Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 16 of 120
Found at i:4791702 original size:22 final size:21
Alignment explanation
Indices: 4791672--4791857 Score: 133
Period size: 22 Copynumber: 9.0 Consensus size: 21
4791662 CTATAATATT
*
4791672 ATTACAATATTCATACAAAAA
1 ATTATAATATTCATACAAAAA
4791693 ATTTATAATATTCATAC--AAA
1 A-TTATAATATTCATACAAAAA
*
4791713 ATTACAATATTCATACAAAAA
1 ATTATAATATTCATACAAAAA
**
4791734 ATTACTAATCCAAAACTATA-AATACAA
1 ATTA-TAAT---ATTC-ATACAA-A-AA
*
4791761 ATT-T-A-ATT-ATA-AAATA
1 ATTATAATATTCATACAAAAA
* *
4791777 ATTACAATATTCATAC--AAC
1 ATTATAATATTCATACAAAAA
*
4791796 ATTACAATATTCATA-AAAAA
1 ATTATAATATTCATACAAAAA
4791816 ATTATAATATTCATACAAAAA
1 ATTATAATATTCATACAAAAA
*
4791837 ATTTAAAATATTCATACAAAA
1 A-TTATAATATTCATACAAAA
4791858 TTCTAATCTA
Statistics
Matches: 132, Mismatches: 14, Indels: 37
0.72 0.08 0.20
Matches are distributed among these distances:
16 4 0.03
17 1 0.01
18 6 0.05
19 33 0.25
20 24 0.18
21 14 0.11
22 35 0.27
24 1 0.01
25 5 0.04
26 4 0.03
27 5 0.04
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.32
Consensus pattern (21 bp):
ATTATAATATTCATACAAAAA
Found at i:4791729 original size:41 final size:41
Alignment explanation
Indices: 4791672--4791857 Score: 170
Period size: 41 Copynumber: 4.5 Consensus size: 41
4791662 CTATAATATT
4791672 ATTACAATATTCATACAAAAAATTTATAATATTCATAC-AAA
1 ATTACAATATTCATACAAAAAA-TTATAATATTCATACAAAA
* * *
4791713 ATTACAATATTCATACAAAAAATTACT-A-ATCCAAAACTATAA
1 ATTACAATATTCATACAAAAAATTA-TAATATTC-ATAC-AAAA
* * * *
4791755 A-TACAA-ATTTAATTATAAAATAATTACAATATTCATAC-AAC
1 ATTACAATA-TTCA-TACAAAA-AATTATAATATTCATACAAAA
4791796 ATTACAATATTCATA-AAAAAATTATAATATTCATACAAAAA
1 ATTACAATATTCATACAAAAAATTATAATATTCATAC-AAAA
*
4791837 ATTTAAAATATTCATACAAAA
1 A-TTACAATATTCATACAAAA
4791858 TTCTAATCTA
Statistics
Matches: 116, Mismatches: 14, Indels: 28
0.73 0.09 0.18
Matches are distributed among these distances:
39 19 0.16
40 12 0.10
41 38 0.33
42 30 0.26
43 14 0.12
44 3 0.03
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.32
Consensus pattern (41 bp):
ATTACAATATTCATACAAAAAATTATAATATTCATACAAAA
Found at i:4791858 original size:83 final size:84
Alignment explanation
Indices: 4791677--4791858 Score: 198
Period size: 83 Copynumber: 2.2 Consensus size: 84
4791667 ATATTATTAC
*
4791677 AATATTCATACAAAA-AATTTATAATATTCATACAAAATTACAATATTCATACAAAAAATTACTA
1 AATATTCATACAAAATAATTTACAATATTCATACAAAATTACAATATTCATACAAAAAATTACTA
* *
4791741 ATCCAAAACTATAAATACA
66 ATCCAAAACAAAAAATACA
* * *
4791760 AAT-TTAATTATAAAATAA-TTACAATATTCATACAACATTACAATATTCATA-AAAAAATTA-T
1 AATATTCA-TACAAAATAATTTACAATATTCATACAAAATTACAATATTCATACAAAAAATTACT
* *
4791821 AATATTC-ATACAAAAAATTTA-A
65 -A-ATCCAAAACAAAAAA--TACA
4791843 AATATTCATACAAAAT
1 AATATTCATACAAAAT
4791859 TCTAATCTAA
Statistics
Matches: 82, Mismatches: 10, Indels: 14
0.77 0.09 0.13
Matches are distributed among these distances:
81 1 0.01
82 20 0.24
83 54 0.66
84 7 0.09
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.32
Consensus pattern (84 bp):
AATATTCATACAAAATAATTTACAATATTCATACAAAATTACAATATTCATACAAAAAATTACTA
ATCCAAAACAAAAAATACA
Found at i:4792036 original size:3 final size:3
Alignment explanation
Indices: 4792028--4792061 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
4792018 TTTATAAACT
*
4792028 TTC TTC TTC TTC TTC TTC TTC TTC TTC TCC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
4792062 CCTCTTCTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:4792267 original size:14 final size:14
Alignment explanation
Indices: 4792248--4792275 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4792238 GATAGGCGCC
4792248 ACCCGACCCGACCG
1 ACCCGACCCGACCG
4792262 ACCCGACCCGACCG
1 ACCCGACCCGACCG
4792276 TATTTTGACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.57, G:0.21, T:0.00
Consensus pattern (14 bp):
ACCCGACCCGACCG
Found at i:4793827 original size:33 final size:34
Alignment explanation
Indices: 4793759--4793827 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
4793749 CAAGCTTCAA
* *
4793759 ATCAGGATATACATATCATTTCAATCTCTTTAAC
1 ATCAGGATATACATATCATTTCAATCTCATAAAC
*
4793793 ATCATGATATACATATCA-TTCAATCAT-ATAAAC
1 ATCAGGATATACATATCATTTCAATC-TCATAAAC
4793826 AT
1 AT
4793828 TTCATATCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 13 0.42
34 18 0.58
ACGTcount: A:0.41, C:0.19, G:0.04, T:0.36
Consensus pattern (34 bp):
ATCAGGATATACATATCATTTCAATCTCATAAAC
Found at i:4798153 original size:10 final size:10
Alignment explanation
Indices: 4798140--4798176 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
4798130 AGAAATTTTT
4798140 ATTTTTAATA
1 ATTTTTAATA
4798150 A-TTTTAATA
1 ATTTTTAATA
*
4798159 ATTTTTAATT
1 ATTTTTAATA
4798169 ATTTTTAA
1 ATTTTTAA
4798177 ATTTTAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:4798154 original size:9 final size:9
Alignment explanation
Indices: 4798142--4798188 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
4798132 AAATTTTTAT
4798142 TTTTAATAA
1 TTTTAATAA
4798151 TTTTAATAA
1 TTTTAATAA
*
4798160 TTTTTAATTA
1 -TTTTAATAA
*
4798170 TTTTTA-AA
1 TTTTAATAA
*
4798178 TTTTAAAAA
1 TTTTAATAA
4798187 TT
1 TT
4798189 AATTAATTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 6 0.19
9 18 0.56
10 8 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TTTTAATAA
Found at i:4801832 original size:23 final size:21
Alignment explanation
Indices: 4801788--4801830 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
4801778 AAAAACCCTA
4801788 AATATTCTCCTTCTTATATAT
1 AATATTCTCCTTCTTATATAT
4801809 AATATTCTCCTTCTTATATAT
1 AATATTCTCCTTCTTATATAT
4801830 A
1 A
4801831 TATAAGAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATTCTCCTTCTTATATAT
Found at i:4804215 original size:29 final size:29
Alignment explanation
Indices: 4804182--4804237 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
4804172 AAAGCCTTTT
4804182 TTTTTCAA-AATTTACCGAAATGGGCCACA
1 TTTTT-AATAATTTACCGAAATGGGCCACA
* * *
4804211 TTTTTAATTATTTATCGGAATGGGCCA
1 TTTTTAATAATTTACCGAAATGGGCCA
4804238 TTTCCACGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 2 0.09
29 21 0.91
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (29 bp):
TTTTTAATAATTTACCGAAATGGGCCACA
Found at i:4805146 original size:42 final size:42
Alignment explanation
Indices: 4805094--4805199 Score: 167
Period size: 42 Copynumber: 2.5 Consensus size: 42
4805084 ATGTAAGCAA
* *
4805094 ATCGCTCTGACGTGGACGCGATGTCCTGACACATACACTGGC
1 ATCGCGCTGACGTGGACGCGATGTCCTGACACATACACTGAC
* *
4805136 ATCGCGCTGACGTGGACGCGATGTCCTGACACGTACCCTGAC
1 ATCGCGCTGACGTGGACGCGATGTCCTGACACATACACTGAC
*
4805178 ATCGCGCTGACATGGACGCGAT
1 ATCGCGCTGACGTGGACGCGAT
4805200 TTCGCGGAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.21, C:0.31, G:0.28, T:0.20
Consensus pattern (42 bp):
ATCGCGCTGACGTGGACGCGATGTCCTGACACATACACTGAC
Found at i:4805264 original size:28 final size:28
Alignment explanation
Indices: 4805207--4805266 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
4805197 GATTTCGCGG
*
4805207 AAAATGGCCCATTCCGGTAAATAATCAA
1 AAAATGGCCCATTCCGGTAAATAATAAA
* *
4805235 AAAATCGGCCCATTTCGGTAAAT-TTAAA
1 AAAAT-GGCCCATTCCGGTAAATAATAAA
4805263 AAAA
1 AAAA
4805267 AAGGGCTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 12 0.43
29 16 0.57
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.23
Consensus pattern (28 bp):
AAAATGGCCCATTCCGGTAAATAATAAA
Found at i:4830451 original size:25 final size:25
Alignment explanation
Indices: 4830423--4830475 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
4830413 TCATGTATTC
*
4830423 CATGTAGTTTATAAACCATGTAAAT
1 CATGTAATTTATAAACCATGTAAAT
* *
