAAGCTTTTTGA
1 ---TTTTTTTCAT-AGCTTTTTGA
2540399 TTCTTTTTCATA
1 TT-TTTTTCATA
2540411 ATTTTTTTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 13
0.79 0.00 0.21
Matches are distributed among these distances:
19 5 0.10
20 8 0.16
21 9 0.18
22 8 0.16
24 17 0.34
25 3 0.06
ACGTcount: A:0.17, C:0.12, G:0.08, T:0.64
Consensus pattern (20 bp):
TTTTTTTCATAGCTTTTTGA
Found at i:2540416 original size:44 final size:43
Alignment explanation
Indices: 2540333--2540416 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 43
2540323 ACAGAATTGC
*
2540333 TTTTTTTTCAATAGCTTTTGATTTTTTTCATAGCTTTTTTGACT
1 TTTTTTTTCAATAGCTTTTGATTTTTTTCATA-CATTTTTGACT
2540377 TTTTTTTTC-ATAAGCTTTTTGATTCTTTTTCATA-ATTTTT
1 TTTTTTTTCAAT-AGC-TTTTGATT-TTTTTCATACATTTTT
2540417 TTTTTTTTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
43 2 0.06
44 17 0.47
45 8 0.22
46 9 0.25
ACGTcount: A:0.17, C:0.11, G:0.07, T:0.65
Consensus pattern (43 bp):
TTTTTTTTCAATAGCTTTTGATTTTTTTCATACATTTTTGACT
Found at i:2540417 original size:22 final size:21
Alignment explanation
Indices: 2540348--2540424 Score: 72
Period size: 24 Copynumber: 3.6 Consensus size: 21
2540338 TTTCAATAGC
*
2540348 TTTTGATTTTTTTCATAGCTT
1 TTTTGATTTTTTTCATAACTT
2540369 TTTTGACTTTTTTTTTCATAAGC-T
1 TTTTGA---TTTTTTTCATAA-CTT
2540393 TTTTGATTCTTTTTCATAA-TT
1 TTTTGATT-TTTTTCATAACTT
2540414 TTTT--TTTTTTT
1 TTTTGATTTTTTT
2540425 AGTTTTTTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 15
0.75 0.02 0.23
Matches are distributed among these distances:
18 5 0.10
19 2 0.04
21 13 0.27
22 10 0.20
24 18 0.37
25 1 0.02
ACGTcount: A:0.14, C:0.09, G:0.06, T:0.70
Consensus pattern (21 bp):
TTTTGATTTTTTTCATAACTT
Found at i:2541797 original size:17 final size:17
Alignment explanation
Indices: 2541775--2541809 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2541765 CTTATGAACA
2541775 ACTTATTAATAAAAATG
1 ACTTATTAATAAAAATG
2541792 ACTTATTAATAAAAATG
1 ACTTATTAATAAAAATG
2541809 A
1 A
2541810 AAATTGAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.34
Consensus pattern (17 bp):
ACTTATTAATAAAAATG
Found at i:2544196 original size:91 final size:90
Alignment explanation
Indices: 2543996--2544530 Score: 521
Period size: 91 Copynumber: 6.0 Consensus size: 90
2543986 TCTATCATGT
* * ** *
2543996 CATTAGTCAAATATTTTCTGTCGTGTCAGAATGAAT-TGAATACTTCATGCATCTGTCGCATCTT
1 CATTAGTCAAATATTTTCTGTCATGTCAGAAGGAATCTG-ATACCCCATGCATCTGTCACATCTT
*
2544060 TCAGGTTCCAAGA--AA--T-TTAGG
65 TCAAGTTCCAAGATTAATTTATTAGG
* * * * *
2544081 TATTAGTCAAATATTTTATGTCATGTCAGAAGGAATCTGATTCCCCGTGCATCTATCACATCTTT
1 CATTAGTCAAATATTTTCTGTCATGTCAGAAGGAATCTGATACCCCATGCATCTGTCACATCTTT
* *
2544146 CAAGCTCCAACATTAATTTTATTAGG
66 CAAGTTCCAAGATTAA-TTTATTAGG
* * * * *
2544172 CATTAGTCAAATATTTTCTGTCATGTCAAAAGGAATCTAATAGCTCATGCATCTATCACATCTTT
1 CATTAGTCAAATATTTTCTGTCATGTCAGAAGGAATCTGATACCCCATGCATCTGTCACATCTTT
* * * *
2544237 CAGGTTTCAAAATTAATTTTATTAGA
66 CAAGTTCCAAGATTAA-TTTATTAGG
* * * * * *
2544263 TATTGGTCAAATATTTTCTATCATGTCAAAAGGAATCTGATGCCCCATGCATTTGTCACATCTTT
1 CATTAGTCAAATATTTTCTGTCATGTCAGAAGGAATCTGATACCCCATGCATCTGTCACATCTTT
** * *
2544328 CGTGTTTCAAGATTAAATTTATTAGA
66 CAAGTTCCAAGATT-AATTTATTAGG
* * * * * * * *
2544354 TATTAGTCAAATATTTTCGGTCATATTATAAAGAAT-TGATACCCCGTGCTTCTGTCACATCTTT
1 CATTAGTCAAATATTTTCTGTCATGTCAGAAGGAATCTGATACCCCATGCATCTGTCACATCTTT
2544418 CAAGTTCCAAGA--AATTTATTAGG
66 CAAGTTCCAAGATTAATTTATTAGG
* * * * * *
2544441 CATTAGTCAAATATTTTCTATCATGTCAGAAGGAATCTAATGCCTCATGCATTTGTCATATCTTT
1 CATTAGTCAAATATTTTCTGTCATGTCAGAAGGAATCTGATACCCCATGCATCTGTCACATCTTT
** *
2544506 CGGGTTCTAAGATTAATTTTATTAG
66 CAAGTTCCAAGATTAA-TTTATTAG
2544531 AATATATTAT
Statistics
Matches: 368, Mismatches: 70, Indels: 18
0.81 0.15 0.04
Matches are distributed among these distances:
85 61 0.17
86 2 0.01
87 41 0.11
88 30 0.08
90 36 0.10
91 196 0.53
92 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (90 bp):
