Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 203 of 206
Found at i:61463504 original size:16 final size:16
Alignment explanation
Indices: 61463463--61463541 Score: 74
Period size: 16 Copynumber: 5.0 Consensus size: 16
61463453 AAGTTCAAAT
* *
61463463 TTCACAACTTACGTAA
1 TTCATAACTTACATAA
61463479 TTTACATAACTTACATAA
1 -TT-CATAACTTACATAA
61463497 TTCATAACTTACATAA
1 TTCATAACTTACATAA
* *
61463513 TT--TAAATT-TATAA
1 TTCATAACTTACATAA
*
61463526 TACATAACTTACATAA
1 TTCATAACTTACATAA
61463542 CTTATTAATA
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
13 5 0.10
14 5 0.10
15 5 0.10
16 20 0.39
17 4 0.08
18 12 0.24
ACGTcount: A:0.44, C:0.16, G:0.01, T:0.38
Consensus pattern (16 bp):
TTCATAACTTACATAA
Found at i:61463657 original size:23 final size:22
Alignment explanation
Indices: 61463607--61463670 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
61463597 TTAAAAATTG
61463607 ATACATTACATAACTTACATAAC
1 ATACA-TACATAACTTACATAAC
*
61463630 CTACATACATAAGCTTACAT---
1 ATACATACATAA-CTTACATAAC
*
61463650 ATA-ATACATAACTTATATAAC
1 ATACATACATAACTTACATAAC
61463671 TTAAATTTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
18 6 0.18
19 8 0.24
20 2 0.06
22 7 0.21
23 11 0.32
ACGTcount: A:0.47, C:0.20, G:0.02, T:0.31
Consensus pattern (22 bp):
ATACATACATAACTTACATAAC
Found at i:61463829 original size:12 final size:12
Alignment explanation
Indices: 61463808--61463847 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
61463798 AAAAACTTAC
61463808 ATAACTTACATA
1 ATAACTTACATA
*
61463820 ATATCTTACATA
1 ATAACTTACATA
61463832 ATAACTTACATA
1 ATAACTTACATA
61463844 ATAA
1 ATAA
61463848 TGCGTACCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:61468846 original size:21 final size:21
Alignment explanation
Indices: 61468820--61468915 Score: 77
Period size: 21 Copynumber: 4.4 Consensus size: 21
61468810 CAACACCTTA
*
61468820 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGAG
** *
61468841 AAGCAGAGGCTACAGCAAGAG
1 AAGCAGAGGCGGCAGCGAGAG
*
61468862 AAGTAGAGGCCGG-AGCGAGAG
1 AAGCAGAGG-CGGCAGCGAGAG
** *
61468883 AAGCAGCGAGAGAAGCAGCGATAG
1 AAGCA--GAG-GCGGCAGCGAGAG
61468907 AAGCAGAGG
1 AAGCAGAGG
61468916 TTCAAAAGAA
Statistics
Matches: 58, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
21 37 0.64
22 4 0.07
23 4 0.07
24 13 0.22
ACGTcount: A:0.38, C:0.17, G:0.43, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGAG
Found at i:61468892 original size:12 final size:12
Alignment explanation
Indices: 61468875--61468912 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
61468865 TAGAGGCCGG
61468875 AGCGAGAGAAGC
1 AGCGAGAGAAGC
61468887 AGCGAGAGAAGC
1 AGCGAGAGAAGC
*
61468899 AGCGATAGAAGC
1 AGCGAGAGAAGC
61468911 AG
1 AG
61468913 AGGTTCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.42, C:0.16, G:0.39, T:0.03
Consensus pattern (12 bp):
AGCGAGAGAAGC
Found at i:61469218 original size:15 final size:15
Alignment explanation
Indices: 61469198--61469231 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
61469188 ATTTATTGTT
61469198 TTTGGTTGCTTTAGA
1 TTTGGTTGCTTTAGA
*
61469213 TTTGGTTGCTTTTGA
1 TTTGGTTGCTTTAGA
61469228 TTTG
1 TTTG
61469232 TTGTTGCAGG
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:0.06, G:0.26, T:0.59
Consensus pattern (15 bp):
TTTGGTTGCTTTAGA
Found at i:61469446 original size:42 final size:43
Alignment explanation
Indices: 61469349--61469553 Score: 303
Period size: 42 Copynumber: 4.8 Consensus size: 43
61469339 TTTGTGAAAT
61469349 AAGCGCCGCTAAAGAACACT-A-CTTTTAGCGGCGTTTTCTTCCC
1 AAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTCTTCCC
61469392 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTT-TTCCC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCTTCCC
*
61469434 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCTTCCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCTTCCC
* * * *
61469477 AAGTGCCG-TAAAGAACATGATATTTAGCAGCGTTTT-TTCCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCTTCCC
*
61469518 AAGCGCCACTAAAGAACATGATCTTTAGCGGCGTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT
61469554 ATTTTCTTAG
Statistics
Matches: 150, Mismatches: 8, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
41 11 0.07
42 94 0.63
43 44 0.29
44 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.29
Consensus pattern (43 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCTTCCC
Found at i:61479230 original size:18 final size:17
Alignment explanation
Indices: 61479203--61479236 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
61479193 AATATTTATT
*
61479203 TATAATAATTAATAATTG
1 TATAAGAATTAA-AATTG
61479221 TATAAGAATTAAAATT
1 TATAAGAATTAAAATT
61479237 AATAGTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
TATAAGAATTAAAATTG
Found at i:61480175 original size:23 final size:23
Alignment explanation
Indices: 61480149--61480197 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
61480139 TATAGACATC
*
61480149 AATGCATAGCAGATACAGATTCA
1 AATGCATAACAGATACAGATTCA
* *
61480172 AATGCATAACATATATAGATTCA
1 AATGCATAACAGATACAGATTCA
61480195 AAT
1 AAT
61480198 CCTACCCCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.27
Consensus pattern (23 bp):
AATGCATAACAGATACAGATTCA
Found at i:61480422 original size:29 final size:29
Alignment explanation
Indices: 61480372--61480485 Score: 156
Period size: 29 Copynumber: 3.9 Consensus size: 29
61480362 AAAAAATAAA
*
61480372 AAATTGCATTTTGACCCCTAAACTTTTTG
1 AAATTACATTTTGACCCCTAAACTTTTTG
* *
61480401 AAACTACATTTTGACCCATAAACTTTTTG
1 AAATTACATTTTGACCCCTAAACTTTTTG
* **
61480430 AAATTACATTTTAACCCCTAAACTTTCTAA
1 AAATTACATTTTGACCCCTAAACTTT-TTG
*
61480460 AAATTACATTTTGACCTCTAAACTTT
1 AAATTACATTTTGACCCCTAAACTTT
61480486 CTCAAAATTA
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
29 49 0.66
30 25 0.34
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.39
Consensus pattern (29 bp):
AAATTACATTTTGACCCCTAAACTTTTTG
Found at i:61480750 original size:16 final size:16
Alignment explanation
Indices: 61480726--61480756 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
61480716 AAAAAGCTTC
61480726 GAGAAAAAGAAAAGAA
1 GAGAAAAAGAAAAGAA
*
61480742 GAGAGAAAGAAAAGA
1 GAGAAAAAGAAAAGA
61480757 GGAAGGAGAA
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:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (16 bp):
GAGAAAAAGAAAAGAA
Found at i:61481971 original size:17 final size:16
Alignment explanation
Indices: 61481958--61482006 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
61481948 TAAAAAATCC
61481958 TCGTGTTTTCAAAAATT
1 TCGTGTTTTC-AAAATT
*
61481975 TCGATGTTTTGAAAATTT
1 TCG-TGTTTTCAAAA-TT
61481993 TCGTGTTTTCAAAA
1 TCGTGTTTTCAAAA
61482007 AAATCTCGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 17 0.61
18 11 0.39
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (16 bp):
TCGTGTTTTCAAAATT
Found at i:61481971 original size:18 final size:17
Alignment explanation
Indices: 61481927--61482042 Score: 76
Period size: 18 Copynumber: 6.7 Consensus size: 17
61481917 NNNNNNNNNT
**
61481927 TGTTTTCAAATTTTTCG
1 TGTTTTCAAAAATTTCG
* * *
61481944 T-ATTTAAAAAATCCTCG
1 TGTTTTCAAAAAT-TTCG
61481961 TGTTTTCAAAAATTTCG
1 TGTTTTCAAAAATTTCG
* *
61481978 ATGTTTTGAAAATTTTCG
1 -TGTTTTCAAAAATTTCG
*
61481996 TGTTTTCAAAAAAATCTCG
1 TGTTTTC--AAAAATTTCG
*
61482015 TG-TTTCATAAATTTTCG
1 TGTTTTCA-AAAATTTCG
*
61482032 T-TTTTTAAAAA
1 TGTTTTCAAAAA
61482043 AAATTGTGTC
Statistics
Matches: 75, Mismatches: 17, Indels: 15
0.70 0.16 0.14
Matches are distributed among these distances:
16 11 0.15
17 26 0.35
18 28 0.37
19 10 0.13
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.47
Consensus pattern (17 bp):
TGTTTTCAAAAATTTCG
Found at i:61482008 original size:36 final size:35
Alignment explanation
Indices: 61481958--61482076 Score: 97
Period size: 36 Copynumber: 3.5 Consensus size: 35
61481948 TAAAAAATCC
* *
61481958 TCGTGTTTTC-AAAAATTTCGATGTTTTGA-AAATTT
1 TCGTGTTTTCAAAAAATCTCG-TG-TTTCATAAATTT
61481993 TCGTGTTTTCAAAAAAATCTCGTGTTTCATAAATTT
1 TCGTGTTTTC-AAAAAATCTCGTGTTTCATAAATTT
* * * *
61482029 TCGTTTTTTAAAAAAAAT-T-GTG-TCCA-AAATTC
1 TCGTGTTTT-CAAAAAATCTCGTGTTTCATAAATTT
*
61482061 TCGTGTTTTTAAAAAA
1 TCGTGTTTTCAAAAAA
61482077 AATTCTCGTG
Statistics
Matches: 72, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
31 6 0.08
32 13 0.18
33 3 0.04
34 3 0.04
35 15 0.21
36 23 0.32
37 9 0.12
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.45
Consensus pattern (35 bp):
TCGTGTTTTCAAAAAATCTCGTGTTTCATAAATTT
Found at i:61488052 original size:14 final size:14
Alignment explanation
Indices: 61488033--61488105 Score: 71
Period size: 14 Copynumber: 5.1 Consensus size: 14
61488023 TATTATGCCT
61488033 AAAAAAACAAAAAC
1 AAAAAAACAAAAAC
61488047 AAAAAAAACAAAAA-
1 -AAAAAAACAAAAAC
*
61488061 AAAACAAAAAAAAAC
1 AAAA-AAACAAAAAC
*
61488076 -AACAAACAAAAAAC
1 AAAAAAAC-AAAAAC
61488090 AAAACAAA-AAAAAC
1 AAAA-AAACAAAAAC
61488104 AA
1 AA
61488106 GGAAAAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
13 7 0.14
14 24 0.49
15 15 0.31
16 3 0.06
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAACAAAAAC
Found at i:61488060 original size:10 final size:10
Alignment explanation
Indices: 61488036--61488102 Score: 84
Period size: 10 Copynumber: 6.8 Consensus size: 10
61488026 TATGCCTAAA
61488036 AAAACAAAAAC
1 AAAA-AAAAAC
61488047 -AAAAAAAAC
1 AAAAAAAAAC