4830448 CATGTAATTTATAATCCTTGTAAAT
1 CATGTAATTTATAAACCATGTAAAT
4830473 CAT
1 CAT
4830476 ATAGCTCTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (25 bp):
CATGTAATTTATAAACCATGTAAAT
Found at i:4830695 original size:23 final size:23
Alignment explanation
Indices: 4830652--4830697 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
4830642 CTAAGCTGGT
*
4830652 AAACGGTAAGCTCCGTAGAGCTG
1 AAACGGTAAGCTCCATAGAGCTG
4830675 AAACGGTAAGCT-CATACGAGCTG
1 AAACGGTAAGCTCCATA-GAGCTG
4830698 TGGTGAGTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.33, C:0.22, G:0.28, T:0.17
Consensus pattern (23 bp):
AAACGGTAAGCTCCATAGAGCTG
Found at i:4835598 original size:11 final size:11
Alignment explanation
Indices: 4835562--4835591 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4835552 TATTCAAACA
4835562 ATAACAATAAT
1 ATAACAATAAT
*
4835573 ATAATAATAAT
1 ATAACAATAAT
4835584 ATAACAAT
1 ATAACAAT
4835592 GAAATAATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (11 bp):
ATAACAATAAT
Found at i:4835599 original size:19 final size:20
Alignment explanation
Indices: 4835575--4835615 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
4835565 ACAATAATAT
*
4835575 AATAATAATATAACAAT-GA
1 AATAATAATAAAACAATAGA
*
4835594 AATAATAGTAAAACAATAGA
1 AATAATAATAAAACAATAGA
4835614 AA
1 AA
4835616 AAACAATGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.66, C:0.05, G:0.07, T:0.22
Consensus pattern (20 bp):
AATAATAATAAAACAATAGA
Found at i:4839082 original size:5 final size:5
Alignment explanation
Indices: 4839052--4839095 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
4839042 AAATATATGT
* *
4839052 TAAAA GTAAAA TAAAA CTTAAG TAAAA TAAAA TAAAA TAAAA TA
1 TAAAA -TAAAA TAAAA -TAAAA TAAAA TAAAA TAAAA TAAAA TA
4839096 CTATCATCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
5 25 0.76
6 8 0.24
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (5 bp):
TAAAA
Found at i:4839490 original size:12 final size:12
Alignment explanation
Indices: 4839473--4839498 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4839463 ACTGTCCTAG
4839473 TTTGTGAATAAA
1 TTTGTGAATAAA
4839485 TTTGTGAATAAA
1 TTTGTGAATAAA
4839497 TT
1 TT
4839499 CGGCTAGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (12 bp):
TTTGTGAATAAA
Found at i:4846490 original size:19 final size:20
Alignment explanation
Indices: 4846465--4846515 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
4846455 TTGAGACAAT
4846465 ATTTTTTTG-AAACAAGA-G
1 ATTTTTTTGAAAACAAGAGG
*
4846483 ATTTTTTTGAAAACACGAGG
1 ATTTTTTTGAAAACAAGAGG
*
4846503 ATTTTTTTTAAAA
1 ATTTTTTTGAAAA
4846516 AAACAAGAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 9 0.31
19 7 0.24
20 13 0.45
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.43
Consensus pattern (20 bp):
ATTTTTTTGAAAACAAGAGG
Found at i:4846920 original size:12 final size:13
Alignment explanation
Indices: 4846903--4846935 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
4846893 ACGACTTGGC
*
4846903 TTTTTTCT-TTTT
1 TTTTTTCTCTTTG
4846915 TTTTTTCTCTTTG
1 TTTTTTCTCTTTG
4846928 TTTTTTCT
1 TTTTTTCT
4846936 GGCTTGCTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (13 bp):
TTTTTTCTCTTTG
Found at i:4847220 original size:3 final size:3
Alignment explanation
Indices: 4847214--4847258 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
4847204 TTAAATTTTT
* * *
4847214 TTC TTC TTC TTC TTT TTC TTT TTC TTT TTC TTTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC TT
4847259 TCTTTCTTTC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (3 bp):
TTC
Found at i:4847238 original size:12 final size:12
Alignment explanation
Indices: 4847217--4847276 Score: 66
Period size: 12 Copynumber: 4.8 Consensus size: 12
4847207 AATTTTTTTC
*
4847217 TTCTTCTTCTTT
1 TTCTTTTTCTTT
4847229 TTCTTTTTCTTT
1 TTCTTTTTCTTT
*
4847241 TTCTTTCTTCTTC
1 TTCTTT-TTCTTT
4847254 TTCTTTCTTTCTTT
1 TTC-TT-TTTCTTT
*
4847268 CTCTTTTTC
1 TTCTTTTTC
4847277 CCTCTTCACC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
12 21 0.51
13 10 0.24
14 9 0.22
15 1 0.02
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (12 bp):
TTCTTTTTCTTT
Found at i:4847248 original size:31 final size:33
Alignment explanation
Indices: 4847209--4847276 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
4847199 TATTTTTAAA
*
4847209 TTTT-TTTCTTCTTCTTC-TT-TTTCTTTTTCT
1 TTTTCTTTCTTCTTCTTCTTTCTTTCTTTCTCT
4847239 TTTTCTTTCTTCTTCTTCTTTCTTTCTTTCTCT
1 TTTTCTTTCTTCTTCTTCTTTCTTTCTTTCTCT
4847272 TTTTC
1 TTTTC
4847277 CCTCTTCACC
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 4 0.12
31 13 0.38
32 2 0.06
33 15 0.44
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (33 bp):
TTTTCTTTCTTCTTCTTCTTTCTTTCTTTCTCT
Found at i:4847385 original size:16 final size:17
Alignment explanation
Indices: 4847359--4847392 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
4847349 GACCCTCTCC
4847359 TCTTCTCCTCTTTCTTT
1 TCTTCTCCTCTTTCTTT
4847376 TCTT-TCCTCTTTCTTT
1 TCTTCTCCTCTTTCTTT
4847392 T
1 T
4847393 GCTGCTGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (17 bp):
TCTTCTCCTCTTTCTTT
Found at i:4847658 original size:29 final size:29
Alignment explanation
Indices: 4847610--4847769 Score: 169
Period size: 29 Copynumber: 5.4 Consensus size: 29
4847600 GACCGAAACA
* *
4847610 TAATTTTGAGAAAGTTTAGGGGTCAAAATG
1 TAATTTT-AAAAAATTTAGGGGTCAAAATG
* * *
4847640 TAATTTCAAAAAATTTAGGGGTTAAAATA
1 TAATTTTAAAAAATTTAGGGGTCAAAATG
*
4847669 TAA-TTTAAAAAATTTAGGGGTAAAAATG
1 TAATTTTAAAAAATTTAGGGGTCAAAATG
* *
4847697 TAATTTTAAGAAAGTTTAGAGGTCAAAATG
1 TAATTTTAA-AAAATTTAGGGGTCAAAATG
* * * *
4847727 CAATTTTTAAAAATTGAGGGGTCAAAATAC
1 TAATTTTAAAAAATTTAGGGGTCAAAAT-G
*
4847757 AAATTTTAAAAAA
1 TAATTTTAAAAAA
4847770 ATAAAATCGA
Statistics
Matches: 108, Mismatches: 19, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
28 25 0.23
29 42 0.39
30 41 0.38
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.33
Consensus pattern (29 bp):
TAATTTTAAAAAATTTAGGGGTCAAAATG
Found at i:4849035 original size:20 final size:18
Alignment explanation
Indices: 4848970--4849035 Score: 53
Period size: 18 Copynumber: 3.4 Consensus size: 18
4848960 TTTTTTTATT
*
4848970 TTATAAAAACTATAAAAA
1 TTATAAAAAATATAAAAA
*
4848988 TTATAAAAAATGTATTAAAAG
1 TTATAAAAAA--TA-TAAAAA
*
4849009 TT-GAAAAAATATAGAATAA
1 TTATAAAAAATATA-AA-AA
4849028 TTATAAAA
1 TTATAAAA
4849036 TTATAAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
17 2 0.05
18 13 0.35
19 3 0.08
20 12 0.32
21 7 0.19
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (18 bp):
TTATAAAAAATATAAAAA
Found at i:4852297 original size:34 final size:35
Alignment explanation
Indices: 4852253--4852319 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
4852243 CAGTAAAATG
4852253 TTTTCCGTAAAATGATTT-CTGAAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
* *
4852287 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
4852320 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:4852502 original size:22 final size:24
Alignment explanation
Indices: 4852477--4852527 Score: 56
Period size: 26 Copynumber: 2.2 Consensus size: 24
4852467 TTATTTATAA
4852477 ATAAATAA-A-TCAA-ATT-AAAT
1 ATAAATAATACTCAATATTAAAAT
4852497 ATATAATAATACTCAATTATTAAAAT
1 ATA-AATAATACTCAA-TATTAAAAT
4852523 ATAAA
1 ATAAA
4852528 AGCATTGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
20 3 0.12
21 5 0.20
22 1 0.04
23 4 0.16
25 5 0.20
26 7 0.28
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (24 bp):
ATAAATAATACTCAATATTAAAAT
Found at i:4858249 original size:16 final size:16
Alignment explanation
Indices: 4858222--4858259 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