CATTAGTCAAATATTTTCTGTCATGTCAGAAGGAATCTGATACCCCATGCATCTGTCACATCTTT
CAAGTTCCAAGATTAATTTATTAGG
Found at i:2544492 original size:178 final size:176
Alignment explanation
Indices: 2543996--2544531 Score: 619
Period size: 182 Copynumber: 3.0 Consensus size: 176
2543986 TCTATCATGT
* * * *
2543996 CATTAGTCAAATATTTTCTGTCGTGTCAGAATGAATTGAATACTTCATGCATCTGTCGCATCTTT
1 CATTAGTCAAATATTTTCTGTCATGTCA-AAAGAATTG-ATACCTCATGCATCTGTCACATCTTT
* * *
2544061 CAGGTTCCAAGAAA--T-TTAGGTATTAGTCAAATATTTTATGTCATGTCAGAAGGAATCTGATT
64 CAGGTTCCAAGAAATTTATTAGGTATTAGTCAAATATTTTCTATCATGTCAGAAGGAATCTGATG
* * * * * * *
2544123 CCCCGTGCATCTATCACATCTTTCAAGCTCCAACATTAATTTTATTAGG
129 CCCCATGCATTTGTCACATCTTTC-GGCTTCAAGATTAATTTTATTAGA
* * *
2544172 CATTAGTCAAATATTTTCTGTCATGTCAAAAGGAATCTAATAGCTCATGCATCTATCACATCTTT
1 CATTAGTCAAATATTTTCTGTCATGTCAAAA-GAAT-TGATACCTCATGCATCTGTCACATCTTT
* * * * *
2544237 CAGGTTTCAAAATTAATTTTATTAGATATTGGTCAAATATTTTCTATCATGTCAAAAGGAATCTG
64 CAGGTTCCAAGA--AA-TTTATTAGGTATTAGTCAAATATTTTCTATCATGTCAGAAGGAATCTG
* *
2544302 ATGCCCCATGCATTTGTCACATCTTTCGTGTTTCAAGATTAAATTTATTAGA
126 ATGCCCCATGCATTTGTCACATCTTTCG-GCTTCAAGATTAATTTTATTAGA
* * * * * * *
2544354 TATTAGTCAAATATTTTCGGTCATATTATAAAGAATTGATACCCCGTGCTTCTGTCACATCTTTC
1 CATTAGTCAAATATTTTCTGTCATGTCA-AAAGAATTGATACCTCATGCATCTGTCACATCTTTC
* * *
2544419 AAGTTCCAAGAAATTTATTAGGCATTAGTCAAATATTTTCTATCATGTCAGAAGGAATCTAATGC
65 AGGTTCCAAGAAATTTATTAGGTATTAGTCAAATATTTTCTATCATGTCAGAAGGAATCTGATGC
* * *
2544484 CTCATGCATTTGTCATATCTTTCGGGTTCTAAGATTAATTTTATTAGA
130 CCCATGCATTTGTCACATCTTTCGGCTTC-AAGATTAATTTTATTAGA
2544532 ATATATTATA
Statistics
Matches: 303, Mismatches: 46, Indels: 20
0.82 0.12 0.05
Matches are distributed among these distances:
175 2 0.01
176 63 0.21
177 5 0.02
178 88 0.29
179 2 0.01
181 32 0.11
182 108 0.36
183 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.38
Consensus pattern (176 bp):
CATTAGTCAAATATTTTCTGTCATGTCAAAAGAATTGATACCTCATGCATCTGTCACATCTTTCA
GGTTCCAAGAAATTTATTAGGTATTAGTCAAATATTTTCTATCATGTCAGAAGGAATCTGATGCC
CCATGCATTTGTCACATCTTTCGGCTTCAAGATTAATTTTATTAGA
Found at i:2544856 original size:15 final size:15
Alignment explanation
Indices: 2544838--2544871 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2544828 TCCTGAATGC
2544838 CTTCTTCTTGAGTAG
1 CTTCTTCTTGAGTAG
*
2544853 CTTCTTCTTGAGTGG
1 CTTCTTCTTGAGTAG
2544868 CTTC
1 CTTC
2544872 ATCTGTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (15 bp):
CTTCTTCTTGAGTAG
Found at i:2545768 original size:144 final size:143
Alignment explanation
Indices: 2545508--2545804 Score: 495
Period size: 144 Copynumber: 2.1 Consensus size: 143
2545498 TTAGTTGTTA
* *
2545508 CATCCCAAATTAGCATAGGACCCTATCCACCTATTTCCACTCTCCAACTTGGAAGTATATCAGTG
1 CATCCCAAATTAGCATAGGACCCTATCCACCTATTTCCACACTCCAACTTGGAAGCATATCAGTG
* *
2545573 TCATATTTGCACACCATATGTGACTACTTCTGTATGCTTCCTCTGAGAGGCACGCCATTAACTCA
66 TCATATTTACACACCATATATGACTACTTCTGTATGCTTCCTCTGAGAGGCACGCCATTAACTCA
2545638 TCAAAGCGATATGG
131 TCAAA-CGATATGG
***
2545652 CATCCCAAATTAGCATAGGACCCTATTTGCCTATTTCCACACTCCAACTTGGAAGCATATCAGTG
1 CATCCCAAATTAGCATAGGACCCTATCCACCTATTTCCACACTCCAACTTGGAAGCATATCAGTG
* *
2545717 TCATATTTACACATCATATATGGCTACTTCTGTATGCTTCCTCTGAGAGGCACGCCATTAACTCA
66 TCATATTTACACACCATATATGACTACTTCTGTATGCTTCCTCTGAGAGGCACGCCATTAACTCA
2545782 TCAAACGATATGG
131 TCAAACGATATGG
2545795 CATCCACAAA
1 CATCC-CAAA
2545805 AACTGTAAAA
Statistics
Matches: 143, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
143 13 0.09
144 130 0.91
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (143 bp):
CATCCCAAATTAGCATAGGACCCTATCCACCTATTTCCACACTCCAACTTGGAAGCATATCAGTG
TCATATTTACACACCATATATGACTACTTCTGTATGCTTCCTCTGAGAGGCACGCCATTAACTCA
TCAAACGATATGG
Found at i:2548234 original size:22 final size:22
Alignment explanation
Indices: 2548204--2548277 Score: 75
Period size: 21 Copynumber: 3.5 Consensus size: 22