61488056 AAAAAAAAAC
1 AAAAAAAAAC
61488066 AAAAAAAAAC
1 AAAAAAAAAC
* *
61488076 AACAAACAA-
1 AAAAAAAAAC
*
61488085 AAAACAAAAC
1 AAAAAAAAAC
61488095 AAAAAAAA
1 AAAAAAAA
61488103 CAAGGAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
9 12 0.25
10 36 0.75
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:61488065 original size:25 final size:24
Alignment explanation
Indices: 61488033--61488114 Score: 112
Period size: 25 Copynumber: 3.3 Consensus size: 24
61488023 TATTATGCCT
61488033 AAAAAAACAAAAACAAAAAAAACAA
1 AAAAAAAC-AAAACAAAAAAAACAA
*
61488058 AAAAAAACAAAA-AAAAACAACAA
1 AAAAAAACAAAACAAAAAAAACAA
61488081 ACAAAAAACAAAACAAAAAAAACAA
1 A-AAAAAACAAAACAAAAAAAACAA
61488106 GGAAAAAAA
1 --AAAAAAA
61488115 TCAAGATGAA
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
23 11 0.22
24 15 0.29
25 18 0.35
26 6 0.12
27 1 0.02
ACGTcount: A:0.85, C:0.12, G:0.02, T:0.00
Consensus pattern (24 bp):
AAAAAAACAAAACAAAAAAAACAA
Found at i:61488111 original size:13 final size:13
Alignment explanation
Indices: 61488033--61488120 Score: 69
Period size: 13 Copynumber: 6.9 Consensus size: 13
61488023 TATTATGCCT
61488033 AAAAAAACAA-AA
1 AAAAAAACAAGAA
*
61488045 ACAAAAAA-AACAA
1 A-AAAAAACAAGAA
61488058 AAAAAAACAA-AA
1 AAAAAAACAAGAA
61488070 AAAAACAAC-A-AA
1 AAAAA-AACAAGAA
* *
61488082 CAAAAAACAAAACA
1 AAAAAAACAAGA-A
*
61488096 AAAAAAACAAGGA
1 AAAAAAACAAGAA
*
61488109 AAAAAATCAAGA
1 AAAAAAACAAGA
61488121 TGAAAACCCG
Statistics
Matches: 63, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
11 3 0.05
12 24 0.38
13 26 0.41
14 10 0.16
ACGTcount: A:0.83, C:0.12, G:0.03, T:0.01
Consensus pattern (13 bp):
AAAAAAACAAGAA
Found at i:61488114 original size:1 final size:1
Alignment explanation
Indices: 61488033--61488102 Score: 59
Period size: 1 Copynumber: 70.0 Consensus size: 1
61488023 TATTATGCCT
* * * * * * * * *
61488033 AAAAAAACAAAAACAAAAAAAACAAAAAAAAACAAAAAAAAACAACAAACAAAAAACAAAACAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
61488098 AAAAA
1 AAAAA
61488103 CAAGGAAAAA
Statistics
Matches: 51, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:61488114 original size:14 final size:13
Alignment explanation
Indices: 61488033--61488105 Score: 80
Period size: 13 Copynumber: 5.8 Consensus size: 13
61488023 TATTATGCCT
61488033 AAAAAAACAAAAA
1 AAAAAAACAAAAA
* *
61488046 CAAAAAA-AACAA
1 AAAAAAACAAAAA
61488058 AAAAAAACAAAAA
1 AAAAAAACAAAAA
*
61488071 AAAACAAC--AAA
1 AAAAAAACAAAAA
*
61488082 CAAAAAACAAAACA
1 AAAAAAACAAAA-A
61488096 AAAAAAACAA
1 AAAAAAACAA
61488106 GGAAAAAAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
11 9 0.19
12 10 0.21
13 19 0.40
14 10 0.21
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAA
Found at i:61489228 original size:78 final size:78
Alignment explanation
Indices: 61488989--61489498 Score: 624
Period size: 78 Copynumber: 6.7 Consensus size: 78
61488979 TATTTTCCAG
* *
61488989 TTTCTGTTTTT-TAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC--GCTGAG
1 TTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGTCACATGCCGAG
*
61489051 GAATTTTCAATTTT-T-
65 GTA-TTTC--TTTTATA
* * *
61489066 TTTC---TTTT--AAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGAGTCAC--GTCGAG
1 TTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG-GTCACATGCCGAG
61489124 GTATTTCTTTTATA
65 GTATTTCTTTTATA
61489138 TTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTCACATGCCGAGG
1 TTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTCACATGCCGAGG
61489203 TATTTCTTTTATA
66 TATTTCTTTTATA
*
61489216 TTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGG
1 TTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTCACATGCCGAGG
* *
61489281 TATTTCGTTTAAA
66 TATTTCTTTTATA
** * *
61489294 TTTCTGTTCTTT-TTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAA
1 TTTCTGTT-TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTCACATGCCGAG
*
61489358 GTA-TT-TTTCA-A
65 GTATTTCTTTTATA
* * * * * *
61489369 TTCCTGTTTTTCAAAAATCAACTCATACTGCAAGGGGTGAGTTGAGCCTCGGGTCTCATGCCAAG
1 TTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGTCACATGCCGAG
61489434 GTA-TTCTTTTCA-A
65 GTATTTCTTTT-ATA
* *
61489447 ATTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCATCGG
1 TTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
61489499 GTCGCACGTC
Statistics
Matches: 385, Mismatches: 33, Indels: 30
0.86 0.07 0.07
Matches are distributed among these distances:
70 4 0.01
71 1 0.00
72 9 0.02
73 46 0.12
74 7 0.02
75 45 0.12
76 23 0.06
77 47 0.12
78 200 0.52
79 3 0.01
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (78 bp):
TTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTCACATGCCGAGG
TATTTCTTTTATA
Found at i:61489418 original size:231 final size:227
Alignment explanation
Indices: 61488989--61489498 Score: 674
Period size: 231 Copynumber: 2.2 Consensus size: 227
61488979 TATTTTCCAG
* * *
61488989 TTTCTGTTTTT-TAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGA
1 TTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACGCCGAGGA
* * * * *
61489053 ATTTTCAATTTTTTTTCTTTTAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGAGTCAC
65 ATTTTAAATTTCTGTTCTTTTAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGACAC
* * * * * *
61489118 GTCGAGGTATTTCTTTTATATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
130 GCCGAAGTATTTCTTTCATATTCCTGTTTTTCAAAAATCAACTCATACTGCAAGAGGTGAGTTGA
*
61489183 GCCTC-GGTCACATGCCGAGGTATTTCTTTT-ATA
195 GCCTCGGGTCACATGCCAAGGTA-TTCTTTTCA-A
61489216 TTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGG
1 TTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACAC--GCCGAGG
* * *
61489281 TATTTCGTTTAAATTTCTGTTCTTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG-
64 -A-AT--TTTAAATTTCTGTTCTTTTAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGA
*
61489345 GACACATGCCGAAGTA-TT-TTTCA-ATTCCTGTTTTTCAAAAATCAACTCATACTGCAAGGGGT
125 GACAC--GCCGAAGTATTTCTTTCATATTCCTGTTTTTCAAAAATCAACTCATACTGCAAGAGGT
*
61489407 GAGTTGAGCCTCGGGTCTCATGCCAAGGTATTCTTTTCAA
188 GAGTTGAGCCTCGGGTCACATGCCAAGGTATTCTTTTCAA
* *
61489447 ATTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCATCGG
1 TTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
61489499 GTCGCACGTC
Statistics
Matches: 250, Mismatches: 22, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
227 16 0.06
228 37 0.15
229 6 0.02
230 1 0.00
231 106 0.42
232 24 0.10
233 53 0.21
234 7 0.03
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (227 bp):
TTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACGCCGAGGAA
TTTTAAATTTCTGTTCTTTTAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGACACG
CCGAAGTATTTCTTTCATATTCCTGTTTTTCAAAAATCAACTCATACTGCAAGAGGTGAGTTGAG
CCTCGGGTCACATGCCAAGGTATTCTTTTCAA
Found at i:61489466 original size:153 final size:150
Alignment explanation
Indices: 61488990--61489498 Score: 614
Period size: 153 Copynumber: 3.3 Consensus size: 150
61488980 ATTTTCCAGT
* * *
61488990 TTCTGTTTTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC--GCTG-AGG
1 TTCTGTTTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGTCACATGCCGAAGT
* * * ** * * *
61489052 AATTTTCAATTTTTTTTCTTTTAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGAG-TC
65 ATTTTTCAATTCTGTTT-TTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCTC
* * *
61489116 ACGTCGAGGTATTTCTTTTATAT
129 ATGCCGAGGTATTTCTTTTA-AA
*
61489139 TTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTCACATGCCGAGGT
1 TTCTGTTTTT-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTCACATGCCGAAGT
* *
61489204 ATTTCTTTTATATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGA
65 A-TT-TTTCA-A-TTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
* *
61489269 CACATGCCGAGGTATTTCGTTTAAA
126 CTCATGCCGAGGTATTTCTTTTAAA
** *
61489294 TTTCTGTTCTTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAAG
1 -TTCTGTT-TTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTCACATGCCGAAG
* * *
61489359 TATTTTTCAATTCCTGTTTTTCAAAAATCAACTCATACTGCAAGGGGTGAGTTGAGCCTCGGGTC
64 TATTTTTCAATT-CTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-C
*
61489424 TCATGCCAAGGTA-TTCTTTTCAAA
127 TCATGCCGAGGTATTTCTTTT-AAA
*
61489448 TTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCATCGG
1 TTCTGTTTTT-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
61489499 GTCGCACGTC
Statistics
Matches: 311, Mismatches: 34, Indels: 26
0.84 0.09 0.07
Matches are distributed among these distances:
149 16 0.05
150 37 0.12
151 3 0.01
152 7 0.02
153 98 0.32
154 23 0.07
155 42 0.14
156 82 0.26
157 3 0.01
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (150 bp):
TTCTGTTTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTCACATGCCGAAGTA
TTTTTCAATTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCTCAT
GCCGAGGTATTTCTTTTAAA
Found at i:61489743 original size:29 final size:29
Alignment explanation
Indices: 61489701--61489814 Score: 165
Period size: 29 Copynumber: 3.9 Consensus size: 29
61489691 AAAAAATAAA
*
61489701 AAATTGCATTTTGACCCCTAAACTTTTTG
1 AAATTACATTTTGACCCCTAAACTTTTTG
*
61489730 AAATTACATTTTGACCCATAAACTTTTTG
1 AAATTACATTTTGACCCCTAAACTTTTTG
* **
61489759 AAATTACATTTTAACCCCTAAACTTTCTAA
1 AAATTACATTTTGACCCCTAAACTTT-TTG
*
61489789 AAATTACATTTTGACCTCTAAACTTT
1 AAATTACATTTTGACCCCTAAACTTT
61489815 CTCAAAATTA
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
29 51 0.67
30 25 0.33