4858212 TTCATTAAAA
*
4858222 AATATA-AATAAATCT
1 AATATATAATAAAACT
*
4858237 AATATATAATAAAAGT
1 AATATATAATAAAACT
4858253 AATATAT
1 AATATAT
4858260 TACTAAGACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (16 bp):
AATATATAATAAAACT
Found at i:4859995 original size:22 final size:20
Alignment explanation
Indices: 4859949--4859988 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4859939 TTTTTTAGAT
*
4859949 AATTAAGTTTATTTTCTTTA
1 AATTAAGTTTATTTTCTTAA
4859969 AATTAAGATTTATTTT-TTAA
1 AATTAAG-TTTATTTTCTTAA
4859989 CGAATTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (20 bp):
AATTAAGTTTATTTTCTTAA
Found at i:4871849 original size:23 final size:23
Alignment explanation
Indices: 4871795--4871849 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
4871785 ATCTTAATTA
4871795 ACAGTATTTTTTCTGCTTTGTAGC
1 ACAGT-TTTTTTCTGCTTTGTAGC
* *
4871819 ACGGTTTTTTTCTGTTTTGTAGC
1 ACAGTTTTTTTCTGCTTTGTAGC
4871842 ACA-TTTTT
1 ACAGTTTTT
4871850 CCTTTTCTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 5 0.18
23 19 0.68
24 4 0.14
ACGTcount: A:0.15, C:0.15, G:0.16, T:0.55
Consensus pattern (23 bp):
ACAGTTTTTTTCTGCTTTGTAGC
Found at i:4879425 original size:31 final size:30
Alignment explanation
Indices: 4879356--4879441 Score: 81
Period size: 31 Copynumber: 2.9 Consensus size: 30
4879346 AATATCTTAA
* *
4879356 AAAC-TTTTGAATGGTTTAGTGACTAGAATG
1 AAACTTTTTGAATAGTTTAGTGACCA-AATG
* *
4879386 AAAGTTTTTGAATAGTTTAGTGACCAAATT
1 AAACTTTTTGAATAGTTTAGTGACCAAATG
*
4879416 ATAACTTTTT---TAGTTAAGTGACCAAA
1 A-AACTTTTTGAATAGTTTAGTGACCAAA
4879442 ACAAAAACCT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
28 15 0.31
30 7 0.15
31 26 0.54
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.38
Consensus pattern (30 bp):
AAACTTTTTGAATAGTTTAGTGACCAAATG
Found at i:4881181 original size:2 final size:2
Alignment explanation
Indices: 4881174--4881202 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4881164 ATGCTTATTC
4881174 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4881203 TAGTATCATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4883696 original size:15 final size:15
Alignment explanation
Indices: 4883664--4883703 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
4883654 CTTCCATCAT
*
4883664 CATCATCATCATCAC
1 CATCATCATCAGCAC
* *
4883679 CATCACCATCAGCCC
1 CATCATCATCAGCAC
4883694 CATCATCATC
1 CATCATCATC
4883704 TTCATCTTCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.30, C:0.45, G:0.03, T:0.23
Consensus pattern (15 bp):
CATCATCATCAGCAC
Found at i:4883703 original size:6 final size:6
Alignment explanation
Indices: 4883634--4883717 Score: 62
Period size: 6 Copynumber: 14.0 Consensus size: 6
4883624 GTGTTGCATG
* * * *
4883634 CATCAC CATCAC CATCAT CA-CTT CCATCAT CATCAT CATCAT CACCAT
1 CATCAT CATCAT CATCAT CATCAT -CATCAT CATCAT CATCAT CATCAT
* * ** * *
4883682 CACCAT CAGCCC CATCAT CATCTT CATCTT CATCAT
1 CATCAT CATCAT CATCAT CATCAT CATCAT CATCAT
4883718 AAACAATGCC
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
5 2 0.03
6 60 0.94
7 2 0.03
ACGTcount: A:0.29, C:0.42, G:0.01, T:0.29
Consensus pattern (6 bp):
CATCAT
Found at i:4883708 original size:9 final size:9
Alignment explanation
Indices: 4883634--4883717 Score: 62
Period size: 9 Copynumber: 9.3 Consensus size: 9
4883624 GTGTTGCATG
*
4883634 CATCACCAT
1 CATCATCAT
*
4883643 CACCATCAT
1 CATCATCAT
*
4883652 CA-CTTCCAT
1 CATCAT-CAT
4883661 CATCATCAT
1 CATCATCAT
*
4883670 CATCATCAC
1 CATCATCAT
*
4883679 CATCACCAT
1 CATCATCAT
* **
4883688 CAGCCCCAT
1 CATCATCAT
*
4883697 CATCATCTT
1 CATCATCAT
*
4883706 CATCTTCAT
1 CATCATCAT
4883715 CAT
1 CAT
4883718 AAACAATGCC
Statistics
Matches: 58, Mismatches: 15, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
8 2 0.03
9 54 0.93
10 2 0.03
ACGTcount: A:0.29, C:0.42, G:0.01, T:0.29
Consensus pattern (9 bp):
CATCATCAT
Found at i:4898606 original size:44 final size:44
Alignment explanation
Indices: 4898543--4898746 Score: 266
Period size: 44 Copynumber: 4.5 Consensus size: 44
4898533 AGTACTTCTA
*
4898543 ATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATTTG
1 ATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTG
*
4898587 ATCAGTGACAAGTGATAAGTGAG-AGCTTTAGCTACACTTATCTA
1 ATCAGTGACAAGTGATAAGTG-GTAGCTTTAGCTACACTTATCTG
*
4898631 ATCAGTGACAAGTGACAAGTGATGAGTGGTAACTTTAGCTACACTTATCTG
1 ATCAGTGACAAGTG---A-T-A--AGTGGTAGCTTTAGCTACACTTATCTG
*
4898682 ATCAGTGACAAGTGATGAGTGGTAGCTTTAGCTACACTTATCTG
1 ATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTG
* * *
4898726 ATCTGGGACAAGTGACAAGTG
1 ATCAGTGACAAGTGATAAGTG
4898747 ATAAATGTGA
Statistics
Matches: 141, Mismatches: 10, Indels: 18
0.83 0.06 0.11
Matches are distributed among these distances:
44 97 0.69
45 1 0.01
47 2 0.01
48 2 0.01
49 1 0.01
50 1 0.01
51 37 0.26
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (44 bp):
ATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTG
Found at i:4898695 original size:95 final size:95
Alignment explanation
Indices: 4898546--4898750 Score: 331
Period size: 95 Copynumber: 2.2 Consensus size: 95
4898536 ACTTCTAATC
* *
4898546 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATTTGATCAGTGACAAGTGATAAGTGAG-
1 AGTGACAAGTGATAAGTGGTAACTTTAGCTACACTTATCTGATCAGTGACAAGTGATAAGTG-GT
*
4898610 AGCTTTAGCTACACTTATCTAATCAGTGACA
65 AGCTTTAGCTACACTTATCTAATCAGGGACA
* *
4898641 AGTGACAAGTGATGAGTGGTAACTTTAGCTACACTTATCTGATCAGTGACAAGTGATGAGTGGTA
1 AGTGACAAGTGATAAGTGGTAACTTTAGCTACACTTATCTGATCAGTGACAAGTGATAAGTGGTA
* *
4898706 GCTTTAGCTACACTTATCTGATCTGGGACA
66 GCTTTAGCTACACTTATCTAATCAGGGACA
4898736 AGTGACAAGTGATAA
1 AGTGACAAGTGATAA
4898751 ATGTGATCCG
Statistics
Matches: 101, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
94 1 0.01
95 100 0.99
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.30
Consensus pattern (95 bp):
AGTGACAAGTGATAAGTGGTAACTTTAGCTACACTTATCTGATCAGTGACAAGTGATAAGTGGTA
GCTTTAGCTACACTTATCTAATCAGGGACA
Found at i:4899992 original size:31 final size:31
Alignment explanation
Indices: 4899955--4900026 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 31
4899945 TATAGAATAT
*
4899955 AATTTAGTCACCCTTATTAGATAAGTTGT-C
1 AATTTAGTCACCCTCATTAGATAAGTTGTCC
*
4899985 AATTTTAGTCA-CCTCGTTAGATAAGTTGTCC
1 AA-TTTAGTCACCCTCATTAGATAAGTTGTCC
4900016 AATTTAGTCAC
1 AATTTAGTCAC
4900027 TCTACTGTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
30 26 0.70
31 11 0.30
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (31 bp):
AATTTAGTCACCCTCATTAGATAAGTTGTCC
Found at i:4900850 original size:7 final size:7
Alignment explanation
Indices: 4900838--4900867 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
4900828 GATCCCAATT
4900838 CAATCCA
1 CAATCCA
4900845 CAATCCA
1 CAATCCA
4900852 CAATCCA
1 CAATCCA
*
4900859 CAATTCA
1 CAATCCA
4900866 CA
1 CA
4900868 TTTCATTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.43, C:0.40, G:0.00, T:0.17
Consensus pattern (7 bp):
CAATCCA
Found at i:4911059 original size:23 final size:22
Alignment explanation
Indices: 4911016--4911063 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
4911006 TTAACTAATG
4911016 TTTTTAATTAATAAATATTTTTA
1 TTTTTAATTAATAAATA-TTTTA
* *
4911039 TTTTTAATTAATAATTCTTTTA
1 TTTTTAATTAATAAATATTTTA
4911061 TTT
1 TTT
4911064 ATATAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTTTAATTAATAAATATTTTA
Found at i:4913962 original size:2 final size:2
Alignment explanation
Indices: 4913955--4913996 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
4913945 CTTTTGCTTG
4913955 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
4913997 GATCTGCTGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4926281 original size:2 final size:2