2548194 CAAAAAAATT
2548204 AAAAA-CAAAAATAAATATTAA
1 AAAAATCAAAAATAAATATTAA
*
2548225 AAAAATCAAAAAGTTAATA--AA
1 AAAAATCAAAAA-TAAATATTAA
* **
2548246 AAAATTCAAAAA-AGCTATTAA
1 AAAAATCAAAAATAAATATTAA
2548267 AAAAATCAAAA
1 AAAAATCAAAA
2548278 GCTTGAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
19 2 0.05
21 30 0.70
22 6 0.14
23 5 0.12
ACGTcount: A:0.72, C:0.07, G:0.03, T:0.19
Consensus pattern (22 bp):
AAAAATCAAAAATAAATATTAA
Found at i:2548235 original size:21 final size:20
Alignment explanation
Indices: 2548195--2548277 Score: 73
Period size: 20 Copynumber: 4.2 Consensus size: 20
2548185 AAAAGTTAAC
2548195 AAAAAA-ATTAAAAACAA--A
1 AAAAAATATTAAAAA-AATCA
*
2548213 AATAAATATTAAAAAAATCA
1 AAAAAATATTAAAAAAATCA
** *
2548233 AAAAGTTAATAAAAAAATTCA
1 AAAAAATATTAAAAAAA-TCA
*
2548254 AAAAAGCTATTAAAAAAATCA
1 AAAAA-ATATTAAAAAAATCA
2548275 AAA
1 AAA
2548278 GCTTGAAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
18 7 0.13
19 8 0.15
20 14 0.27
21 13 0.25
22 10 0.19
ACGTcount: A:0.72, C:0.06, G:0.02, T:0.19
Consensus pattern (20 bp):
AAAAAATATTAAAAAAATCA
Found at i:2548290 original size:33 final size:33
Alignment explanation
Indices: 2548253--2548324 Score: 101
Period size: 32 Copynumber: 2.2 Consensus size: 33
2548243 AAAAAAATTC
*
2548253 AAAAAAGCTATTAAAAAAATCAAAAGC-TTGAAA
1 AAAAAACCTA-TAAAAAAATCAAAAGCATTGAAA
*
2548286 AAAAAACCTATGAAAAAATCAAAAGCTATTGAAA
1 AAAAAACCTATAAAAAAATCAAAAGC-ATTGAAA
2548320 AAAAA
1 AAAAA
2548325 GTAATTGCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
32 15 0.43
33 9 0.26
34 11 0.31
ACGTcount: A:0.65, C:0.10, G:0.08, T:0.17
Consensus pattern (33 bp):
AAAAAACCTATAAAAAAATCAAAAGCATTGAAA
Found at i:2549265 original size:16 final size:17
Alignment explanation
Indices: 2549240--2549272 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2549230 TAAAATAATA
2549240 TTAATATTATAT-TATT
1 TTAATATTATATCTATT
*
2549256 TTAATTTTATATCTATT
1 TTAATATTATATCTATT
2549273 CGTATCGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
TTAATATTATATCTATT
Found at i:2549359 original size:6 final size:6
Alignment explanation
Indices: 2549348--2549380 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
2549338 TAGATACAAG
2549348 ATTTTA ATTTTA ATTTTA ATTTT- -TTTTA ATTTT
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTT
2549381 TTTAATTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 4 0.16
6 21 0.84
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (6 bp):
ATTTTA
Found at i:2549376 original size:10 final size:10
Alignment explanation
Indices: 2549349--2549388 Score: 55
Period size: 12 Copynumber: 3.9 Consensus size: 10
2549339 AGATACAAGA
2549349 TTTTAATTTT
1 TTTTAATTTT
2549359 AATTTTAATTTT
1 --TTTTAATTTT
2549371 TTTTAA-TTT
1 TTTTAATTTT
2549380 TTTTAATTT
1 TTTTAATTT
2549389 CACTAATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 9 0.33
10 8 0.30
12 10 0.37
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTAATTTT
Found at i:2549547 original size:15 final size:14
Alignment explanation
Indices: 2549529--2549587 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 14
2549519 AGATTTATTT
2549529 ATTTGATATTTAAAA
1 ATTT-ATATTTAAAA
* *
2549544 ATTTTAGATATTAAAT
1 A-TTTATAT-TTAAAA
*
2549560 ATTTATAATTTTAAA
1 ATTTAT-ATTTAAAA
2549575 ATTTATATTTAAA
1 ATTTATATTTAAA
2549588 TCTAAACTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
14 6 0.17
15 18 0.51
16 11 0.31
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (14 bp):
ATTTATATTTAAAA
Found at i:2549576 original size:31 final size:30
Alignment explanation
Indices: 2549506--2549588 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 30
2549496 ACTATATATT
**
2549506 TTTTAAATATTTTAGATTTATTTATTTGATA
1 TTTTAAA-ATTTTAGATTTAAATATTTGATA
*
2549537 TTTAAAAATTTTAGATATTAAATATTT-ATAA
1 TTTTAAAATTTTAGAT-TTAAATATTTGAT-A
*
2549568 TTTTAAAA-TTTATATTTAAAT