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.40
Consensus pattern (29 bp):
AAATTACATTTTGACCCCTAAACTTTTTG
Found at i:61489814 original size:59 final size:58
Alignment explanation
Indices: 61489701--61489814 Score: 167
Period size: 59 Copynumber: 1.9 Consensus size: 58
61489691 AAAAAATAAA
* * **
61489701 AAATTGCATTTTGACCCCTAAACTTTTTGAAATTACATTTTGACCCATAAACTTTTTG
1 AAATTACATTTTAACCCCTAAACTTTTAAAAATTACATTTTGACCCATAAACTTTTTG
61489759 AAATTACATTTTAACCCCTAAACTTTCTAAAAATTACATTTTGACCTC-TAAACTTT
1 AAATTACATTTTAACCCCTAAACTTT-TAAAAATTACATTTTGACC-CATAAACTTT
61489815 CTCAAAATTA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
58 24 0.48
59 25 0.50
60 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.40
Consensus pattern (58 bp):
AAATTACATTTTAACCCCTAAACTTTTAAAAATTACATTTTGACCCATAAACTTTTTG
Found at i:61490079 original size:16 final size:16
Alignment explanation
Indices: 61490055--61490085 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
61490045 AAAAAGCTTC
61490055 GAGAAAAAGAAAAGAA
1 GAGAAAAAGAAAAGAA
*
61490071 GAGAGAAAGAAAAGA
1 GAGAAAAAGAAAAGA
61490086 GGAAGGAGAA
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:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (16 bp):
GAGAAAAAGAAAAGAA
Found at i:61490342 original size:20 final size:19
Alignment explanation
Indices: 61490310--61490365 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
61490300 GCCCAAGAAA
* *
61490310 AAAAACAACAAAAAAAAGC
1 AAAAACAAAAAAAAAAAAC
61490329 AAAAACAAAAAAAAAGAAAC
1 AAAAACAAAAAAAAA-AAAC
***
61490349 AAGCCCAAAAAAAAAAA
1 AAAAACAAAAAAAAAAA
61490366 GAAGAGAAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.80, C:0.14, G:0.05, T:0.00
Consensus pattern (19 bp):
AAAAACAAAAAAAAAAAAC
Found at i:61490517 original size:11 final size:11
Alignment explanation
Indices: 61490501--61490564 Score: 56
Period size: 11 Copynumber: 5.7 Consensus size: 11
61490491 GGCCCAGCAG
61490501 AGAAAAAAAAA
1 AGAAAAAAAAA
*
61490512 AGAAAAGAAAA
1 AGAAAAAAAAA
* * *
61490523 CGAAGAAAAAG
1 AGAAAAAAAAA
**
61490534 AGAAGGAAAAA
1 AGAAAAAAAAA
*
61490545 AGAAGGAAAAAA
1 AGAA-AAAAAAA
61490557 AGAAAAAA
1 AGAAAAAA
61490565 GATGTTCAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
11 32 0.76
12 10 0.24
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (11 bp):
AGAAAAAAAAA
Found at i:61490714 original size:10 final size:9
Alignment explanation
Indices: 61490687--61490711 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
61490677 AATATTATTA
61490687 GCATTTTAT
1 GCATTTTAT
61490696 GCATTTTAT
1 GCATTTTAT
61490705 GCATTTT
1 GCATTTT
61490712 TATATTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.12, G:0.12, T:0.56
Consensus pattern (9 bp):
GCATTTTAT
Found at i:61490747 original size:16 final size:17
Alignment explanation
Indices: 61490721--61490758 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
61490711 TTATATTTAT
61490721 ATTTTTAATTTAATTTG
1 ATTTTTAATTTAATTTG
* *
61490738 ATTTTT-ATTTTATTTT
1 ATTTTTAATTTAATTTG
61490754 ATTTT
1 ATTTT
61490759 AAATAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTTTAATTTAATTTG
Found at i:61490956 original size:21 final size:20
Alignment explanation
Indices: 61490924--61490965 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
61490914 TCGGGTTTCG
61490924 AAATTTTCGTGTCTTCAAAA
1 AAATTTTCGTGTCTTCAAAA
*
61490944 AAATTTCTCGTGTTTTCAAAA
1 AAATTT-TCGTGTCTTCAAAA
61490965 A
1 A
61490966 TAAGGTAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
AAATTTTCGTGTCTTCAAAA
Found at i:61490966 original size:19 final size:19
Alignment explanation
Indices: 61490924--61490965 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
61490914 TCGGGTTTCG
61490924 AAATTTTCGTGTCTTCAAAA
1 AAATTTTCGTGTCTTC-AAA
*
61490944 AAATTTCTCGTGTTTTCAAA
1 AAATTT-TCGTGTCTTCAAA
61490964 AA
1 AA
61490966 TAAGGTAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (19 bp):
AAATTTTCGTGTCTTCAAA
Found at i:61491124 original size:36 final size:35
Alignment explanation
Indices: 61491071--61491139 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 35
61491061 AAAAAATCGG
* *
61491071 AAAATTTTTCGTGTTTTCAAAAATTCCCGTGTTGC
1 AAAAATTTTCATGTTTTCAAAAATTCCCGTGTTGC
*
61491106 AAAAATTTTCATGTTTTTCAAAAATTCTCGTGTT
1 AAAAATTTTCATG-TTTTCAAAAATTCCCGTGTT
61491140 TTCAAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 11 0.37
36 19 0.63
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (35 bp):
AAAAATTTTCATGTTTTCAAAAATTCCCGTGTTGC
Found at i:61491160 original size:36 final size:35
Alignment explanation
Indices: 61491120--61491212 Score: 105
Period size: 36 Copynumber: 2.6 Consensus size: 35
61491110 ATTTTCATGT
*
61491120 TTTTCAAAAATTCTCGTGTTTTCAAAAAAATTCCAA
1 TTTTCAAAAATTTTCGTGTTTTCAAAAAAATT-CAA
* * * * **
61491156 TTTTCAAAATTTTTCGTTTTTTCTAAAAACTTCTG
1 TTTTCAAAAATTTTCGTGTTTTCAAAAAAATTCAA
61491191 TGTTTCAAAAATTTTCGTGTTT
1 T-TTTCAAAAATTTTCGTGTTT
61491213 CTAAAATTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
35 2 0.04
36 45 0.96
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.48
Consensus pattern (35 bp):
TTTTCAAAAATTTTCGTGTTTTCAAAAAAATTCAA
Found at i:61491176 original size:17 final size:17
Alignment explanation
Indices: 61491071--61491268 Score: 107
Period size: 17 Copynumber: 11.4 Consensus size: 17
61491061 AAAAAATCGG
*
61491071 AAAATTTTTCGTGTTTTC
1 AAAAATTTTCGT-TTTTC
** * *
61491089 AAAAATTCCCGTGTTGC
1 AAAAATTTTCGTTTTTC
61491106 AAAAATTTTCATGTTTTTC
1 AAAAATTTTC--GTTTTTC
*
61491125 AAAAATTCTCGTGTTTTC
1 AAAAATTTTCGT-TTTTC
* * **
61491143 AAAAAAATTCCAATTTTC
1 -AAAAATTTTCGTTTTTC
*
61491161 AAAATTTTTCGTTTTTTC
1 AAAAATTTTCG-TTTTTC
* *
61491179 TAAAAA-CTTCTGTGTTTC
1 -AAAAATTTTC-GTTTTTC
*
61491197 AAAAATTTTCGTGTTTC
1 AAAAATTTTCGTTTTTC
* *
61491214 TAAAATTTTCG-TATTC
1 AAAAATTTTCGTTTTTC
*
61491230 -AAAATTTTCTTGTTTTC
1 AAAAATTTTCGT-TTTTC
* * *
61491247 -AAATTTTTCGTATTTA
1 AAAAATTTTCGTTTTTC
61491263 AAAAAT
1 AAAAAT
61491269 CNNNNNNNNN
Statistics
Matches: 135, Mismatches: 34, Indels: 23
0.70 0.18 0.12
Matches are distributed among these distances:
15 9 0.07
16 6 0.04
17 59 0.44
18 35 0.26
19 26 0.19
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.47
Consensus pattern (17 bp):
AAAAATTTTCGTTTTTC
Found at i:61491238 original size:32 final size:32
Alignment explanation
Indices: 61491198--61491265 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
61491188 CTGTGTTTCA
61491198 AAAATTTTCGTG-TTTCTAAAATTTTCGTATTC
1 AAAATTTTCGTGTTTTC-AAAATTTTCGTATTC
* * *
61491230 AAAATTTTCTTGTTTTCAAATTTTTCGTATTT
1 AAAATTTTCGTGTTTTCAAAATTTTCGTATTC
61491262 AAAA
1 AAAA
61491266 AATCNNNNNN
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 28 0.88
33 4 0.12
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.51
Consensus pattern (32 bp):
AAAATTTTCGTGTTTTCAAAATTTTCGTATTC
Found at i:61491429 original size:36 final size:34
Alignment explanation
Indices: 61491372--61491475 Score: 106
Period size: 36 Copynumber: 3.0 Consensus size: 34
61491362 NNNNNNNNTG
61491372 AAAATTTTCGTGTTTTCAAAAAAATCTCGTGTTTC
1 AAAATTTTCGTGTTTT-AAAAAAATCTCGTGTTTC
* *
61491407 ATAAATTTTCGT-TTGTTAAAAAAAT-TTGTG-TCC
1 A-AAATTTTCGTGTT-TTAAAAAAATCTCGTGTTTC
*
61491440 AAAATTCTCGTGTTTTTAAAAAAAATTCTCGTGTTT
1 AAAATTTTCGTG-TTTT-AAAAAAA-TCTCGTGTTT
61491476 TAATCGGATC
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
32 9 0.16
33 5 0.09
34 13 0.23
35 12 0.21
36 16 0.29
37 1 0.02
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (34 bp):
AAAATTTTCGTGTTTTAAAAAAATCTCGTGTTTC
Found at i:61494810 original size:58 final size:58
Alignment explanation
Indices: 61494741--61494856 Score: 180
Period size: 58 Copynumber: 2.0 Consensus size: 58
61494731 TATTCTGTAA
* * *
61494741 AATTGGAATCGATGAAGAGA-ATTATCACCATAAACTTGAGACCTAAAACTTCTAGAGT
1 AATTGGAATCGATGAAGA-ATATTATCACAATAAACTTGAGAACTAAAACTGCTAGAGT
*
61494799 AATTGGAATCGATGAAGAATATTATCACAATAAACTTGAGAACTAAATCTGCTAGAGT
1 AATTGGAATCGATGAAGAATATTATCACAATAAACTTGAGAACTAAAACTGCTAGAGT
61494857 TTTTAGTATT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
57 1 0.02
58 52 0.98
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (58 bp):
AATTGGAATCGATGAAGAATATTATCACAATAAACTTGAGAACTAAAACTGCTAGAGT
Found at i:61495351 original size:52 final size:52
Alignment explanation
Indices: 61495289--61495387 Score: 164
Period size: 52 Copynumber: 1.9 Consensus size: 52
61495279 CTAATGTACG
*
61495289 AGAACTAATTTTCTCGTTTTATTAATAGATGAG-GCAAAATACAATTTGAACA
1 AGAACTAATTTGCTCGTTTTATTAATAGA-GAGAGCAAAATACAATTTGAACA
*
61495341 AGAACTAATTTGCTCGTTTTATTAATAGAGGGAGCAAAATACAATTT
1 AGAACTAATTTGCTCGTTTTATTAATAGAGAGAGCAAAATACAATTT
61495388 AAGTCATAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
51 2 0.05
52 42 0.95
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.34
Consensus pattern (52 bp):
AGAACTAATTTGCTCGTTTTATTAATAGAGAGAGCAAAATACAATTTGAACA
Found at i:61499067 original size:21 final size:19
Alignment explanation
Indices: 61499017--61499114 Score: 115
Period size: 19 Copynumber: 4.8 Consensus size: 19
61499007 AATCTTCGAG
*
61499017 GATATGCAATCTTAGATAT
1 GATATGTAATCTTAGATAT
*
61499036 GATATGCAATCTTAGATAT
1 GATATGTAATCTTAGATAT
61499055 GATATATGTAATCTTAGATAT
1 G--ATATGTAATCTTAGATAT
61499076 GATATGTAATCTTAGAAGATAT
1 GATATGTAATCTT---AGATAT
*
61499098 GATTTTGTAATCTTAGA
1 GA-TATGTAATCTTAGA