Alignment explanation
Indices: 4926274--4926319 Score: 76
Period size: 2 Copynumber: 23.0 Consensus size: 2
4926264 NNNNNNNNNN
4926274 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TCA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
4926316 TA TA
1 TA TA
4926320 ACTAGGTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 40 0.95
3 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4933769 original size:62 final size:62
Alignment explanation
Indices: 4933667--4933798 Score: 255
Period size: 62 Copynumber: 2.1 Consensus size: 62
4933657 GAGAAAGAAG
*
4933667 ATAGACTATTTATTGTGTCCAATTAATTAATCAAAATATATCATCATAACAATTTGACGATA
1 ATAGGCTATTTATTGTGTCCAATTAATTAATCAAAATATATCATCATAACAATTTGACGATA
4933729 ATAGGCTATTTATTGTGTCCAATTAATTAATCAAAATATATCATCATAACAATTTGACGATA
1 ATAGGCTATTTATTGTGTCCAATTAATTAATCAAAATATATCATCATAACAATTTGACGATA
4933791 ATAGGCTA
1 ATAGGCTA
4933799 ATATGCATTA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
62 69 1.00
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (62 bp):
ATAGGCTATTTATTGTGTCCAATTAATTAATCAAAATATATCATCATAACAATTTGACGATA
Found at i:4955089 original size:11 final size:12
Alignment explanation
Indices: 4955061--4955094 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
4955051 GCCCAAACGT
4955061 CGAAATTTTTGAA
1 CGAAATTTTT-AA
4955074 CGAAATTTTT-A
1 CGAAATTTTTAA
4955085 CGAAATTTTT
1 CGAAATTTTT
4955095 CCTCAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
13 10 0.48
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (12 bp):
CGAAATTTTTAA
Found at i:4956052 original size:22 final size:24
Alignment explanation
Indices: 4956009--4956052 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
4955999 TGATAATATA
4956009 TTTTGATATAACAAATTAAAGTGT
1 TTTTGATATAACAAATTAAAGTGT
*
4956033 TTTTGA-ATAA-AAGTTAAAGT
1 TTTTGATATAACAAATTAAAGT
4956053 TAAACAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.43, C:0.02, G:0.14, T:0.41
Consensus pattern (24 bp):
TTTTGATATAACAAATTAAAGTGT
Found at i:4956312 original size:97 final size:97
Alignment explanation
Indices: 4956141--4956429 Score: 551
Period size: 97 Copynumber: 3.0 Consensus size: 97
4956131 ATCAACTTTA
* *
4956141 AAATAAAGTTAAAATGATTTTAATCAAGTAATAATTATTTCAACTAGTCAAACTGTTTTTAAAAC
1 AAATCAAGTTAAAATGATTTTAATCAAGTAATAATTCTTTCAACTAGTCAAACTGTTTTTAAAAC
4956206 AAGTCAGTATAGCTCCAGGCCAAAAAGTATTG
66 AAGTCAGTATAGCTCCAGGCCAAAAAGTATTG
4956238 AAATCAAGTTAAAATGATTTTAATCAAGTAATAATTCTTTCAACTAGTCAAACTGTTTTTAAAAC
1 AAATCAAGTTAAAATGATTTTAATCAAGTAATAATTCTTTCAACTAGTCAAACTGTTTTTAAAAC
4956303 AAGTCAGTATAGCTCCAGGCCAAAAAGTATTG
66 AAGTCAGTATAGCTCCAGGCCAAAAAGTATTG
4956335 AAATCAAGTTAAAATGATTTTAATCAAGTAATAATTCTTTCAACTAGTCAAACTGTTTTTAAAAC
1 AAATCAAGTTAAAATGATTTTAATCAAGTAATAATTCTTTCAACTAGTCAAACTGTTTTTAAAAC
*
4956400 AAGTCAGTATAGCTCCAAGCCAAAAAGTAT
66 AAGTCAGTATAGCTCCAGGCCAAAAAGTAT
4956430 CGATAGTTTT
Statistics
Matches: 189, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 189 1.00
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.32
Consensus pattern (97 bp):
AAATCAAGTTAAAATGATTTTAATCAAGTAATAATTCTTTCAACTAGTCAAACTGTTTTTAAAAC
AAGTCAGTATAGCTCCAGGCCAAAAAGTATTG
Found at i:4958122 original size:27 final size:27
Alignment explanation
Indices: 4958092--4958171 Score: 97
Period size: 27 Copynumber: 3.0 Consensus size: 27
4958082 TAGACGCGAT
4958092 TAGTTGAGCCTATCTCAGAGGCGTGAC
1 TAGTTGAGCCTATCTCAGAGGCGTGAC
* * **
4958119 TAGTTGAGCCTATCTGACAGGCGCAAC
1 TAGTTGAGCCTATCTCAGAGGCGTGAC
* * *
4958146 TAATTGTGCCTAACTCAGAGGCGTGA
1 TAGTTGAGCCTATCTCAGAGGCGTGA
4958172 ATGGTGGGGC
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (27 bp):
TAGTTGAGCCTATCTCAGAGGCGTGAC
Found at i:4958506 original size:20 final size:20
Alignment explanation
Indices: 4958471--4958508 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4958461 ATTTTTTTGC
*
4958471 ATTTCGAAACTGTTTTAAGA
1 ATTTCGAAAATGTTTTAAGA
*
4958491 ATTTCGAAAATTTTTTAA
1 ATTTCGAAAATGTTTTAA
4958509 CAGATATAGT
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:0.37, C:0.08, G:0.11, T:0.45
Consensus pattern (20 bp):
ATTTCGAAAATGTTTTAAGA
Found at i:4963492 original size:34 final size:33
Alignment explanation
Indices: 4963454--4963553 Score: 90
Period size: 34 Copynumber: 3.2 Consensus size: 33
4963444 CTAAACACAA
*
4963454 TAATTTATAACTTAATCCTAAATTACTAATAAAT
1 TAATTTATAAC-TAATCCTAAATTACTAACAAAT
*
4963488 TAATTT-TAA--AA---T-AATTACAAACACAA-
1 TAATTTATAACTAATCCTAAATTACTAACA-AAT
*
4963514 AAATTTATAACATAATCCTAAATTACTAACAAAT
1 TAATTTATAAC-TAATCCTAAATTACTAACAAAT
4963548 TAATTT
1 TAATTT
4963554 TAAAATAATT
Statistics
Matches: 51, Mismatches: 5, Indels: 20
0.67 0.07 0.26
Matches are distributed among these distances:
26 14 0.27
27 6 0.12
30 4 0.08
33 6 0.12
34 21 0.41
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (33 bp):
TAATTTATAACTAATCCTAAATTACTAACAAAT
Found at i:4963539 original size:60 final size:60
Alignment explanation
Indices: 4963446--4963564 Score: 211
Period size: 60 Copynumber: 2.0 Consensus size: 60
4963436 ATACTAAACT
* * *
4963446 AAACACAATAATTTATAACTTAATCCTAAATTACTAATAAATTAATTTTAAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
4963506 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
4963565 TAAAAAGCAA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (60 bp):
AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
Found at i:4963598 original size:60 final size:59
Alignment explanation
Indices: 4963460--4963585 Score: 155
Period size: 60 Copynumber: 2.1 Consensus size: 59
4963450 ACAATAATTT
* * * * *
4963460 ATAACTTAATCCTAAATTACTAATAAATTAATTTTAAAATAATTACAAACACAAAAATTT
1 ATAACATAATCCAAAATTACTAACAAATTAATTTTAAAATAATTACAAAAACAAAAA-TA
* *
4963520 ATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTATAAAAAGCAAAAA-A
1 ATAACATAATCCAAAATTACTAACAAATTAATTTTAAAATAATTACAAAAA-CAAAAATA
*
4963579 ATTACAT
1 ATAACAT
4963586 TCATTCAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
59 6 0.10
60 47 0.80
61 6 0.10
ACGTcount: A:0.56, C:0.11, G:0.01, T:0.33
Consensus pattern (59 bp):
ATAACATAATCCAAAATTACTAACAAATTAATTTTAAAATAATTACAAAAACAAAAATA
Found at i:4963884 original size:27 final size:27
Alignment explanation
Indices: 4963815--4963885 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 27
4963805 CACCATTCAT
* * * *
4963815 GCCTACTTGTCAGGCGCGATTAGTAGC
1 GCCTATTTGACAGGCTCAATTAGTAGC
* * * *
4963842 ACCTATCTGGCAGGCTCAATTAGTCGC
1 GCCTATTTGACAGGCTCAATTAGTAGC
4963869 GCCTATTTGACAGGCTC
1 GCCTATTTGACAGGCTC
4963886 GACCCGTTTT
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.20, C:0.28, G:0.25, T:0.27
Consensus pattern (27 bp):
GCCTATTTGACAGGCTCAATTAGTAGC
Found at i:4964665 original size:3 final size:3
Alignment explanation
Indices: 4964657--4964702 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
4964647 TTTGTTTAGT
4964657 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
4964703 TTATTGGTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:4992773 original size:60 final size:59
Alignment explanation
Indices: 4992674--4992816 Score: 196
Period size: 60 Copynumber: 2.4 Consensus size: 59
4992664 AGTAGTTTTA
* * *
4992674 AATCTGATGAAGAAAAAACTTCATCAGACCAGAAAGAAGACATAAATGTTACTAGTAAT
1 AATCTGATGAAGAAAAAACTTCAACAGACCAGAAAGAAGACATAAAAGTCACTAGTAAT
* * * *
4992733 CAATCTGATGAAGAAAAAACTTCAACAGATCAGGATGAAGACATAAAAGTCACTAGTTAT
1 -AATCTGATGAAGAAAAAACTTCAACAGACCAGAAAGAAGACATAAAAGTCACTAGTAAT
*
4992793 AATTCTGATGAAGAAAACACTTCA
1 AA-TCTGATGAAGAAAAAACTTCA
4992817 TCTGAAGATG
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
59 2 0.03
60 72 0.97
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (59 bp):