1 TTTTAAAATTTTAGATTTAAAT
2549589 CTAAACTTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
29 6 0.13
30 17 0.38
31 22 0.49
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (30 bp):
TTTTAAAATTTTAGATTTAAATATTTGATA
Found at i:2550402 original size:18 final size:21
Alignment explanation
Indices: 2550353--2550403 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 21
2550343 TATATATCGT
2550353 GTATTTATATATAATAATTTAC
1 GTATTTATATAT-ATAATTTAC
* *
2550375 ATATTGATATAT-T-ATTT-C
1 GTATTTATATATATAATTTAC
2550393 GTATTTATATA
1 GTATTTATATA
2550404 CACTTATTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 10 0.40
19 4 0.16
20 1 0.04
22 10 0.40
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.53
Consensus pattern (21 bp):
GTATTTATATATATAATTTAC
Found at i:2551948 original size:28 final size:27
Alignment explanation
Indices: 2551894--2551948 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
2551884 TCAAATAAAA
* *
2551894 AATAAAAAAATAATTAAAACATAATAT
1 AATAAAAAAATAATAAAAACACAATAT
* *
2551921 AATATAAAAAATTATAAAAACACGATAT
1 AATA-AAAAAATAATAAAAACACAATAT
2551949 TTCATTCATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.25
Consensus pattern (27 bp):
AATAAAAAAATAATAAAAACACAATAT
Found at i:2552009 original size:11 final size:11
Alignment explanation
Indices: 2551993--2552043 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
2551983 TTTATACTTT
2551993 AAATAAATAAA
1 AAATAAATAAA
2552004 AAATAACATTAAA
1 AAATAA-A-TAAA
2552017 AACA-AAATAAA
1 AA-ATAAATAAA
2552028 AAATAAA-ACAA
1 AAATAAATA-AA
2552039 AAATA
1 AAATA
2552044 TCTACACAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
10 2 0.06
11 22 0.63
12 2 0.06
13 8 0.23
14 1 0.03
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.16
Consensus pattern (11 bp):
AAATAAATAAA
Found at i:2552029 original size:12 final size:12
Alignment explanation
Indices: 2551993--2552041 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
2551983 TTTATACTTT
2551993 AAAT-AAATAAA
1 AAATAAAATAAA
* *
2552004 AAATAACATTAA
1 AAATAAAATAAA
*
2552016 AAACAAAATAAA
1 AAATAAAATAAA
*
2552028 AAATAAAACAAA
1 AAATAAAATAAA
2552040 AA
1 AA
2552042 TATCTACACA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
11 4 0.13
12 26 0.87
ACGTcount: A:0.80, C:0.06, G:0.00, T:0.14
Consensus pattern (12 bp):
AAATAAAATAAA
Found at i:2552121 original size:18 final size:18
Alignment explanation
Indices: 2552071--2552122 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 18
2552061 CTTTCTTTCC
2552071 CTCTCTCTTGTTC-CTTTTT
1 CTCT-TCTT-TTCTCTTTTT
*
2552090 CTTCCTTCTATTCTCTTTTT
1 C-T-CTTCTTTTCTCTTTTT
2552110 CTCTTCTTTTCTC
1 CTCTTCTTTTCTC
2552123 CTCCATCCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
18 10 0.36
19 5 0.18
20 11 0.39
21 2 0.07
ACGTcount: A:0.02, C:0.33, G:0.02, T:0.63
Consensus pattern (18 bp):
CTCTTCTTTTCTCTTTTT
Found at i:2552709 original size:23 final size:23
Alignment explanation
Indices: 2552682--2552725 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2552672 ATAAATAAAT
* *
2552682 TTAAAGAAGCTTTAAATGATTTA
1 TTAAAGAAGCATTAAACGATTTA
*
2552705 TTAAATAAGCATTAAACGATT
1 TTAAAGAAGCATTAAACGATT
2552726 CATATATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.36
Consensus pattern (23 bp):
TTAAAGAAGCATTAAACGATTTA
Found at i:2553319 original size:26 final size:26
Alignment explanation
Indices: 2553289--2553350 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
2553279 TAAACATTAA
* *
2553289 ATAAAAATGTATATGTAATAAATAAT
1 ATAAAAATATATATATAATAAATAAT
* * *
2553315 TTAAAAATATATTTATATTAAATAAT
1 ATAAAAATATATATATAATAAATAAT
2553341 ATATAAAATA
1 ATA-AAAATA
2553351 AAATTATATT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
26 23 0.79
27 6 0.21
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (26 bp):
ATAAAAATATATATATAATAAATAAT
Found at i:2553343 original size:18 final size:17
Alignment explanation