61499115 GATTTAATTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
19 32 0.45
20 3 0.04
21 18 0.25
22 8 0.11
23 10 0.14
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.40
Consensus pattern (19 bp):
GATATGTAATCTTAGATAT
Found at i:61499068 original size:40 final size:41
Alignment explanation
Indices: 61499018--61499114 Score: 135
Period size: 40 Copynumber: 2.4 Consensus size: 41
61499008 ATCTTCGAGG
*
61499018 ATATGCAATCTTAGATATGATATGCAATCTT-AGATATGAT
1 ATATGTAATCTTAGATATGATATGCAATCTTAAGATATGAT
*
61499058 ATATGTAATCTTAGATATGATATGTAATCTTAGAAGATATGAT
1 ATATGTAATCTTAGATATGATATGCAATCTT--AAGATATGAT
*
61499101 -TTTGTAATCTTAGA
1 ATATGTAATCTTAGA
61499115 GATTTAATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
40 29 0.57
42 13 0.25
43 9 0.18
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.40
Consensus pattern (41 bp):
ATATGTAATCTTAGATATGATATGCAATCTTAAGATATGAT
Found at i:61499124 original size:22 final size:22
Alignment explanation
Indices: 61499070--61499128 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 22
61499060 ATGTAATCTT
* *
61499070 AGATATGATATGTAATCTTAGA
1 AGATATAATTTGTAATCTTAGA
*
61499092 AGATATGATTTTGTAATCTTAG-
1 AGATAT-AATTTGTAATCTTAGA
*
61499114 AGATTTAATTTGTAA
1 AGATATAATTTGTAA
61499129 ATACCTTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 8 0.26
22 11 0.35
23 12 0.39
ACGTcount: A:0.37, C:0.03, G:0.17, T:0.42
Consensus pattern (22 bp):
AGATATAATTTGTAATCTTAGA
Found at i:61499127 original size:21 final size:23
Alignment explanation
Indices: 61499049--61499128 Score: 73
Period size: 21 Copynumber: 3.7 Consensus size: 23
61499039 ATGCAATCTT
*
61499049 AGATATGATATATGTAATCTT---
1 AGATATGA-ATTTGTAATCTTAGA
*
61499070 AGATATG-ATATGTAATCTTAGA
1 AGATATGAATTTGTAATCTTAGA
*
61499092 AGATATGATTTTGTAATCTTAG-
1 AGATATGAATTTGTAATCTTAGA
*
61499114 AGAT-TTAATTTGTAA
1 AGATATGAATTTGTAA
61499129 ATACCTTTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
19 12 0.24
21 16 0.31
22 11 0.22
23 12 0.24
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.42
Consensus pattern (23 bp):
AGATATGAATTTGTAATCTTAGA
Found at i:61499941 original size:51 final size:52
Alignment explanation
Indices: 61499827--61499942 Score: 132
Period size: 51 Copynumber: 2.3 Consensus size: 52
61499817 ATTTTCCACG
**
61499827 TTTT-TATAT-TATACTTATATATTTCATTTTTTTGTAAATGCATGAATATA
1 TTTTATATATATATACTTATATATTTCATTTTTTCATAAATGCATGAATATA
* * * * *
61499877 TTTTATATGTATATATTTATAT-TTTCCTTGTTTTCATAAATGCAT-TATGTA
1 TTTTATATATATATACTTATATATTTCATT-TTTTCATAAATGCATGAATATA
61499928 TTTTATATATATATA
1 TTTTATATATATATA
61499943 AGTTTTATAA
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
50 4 0.07
51 28 0.51
52 23 0.42
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (52 bp):
TTTTATATATATATACTTATATATTTCATTTTTTCATAAATGCATGAATATA
Found at i:61503287 original size:31 final size:29
Alignment explanation
Indices: 61503219--61503287 Score: 70
Period size: 31 Copynumber: 2.3 Consensus size: 29
61503209 AATAGATGAA
61503219 TTTTTT-AATAAAAATAATTAATTTACTT
1 TTTTTTAAATAAAAATAATTAATTTACTT
*
61503247 TTTAATTTAACATAAAAAT-ATTATTTTACTCAT
1 TTT--TTTAA-ATAAAAATAATTAATTTACT--T
61503280 TTTTTTAA
1 TTTTTTAA
61503288 GAAGAACTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
28 3 0.09
30 3 0.09
31 16 0.47
32 8 0.24
33 4 0.12
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.54
Consensus pattern (29 bp):
TTTTTTAAATAAAAATAATTAATTTACTT
Found at i:61508655 original size:4 final size:4
Alignment explanation
Indices: 61508639--61508677 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
61508629 ATACTGCACA
* *
61508639 TATG TATG AATG TATG TATG CATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
61508678 ACACACATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.28, C:0.03, G:0.23, T:0.46
Consensus pattern (4 bp):
TATG
Found at i:61510951 original size:15 final size:15
Alignment explanation
Indices: 61510920--61510960 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
61510910 TATTGTCAGG
61510920 AAGAAAGAAAGATATTT
1 AAGAAA-AAA-ATATTT
61510937 AAGAAAAAAATATTT
1 AAGAAAAAAATATTT
61510952 AA-AAAAAAA
1 AAGAAAAAAA
61510961 GGAAATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.29
15 8 0.33
16 3 0.12
17 6 0.25
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.20
Consensus pattern (15 bp):
AAGAAAAAAATATTT
Found at i:61512760 original size:25 final size:25
Alignment explanation
Indices: 61512726--61512778 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
61512716 TTTAAAAAAG
61512726 AAATAATATTTGATACATTGTCGAT
1 AAATAATATTTGATACATTGTCGAT
61512751 AAATAATATTTGATACATTGTCGAT
1 AAATAATATTTGATACATTGTCGAT
61512776 AAA
1 AAA
61512779 GGTGCTCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (25 bp):
AAATAATATTTGATACATTGTCGAT
Found at i:61513014 original size:29 final size:28
Alignment explanation
Indices: 61512932--61513012 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 28
61512922 CCCATTTTTT
*
61512932 AATAAAACACTAAAAAT-T-TATTTTAAA
1 AATAAAA-AATAAAAATATATATTTTAAA
61512959 AATAAAAAAATTAAAAA-A-AGTATTTTAAA
1 AAT-AAAAAA-TAAAAATATA-TATTTTAAA
61512988 AATAAAAAATAAAAATATATATTTT
1 AATAAAAAATAAAAATATATATTTT
61513013 TATTATATTC
Statistics
Matches: 46, Mismatches: 1, Indels: 13
0.77 0.02 0.22
Matches are distributed among these distances:
27 10 0.22
28 23 0.50
29 13 0.28
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.32
Consensus pattern (28 bp):
AATAAAAAATAAAAATATATATTTTAAA
Found at i:61513608 original size:25 final size:26
Alignment explanation
Indices: 61513580--61513633 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
61513570 ATTATCGTGG
61513580 TTTGTCCACA-GTTTCGTGATTTTAT
1 TTTGTCCACATGTTTCGTGATTTTAT
* * * *
61513605 TTTGTTCACATTTTTCGTGGTTTTTT
1 TTTGTCCACATGTTTCGTGATTTTAT
61513631 TTT
1 TTT
61513634 AATTTGTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.11, C:0.13, G:0.15, T:0.61
Consensus pattern (26 bp):
TTTGTCCACATGTTTCGTGATTTTAT
Found at i:61515871 original size:5 final size:5
Alignment explanation
Indices: 61515861--61515888 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
61515851 ATTTAAATCG
61515861 ATTAA ATTAA ATTAA ATTAA ATTAA ATT
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATT
61515889 CTTTTGTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
ATTAA
Found at i:61522650 original size:64 final size:64
Alignment explanation
Indices: 61522577--61522704 Score: 247
Period size: 64 Copynumber: 2.0 Consensus size: 64
61522567 GGTCAAAAAA
61522577 TGACCAACAATGGTATTAAACAGCAGCAACCCTTATTGTTAATAGCAATAATATATTAACAAAT
1 TGACCAACAATGGTATTAAACAGCAGCAACCCTTATTGTTAATAGCAATAATATATTAACAAAT
*
61522641 TGACCAACAATGGTATTAAACAGCAGCAACCCTTATTGTTAATAGCAATAGTATATTAACAAAT
1 TGACCAACAATGGTATTAAACAGCAGCAACCCTTATTGTTAATAGCAATAATATATTAACAAAT
61522705 ATACGTGTAT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.28
Consensus pattern (64 bp):
TGACCAACAATGGTATTAAACAGCAGCAACCCTTATTGTTAATAGCAATAATATATTAACAAAT
Found at i:61544539 original size:17 final size:17
Alignment explanation
Indices: 61544519--61544565 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 17
61544509 TAATTATGAG
*
61544519 TTTAAATTAATTTTAGA
1 TTTAAATTAATTTTACA
61544536 TTTAAA-TAATTTTACA
1 TTTAAATTAATTTTACA
*
61544552 TTCAAATT-ATTTTA
1 TTTAAATTAATTTTA
61544566 ACTTAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 20 0.74
17 7 0.26
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (17 bp):
TTTAAATTAATTTTACA
Found at i:61544547 original size:16 final size:16
Alignment explanation
Indices: 61544505--61544565 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
61544495 GTTTCGAACA
*
61544505 TAAATAATTAT-GAGTT
1 TAAATAATTTTAGA-TT
61544521 TAAATTAATTTTAGATT
1 TAAA-TAATTTTAGATT
*
61544538 TAAATAATTTTACATT
1 TAAATAATTTTAGATT
* *
61544554 CAAATTATTTTA
1 TAAATAATTTTA
61544566 ACTTAAAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
16 25 0.64
17 12 0.31
18 2 0.05
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (16 bp):
TAAATAATTTTAGATT
Found at i:61545051 original size:19 final size:21
Alignment explanation
Indices: 61545024--61545062 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
61545014 CCTAGATACA
61545024 TGCCTAAA-GTATCAATACTT
1 TGCCTAAAGGTATCAATACTT
61545044 TGCC-AAAGGTATCAATACT
1 TGCCTAAAGGTATCAATACT
61545063 CAGACAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.31
Consensus pattern (21 bp):
TGCCTAAAGGTATCAATACTT
Found at i:61548664 original size:31 final size:31
Alignment explanation
Indices: 61548629--61548689 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
61548619 ATTAATATAA
* *
61548629 ATTCAAAATAGATAAAATAAATCACCTCTAC
1 ATTCAAAACAAATAAAATAAATCACCTCTAC
61548660 ATTCAAAACAAATAAAATAAATCACCTCTA
1 ATTCAAAACAAATAAAATAAATCACCTCTA
61548690 GACAAATGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.54, C:0.20, G:0.02, T:0.25
Consensus pattern (31 bp):
ATTCAAAACAAATAAAATAAATCACCTCTAC
Found at i:61549015 original size:22 final size:23
Alignment explanation
Indices: 61548990--61549034 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
61548980 AGACTCACAC
61548990 AACCA-TATCAACTTCAG-AAGCA
1 AACCATTATCAAC-TCAGTAAGCA
61549012 AACCATTATCAACTCAGTAAGCA
1 AACCATTATCAACTCAGTAAGCA
61549035 TACAGATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.44, C:0.27, G:0.09, T:0.20
Consensus pattern (23 bp):