AATCTGATGAAGAAAAAACTTCAACAGACCAGAAAGAAGACATAAAAGTCACTAGTAAT
Found at i:4995160 original size:13 final size:13
Alignment explanation
Indices: 4995142--4995166 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4995132 ATTGAAGAAG
4995142 AAAAAGAAATTTC
1 AAAAAGAAATTTC
4995155 AAAAAGAAATTT
1 AAAAAGAAATTT
4995167 TTTTTATAAT
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:0.04, G:0.08, T:0.24
Consensus pattern (13 bp):
AAAAAGAAATTTC
Found at i:5005709 original size:5 final size:5
Alignment explanation
Indices: 5005701--5005727 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
5005691 AAAAAAAATT
5005701 GAAAA GAAAA GAAAA GAAAA GAAAA GA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GA
5005728 GCAAAATCTA
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:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:5006046 original size:20 final size:19
Alignment explanation
Indices: 5006021--5006059 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5006011 ATTTTACCCA
5006021 CCCCTTCTCCTTTTCTTTTC
1 CCCCTT-TCCTTTTCTTTTC
**
5006041 CCCCTTTTTTTTTCTTTTC
1 CCCCTTTCCTTTTCTTTTC
5006060 ATTATATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (19 bp):
CCCCTTTCCTTTTCTTTTC
Found at i:5011995 original size:57 final size:56
Alignment explanation
Indices: 5011874--5012003 Score: 133
Period size: 57 Copynumber: 2.3 Consensus size: 56
5011864 ATGATTTTTT
*
5011874 TTCTTTTTTAGTCACCAACTACGAAAAAGTATAAAATGGTCAAATAACTATTAGTAAG
1 TTCTTTTTT-GTCACCAACTACGAAAAAGTACAAAATGGTCAAATAACTATTA-TAAG
* * *
5011932 TT-TTTTTTGTCACCTAACTATG-AAAAGTTACAAAATGGTC-ACTCAACTATT-TAAT
1 TTCTTTTTTGTCACC-AACTACGAAAAAG-TACAAAATGGTCAAAT-AACTATTATAAG
5011987 TATCTTTTTTGATCACC
1 T-TCTTTTTTG-TCACC
5012004 CATCTATCTT
Statistics
Matches: 62, Mismatches: 4, Indels: 12
0.79 0.05 0.15
Matches are distributed among these distances:
55 4 0.06
56 14 0.23
57 37 0.60
58 7 0.11
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (56 bp):
TTCTTTTTTGTCACCAACTACGAAAAAGTACAAAATGGTCAAATAACTATTATAAG
Found at i:5012692 original size:4 final size:4
Alignment explanation
Indices: 5012663--5012709 Score: 58
Period size: 4 Copynumber: 10.8 Consensus size: 4
5012653 TTTTATTTCA
5012663 AAAT AAAT CAACAT AAAAT GAAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT -AA-AT -AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAA
5012710 GAATTAGATT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
4 27 0.69
5 8 0.21
6 4 0.10
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:5012707 original size:20 final size:24
Alignment explanation
Indices: 5012663--5012709 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
5012653 TTTTATTTCA
5012663 AAATAAATCAACATAAAATGAAAT
1 AAATAAATCAACATAAAATGAAAT
5012687 AAATAAAT-AA-AT-AAAT-AAAT
1 AAATAAATCAACATAAAATGAAAT
5012707 AAA
1 AAA
5012710 GAATTAGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.30
21 4 0.17
22 2 0.09
23 2 0.09
24 8 0.35
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (24 bp):
AAATAAATCAACATAAAATGAAAT
Found at i:5032505 original size:97 final size:97
Alignment explanation
Indices: 5032331--5032528 Score: 371
Period size: 97 Copynumber: 2.1 Consensus size: 97
5032321 ATATTCACAT
5032331 AACC-TAATCTAGCATGCCACATGTCAATGGATTCAGCAATATAAGTAGAAGTGGTGGCTGTATT
1 AACCTTAATCTAGCATGCCACATGTCAATGGATTCAGCAATATAAGTAGAAGTGGTGGCTGTATT
*
5032395 ATTATCATTAAACATGGTCTCAATCACAAATA
66 ATTATCATGAAACATGGTCTCAATCACAAATA
*
5032427 AACCTTAATCTAGCATGCCACATGTCAATGGATTCAGCAATATAAGTAGAAGTGGTGGCTTTATT
1 AACCTTAATCTAGCATGCCACATGTCAATGGATTCAGCAATATAAGTAGAAGTGGTGGCTGTATT
5032492 ATTATCATGAAACATGGTCTCAATCACAAATA
66 ATTATCATGAAACATGGTCTCAATCACAAATA
5032524 AACCT
1 AACCT
5032529 CCACTCAGAT
Statistics
Matches: 99, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
96 4 0.04
97 95 0.96
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.29
Consensus pattern (97 bp):
AACCTTAATCTAGCATGCCACATGTCAATGGATTCAGCAATATAAGTAGAAGTGGTGGCTGTATT
ATTATCATGAAACATGGTCTCAATCACAAATA
Found at i:5034202 original size:28 final size:27
Alignment explanation
Indices: 5034171--5034240 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 27
5034161 CATCCAGACG
*
5034171 GACTTCCTCATTTAAGATTGTCTTGGAC
1 GACTTCCTCATTTAAGATCGTCTT-GAC
* *
5034199 GACTTCCACATTTAAGATCGTCTTGAG
1 GACTTCCTCATTTAAGATCGTCTTGAC
*
5034226 GACTTCTTACATTTA
1 GACTTCCT-CATTTA
5034241 GACAGTCTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
27 8 0.22
28 28 0.78
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (27 bp):
GACTTCCTCATTTAAGATCGTCTTGAC
Found at i:5034347 original size:22 final size:22
Alignment explanation
Indices: 5034322--5034389 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 22
5034312 CATGGTCTTC
5034322 CATACGTCCCATAAAGGGCTCT
1 CATACGTCCCATAAAGGGCTCT
* *
5034344 CATACGTCCTACATAAGGGGATCT
1 CATACGTCC--CATAAAGGGCTCT
* *
5034368 CAAACGTCCCTTAAAGGGCTCT
1 CATACGTCCCATAAAGGGCTCT
5034390 ATATACTGGT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
22 19 0.50
24 19 0.50
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (22 bp):
CATACGTCCCATAAAGGGCTCT
Found at i:5034368 original size:24 final size:22
Alignment explanation
Indices: 5034322--5034385 Score: 74
Period size: 24 Copynumber: 2.8 Consensus size: 22
5034312 CATGGTCTTC
*
5034322 CATACGTCCCATAAAGGGCTCT
1 CATACGTCCCATAAAGGGATCT
*
5034344 CATACGTCCTACATAAGGGGATCT
1 CATACGTCC--CATAAAGGGATCT
* *
5034368 CAAACGTCCCTTAAAGGG
1 CATACGTCCCATAAAGGG
5034386 CTCTATATAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 16 0.46
24 19 0.54
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (22 bp):
CATACGTCCCATAAAGGGATCT
Found at i:5059788 original size:2 final size:2
Alignment explanation
Indices: 5059781--5059814 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5059771 TATCATTGTA
5059781 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
5059815 CACTTGAAAT
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:5062327 original size:23 final size:25
Alignment explanation
Indices: 5062296--5062346 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 25
5062286 ATATTTTGAA
5062296 AAACATATAAAATTTATAA-TATAT
1 AAACATATAAAATTTATAAGTATAT
** *
5062320 AAAC-TATATTATTTATAAGTTTAT
1 AAACATATAAAATTTATAAGTATAT
5062344 AAA
1 AAA
5062347 AAATTAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (25 bp):
AAACATATAAAATTTATAAGTATAT
Found at i:5063544 original size:29 final size:30
Alignment explanation
Indices: 5063487--5063544 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
5063477 TTAATTTATG
*
5063487 GTAAAATTACATTTTAGCCCTCCAAAAAAA
1 GTAAAATTACATTTAAGCCCTCCAAAAAAA
* * *
5063517 GTAAAATTACGTTTAATCCCTTCAAAAA
1 GTAAAATTACATTTAAGCCCTCCAAAAA
5063545 TGATGAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.45, C:0.19, G:0.07, T:0.29
Consensus pattern (30 bp):
GTAAAATTACATTTAAGCCCTCCAAAAAAA
Found at i:5064769 original size:20 final size:21
Alignment explanation
Indices: 5064719--5064759 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
5064709 AGATGGTTTT
*
5064719 CAAAATTAAAAATATATATAA
1 CAAAAATAAAAATATATATAA
5064740 CAAATAATAAAAATATATAT
1 CAAA-AATAAAAATATATAT
5064760 TTAAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (21 bp):
CAAAAATAAAAATATATATAA
Found at i:5075239 original size:2 final size:2
Alignment explanation
Indices: 5075232--5075257 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5075222 AAATAGTTAA
5075232 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
5075258 TAAAGTTTGA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5092391 original size:71 final size:69