Indices: 2553315--2553386 Score: 76
Period size: 18 Copynumber: 4.2 Consensus size: 17
2553305 AATAAATAAT
2553315 TTAAAAATATATTTATA
1 TTAAAAATATATTTATA
*
2553332 TTAAATAATATA--TAAA
1 TTAAA-AATATATTTATA
* *
2553348 ATAAAATTATATTTATA
1 TTAAAAATATATTTATA
*
2553365 TTAAAAATTATATTTATT
1 TTAAAAA-TATATTTATA
2553383 TTAA
1 TTAA
2553387 TTATTAATTA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
15 5 0.11
16 7 0.16
17 13 0.30
18 19 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAAAAATATATTTATA
Found at i:2553357 original size:27 final size:26
Alignment explanation
Indices: 2553307--2553360 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
2553297 GTATATGTAA
* * *
2553307 TAAATAATTTAAAAATATATTTATAT
1 TAAATAATATAAAAATAAAATTATAT
2553333 TAAATAATATATAAAATAAAATTATAT
1 TAAATAATATA-AAAATAAAATTATAT
2553360 T
1 T
2553361 TATATTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 10 0.42
27 14 0.58
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
TAAATAATATAAAAATAAAATTATAT
Found at i:2553392 original size:18 final size:18
Alignment explanation
Indices: 2553315--2553416 Score: 75
Period size: 18 Copynumber: 6.3 Consensus size: 18
2553305 AATAAATAAT
2553315 TTAAAAA-TATATTTATA
1 TTAAAAATTATATTTATA
*
2553332 TTAAATAA-TATA--TAAA
1 TTAAA-AATTATATTTATA
*
2553348 AT-AAAATTATATTTATA
1 TTAAAAATTATATTTATA
2553365 TTAAAAATTATATTTAT-
1 TTAAAAATTATATTTATA
*
2553382 TT--TAA-T-TA-TTA-A
1 TTAAAAATTATATTTATA
2553394 TTAAAAATTATATTTATA
1 TTAAAAATTATATTTATA
*
2553412 CTAAA
1 TTAAA
2553417 CTAAATATTA
Statistics
Matches: 66, Mismatches: 7, Indels: 23
0.69 0.07 0.24
Matches are distributed among these distances:
12 5 0.08
13 2 0.03
14 5 0.08
15 9 0.14
16 6 0.09
17 14 0.21
18 25 0.38
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAAAAATTATATTTATA
Found at i:2561473 original size:35 final size:35
Alignment explanation
Indices: 2561434--2561503 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
2561424 AGCTACAAGG
*
2561434 CGTGCCTTGTATTTTCCAATAGTCTTACTAGACTT
1 CGTGCCTTGTATTTTCCAATAGTCCTACTAGACTT
2561469 CGTGCCTTGTATTTTCCAATAGTCCTACTAGACTT
1 CGTGCCTTGTATTTTCCAATAGTCCTACTAGACTT
2561504 ACATGTAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.41
Consensus pattern (35 bp):
CGTGCCTTGTATTTTCCAATAGTCCTACTAGACTT
Found at i:2562783 original size:27 final size:27
Alignment explanation
Indices: 2562732--2562784 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
2562722 ATTCAAAAAC
** *
2562732 GGGGTTGGAGTATCCCCTCGGAATAAT
1 GGGGTTGGAGTATCCCCGAGAAATAAT
*
2562759 GGGGTTGGAGTATCCCCGATAAATAA
1 GGGGTTGGAGTATCCCCGAGAAATAA
2562785 AATTTGGTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.25
Consensus pattern (27 bp):
GGGGTTGGAGTATCCCCGAGAAATAAT
Found at i:2565005 original size:20 final size:19
Alignment explanation
Indices: 2564980--2565035 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 19
2564970 AAATTTGCTT
*
2564980 TAATGTATCGATACATTGAA
1 TAATGTATCGATACAATG-A
2565000 TAATGTATCGATACAATGA
1 TAATGTATCGATACAATGA
2565019 TAAATGTATCGATACAA
1 T-AATGTATCGATACAA
2565036 AACTTATGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 2 0.06
20 32 0.94
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (19 bp):
TAATGTATCGATACAATGA
Found at i:2570483 original size:78 final size:80
Alignment explanation
Indices: 2570371--2570543 Score: 271
Period size: 81 Copynumber: 2.2 Consensus size: 80
2570361 GAATTACATG
* *
2570371 AGGTGGTGGTGGTGGATGGAATGGATGA-T-GTGGTGGTGGTGGTGGTGTCAC-GATAGGGGAAG
1 AGGTGGTGGTGGTGCATGGAATGGATGAGTGGTGGTGGTGGTGGTGGTGTCACAG-TAGGAGAAG
2570433 GAGGTGGTTTCGTTGC
65 GAGGTGGTTTCGTTGC
*
2570449 AGGTGGTGGTGGTGCATGGAATGGATGATGTGGTGGTGGTGGTGGTGGTGTCACAGTAGGAGAGG
1 AGGTGGTGGTGGTGCATGGAATGGATGA-GTGGTGGTGGTGGTGGTGGTGTCACAGTAGGAGAAG
*
2570514 GAGGTGGTTTTGTTGC
65 GAGGTGGTTTCGTTGC
2570530 AGGTGGTGGTGGTG
1 AGGTGGTGGTGGTG
2570544 GTTTTACAAT