AACCATTATCAACTCAGTAAGCA
Found at i:61553794 original size:2 final size:2
Alignment explanation
Indices: 61553787--61553814 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
61553777 CTGTGGAGAA
61553787 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
61553815 TCTACAGCTG
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:61557544 original size:2 final size:2
Alignment explanation
Indices: 61557537--61557569 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
61557527 TCATACATAC
*
61557537 AT AT AT AT AT AT AT AT AT AT AT -T AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61557570 CTTAAGATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
AT
Found at i:61561149 original size:2 final size:2
Alignment explanation
Indices: 61561142--61561179 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
61561132 GCTAAGCTTA
61561142 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
61561180 ATAATTGGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61561895 original size:28 final size:28
Alignment explanation
Indices: 61561864--61561924 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
61561854 TCAAGTCATC
61561864 AGCAGCAATGCTAAACGCCGGTGGAAAG
1 AGCAGCAATGCTAAACGCCGGTGGAAAG
61561892 AGCAGCAATGCTAAACGCCGGTGGAAAG
1 AGCAGCAATGCTAAACGCCGGTGGAAAG
61561920 AGCAG
1 AGCAG
61561925 AGGAAGAATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.36, C:0.21, G:0.33, T:0.10
Consensus pattern (28 bp):
AGCAGCAATGCTAAACGCCGGTGGAAAG
Found at i:61570667 original size:2 final size:2
Alignment explanation
Indices: 61570660--61570705 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
61570650 TTCAAACAAT
61570660 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
61570702 TA TA
1 TA TA
61570706 CACACACACA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:61572892 original size:30 final size:30
Alignment explanation
Indices: 61572858--61572919 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
61572848 ACTTAACAAG
61572858 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* ** *
61572888 CAAATGCCTTTAAAATGGTAATAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
61572918 CA
1 CA
61572920 TTAAAATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.53, C:0.15, G:0.06, T:0.26
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:61573005 original size:22 final size:22
Alignment explanation
Indices: 61572958--61573007 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
61572948 CAATAACAAT
* *
61572958 AAAATAGTAGCAACATAATAGC
1 AAAATAGTAGCAAAATAAGAGC
*
61572980 AAAATGGTAGCAAAATAGAGAG-
1 AAAATAGTAGCAAAATA-AGAGC
61573002 AAAATA
1 AAAATA
61573008 ACAAAAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.58, C:0.08, G:0.18, T:0.16
Consensus pattern (22 bp):
AAAATAGTAGCAAAATAAGAGC
Found at i:61580931 original size:16 final size:16
Alignment explanation
Indices: 61580906--61580993 Score: 58
Period size: 16 Copynumber: 5.5 Consensus size: 16
61580896 CTAAAAAAAT
61580906 TTCTAAACAAGAGTTGA
1 TTCTAAACAAGAGTT-A
*
61580923 TTC-AAACAAGGGTTA
1 TTCTAAACAAGAGTTA
*
61580938 TTCTAAACATA-A-CTA
1 TTCTAAACA-AGAGTTA
**
61580953 TTCTTAAAACATCA-TTA
1 TTC-T-AAACAAGAGTTA
* *
61580970 TTCTAAACAAAAGTTG
1 TTCTAAACAAGAGTTA
61580986 TTCTAAAC
1 TTCTAAAC
61580994 TTTAACCGTT
Statistics
Matches: 57, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
15 15 0.26
16 27 0.47
17 15 0.26
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (16 bp):
TTCTAAACAAGAGTTA
Found at i:61580954 original size:15 final size:15
Alignment explanation
Indices: 61580936--61580978 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
61580926 AAACAAGGGT
61580936 TATTCTAAACATAAC
1 TATTCTAAACATAAC
* *
61580951 TATTCTTAAAACATCAT
1 TATTC-T-AAACATAAC
61580968 TATTCTAAACA
1 TATTCTAAACA
61580979 AAAGTTGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 10 0.42
16 2 0.08
17 12 0.50
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (15 bp):
TATTCTAAACATAAC
Found at i:61591829 original size:6 final size:7
Alignment explanation
Indices: 61591790--61591842 Score: 56
Period size: 7 Copynumber: 7.6 Consensus size: 7
61591780 AAAAGTGAAG
61591790 TTTTTAC
1 TTTTTAC
61591797 TTTTTAC
1 TTTTTAC
* *
61591804 TACATATA-
1 T--TTTTAC
61591812 TTTTTAC
1 TTTTTAC
61591819 TTTTTAC
1 TTTTTAC
61591826 -TTTTAC
1 TTTTTAC
61591832 TTTTTAC
1 TTTTTAC
61591839 TTTT
1 TTTT
61591843 GATGTCCTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
6 9 0.24
7 25 0.66
8 1 0.03
9 3 0.08
ACGTcount: A:0.19, C:0.13, G:0.00, T:0.68
Consensus pattern (7 bp):
TTTTTAC
Found at i:61591831 original size:13 final size:13
Alignment explanation
Indices: 61591813--61591842 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
61591803 CTACATATAT
61591813 TTTTACTTTTTAC
1 TTTTACTTTTTAC
61591826 TTTTACTTTTTAC
1 TTTTACTTTTTAC
61591839 TTTT
1 TTTT
61591843 GATGTCCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTACTTTTTAC
Found at i:61604776 original size:95 final size:95
Alignment explanation
Indices: 61604613--61604802 Score: 326
Period size: 95 Copynumber: 2.0 Consensus size: 95
61604603 TGTGAATCAT
*
61604613 TTGGGCTCTTCTCGAAGTAAGGAGATAAAAACCCAAGACTAAAACTCTACATAGACACTGAAAAC
1 TTGGGCTCTTCTCAAAGTAAGGAGATAAAAACCCAAGACTAAAACTCTACATAGACACTGAAAAC
* *
61604678 AATATTTTCATTCGAAGATTCAATTGACTG
66 AATATTTCCATTCGAACATTCAATTGACTG
*
61604708 TTGGGCTCTTCTCAAAGTAAGGAGATAAAAACCCAAGACTAAAACTCTATATAGACACTGAAAAC
1 TTGGGCTCTTCTCAAAGTAAGGAGATAAAAACCCAAGACTAAAACTCTACATAGACACTGAAAAC
**
61604773 AATATTTCCATTCGAACATTTGATTGACTG
66 AATATTTCCATTCGAACATTCAATTGACTG
61604803 CTCTACGAAC
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
95 89 1.00
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (95 bp):
TTGGGCTCTTCTCAAAGTAAGGAGATAAAAACCCAAGACTAAAACTCTACATAGACACTGAAAAC
AATATTTCCATTCGAACATTCAATTGACTG
Found at i:61606844 original size:20 final size:20
Alignment explanation
Indices: 61606811--61606849 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
61606801 TTGAACAAAG
* *
61606811 AAATTTTATTATTTAATTTC
1 AAATTTAATAATTTAATTTC
*
61606831 AAATTTAATAATTTTATTT
1 AAATTTAATAATTTAATTT
61606850 AGAGGTTCAT
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:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
AAATTTAATAATTTAATTTC
Found at i:61609973 original size:15 final size:14
Alignment explanation
Indices: 61609926--61609995 Score: 52
Period size: 15 Copynumber: 4.7 Consensus size: 14
61609916 TTTTATACAT
*
61609926 TTAATTAAAACTAA
1 TTAATTAAAATTAA
* *
61609940 TTAATTATAATTTAT
1 TTAATTA-AAATTAA
61609955 TTAATTAAACATTAA
1 TTAATTAAA-ATTAA
*
61609970 TTAA-CAAAACTTAA
1 TTAATTAAAA-TTAA
61609984 TGATAATTAAAA
1 T--TAATTAAAA
61609996 AAGTTGGTGG
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
13 1 0.02
14 17 0.40
15 18 0.42
16 3 0.07
17 4 0.09
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.40
Consensus pattern (14 bp):
TTAATTAAAATTAA
Found at i:61616692 original size:17 final size:16
Alignment explanation
Indices: 61616661--61616694 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
61616651 GCAAAATAAA
61616661 AAATAATAATAAACTT
1 AAATAATAATAAACTT
*
61616677 AAATAATTAATTAACTT
1 AAATAA-TAATAAACTT
61616694 A
1 A
61616695 TTTAGGTTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATAATAATAAACTT
Found at i:61616825 original size:19 final size:20
Alignment explanation
Indices: 61616795--61616846 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
61616785 AAATATATAA
61616795 ATTTTGGAATTTTT-AAAAAT
1 ATTTT-GAATTTTTGAAAAAT
*
61616815 ATTTTGAATTTTTGAAAATT
1 ATTTTGAATTTTTGAAAAAT
*
61616835 ACTTT-AATTTTT
1 ATTTTGAATTTTT
61616847 TTTTTGTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.56
Consensus pattern (20 bp):
ATTTTGAATTTTTGAAAAAT
Found at i:61618246 original size:2 final size:2
Alignment explanation
Indices: 61618239--61618264 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
61618229 ACTATAATTC
61618239 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
61618265 CAATTATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61628157 original size:216 final size:216
Alignment explanation
Indices: 61627745--61628158 Score: 474
Period size: 216 Copynumber: 1.9 Consensus size: 216
61627735 CTTATATTAA
* * * * *
61627745 TTCAAATAGTACGGCAGAATTGAGGCTTAACTCGATTAGGATGGGTATTGTCGTTAATGTAGTAG
1 TTCAAATAGTACGACAGAATTGAGGCTTAACTCGATTAGGATGCGTATTGTCGCTAATGTAGGAA
* * * * * *
61627810 GATGTGGGTTTGAGTGCGTCGAAGTGCATTATCCTCTTATTTATGAGCTGTGGAAGAACTATTAG
66 GATGTGAGTTTAAGTGCGCCGAAGCGCATTATCCTCCTATTTATGAGCTGTGGAAGAACTATAAG
* * * *
61627875 TAGTTTTAAATATTGTGTCATAAAAAGTAGGTATGATCAAAACCTATAATGAGATTATTAAAAAA
131 TAATTCTAAATATCGTGTCATAAAAAGTA-GTATGATCAAAACCTATAATAAGATTATTAAAAAA
61627940 AAAAATCAATGATGTTTATCGT
195 AAAAATCAATGATGTTTATCGT
* * * * * *
61627962 TTCAAATTGTATGACAG-ATTGAGTCTTAGCTCGATTAGTATGCGTATTGTTGCTAATGTAGGAA
1 TTCAAATAGTACGACAGAATTGAGGCTTAACTCGATTAGGATGCGTATTGTCGCTAATGTAGGAA
* * * * * * **
61628026 GATGTGAGTTTAAGTGTGCCGATGCGCATTATTCTCCTATTTCTGGGTTAG-GGAAGAGTTATAA
66 GATGTGAGTTTAAGTGCGCCGAAGCGCATTATCCTCCTATTTATGAGCT-GTGGAAGAACTATAA
* * *
61628090 GTAATTCTAGATATCGTGTCATAAAAACGATA-TATGGTCAAAACTTATAATAAGATTATCTAAA
130 GTAATTCTAAATATCGTGTCATAAAAA-G-TAGTATGATCAAAACCTATAATAAGATTAT-TAAA
61628154 AAAAA
192 AAAAA
61628159 TCAAATAATT
Statistics