Alignment explanation
Indices: 5092277--5092419 Score: 241
Period size: 71 Copynumber: 2.0 Consensus size: 69
5092267 AACTCTTCAA
* *
5092277 TTACCAATCTTACCTATGCTATGATGCATTAAAACTTATCATTTTATATACATGTGAGCATTATA
1 TTACCAATCTTACCTATGCTATAATGCATTAAAACTTATCATTTTATATACATGTGAACATTATA
5092342 TACC
66 TACC
*
5092346 TTACCAATCTTACCTATTTGCTATAATGCATTAAAACTTATCATTTTATCTACATGTGAACATTA
1 TTACCAATCTTACCTA--TGCTATAATGCATTAAAACTTATCATTTTATATACATGTGAACATTA
5092411 TATACC
64 TATACC
5092417 TTA
1 TTA
5092420 ATGATTTAAG
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
69 16 0.23
71 53 0.77
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.41
Consensus pattern (69 bp):
TTACCAATCTTACCTATGCTATAATGCATTAAAACTTATCATTTTATATACATGTGAACATTATA
TACC
Found at i:5095822 original size:25 final size:25
Alignment explanation
Indices: 5095792--5095946 Score: 79
Period size: 26 Copynumber: 6.2 Consensus size: 25
5095782 AATAACGAGT
5095792 AGCTCCGAAGAGCCATTAATCAGGA
1 AGCTCCGAAGAGCCATTAATCAGGA
* * **
5095817 AGCTCCGGATAATCA-TATATCAGGA
1 AGCTCCGAAGAGCCATTA-ATCAGGA
* * **
5095842 AG-TTC-AAGCGAGCCA--CATTGGGA
1 AGCTCCGAA--GAGCCATTAATCAGGA
* *
5095865 AGCTCTGGAGAGCCATTAATCAGGA
1 AGCTCCGAAGAGCCATTAATCAGGA
* * *
5095890 AGCTCACAAAGAGCCTTTAATCGGGA
1 AGCTC-CGAAGAGCCATTAATCAGGA
*
5095916 AGCTCACGAAAAGCCATATAA-CAGGA
1 AGCTC-CGAAGAGCCAT-TAATCAGGA
*
5095942 TGCTC
1 AGCTC
5095947 ATAAGAGTTG
Statistics
Matches: 93, Mismatches: 28, Indels: 17
0.67 0.20 0.12
Matches are distributed among these distances:
23 14 0.15
24 5 0.05
25 34 0.37
26 37 0.40
27 3 0.03
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.19
Consensus pattern (25 bp):
AGCTCCGAAGAGCCATTAATCAGGA
Found at i:5095834 original size:73 final size:73
Alignment explanation
Indices: 5095757--5095894 Score: 163
Period size: 73 Copynumber: 1.9 Consensus size: 73
5095747 TCATAAGAGC
* * *
5095757 CATAT-TCAAGAAGCTCATGTGAGCCA-ATAACGAGTAGCTCCGAAGAGCCATTAATCAGGAAGC
1 CATATATCAAGAAGCTCAAGCGAGCCACAT--CGAGAAGCTCCGAAGAGCCATTAATCAGGAAGC
5095820 TCCGGATAAT
64 TCCGGATAAT
* * * * * *
5095830 CATATATCAGGAAGTTCAAGCGAGCCACATTGGGAAGCTCTGGAGAGCCATTAATCAGGAAGCTC
1 CATATATCAAGAAGCTCAAGCGAGCCACATCGAGAAGCTCCGAAGAGCCATTAATCAGGAAGCTC
5095895 ACAAAGAGCC
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
73 35 0.65
74 17 0.31
75 2 0.04
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (73 bp):
CATATATCAAGAAGCTCAAGCGAGCCACATCGAGAAGCTCCGAAGAGCCATTAATCAGGAAGCTC
CGGATAAT
Found at i:5095909 original size:26 final size:27
Alignment explanation
Indices: 5095873--5095947 Score: 84
Period size: 26 Copynumber: 2.9 Consensus size: 27
5095863 GAAGCTCTGG
*
5095873 AGAGCCATTAATCAGGAAGCTCAC-AA
1 AGAGCCTTTAATCAGGAAGCTCACGAA
*
5095899 AGAGCCTTTAATCGGGAAGCTCACGAA
1 AGAGCCTTTAATCAGGAAGCTCACGAA
* *
5095926 A-AGCCATATAA-CAGGATGCTCA
1 AGAGCC-TTTAATCAGGAAGCTCA
5095948 TAAGAGTTGT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 35 0.83
27 7 0.17
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (27 bp):
AGAGCCTTTAATCAGGAAGCTCACGAA
Found at i:5096986 original size:16 final size:13
Alignment explanation
Indices: 5096952--5096979 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5096942 TTTTATTTTA
5096952 TTATTTATCATCT
1 TTATTTATCATCT
5096965 TTATTTATCATCT
1 TTATTTATCATCT
5096978 TT
1 TT
5096980 CCAATTTTGT
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:0.21, C:0.14, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTTATCATCT
Found at i:5114515 original size:23 final size:24
Alignment explanation
Indices: 5114489--5114533 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5114479 ATTTATGAAG
5114489 TTAGT-ATAAAATTTTATTAAAAT
1 TTAGTCATAAAATTTTATTAAAAT
* *
5114512 TTAGTCCTATAATTTTATTAAA
1 TTAGTCATAAAATTTTATTAAA
5114534 TTCATTGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.49
Consensus pattern (24 bp):
TTAGTCATAAAATTTTATTAAAAT
Found at i:5120786 original size:33 final size:32
Alignment explanation
Indices: 5120732--5120891 Score: 87
Period size: 33 Copynumber: 4.8 Consensus size: 32
5120722 TTGTTCGTTA
* *
5120732 TCGGTGGATTCAGCACCTAGCAACCACCAGTGAT
1 TCGG-GGAATCAGCACTTAGCAACCACCA-TGAT
*
5120766 TCGGGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGAT
1 TCGGGGAATCAGCACTTAGCAA--CC--AC-CA--T--GAT
* * * * *
5120807 ACAGTGGGATCAGCACTTAGTAACCACCAATGAG
1 TC-GGGGAATCAGCACTTAGCAACCACC-ATGAT
5120841 TCGGGGAATCAGCACTTAGCAA-C-CC---AT
1 TCGGGGAATCAGCACTTAGCAACCACCATGAT
*
5120868 TGGGGGAATCAGCACTTAGCAACC
1 TCGGGGAATCAGCACTTAGCAACC
5120892 CCCTTTATAT
Statistics
Matches: 99, Mismatches: 16, Indels: 28
0.69 0.11 0.20
Matches are distributed among these distances:
27 22 0.22
28 1 0.01
31 2 0.02
32 1 0.01
33 33 0.33
34 7 0.07
35 2 0.02
36 1 0.01
37 2 0.02
38 4 0.04
39 1 0.01
40 2 0.02
41 4 0.04
42 17 0.17
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.21
Consensus pattern (32 bp):
TCGGGGAATCAGCACTTAGCAACCACCATGAT
Found at i:5122230 original size:28 final size:28
Alignment explanation
Indices: 5122149--5122230 Score: 103
Period size: 28 Copynumber: 2.9 Consensus size: 28
5122139 AAAATAGCCT
*
5122149 TGACGGATTTCCACTTATAATATAGTTC
1 TGACGGATTTCCACTTATAATATAGTCC
* * *
5122177 TGACAGACTTCCA-TATATAAGATAGTCC
1 TGACGGATTTCCACT-TATAATATAGTCC
*
5122205 TGATGGATTTCCACTTATAATATAGT
1 TGACGGATTTCCACTTATAATATAGT
5122231 TCTAACGAAC
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
27 1 0.02
28 42 0.95
29 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.37
Consensus pattern (28 bp):
TGACGGATTTCCACTTATAATATAGTCC
Found at i:5122254 original size:56 final size:56
Alignment explanation
Indices: 5122151--5122330 Score: 166
Period size: 56 Copynumber: 3.2 Consensus size: 56
5122141 AATAGCCTTG
* *
5122151 ACGGATTTCCACTTATAATATAGTTCTGACAGACTTCCATATATAAGATAGTCCTG
1 ACGGATTTCCACTTATAATATAGTTCTAACAGACTTCCATATATAAGATAGTCCTA
* * * * *
5122207 ATGGATTTCCACTTATAATATAGTTCTAAC-GAACTTTCGTATTTAAGATAGTCTTA
1 ACGGATTTCCACTTATAATATAGTTCTAACAG-ACTTCCATATATAAGATAGTCCTA
* * * * * * * * *
5122263 ACGGACTTCCACATATAAGATAG-TCTTGACAAATTTCAACATATAAAATAGTCCTA
1 ACGGATTTCCACTTATAATATAGTTC-TAACAGACTTCCATATATAAGATAGTCCTA
* *
5122319 ACGAACTTCCAC
1 ACGGATTTCCAC
5122331 ATTTACAGTA
Statistics
Matches: 99, Mismatches: 22, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
55 3 0.03
56 96 0.97
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.33
Consensus pattern (56 bp):
ACGGATTTCCACTTATAATATAGTTCTAACAGACTTCCATATATAAGATAGTCCTA
Found at i:5122264 original size:28 final size:28
Alignment explanation
Indices: 5122183--5122332 Score: 113
Period size: 28 Copynumber: 5.4 Consensus size: 28
5122173 GTTCTGACAG
* * * * *
5122183 ACTTCCATATATAAGATAGTCCTGATGG
1 ACTTCCACATATAAGATAGTCTTAACGA
* * *
5122211 ATTTCCACTTATAATATAGT-TCTAACGA
1 ACTTCCACATATAAGATAGTCT-TAACGA
* ** * *
5122239 ACTTTCGTATTTAAGATAGTCTTAACGG
1 ACTTCCACATATAAGATAGTCTTAACGA
* *
5122267 ACTTCCACATATAAGATAGTCTTGACAA
1 ACTTCCACATATAAGATAGTCTTAACGA
* * * *
5122295 ATTTCAACATATAAAATAGTCCTAACGA
1 ACTTCCACATATAAGATAGTCTTAACGA
5122323 ACTTCCACAT
1 ACTTCCACAT
5122333 TTACAGTAAT
Statistics
Matches: 89, Mismatches: 31, Indels: 4
0.72 0.25 0.03
Matches are distributed among these distances:
28 88 0.99
29 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.33
Consensus pattern (28 bp):
ACTTCCACATATAAGATAGTCTTAACGA
Found at i:5122335 original size:84 final size:84
Alignment explanation
Indices: 5122182--5122335 Score: 200
Period size: 84 Copynumber: 1.8 Consensus size: 84
5122172 AGTTCTGACA
* *** * * * * * **
5122182 GACTTCCATATATAAGATAGTCCTGATGGATTTCCACTTATAATATAGTTCTAACGAACTTTCGT
1 GACTTCCACATATAAGATAGTCCTGACAAATTTCAACATATAAAATAGTCCTAACGAACTTCCAC