Statistics
Matches: 87, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
78 27 0.31
80 1 0.01
81 58 0.67
82 1 0.01
ACGTcount: A:0.14, C:0.05, G:0.52, T:0.29
Consensus pattern (80 bp):
AGGTGGTGGTGGTGCATGGAATGGATGAGTGGTGGTGGTGGTGGTGGTGTCACAGTAGGAGAAGG
AGGTGGTTTCGTTGC
Found at i:2570581 original size:24 final size:24
Alignment explanation
Indices: 2570506--2570582 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
2570496 GTGTCACAGT
2570506 AGGAGAGGGAGGTGGTTTTGTTGC
1 AGGAGAGGGAGGTGGTTTTGTTGC
* * *****
2570530 AGGTG-GTGGTGGTGGTTTTACAAT
1 AGGAGAG-GGAGGTGGTTTTGTTGC
2570554 AGGAGAGGGAGGTGGTTTTGTTGC
1 AGGAGAGGGAGGTGGTTTTGTTGC
2570578 AGGAG
1 AGGAG
2570583 GTGGTGGTGT
Statistics
Matches: 37, Mismatches: 14, Indels: 4
0.67 0.25 0.07
Matches are distributed among these distances:
23 1 0.03
24 35 0.95
25 1 0.03
ACGTcount: A:0.18, C:0.04, G:0.48, T:0.30
Consensus pattern (24 bp):
AGGAGAGGGAGGTGGTTTTGTTGC
Found at i:2570586 original size:45 final size:45
Alignment explanation
Indices: 2570486--2570810 Score: 425
Period size: 45 Copynumber: 7.2 Consensus size: 45
2570476 ATGTGGTGGT
2570486 GGTGGTGGTGGTGTCACAGTAGGAGAGGGAGGTGGTTTTGTTGCA
1 GGTGGTGGTGGTGTCACAGTAGGAGAGGGAGGTGGTTTTGTTGCA
* *
2570531 GGTGGTGGTGGTGGTTTTACAATAGGAGAGGGAGGTGGTTTTGTTGCA
1 GGTGGTGGTGGT-G--TCACAGTAGGAGAGGGAGGTGGTTTTGTTGCA
* * *
2570579 GGAGGTGGTGGTGTCCCAGTAGGAGAGGGCGGTGGTTTTGTTGCA
1 GGTGGTGGTGGTGTCACAGTAGGAGAGGGAGGTGGTTTTGTTGCA
* * * * *
2570624 GGTGGTGGCGGTGTCACGGTAGGAGAGGGAGGCGGTCTTCTTGCA
1 GGTGGTGGTGGTGTCACAGTAGGAGAGGGAGGTGGTTTTGTTGCA
* * * * *
2570669 GGTGGCGGTGGTCTCACAGTAGGAGAGGGAGGCGGTTTTATCGCA
1 GGTGGTGGTGGTGTCACAGTAGGAGAGGGAGGTGGTTTTGTTGCA
* * *
2570714 GGTGGCGGTGGTGTCACGGTAGGAGAGGGAGGTGGTTTTATTGCA
1 GGTGGTGGTGGTGTCACAGTAGGAGAGGGAGGTGGTTTTGTTGCA
* * * *
2570759 GGTGGCGGTGGTGTCACAGTAGGAGAGGGAGGCGGTTTTCTTGCT
1 GGTGGTGGTGGTGTCACAGTAGGAGAGGGAGGTGGTTTTGTTGCA
2570804 GGTGGTG
1 GGTGGTG
2570811 ATGGATAGAA
Statistics
Matches: 246, Mismatches: 31, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
45 203 0.83
46 1 0.00
47 1 0.00
48 41 0.17
ACGTcount: A:0.15, C:0.10, G:0.48, T:0.27
Consensus pattern (45 bp):
GGTGGTGGTGGTGTCACAGTAGGAGAGGGAGGTGGTTTTGTTGCA
Found at i:2570591 original size:24 final size:24
Alignment explanation
Indices: 2570516--2570591 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
2570506 AGGAGAGGGA
*
2570516 GGTGGTTTTGTTGCAGGTGGTGGT
1 GGTGGTTTTGTTGCAGGAGGTGGT
***** *
2570540 GGTGGTTTTACAATAGGAGAG-GGA
1 GGTGGTTTTGTTGCAGGAG-GTGGT
2570564 GGTGGTTTTGTTGCAGGAGGTGGT
1 GGTGGTTTTGTTGCAGGAGGTGGT
2570588 GGTG
1 GGTG
2570592 TCCCAGTAGG
Statistics
Matches: 37, Mismatches: 13, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
23 1 0.03
24 35 0.95
25 1 0.03
ACGTcount: A:0.13, C:0.04, G:0.49, T:0.34
Consensus pattern (24 bp):
GGTGGTTTTGTTGCAGGAGGTGGT
Found at i:2573323 original size:2 final size:2
Alignment explanation
Indices: 2573316--2573344 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2573306 CAGTTTTAAT
2573316 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
2573345 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2573451 original size:128 final size:128
Alignment explanation
Indices: 2573319--2573574 Score: 494
Period size: 128 Copynumber: 2.0 Consensus size: 128
2573309 TTTTAATACA
2573319 CACACACACACACACACACACACACATATATATATATAATTTAGAACCTAAAAGGAATTTTCGAC
1 CACACACACACACACACACACACACATATATATATATAATTTAGAACCTAAAAGGAATTTTCGAC
2573384 CAGTGTGTTTTCTAAAAGAGCATCATGGTGCAGCTGAGCATTCGGCTCAGTCCCAGGTGCATG
66 CAGTGTGTTTTCTAAAAGAGCATCATGGTGCAGCTGAGCATTCGGCTCAGTCCCAGGTGCATG
* *
2573447 CACACACACACACACACACACATATATATATATATATAATTTAGAACCTAAAAGGAATTTTCGAC
1 CACACACACACACACACACACACACATATATATATATAATTTAGAACCTAAAAGGAATTTTCGAC
2573512 CAGTGTGTTTTCTAAAAGAGCATCATGGTGCAGCTGAGCATTCGGCTCAGTCCCAGGTGCATG
66 CAGTGTGTTTTCTAAAAGAGCATCATGGTGCAGCTGAGCATTCGGCTCAGTCCCAGGTGCATG