Matches: 161, Mismatches: 32, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
216 134 0.83
217 25 0.16
218 2 0.01
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.34
Consensus pattern (216 bp):
TTCAAATAGTACGACAGAATTGAGGCTTAACTCGATTAGGATGCGTATTGTCGCTAATGTAGGAA
GATGTGAGTTTAAGTGCGCCGAAGCGCATTATCCTCCTATTTATGAGCTGTGGAAGAACTATAAG
TAATTCTAAATATCGTGTCATAAAAAGTAGTATGATCAAAACCTATAATAAGATTATTAAAAAAA
AAAATCAATGATGTTTATCGT
Found at i:61628455 original size:26 final size:27
Alignment explanation
Indices: 61628397--61628455 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 27
61628387 AATTCGAGAT
* * *
61628397 TTAATTTATATATTTTAATACGACTTA
1 TTAATATATATATTTTAATACAACTCA
*
61628424 TGTAATATATATATTTTTATA-AACTCA
1 T-TAATATATATATTTTAATACAACTCA
61628451 TTAAT
1 TTAAT
61628456 TAATCTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 4 0.15
27 6 0.22
28 17 0.63
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.51
Consensus pattern (27 bp):
TTAATATATATATTTTAATACAACTCA
Found at i:61629498 original size:18 final size:18
Alignment explanation
Indices: 61629475--61629510 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
61629465 TTGGTACTTA
61629475 AATTTAGT-TTTAATATTT
1 AATTTAGTATTTAA-ATTT
61629493 AATTTAGTATTTAAATTT
1 AATTTAGTATTTAAATTT
61629511 GATATTCGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (18 bp):
AATTTAGTATTTAAATTT
Found at i:61631296 original size:27 final size:26
Alignment explanation
Indices: 61631266--61631339 Score: 69
Period size: 27 Copynumber: 2.8 Consensus size: 26
61631256 TACCCTTAAT
61631266 CTTGAACCTTGAACTCTAAACCCCAAA
1 CTTGAACCTTGAAC-CTAAACCCCAAA
* * * * *
61631293 CTTGAACC-CGAACCCTGAACGCTAAT
1 CTTGAACCTTGAA-CCTAAACCCCAAA
61631319 CTTCGAACCTTGAACCTAAAC
1 CTT-GAACCTTGAACCTAAAC
61631340 TCAAACCCAA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
26 14 0.38
27 20 0.54
28 3 0.08
ACGTcount: A:0.34, C:0.34, G:0.11, T:0.22
Consensus pattern (26 bp):
CTTGAACCTTGAACCTAAACCCCAAA
Found at i:61631394 original size:20 final size:20
Alignment explanation
Indices: 61631369--61631406 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
61631359 TGGGTTTAGG
61631369 GTTTGGGATTCAAGATTTGA
1 GTTTGGGATTCAAGATTTGA
* *
61631389 GTTTGGGGTTCGAGATTT
1 GTTTGGGATTCAAGATTT
61631407 AGAATAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.05, G:0.34, T:0.42
Consensus pattern (20 bp):
GTTTGGGATTCAAGATTTGA
Found at i:61637526 original size:6 final size:6
Alignment explanation
Indices: 61637509--61637583 Score: 70
Period size: 6 Copynumber: 13.2 Consensus size: 6
61637499 GATTATTTAC
* * *
61637509 CCCTCT CTCTCT CCCTCT --CTCT CTCTCT CTCTCT CCCTCT CCCTCT
1 CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT
*
61637555 --CTCT CCCTCT CTCC-CT CTCTCT CCCTCT C
1 CCCTCT CCCTCT C-CCTCT CCCTCT CCCTCT C
61637584 TCTCCCTNNN
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
4 8 0.14
5 1 0.02
6 47 0.81
7 2 0.03
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (6 bp):
CCCTCT
Found at i:61637528 original size:8 final size:8
Alignment explanation
Indices: 61637515--61637585 Score: 85
Period size: 8 Copynumber: 8.9 Consensus size: 8
61637505 TTACCCCTCT
61637515 CTCTCTCC
1 CTCTCTCC
61637523 CTCTCT--
1 CTCTCTCC
*
61637529 CTCTCTCT
1 CTCTCTCC
61637537 CTCTCTCC
1 CTCTCTCC
61637545 CTCTC-CC
1 CTCTCTCC
61637552 TCTCTCTCC
1 -CTCTCTCC
61637561 CTCTCTCCC
1 CTCTCT-CC
61637570 TCTCTCTCC
1 -CTCTCTCC
61637579 CTCTCTC
1 CTCTCTC
61637586 TCCCTNNNNN
Statistics
Matches: 56, Mismatches: 1, Indels: 12
0.81 0.01 0.17
Matches are distributed among these distances:
6 6 0.11
7 2 0.04
8 36 0.64
9 6 0.11
10 6 0.11
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (8 bp):
CTCTCTCC
Found at i:61637528 original size:10 final size:10
Alignment explanation
Indices: 61637513--61637590 Score: 110
Period size: 10 Copynumber: 8.2 Consensus size: 10
61637503 ATTTACCCCT
61637513 CTCTCTCTCC
1 CTCTCTCTCC
61637523 CTCTCTCT--
1 CTCTCTCTCC
*
61637531 CTCTCTCTCT
1 CTCTCTCTCC
*
61637541 CTCCCTCTCC
1 CTCTCTCTCC
61637551 CTCTCTCT-C
1 CTCTCTCTCC
61637560 C-CTCTCTCC
1 CTCTCTCTCC
61637569 CTCTCTCTCC
1 CTCTCTCTCC
61637579 CTCTCTCTCC
1 CTCTCTCTCC
61637589 CT
1 CT
61637591 NNNNNNNNNN
Statistics
Matches: 61, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
8 14 0.23
9 4 0.07
10 43 0.70
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (10 bp):
CTCTCTCTCC
Found at i:61637534 original size:18 final size:18
Alignment explanation
Indices: 61637511--61637587 Score: 113
Period size: 18 Copynumber: 4.4 Consensus size: 18
61637501 TTATTTACCC
* *
61637511 CTCTCTCTCTCCCTCTCT
1 CTCTCTCTCTCTCTCCCT
61637529 CTCTCTCTCTCTCTCCCT
1 CTCTCTCTCTCTCTCCCT
61637547 CTC-C-CTCTCTCTCCCT
1 CTCTCTCTCTCTCTCCCT
*
61637563 CTCTCCCTCTCTCTCCCT
1 CTCTCTCTCTCTCTCCCT
61637581 CTCTCTC
1 CTCTCTC
61637588 CCTNNNNNNN
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
16 15 0.28
17 2 0.04
18 37 0.69
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (18 bp):
CTCTCTCTCTCTCTCCCT
Found at i:61638311 original size:8 final size:8
Alignment explanation
Indices: 61638298--61638325 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
61638288 GACGTCTACT
61638298 TATATATC
1 TATATATC
61638306 TATATATC
1 TATATATC
61638314 TATATATC
1 TATATATC
61638322 TATA
1 TATA
61638326 CATACATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (8 bp):
TATATATC
Found at i:61641978 original size:6 final size:6
Alignment explanation
Indices: 61641967--61641994 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
61641957 TGATCTCTCC
61641967 TAAAAA TAAAAA TAAAAA TAAAAA TAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAA
61641995 TTTTCAATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:61644960 original size:195 final size:192
Alignment explanation
Indices: 61644370--61645255 Score: 847
Period size: 195 Copynumber: 4.6 Consensus size: 192
61644360 TATTTGATTG
** * * *
61644370 AATGGGTTTTTGTTTTCCATTGAA-TATGCTTATTTTAGATCTTTAACTTGGTGGGATTACAAGA
1 AATGGGTTTTTGTTTTTTATTGAATTATGCTTATTTGAGATCCTTAACTTGGTGAGATTACAAGA
** * * ** ** * *
61644434 AACTTGTCATGGGTAAC-CTTAATATGTTGAAGCTTGCAAAGAGACTAAAATTAATGGGGTTTTG
66 AAAATGTGATGGGT-ACTATTAATATGTTGGGGCTTGCAAAGAGTGTGAAATTAAT-GGTTTTTG
* * ** * * * * * *** *
61644498 TGTCAGTTTTGCATTAGTTTTTGGTTTTTTTCTTTACACTTCTATGGTAGTT--TATGTTATTTG
129 TAT-TGAATTGCATTAGATTTTGGTGTTTTTCTTTAGA-TTTTAT-GT--TTAACAAAATATTCG
*
61644561 A-TAG
189 AGT-T
* * *
61644565 AATGGG-TTTTGTTTTTTATTGAATTATGCTTATTTAAGATCATTAACTTGGTGACATTACAAGA
1 AATGGGTTTTTGTTTTTTATTGAATTATGCTTATTTGAGATCCTTAACTTGGTGAGATTACAAGA
** * * * *
61644629 AATTTGTGATGGG-ACTCTTAATATGTTGAGGCTTGCAAAGAGAGTGAAATTAATGGGGTTTTGT
66 AAAATGTGATGGGTACTATTAATATGTTGGGGCTTGCAAAGAGTGTGAAATTAAT-GGTTTTTGT
* * * * * * *
61644693 -GTAAATTTTGCGTTAGTTTTTGTTTTTTTTCTTTAGATTTTATGTTTAACAATACTATTCGAGT
130 ATTGAA--TTGCATTAGATTTTGGTGTTTTTCTTTAGATTTTATGTTTAACAA-AATATTCGAGT
61644757 T
192 T
* *
61644758 AATGGGTTTTTGTTTTTTATTGAATTATGCTTATTTGAGATCTTTAACTTAGTGAGATTACAAGA
1 AATGGGTTTTTGTTTTTTATTGAATTATGCTTATTTGAGATCCTTAACTTGGTGAGATTACAAGA
* *
61644823 AAAATGTGATGGGTACTATTGATATGTTGGGGCTTGCAAAGAGTGTGAATTTAATGGTTTTTTGT
66 AAAATGTGATGGGTACTATTAATATGTTGGGGCTTGCAAAGAGTGTGAAATTAATGG-TTTTTGT
* * * * * *
61644888 ATTGAATATGTATTAGGTTTTGGGGTTTTTCTTTAGATTTTATGTTTAACAAAATGGTTCAAATT
130 ATTGAAT-TGCATTAGATTTTGGTGTTTTTCTTTAGATTTTATGTTTAACAAAAT-ATTCGAGTT
* * *
61644953 GATGGGTTTTTGTTATTGT-TTGAATTATTGCTTATTTGAGATCCTTACCTTGGTGAGATTACAA
1 AATGGGTTTTTGTT-TTTTATTGAATTA-TGCTTATTTGAGATCCTTAACTTGGTGAGATTACAA
* * * *
61645017 GAAAAATGTGATGGGTACTATTAATATGTTGGGGCTTGTAAAGAGTGTAAAATTAGTGGTTTTTC
64 GAAAAATGTGATGGGTACTATTAATATGTTGGGGCTTGCAAAGAGTGTGAAATTAATGGTTTTTG
* * * * **
61645082 TATCGAATTCACAGTAGATTTTGGTGTTTTTCTTTAGCTTTTATGTTTAACGAAACCATTCGAGT
129 TATTGAATT-GCATTAGATTTTGGTGTTTTTCTTTAGATTTTATGTTTAAC-AAAATATTCGAGT
61645147 T
192 T
* ** *
61645148 AATGGGTTTTTGTTATTGGTTGAATTATGTTTATTTGAGATCCTTAACTTGGTGA-AGTTACAAG
1 AATGGGTTTTTGTTTTTTATTGAATTATGCTTATTTGAGATCCTTAACTTGGTGAGA-TTACAAG
* * *
61645212 ACAAATGTGATGGGTACTCTTAACATGTTGGGGCTTGCAAAGAG
65 AAAAATGTGATGGGTACTATTAATATGTTGGGGCTTGCAAAGAG
61645256 AGTTGGGGCC
Statistics
Matches: 588, Mismatches: 83, Indels: 41
0.83 0.12 0.06
Matches are distributed among these distances:
190 2 0.00
192 3 0.01
193 20 0.03
194 233 0.40
195 234 0.40
196 96 0.16
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (192 bp):
AATGGGTTTTTGTTTTTTATTGAATTATGCTTATTTGAGATCCTTAACTTGGTGAGATTACAAGA
AAAATGTGATGGGTACTATTAATATGTTGGGGCTTGCAAAGAGTGTGAAATTAATGGTTTTTGTA
TTGAATTGCATTAGATTTTGGTGTTTTTCTTTAGATTTTATGTTTAACAAAATATTCGAGTT
Found at i:61649874 original size:24 final size:23
Alignment explanation
Indices: 61649847--61649891 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
61649837 ATATTATAAC
61649847 ATTTAATAATTTTATATATTTTTT
1 ATTTAATAATTTT-TATATTTTTT
* *
61649871 ATTTATTAATTTTTTTATTTT
1 ATTTAATAATTTTTATATTTT
61649892 AATGTTTACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (23 bp):
ATTTAATAATTTTTATATTTTTT
Found at i:61655455 original size:9 final size:9
Alignment explanation
Indices: 61655432--61655466 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
61655422 TATCACTTCA
61655432 AAAATAAATT
1 AAAA-AAATT
*
61655442 TAAAAAATT
1 AAAAAAATT
61655451 AAAAAAATT
1 AAAAAAATT
61655460 AAAAAAA
1 AAAAAAA