5122247 ATTTAAGATAGTCTTAACG
66 ATTTAAGATAGTCTTAACG
*
5122266 GACTTCCACATATAAGATAGTCTTGACAAATTTCAACATATAAAATAGTCCTAACGAACTTCCAC
1 GACTTCCACATATAAGATAGTCCTGACAAATTTCAACATATAAAATAGTCCTAACGAACTTCCAC
5122331 ATTTA
66 ATTTA
5122336 CAGTAATGTC
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
84 58 1.00
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.34
Consensus pattern (84 bp):
GACTTCCACATATAAGATAGTCCTGACAAATTTCAACATATAAAATAGTCCTAACGAACTTCCAC
ATTTAAGATAGTCTTAACG
Found at i:5126840 original size:13 final size:14
Alignment explanation
Indices: 5126822--5126850 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5126812 ATAATTTAAT
5126822 AATAAAT-AAACAA
1 AATAAATAAAACAA
5126835 AATAAATAAAACAA
1 AATAAATAAAACAA
5126849 AA
1 AA
5126851 ATCACATTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (14 bp):
AATAAATAAAACAA
Found at i:5136737 original size:25 final size:24
Alignment explanation
Indices: 5136693--5136757 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 24
5136683 AAGTTCAAAA
*
5136693 TTAAAAAAAAAAACATAATACAA-TAT
1 TTAAAAAAAATAA-A-AATA-AAGTAT
5136719 TTATAAAAAAATAAAAATAAAGTAT
1 TTA-AAAAAAATAAAAATAAAGTAT
*
5136744 TTAATAAAAATAAA
1 TTAAAAAAAATAAA
5136758 GTTAAATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 12 0.34
25 10 0.29
26 4 0.11
27 9 0.26
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (24 bp):
TTAAAAAAAATAAAAATAAAGTAT
Found at i:5137195 original size:35 final size:35
Alignment explanation
Indices: 5137149--5137219 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
5137139 CATGTTAAGG
5137149 ACAGAGTATCCCTATAGGCAATTGTAGTAATCCAA
1 ACAGAGTATCCCTATAGGCAATTGTAGTAATCCAA
5137184 ACAGAGTATCCCTATAGGCAATTGTAGTAATCCAA
1 ACAGAGTATCCCTATAGGCAATTGTAGTAATCCAA
5137219 A
1 A
5137220 AATTATGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (35 bp):
ACAGAGTATCCCTATAGGCAATTGTAGTAATCCAA
Found at i:5142732 original size:27 final size:28
Alignment explanation
Indices: 5142678--5142738 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
5142668 ACACAATTTT
* *
5142678 AATTT-TTAATTTTAAAATTTGAATTTA
1 AATTTATTAATTTCAAAATTTGAACTTA
*
5142705 AATTTATTAATTTCAATATTT-AACTTA
1 AATTTATTAATTTCAAAATTTGAACTTA
*
5142732 AAGTTAT
1 AATTTAT
5142739 AAATCTCATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 16 0.55
28 13 0.45
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.52
Consensus pattern (28 bp):
AATTTATTAATTTCAAAATTTGAACTTA
Found at i:5143636 original size:20 final size:20
Alignment explanation
Indices: 5143613--5143650 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5143603 AAAACTTAAG
5143613 TATATTTTTAAA-ATTATTCA
1 TATA-TTTTAAATATTATTCA
5143633 TATATTTTAAATATTATT
1 TATATTTTAAATATTATT
5143651 TTATCAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (20 bp):
TATATTTTAAATATTATTCA
Found at i:5143666 original size:17 final size:17
Alignment explanation
Indices: 5143646--5143699 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
5143636 ATTTTAAATA
5143646 TTATTTTATCAATAATT
1 TTATTTTATCAATAATT
*
5143663 TTATTTTA-CCAT-ATT
1 TTATTTTATCAATAATT
*
5143678 GTTATTTAAAT-AATAATT
1 -TTATTT-TATCAATAATT
5143696 TTAT
1 TTAT
5143700 AAAACACGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 3 0.10
16 9 0.30
17 15 0.50
18 3 0.10
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (17 bp):
TTATTTTATCAATAATT
Found at i:5144234 original size:15 final size:17
Alignment explanation
Indices: 5144200--5144236 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
5144190 TATCCTCTTA
5144200 ATTTACCTTAAATAATT
1 ATTTACCTTAAATAATT
*
5144217 ATTTA-CTTATAT-ATT
1 ATTTACCTTAAATAATT
5144232 ATTTA
1 ATTTA
5144237 TATAATTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
16 6 0.32
17 5 0.26
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTACCTTAAATAATT
Found at i:5144494 original size:24 final size:24
Alignment explanation
Indices: 5144437--5144488 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
5144427 ATTTTCTTTG
* **
5144437 TTTAGTTTTAATTCTATTTTTTAT
1 TTTAGATTTAATTCTATAATTTAT
5144461 TTTAGATTTAATTCTAATAATTTAT
1 TTTAGATTTAATTCT-ATAATTTAT
5144486 TTT
1 TTT
5144489 TATTTAGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (24 bp):
TTTAGATTTAATTCTATAATTTAT
Found at i:5144582 original size:20 final size:21
Alignment explanation
Indices: 5144539--5144582 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
5144529 TATGTTATTA
*
5144539 TTATTTGATTTCACTTTTTGG
1 TTATTTGATTTCACTATTTGG
5144560 TTATTT-ATTTCA-TATTTGTG
1 TTATTTGATTTCACTATTTG-G
5144580 TTA
1 TTA
5144583 GGTTAATTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 10 0.48
21 6 0.29
ACGTcount: A:0.18, C:0.07, G:0.11, T:0.64
Consensus pattern (21 bp):
TTATTTGATTTCACTATTTGG
Found at i:5146612 original size:8 final size:8
Alignment explanation
Indices: 5146599--5146626 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
5146589 GAAGAATTTT
5146599 AATTATAA
1 AATTATAA
5146607 AATTATAA
1 AATTATAA
5146615 AATTATAA
1 AATTATAA
5146623 AATT
1 AATT
5146627 GTGTATAAGA
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
AATTATAA
Found at i:5148746 original size:24 final size:24
Alignment explanation
Indices: 5148701--5148746 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
5148691 TTTGAACTAA
* *
5148701 TATGCGAAACCTTATGTGAATAAG
1 TATGCGAAACCTTAAGTAAATAAG
5148725 TATGCGAAA-CTTAAAGTAAATA
1 TATGCGAAACCTT-AAGTAAATA
5148747 TGCATGTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.28
Consensus pattern (24 bp):
TATGCGAAACCTTAAGTAAATAAG
Found at i:5151704 original size:32 final size:32
Alignment explanation
Indices: 5151621--5151715 Score: 88
Period size: 32 Copynumber: 2.9 Consensus size: 32
5151611 GATGATATTA
5151621 GAGATATTTTGATGATATTTTA-TAAT-TATTTAAT
1 GAGATATTTT-AT--TATTTTATTAATAT-TTTAAT
* **
5151655 TAGATA-AATATTATTTTATTAATATTTTAAT
1 GAGATATTTTATTATTTTATTAATATTTTAAT
**
5151686 GAGATATTTTATTATTTTATTGTTATTTTA
1 GAGATATTTTATTATTTTATTAATATTTTA
5151716 TTTAGTATAT
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
30 7 0.14
31 15 0.30
32 22 0.44
33 1 0.02
34 5 0.10
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (32 bp):
GAGATATTTTATTATTTTATTAATATTTTAAT
Found at i:5153511 original size:26 final size:25
Alignment explanation
Indices: 5153474--5153522 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
5153464 ACATACCACA
5153474 GCTCTTATGAGCGTCCCGATATATG
1 GCTCTTATGAGCGTCCCGATATATG
*
5153499 GCTCTTCATGAGCTTCCCGATATA
1 GCTCTT-ATGAGCGTCCCGATATA
5153523 GCTCGCTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (25 bp):
GCTCTTATGAGCGTCCCGATATATG
Found at i:5159276 original size:5 final size:5
Alignment explanation
Indices: 5159268--5159298 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
5159258 GTTCTTTTGA
5159268 TTCTT TTCTT TTC-T TTCTT TTCTT TTCTT TT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TT
5159299 TGCATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTCTT
Found at i:5159281 original size:19 final size:19
Alignment explanation
Indices: 5159253--5159298 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
5159243 ACTTTTCATG
*
5159253 TTTCTGTTCTTT-TGATTCT
1 TTTCTTTTCTTTCT-ATTCT
*
5159272 TTTCTTTTCTTTCTTTTCT
1 TTTCTTTTCTTTCTATTCT
5159291 TTTCTTTT
1 TTTCTTTT
5159299 TGCATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 23 0.96
20 1 0.04
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.76
Consensus pattern (19 bp):
TTTCTTTTCTTTCTATTCT
Found at i:5159295 original size:14 final size:14
Alignment explanation
Indices: 5159253--5159297 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