2573575 TGTTCCCCTG
Statistics
Matches: 126, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 126 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.25
Consensus pattern (128 bp):
CACACACACACACACACACACACACATATATATATATAATTTAGAACCTAAAAGGAATTTTCGAC
CAGTGTGTTTTCTAAAAGAGCATCATGGTGCAGCTGAGCATTCGGCTCAGTCCCAGGTGCATG
Found at i:2578471 original size:2 final size:2
Alignment explanation
Indices: 2578464--2578496 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2578454 GTAACCTCAT
2578464 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2578497 AACACCCATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2582777 original size:2 final size:2
Alignment explanation
Indices: 2582772--2582796 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2582762 AAGAATATAT
2582772 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
2582797 ACCCAAAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2584124 original size:3 final size:3
Alignment explanation
Indices: 2584109--2584150 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
2584099 CTTTTACCTC
* *
2584109 ATT ATT CTT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2584151 TATTCTCCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2585118 original size:2 final size:2
Alignment explanation
Indices: 2585100--2585138 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
2585090 ATTAATATTA
* *
2585100 AT AT TT AT AT TT 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 A
2585139 AATGATGACT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:2585356 original size:2 final size:2
Alignment explanation
Indices: 2585351--2585381 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2585341 GAAAAAAGAA
2585351 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2585382 AATAAAAGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2589042 original size:20 final size:20
Alignment explanation
Indices: 2589019--2589089 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
2589009 TTTTACCTAG
* *
2589019 ATGTATTGATACATTTTTTA
1 ATGTATCGATACATTTTTCA
* * * *
2589039 ATGTATCGATATATATATGA
1 ATGTATCGATACATTTTTCA
2589059 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
2589079 ATGTATCGATA
1 ATGTATCGATA
2589090 TATTCTGTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.45
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:2589135 original size:20 final size:21
Alignment explanation
Indices: 2589110--2589148 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
2589100 TGTTATCCAG
2589110 ATGTATCGATACAT-TATTCA
1 ATGTATCGATACATCTATTCA
2589130 ATGTATCGATACATCTATT
1 ATGTATCGATACATCTATT
2589149 TAATTTTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTATTCA
Found at i:2589512 original size:22 final size:22
Alignment explanation
Indices: 2589460--2589505 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
2589450 GGAGAGAAAT
2589460 ATACCAAAACGCCTCACCTTTC
1 ATACCAAAACGCCTCACCTTTC
*
2589482 ATACCAAAACGTCTCACCTTTC
1 ATACCAAAACGCCTCACCTTTC
2589504 AT
1 AT
2589506 CCTAAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.37, G:0.04, T:0.26
Consensus pattern (22 bp):
ATACCAAAACGCCTCACCTTTC
Found at i:2590086 original size:20 final size:20
Alignment explanation
Indices: 2590049--2590087 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2590039 TAGCCTTTAA
* *
2590049 TCATGCATTTTCACTATGTT
1 TCATACATTTTCAATATGTT
*
2590069 TCATACATTTTTAATATGT
1 TCATACATTTTCAATATGT
2590088 CTCGCATCTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.15, G:0.08, T:0.51
Consensus pattern (20 bp):
TCATACATTTTCAATATGTT
Found at i:2592567 original size:28 final size:27
Alignment explanation
Indices: 2592536--2592589 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 27
2592526 ATATATCTAT
* * *
2592536 AAATGATATTTTTAATATATTATATTTC
1 AAATGATATCTATAA-ATAATATATTTC
*
2592564 AAATTATATCTATAAATAATATATTT