61655467 GAGAAAAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 20 0.87
10 3 0.13
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
AAAAAAATT
Found at i:61655845 original size:2 final size:2
Alignment explanation
Indices: 61655838--61655867 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
61655828 AGAGAAACAC
61655838 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
61655868 GGGTTAAGGC
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:61658893 original size:21 final size:20
Alignment explanation
Indices: 61658835--61658898 Score: 74
Period size: 21 Copynumber: 3.1 Consensus size: 20
61658825 CCTGATCAGT
*
61658835 ATACGACACATAAGTGCCTA
1 ATACGACACATAAGTGCCTG
* * *
61658855 AAACGACACACGAGGTGCCTG
1 ATACGACACA-TAAGTGCCTG
61658876 ATACGACACATAAAGTGCCTG
1 ATACGACACAT-AAGTGCCTG
61658897 AT
1 AT
61658899 CGGCAAAGCC
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
20 9 0.26
21 26 0.74
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.17
Consensus pattern (20 bp):
ATACGACACATAAGTGCCTG
Found at i:61662205 original size:5 final size:5
Alignment explanation
Indices: 61662195--61662221 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
61662185 AATAGGTAGT
61662195 GGACC GGACC GGACC GGACC GGACC GG
1 GGACC GGACC GGACC GGACC GGACC GG
61662222 CTAGTGGCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.37, G:0.44, T:0.00
Consensus pattern (5 bp):
GGACC
Found at i:61668780 original size:31 final size:31
Alignment explanation
Indices: 61668743--61668817 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 31
61668733 TTATAAAATA
*
61668743 ATCACTCAATTATTAGCAA-TTT-TCTTTTTTT
1 ATCACTCAACTATT--CAACTTTATCTTTTTTT
61668774 ATCACTCAACTATTCAACTTTATC-TTTTTT
1 ATCACTCAACTATTCAACTTTATCTTTTTTT
*
61668804 AGTCACCCAACTAT
1 A-TCACTCAACTAT
61668818 CTTGGGTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
29 3 0.08
30 10 0.26
31 26 0.67
ACGTcount: A:0.28, C:0.23, G:0.03, T:0.47
Consensus pattern (31 bp):
ATCACTCAACTATTCAACTTTATCTTTTTTT
Found at i:61669780 original size:21 final size:21
Alignment explanation
Indices: 61669747--61669786 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
61669737 AAAAAATAAA
61669747 TAATAAAAATCGAATTAAATT
1 TAATAAAAATCGAATTAAATT
* *
61669768 TAATTAAATTCGAATTAAA
1 TAATAAAAATCGAATTAAA
61669787 CTCAACTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (21 bp):
TAATAAAAATCGAATTAAATT
Found at i:61681600 original size:13 final size:13
Alignment explanation
Indices: 61681582--61681613 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
61681572 AATCTGCAAA
61681582 ACTATTACAACAG
1 ACTATTACAACAG
61681595 ACTATTACAACAG
1 ACTATTACAACAG
*
61681608 ATTATT
1 ACTATT
61681614 TTGTTCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (13 bp):
ACTATTACAACAG
Found at i:61683759 original size:59 final size:59
Alignment explanation
Indices: 61683667--61683783 Score: 198
Period size: 59 Copynumber: 2.0 Consensus size: 59
61683657 CATGGAGCGA
* * *
61683667 CAAGAAACTCGTTGTTGATCATTTTAAGATATTTTGATGCGTTGCATATGCACATATAG
1 CAAGAAACCCGTTGTTGATCATTTTAAGATATTTGGATGCATTGCATATGCACATATAG
*
61683726 CAAGAAACCCGTTGTTGATCATTTTAAGATATTTGGATGTATTGCATATGCACATATA
1 CAAGAAACCCGTTGTTGATCATTTTAAGATATTTGGATGCATTGCATATGCACATATA
61683784 TCTAATGAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.37
Consensus pattern (59 bp):
CAAGAAACCCGTTGTTGATCATTTTAAGATATTTGGATGCATTGCATATGCACATATAG
Found at i:61684094 original size:3 final size:3
Alignment explanation
Indices: 61684086--61684116 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
61684076 ATCAACATTT
61684086 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
61684117 AGGAGATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:61694117 original size:6 final size:6
Alignment explanation
Indices: 61694106--61694133 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
61694096 CAAACTGTTC
61694106 TAGGTT TAGGTT TAGGTT TAGGTT TAGG
1 TAGGTT TAGGTT TAGGTT TAGGTT TAGG
61694134 CATGTTCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.36, T:0.46
Consensus pattern (6 bp):
TAGGTT
Found at i:61704919 original size:31 final size:31
Alignment explanation
Indices: 61704878--61704957 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 31
61704868 AAGTTTTTGG
*
61704878 AAATTCTAATTAAACCCTCTAAAACTTTTAA
1 AAATTTTAATTAAACCCTCTAAAACTTTTAA
* *
61704909 AAATTTTAATTAGACCCT-T--AACTTTTGA
1 AAATTTTAATTAAACCCTCTAAAACTTTTAA
61704937 AAATCTTT-ATTAAACCC-CTAA
1 AAAT-TTTAATTAAACCCTCTAA
61704958 GAGTTTTGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
28 21 0.51
29 3 0.07
30 1 0.02
31 16 0.39
ACGTcount: A:0.41, C:0.19, G:0.03, T:0.38
Consensus pattern (31 bp):
AAATTTTAATTAAACCCTCTAAAACTTTTAA
Found at i:61704955 original size:29 final size:30
Alignment explanation
Indices: 61704878--61704988 Score: 86
Period size: 30 Copynumber: 3.8 Consensus size: 30
61704868 AAGTTTTTGG
*
61704878 AAATTCTAATTAAACCCTCTAAAACTTTTAA
1 AAATTTTAATTAAACCC-CTAAAACTTTTAA
* * *
61704909 AAATTTTAATTAGA-CCCT-TAACTTTTGA
1 AAATTTTAATTAAACCCCTAAAACTTTTAA
* * *
61704937 AAATCTTT-ATTAAACCCCTAAGAGTTTTGA
1 AAAT-TTTAATTAAACCCCTAAAACTTTTAA
* * *
61704967 GAAGTTTAGTTAAACCCC-AAAA
1 AAATTTTAATTAAACCCCTAAAA
61704989 TTAGTGGACC
Statistics
Matches: 64, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
28 17 0.27
29 15 0.23
30 20 0.31
31 12 0.19
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.35
Consensus pattern (30 bp):
AAATTTTAATTAAACCCCTAAAACTTTTAA
Found at i:61707092 original size:108 final size:108
Alignment explanation
Indices: 61706973--61707189 Score: 434
Period size: 108 Copynumber: 2.0 Consensus size: 108
61706963 CAATAATATT
61706973 ATTATTCATTAAACAAAAACAAAAAAGTAAATAAAAAAGGGGTTTTTGTAAAAGTAAAAATTGAA
1 ATTATTCATTAAACAAAAACAAAAAAGTAAATAAAAAAGGGGTTTTTGTAAAAGTAAAAATTGAA
61707038 ATTAAATTAAAAAATAAATTTAAATTGAAAACTCAAATTGAAG
66 ATTAAATTAAAAAATAAATTTAAATTGAAAACTCAAATTGAAG
61707081 ATTATTCATTAAACAAAAACAAAAAAGTAAATAAAAAAGGGGTTTTTGTAAAAGTAAAAATTGAA
1 ATTATTCATTAAACAAAAACAAAAAAGTAAATAAAAAAGGGGTTTTTGTAAAAGTAAAAATTGAA
61707146 ATTAAATTAAAAAATAAATTTAAATTGAAAACTCAAATTGAAG
66 ATTAAATTAAAAAATAAATTTAAATTGAAAACTCAAATTGAAG
61707189 A
1 A
61707190 AAGCAATAAT
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 109 1.00
ACGTcount: A:0.58, C:0.05, G:0.10, T:0.28
Consensus pattern (108 bp):
ATTATTCATTAAACAAAAACAAAAAAGTAAATAAAAAAGGGGTTTTTGTAAAAGTAAAAATTGAA
ATTAAATTAAAAAATAAATTTAAATTGAAAACTCAAATTGAAG
Found at i:61709560 original size:168 final size:168
Alignment explanation
Indices: 61709322--61709652 Score: 536
Period size: 168 Copynumber: 2.0 Consensus size: 168
61709312 CCCTCGCAGA
* * * * *
61709322 TTGTTTTTGGGTCATTTTCTGACATGCCAGCTGACGTATTCTATGATTCAACATTCGACGAAGCA
1 TTGTTTTTGGGTCATTTGCTGACATGCCAGCTCACGTATTCTATCATTCAACATTCAACCAAGCA
* *
61709387 CCACCTTCCAAGGTGGCCCGTGTCTCACCTCGTCCACCGGCACCTTCAGCACCGGCAGGGGCTTC
66 CCACCTTCCAAGGTGGCCCGTGTCTCACCTCCTCCACCGGCACCTCCAGCACCGGCAGGGGCTTC
61709452 TGAAAATGTGGCCAAAGATGATGAGAAACCAAACAAGC
131 TGAAAATGTGGCCAAAGATGATGAGAAACCAAACAAGC
* * * *
61709490 TTGTTTTTGGGTCCTTTGGTGACATGTCAGGTCACGTATTCTATCATTCAACATTCAACCAAGCA
1 TTGTTTTTGGGTCATTTGCTGACATGCCAGCTCACGTATTCTATCATTCAACATTCAACCAAGCA
** *
61709555 CCACCTTCCAAGGTGGCCCGTGTCTCACCTCCTCCACTTGCACCTCCAGCACCGGCAGGGGCTTT
66 CCACCTTCCAAGGTGGCCCGTGTCTCACCTCCTCCACCGGCACCTCCAGCACCGGCAGGGGCTTC
61709620 TGAAAATGTGGCCAAAGATGATGAGAAACCAAA
131 TGAAAATGTGGCCAAAGATGATGAGAAACCAAA
61709653 AAATGCTAAA
Statistics
Matches: 149, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
168 149 1.00
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (168 bp):
TTGTTTTTGGGTCATTTGCTGACATGCCAGCTCACGTATTCTATCATTCAACATTCAACCAAGCA
CCACCTTCCAAGGTGGCCCGTGTCTCACCTCCTCCACCGGCACCTCCAGCACCGGCAGGGGCTTC
TGAAAATGTGGCCAAAGATGATGAGAAACCAAACAAGC
Found at i:61710723 original size:16 final size:17
Alignment explanation
Indices: 61710696--61710727 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
61710686 GCCCGGCCCG
61710696 TTTTTAATTAAAATTAT
1 TTTTTAATTAAAATTAT
61710713 TTTTTAA-TAAAATTA
1 TTTTTAATTAAAATTA
61710728 AAACTAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTTAATTAAAATTAT
Found at i:61710763 original size:16 final size:16
Alignment explanation
Indices: 61710726--61710765 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
61710716 TTAATAAAAT
* *
61710726 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
61710742 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
61710758 TAAAATTA
1 TAAAATTA
61710766 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:61710765 original size:22 final size:22
Alignment explanation
Indices: 61710701--61710750 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
61710691 GCCCGTTTTT
* * *
61710701 AATTAAAATTATTTTTTAATAA
1 AATTAAAACTAATTGTTAATAA
*
61710723 AATTAAAACTAATTGTTATTAA
1 AATTAAAACTAATTGTTAATAA
61710745 AATTAA
1 AATTAA
61710751 TTGTTAGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
AATTAAAACTAATTGTTAATAA
Found at i:61710871 original size:9 final size:9
Alignment explanation
Indices: 61710838--61710865 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
61710828 TTTATCAAAT
61710838 TATTAATTG
1 TATTAATTG
61710847 TATTAATTG
1 TATTAATTG
61710856 TATTAATTG
1 TATTAATTG
61710865 T
1 T
61710866 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:61710875 original size:68 final size:68
Alignment explanation
Indices: 61710754--61710963 Score: 370
Period size: 68 Copynumber: 3.1 Consensus size: 68
61710744 AAATTAATTG
* *
61710754 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAAGCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
61710817 TGA
66 TGA
61710820 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
61710885 TGA
66 TGA
* *
61710888 TTAGTAAATTTATAAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
61710953 TGA
66 TGA
61710956 TTAGTAAA
1 TTAGTAAA
61710964 ACAAATTTGA
Statistics
Matches: 138, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
66 26 0.19
68 112 0.81
ACGTcount: A:0.41, C:0.04, G:0.10, T:0.45
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:61710918 original size:9 final size:9
Alignment explanation
Indices: 61710906--61710933 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
61710896 TTTATAAAAT
61710906 TATTAATTG
1 TATTAATTG
61710915 TATTAATTG
1 TATTAATTG
61710924 TATTAATTG
1 TATTAATTG
61710933 T
1 T
61710934 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:61711070 original size:22 final size:24
Alignment explanation
Indices: 61711030--61711073 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
61711020 AAATAAACTT
61711030 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
61711054 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
61711074 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:61718927 original size:27 final size:26
Alignment explanation
Indices: 61718887--61718946 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
61718877 TAAATATATT
*
61718887 TATTTTTCT-ATTTTTTATTTTTAAAA
1 TATTTTT-TAATTTTTTAATTTTAAAA
*
61718913 TACTTTTTTAATTTTTTAATTTTCAAA
1 TA-TTTTTTAATTTTTTAATTTTAAAA
61718940 TATTTTT
1 TATTTTT
61718947 AAAATACTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 8 0.27
27 22 0.73
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (26 bp):
TATTTTTTAATTTTTTAATTTTAAAA
Found at i:61718966 original size:21 final size:21
Alignment explanation
Indices: 61718940--61718980 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
61718930 AATTTTCAAA
*
61718940 TATTTTTAAAATACTTTTTTT
1 TATTTTTAAAATAATTTTTTT
61718961 TATTTTTAAAATAATTTTTT
1 TATTTTTAAAATAATTTTTT
61718981 GGTATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
TATTTTTAAAATAATTTTTTT
Found at i:61718967 original size:22 final size:22
Alignment explanation
Indices: 61718940--61718987 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
61718930 AATTTTCAAA
* *
61718940 TATTTTTAAAATACTTTTTT-T
1 TATTTTTAAAATAATTTTTTGG
61718961 TATTTTTAAAATAATTTTTTGG
1 TATTTTTAAAATAATTTTTTGG
61718983 TATTT
1 TATTT
61718988 ATTTAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (22 bp):
TATTTTTAAAATAATTTTTTGG
Found at i:61719836 original size:12 final size:12
Alignment explanation
Indices: 61719819--61719855 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
61719809 CAAATAATTT
61719819 AAAAATTATAAA
1 AAAAATTATAAA
*
61719831 AAAAATT-CAAA
1 AAAAATTATAAA
61719842 AAAAATTATAAA
1 AAAAATTATAAA
61719854 AA
1 AA
61719856 GTTCAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (12 bp):
AAAAATTATAAA
Found at i:61719854 original size:21 final size:22
Alignment explanation
Indices: 61719819--61719865 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 22
61719809 CAAATAATTT
61719819 AAAAATTATAAAAAAAATTCAAA
1 AAAAATTAT-AAAAAAATTCAAA
*
61719842 AAAAATTAT-AAAAAGTTCAAA
1 AAAAATTATAAAAAAATTCAAA
61719863 AAA
1 AAA
61719866 TTCAAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.61
23 9 0.39
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (22 bp):
AAAAATTATAAAAAAATTCAAA
Found at i:61719865 original size:11 final size:11
Alignment explanation
Indices: 61719828--61719865 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
61719818 TAAAAATTAT
61719828 AAAAAAAATTC
1 AAAAAAAATTC
61719839 AAAAAAAATT-
1 AAAAAAAATTC
* *
61719849 ATAAAAAGTTC
1 AAAAAAAATTC
61719860 AAAAAA
1 AAAAAA
61719866 TTCAAAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:61720773 original size:20 final size:20
Alignment explanation
Indices: 61720724--61720773 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
61720714 ATAAACACCA
61720724 AAAT-TTTATTTAAAAAAAT
1 AAATATTTATTTAAAAAAAT
* ** *
61720743 AAAAAAGTATTTTAAAAAAT
1 AAATATTTATTTAAAAAAAT
61720763 AAATATTTATT
1 AAATATTTATT
61720774 ATATATTCGG
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
AAATATTTATTTAAAAAAAT
Found at i:61722466 original size:3 final size:3
Alignment explanation
Indices: 61722458--61722505 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
61722448 ATTCACATCC
61722458 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
61722505 T
1 T
61722506 CAAAATTCAC
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:61723660 original size:91 final size:94
Alignment explanation
Indices: 61723509--61723680 Score: 271
Period size: 91 Copynumber: 1.9 Consensus size: 94
61723499 TTTAAAAGTA
*
61723509 ATAGTTTTGTTCTTGAATTTAATCGTATTCCTGGTATTTTTGTGTAAGTTTTCCGCAATCCGACT
1 ATAGTTTTGTTCTTGAATTTAATCGTATTCCTGGTATTTTTGTGTAAGTTTTCAGCAATCCGACT
61723574 GGAT-CTT-CTTTTTTAAGTTTTAAATTG
66 GGATCCTTACTTTTTTAAGTTTTAAATTG
* * *
61723601 ATAG-TTTGTTCTTGAATTTAATCGTATTCCTGGTATTTTTGTGTAA-TTTCTTAGTAATCCGAT
1 ATAGTTTTGTTCTTGAATTTAATCGTATTCCTGGTATTTTTGTGTAAGTTT-TCAGCAATCCGAC
61723664 TGGATCCTTACTTTTTT
65 TGGATCCTTACTTTTTT
61723681 TTTTCTGTTG
Statistics
Matches: 73, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
90 3 0.04
91 56 0.77
92 7 0.10
93 7 0.10
ACGTcount: A:0.20, C:0.13, G:0.16, T:0.51
Consensus pattern (94 bp):
ATAGTTTTGTTCTTGAATTTAATCGTATTCCTGGTATTTTTGTGTAAGTTTTCAGCAATCCGACT
GGATCCTTACTTTTTTAAGTTTTAAATTG
Found at i:61723780 original size:112 final size:110
Alignment explanation
Indices: 61723582--61723781 Score: 303
Period size: 112 Copynumber: 1.8 Consensus size: 110
61723572 CTGGATCTTC
* * *
61723582 TTTTTTAAGTTTTAAATTGATAGTTTGTTCTTGAATTTAATCGTATTCCTGGTATTTTTGTGTAA
1 TTTTTTAAGTTTTAAATTGATAGGTTATTCTTGAATTTAATCGTATTCCTGATATTTTTGTGTAA
* *
61723647 TTTCTTAGTAATCCGATTGGATCCTTACTTTTTTTTTTCTGTTGA
66 TTTCTTAGCAATCCGACTGGATCCTTACTTTTTTTTTTCTGTTGA
**
61723692 TTTTTTAAGTTTTAAATT-AGTAGGTTATTCTTGAATTTAATCGCGTATTTTTGATATTTTTGTG
1 TTTTTTAAGTTTTAAATTGA-TAGGTTATTCTTGAATTTAAT--CGTATTCCTGATATTTTTGTG
61723756 TAATTTCTTAGCAATCCGACTGGATC
63 TAATTTCTTAGCAATCCGACTGGATC
61723782 GTCATTGAAC
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
109 1 0.01
110 37 0.46
112 42 0.52
ACGTcount: A:0.22, C:0.10, G:0.15, T:0.53
Consensus pattern (110 bp):
TTTTTTAAGTTTTAAATTGATAGGTTATTCTTGAATTTAATCGTATTCCTGATATTTTTGTGTAA
TTTCTTAGCAATCCGACTGGATCCTTACTTTTTTTTTTCTGTTGA
Found at i:61724074 original size:110 final size:106
Alignment explanation
Indices: 61723799--61724106 Score: 363
Period size: 110 Copynumber: 2.9 Consensus size: 106
61723789 AACAAATAAA
* * * *
61723799 AATCCGACTGGATCTTCCTTTTTTTGTTGATT--TTTTTTAAGTTTAAAATTAACAGTTTATCCT
1 AATCCGACTGGATCGT-CTTTTTTTGTTG-TTGATTTTTTAAGTTTTAAATTAATAGTTTATTCT
* *
61723862 TGAATTTAATCGTATTTTTTAAATATATTTGTGTAATTTCTAAGC
64 TGAATTTAATCGTA-TTTCT-AATATTTTTGTGTAATTTCTAAGC
* * *
61723907 AATCCGACTGGATCGTCTTTTCTT-TTGTTGATTTTTCAAGTTTTGAATTAATAGTTTATTCTTG
1 AATCCGACTGGATCGTCTTTTTTTGTTGTTGATTTTTTAAGTTTTAAATTAATAGTTTATTCTTG
* * *
61723971 AATTAAAAT-ATATTTCTAATATTTTTGTGTAATTTCTTAGC
66 AATT-TAATCGTATTTCTAATATTTTTGTGTAATTTCTAAGC
* * *
61724012 AATCGGATTGGATCCTTACCTTTTTTTTGTTGTTGATTTTTTAAGTTTTAAATTAATAGTTTATT
1 AATCCGACTGGAT-CGT--C-TTTTTTTGTTGTTGATTTTTTAAGTTTTAAATTAATAGTTTATT
*
61724077 CTTGAATTTAATCGTATTTCTAGTATTTTT
62 CTTGAATTTAATCGTATTTCTAATATTTTT
61724107 TTTAGCAATC
Statistics
Matches: 170, Mismatches: 21, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
105 35 0.21
106 9 0.05
107 41 0.24
108 19 0.11
109 9 0.05
110 57 0.34
ACGTcount: A:0.25, C:0.10, G:0.12, T:0.53
Consensus pattern (106 bp):
AATCCGACTGGATCGTCTTTTTTTGTTGTTGATTTTTTAAGTTTTAAATTAATAGTTTATTCTTG
AATTTAATCGTATTTCTAATATTTTTGTGTAATTTCTAAGC
Found at i:61727606 original size:111 final size:110
Alignment explanation
Indices: 61727414--61727723 Score: 428
Period size: 111 Copynumber: 2.8 Consensus size: 110
61727404 CTTACTTTTA
* ** * *
61727414 AGTTTAAAATTAATAGTTTATCCTTTAATTGAATCGTA-GT-TCTGGTATTTTTGTGTAATTTCT
1 AGTTTTAAATTAATAGTTTATCCTAGAATTAAATC-TATATCTCTGGTATTTTTGTGTAATTTCT
* *
61727477 TAGCAATTCGACTGGATCGTCTTTTTTCTTGTTCATATTTTTGTGT
65 TAGCAATTCGACTGGATCGTCTCTTTTCCTGTTCATATTTTTGTGT
* *
61727523 AGTTTTAAATTAATAGTTTATCCTAGAATTAAATCATATATCTCTGGTATTTTTGTGCAACTTCT
1 AGTTTTAAATTAATAGTTTATCCTAGAATTAAATC-TATATCTCTGGTATTTTTGTGTAATTTCT
* * *
61727588 TAGCAATTCGACTGGATCGTCTCTTTTCCTGTTGATTTTTTTTTGT
65 TAGCAATTCGACTGGATCGTCTCTTTTCCTGTTCATATTTTTGTGT
61727634 AGTTTTAAATTAATAGTTTATCCTAGAATTAAATC-ATATCTCTGGTATTTTTGTGTAATTTCTT
1 AGTTTTAAATTAATAGTTTATCCTAGAATTAAATCTATATCTCTGGTATTTTTGTGTAATTTCTT
* * * * *
61727698 AGTAATCCAACTAGATCCTCTCTTTT
66 AGCAATTCGACTGGATCGTCTCTTTT
61727724 TTTTGTTGAT
Statistics
Matches: 179, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
109 81 0.45
110 1 0.01
111 97 0.54
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.49
Consensus pattern (110 bp):
AGTTTTAAATTAATAGTTTATCCTAGAATTAAATCTATATCTCTGGTATTTTTGTGTAATTTCTT
AGCAATTCGACTGGATCGTCTCTTTTCCTGTTCATATTTTTGTGT
Done.