1 AAATGATATCTATAAATAATATATTT
2592590 ATTTTATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (27 bp):
AAATGATATCTATAAATAATATATTTC
Found at i:2594774 original size:2 final size:2
Alignment explanation
Indices: 2594763--2594806 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
2594753 CTTTCAATGA
2594763 AT AT -T AT AT AT AT A- 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
2594803 AT AT
1 AT AT
2594807 TTGTGTGTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2595615 original size:7 final size:7
Alignment explanation
Indices: 2595603--2595630 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
2595593 TATTTTAAAT
2595603 AATATTA
1 AATATTA
2595610 AATATTA
1 AATATTA
2595617 AATATTA
1 AATATTA
2595624 AATATTA
1 AATATTA
2595631 TTTTTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
AATATTA
Found at i:2595632 original size:17 final size:19
Alignment explanation
Indices: 2595582--2595623 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
2595572 GCTTTAAATT
2595582 TATTATTAAAATATTTTAAA
1 TATTATTAAAATA-TTTAAA
*
2595602 TAATATT-AAATA-TTAAA
1 TATTATTAAAATATTTAAA
2595619 TATTA
1 TATTA
2595624 AATATTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 9 0.45
19 5 0.25
20 6 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TATTATTAAAATATTTAAA
Found at i:2596057 original size:228 final size:229
Alignment explanation
Indices: 2595770--2596369 Score: 697
Period size: 228 Copynumber: 2.6 Consensus size: 229
2595760 CAATTAATTA
* *
2595770 TATCTCATTCTCGTTCATTGAATTTAATATAATATATTAATTTTA-TCATTGCTTTTTAAATTTT
1 TATCTCATTCACATTCATTGAATTTAATATAATATATTAATTTTATTCATTGC-TTTTAAATTTT
* * * * *
2595834 TTTTATTTTTTTTAATATAATTTGAATGGTTAAATTACTGAAAATATAATCTAAAAATTATTATC
65 TTTAACTCTTTTTAATAGAATTTGAATGGTTAAATTACTAAAAATATAATCTAAAAATTATTATC
* * * *
2595899 CATTAATATTCTCTCGGTTCATTAAACTTAAATTTAATATAATATATTAGTTTTACTAATAAA-T
130 CATTAATATTCTCTC-GTTCATTAAACTTAAATTTAAAAAAATATATTAATTTTACCAATAAATT
** *
2595963 -TCTCGTTCATTGTGTTTAATATAATATATTACTTT
194 ATCTCACTCATTATGTTTAATATAATATATTACTTT
* ** * * *
2595998 TATTTCATTCTTATTTATTGAATTTAATATAATGTATTAATTTTATTCATTGCTTTTAAATTTCA
1 TATCTCATTCACATTCATTGAATTTAATATAATATATTAATTTTATTCATTGCTTTTAAATTT-T
* ** *
2596063 TTTAACTCTTTTTAATAGAATTTGAATAGTTAAATTACTAAAAATATAAAATAAAAATTATCA-C
65 TTTAACTCTTTTTAATAGAATTTGAATGGTTAAATTACTAAAAATATAATCTAAAAATTATTATC
* * * * *
2596127 CAACTAATATTTTCTCTTTCATTGAATTTAAATTTAAAAAAATATATTAATTTTACCAATAAATT
130 C-ATTAATATTCTCTCGTTCATTAAACTTAAATTTAAAAAAATATATTAATTTTACCAATAAA--
*
2596192 TTATCTCACTCATTATGTTTAATATAATATATTAGTTT
192 TTATCTCACTCATTATGTTTAATATAATATATTACTTT
* * * *
2596230 TATCTCATTCACATTCATTGAATTTAATATAATACATTAATTCTATTTATTACTTTTCGAAATTC
1 TATCTCATTCACATTCATTGAATTTAATATAATATATTAATTTTATTCATTGCTTTT--AAATT-
* * * * * *
2596295 CTTTTAACACTTTTTAATAGAATTTAAATGGCTAAATTATTAAAAATATAGTAC-AAAAATTATT
63 TTTTTAACTCTTTTTAATAGAATTTGAATGGTTAAATTACTAAAAATATAAT-CTAAAAATTATT
* *
2596359 GTCAATTAATA
127 ATCCATTAATA
2596370 ATTTAGCATT
Statistics
Matches: 309, Mismatches: 51, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
228 92 0.30
229 73 0.24
231 1 0.00
232 79 0.26
234 63 0.20
235 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.48
Consensus pattern (229 bp):
TATCTCATTCACATTCATTGAATTTAATATAATATATTAATTTTATTCATTGCTTTTAAATTTTT
TTAACTCTTTTTAATAGAATTTGAATGGTTAAATTACTAAAAATATAATCTAAAAATTATTATCC
ATTAATATTCTCTCGTTCATTAAACTTAAATTTAAAAAAATATATTAATTTTACCAATAAATTAT
CTCACTCATTATGTTTAATATAATATATTACTTT
Found at i:2596524 original size:22 final size:22
Alignment explanation
Indices: 2596498--2596539 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
2596488 TGTTTAATAT
2596498 TATTTTTATAA-TAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
2596520 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
2596540 AATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Done.