5159243 ACTTTTCATG
* *
5159253 TTTCTGTTCTTTTG
1 TTTCTTTTCTTTTC
*
5159267 ATTCTTTTCTTTTC
1 TTTCTTTTCTTTTC
5159281 TTTCTTTTCTTTTC
1 TTTCTTTTCTTTTC
5159295 TTT
1 TTT
5159298 TTGCATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (14 bp):
TTTCTTTTCTTTTC
Found at i:5160153 original size:34 final size:34
Alignment explanation
Indices: 5160110--5160181 Score: 144
Period size: 34 Copynumber: 2.1 Consensus size: 34
5160100 GTTGGCATTT
5160110 CAATAGTGACTTTATTTTTCTGTCTTTAAACTTC
1 CAATAGTGACTTTATTTTTCTGTCTTTAAACTTC
5160144 CAATAGTGACTTTATTTTTCTGTCTTTAAACTTC
1 CAATAGTGACTTTATTTTTCTGTCTTTAAACTTC
5160178 CAAT
1 CAAT
5160182 GTTTACAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.25, C:0.18, G:0.08, T:0.49
Consensus pattern (34 bp):
CAATAGTGACTTTATTTTTCTGTCTTTAAACTTC
Found at i:5169987 original size:6 final size:6
Alignment explanation
Indices: 5169976--5170032 Score: 55
Period size: 6 Copynumber: 9.5 Consensus size: 6
5169966 GATTGGAGGG
* * *
5169976 AAAGAA AAAGAA AAAGAA AAA-AA AAATGAA AATGAA AGAGAA AGAGGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAA-GAA AAAGAA AAAGAA A-AAGAA
5170025 AAA-AA AAA
1 AAAGAA AAA
5170033 CAAAGTTCTC
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
5 10 0.24
6 24 0.57
7 8 0.19
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (6 bp):
AAAGAA
Found at i:5174566 original size:30 final size:31
Alignment explanation
Indices: 5174511--5174569 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
5174501 ATTTTTTTGA
* *
5174511 AGTTTTTTATATTTTAATTTAAATTTTGATTT
1 AGTTATTTATATTTT-ATATAAATTTTGATTT
5174543 AGTTATTTATATTTT-TATAAATTTTGA
1 AGTTATTTATATTTTATATAAATTTTGA
5174570 ATTATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 11 0.44
32 14 0.56
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.63
Consensus pattern (31 bp):
AGTTATTTATATTTTATATAAATTTTGATTT
Found at i:5186700 original size:23 final size:21
Alignment explanation
Indices: 5186670--5186713 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
5186660 ATTTGATAAT
5186670 ATGTTTTGATATAACAAATTAAA
1 ATGTTTTGA-ATAA-AAATTAAA
*
5186693 ATGTTTTGAATAAAAGTTAAA
1 ATGTTTTGAATAAAAATTAAA
5186714 GTTGAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 4 0.20
23 9 0.45
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39
Consensus pattern (21 bp):
ATGTTTTGAATAAAAATTAAA
Found at i:5188142 original size:19 final size:21
Alignment explanation
Indices: 5188106--5188146 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5188096 TAATTTTCAT
5188106 ATTTTATGACTAAAAATATAA
1 ATTTTATGACTAAAAATATAA
5188127 ATTTTATGA-TAAAATATATA
1 ATTTTATGACTAAAA-ATATA
5188147 TGCTATTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.41
Consensus pattern (21 bp):
ATTTTATGACTAAAAATATAA
Found at i:5191518 original size:22 final size:22
Alignment explanation
Indices: 5191490--5191533 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
5191480 AAATAAGAAG
5191490 AAGAATAAACATCATATGCAAT
1 AAGAATAAACATCATATGCAAT
5191512 AAGAATAAACATCATATGCAAT
1 AAGAATAAACATCATATGCAAT
5191534 TTTATCTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.55, C:0.14, G:0.09, T:0.23
Consensus pattern (22 bp):
AAGAATAAACATCATATGCAAT
Found at i:5195783 original size:44 final size:43
Alignment explanation
Indices: 5195728--5195868 Score: 165
Period size: 44 Copynumber: 3.2 Consensus size: 43
5195718 AGTTGTTAAA
*
5195728 TGGTAAGAAATGAACATGCATTATAATTGTTTGATTGGTTGTCT
1 TGGTAAGAAATGAACATGCATTATAATTGTTTGATTGATTGT-T
* * * *
5195772 TGGTAATAAATGAACACGCATTATAAATGTTTGGTTGATTGTT
1 TGGTAAGAAATGAACATGCATTATAATTGTTTGATTGATTGTT
* * * * *
5195815 TGGCAAGAAATGGACATGTAATATAATTGTCTTGGTTGATTGTT
1 TGGTAAGAAATGAACATGCATTATAATTGT-TTGATTGATTGTT
5195859 TAGGTAAGAA
1 T-GGTAAGAA
5195869 TTTAAATGGT
Statistics
Matches: 82, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
43 24 0.29
44 51 0.62
45 7 0.09
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.38
Consensus pattern (43 bp):
TGGTAAGAAATGAACATGCATTATAATTGTTTGATTGATTGTT
Found at i:5196088 original size:2 final size:2
Alignment explanation
Indices: 5196081--5196113 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5196071 TGAGATTAGG
*
5196081 TA TA TA TA TA TA TA TC TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5196114 GCGAATTAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5199824 original size:8 final size:8
Alignment explanation
Indices: 5199813--5199843 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
5199803 TATATTGTTA
5199813 TATTATAT
1 TATTATAT
*
5199821 TATTATAA
1 TATTATAT
5199829 TATTATAT
1 TATTATAT
5199837 TATTATA
1 TATTATA
5199844 ATAATAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
TATTATAT
Found at i:5199831 original size:16 final size:16
Alignment explanation
Indices: 5199812--5199846 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
5199802 ATATATTGTT
5199812 ATATTATATTATTATA
1 ATATTATATTATTATA
5199828 ATATTATATTATTATA
1 ATATTATATTATTATA
5199844 ATA
1 ATA
5199847 ATAAAACAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATATTATATTATTATA
Found at i:5201322 original size:25 final size:27
Alignment explanation
Indices: 5201294--5201352 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 27
5201284 GTATATGAAT
*
5201294 TGAAATGAA-CTATTGGAA-TGAGAT-G
1 TGAAAT-AATCTAATGGAATTGAGATAG
5201319 TGAAA-AATCTAATGGAATTGAGATAG
1 TGAAATAATCTAATGGAATTGAGATAG
5201345 TGAAATAA
1 TGAAATAA
5201353 GGTATGAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
23 2 0.07
24 8 0.28
25 11 0.38
26 6 0.21
27 2 0.07
ACGTcount: A:0.46, C:0.03, G:0.24, T:0.27
Consensus pattern (27 bp):
TGAAATAATCTAATGGAATTGAGATAG
Found at i:5214022 original size:418 final size:419
Alignment explanation
Indices: 5213030--5214076 Score: 1624
Period size: 421 Copynumber: 2.5 Consensus size: 419
5213020 TCTAACAGGT
* * *
5213030 ATAACCTTCACAAC-ACTCTATTATTTACTTGGGGCTAAGATAGAACCATTTCATAGGTTTTGTA
1 ATAACATTCACAACTA-TCTATTATTTACTT-GGGTTAAGATAGAACCATTTCATAGTTTTTGTA
* * ** *
5213094 GCCTAACTAAAACCTTCTAACTTTTCGAAGGCTTAACTAAAAACTTATCTAGTTTTTATGGCTCA
64 GCTTAACTAGAACCTTCTAACTTTTCGAAGGCCCAACTAAAAACTTCTCTAGTTTTTATGGCTCA
* * *
5213159 ATTAGTAATCCTCCGAATATACAAATTGGTGATTTGTATAAACAAATGAAAAACCTCAAAAATGT
129 ATTAGTAATCCTCTGAATATACAAATTGGTGATTTGTGTAAA-AAATGAAAAACCTCTAAAATGT
* *
5213224 TTGAGTGTTTGCAAAGTCATATAGTAATTGGATTTTGGTGTAATTACTTGCGTAATTACTCCAAT
193 ATGAGTGTTTGCAAAGCCATATAGTAATTGGATTTTGGTGTAATTACTTGCGTAATTACTCCAAT
* *
5213289 TCTCACCCTCGCCTAAGAGTTGGAAAGTGTAATTGGGGTGCTTCAATTATACACAATTTAATGGG
258 TCTCACCCTCACCGAAGAGTTGGAAAGTGTAATTGGGGTGCTTCAATTATACACAATTTAATGGG
5213354 ATCCACCAATTACACCCAAATTCAATTACTAAGTTGTTTTCCAAACATAGCCAAAAGGTTTTCCC
323 ATCCACCAATTACACCCAAATTCAATTACTAAGTTGTTTTCCAAACATAGCCAAAAGGTTTTCCC
* * *
5213419 AGTTCAGTAATTGGTATCTTTCAATAACAAGG
388 AGTTCACTAATTGGCATCTTTCAAGAACAAGG
* * *
5213451 TATAACTTTCACAACTCTTTATTATTTACTTGGGTTAAGATAGAACCATTTCATAGTTTTTGTAG
1 -ATAACATTCACAACTATCTATTATTTACTTGGGTTAAGATAGAACCATTTCATAGTTTTTGTAG
5213516 CTTAACTAGAACCTTCTAACTTTTCGAAGGCCCAACTAAAAACTTCTCTAGTTTTTATGGCTCAA
65 CTTAACTAGAACCTTCTAACTTTTCGAAGGCCCAACTAAAAACTTCTCTAGTTTTTATGGCTCAA
*
5213581 TTAGTAATCCT-TCGAATATACAAATTGGTGATATGTGTAAGAAAATGAAAAACCTCTAAAATGT
130 TTAGTAATCCTCT-GAATATACAAATTGGTGATTTGTGTAA-AAAATGAAAAACCTCTAAAATGT
*
5213645 ATGAGTGTTTGGAAAGCCATATAGTAATTGGATTTTGGTGTAATTACTTGCGTAATTACTCCAAT
193 ATGAGTGTTTGCAAAGCCATATAGTAATTGGATTTTGGTGTAATTACTTGCGTAATTACTCCAAT
* * *
5213710 TCTCACCCTCACCGAAGAGTTGGAAAGTGTAATT-GGGTGCTTCAATTATACCCATTTTAATGTG
258 TCTCACCCTCACCGAAGAGTTGGAAAGTGTAATTGGGGTGCTTCAATTATACACAATTTAATGGG
* * *
5213774 ATCCACCAGTTACACCCAAATTCAATTACTAAGTTGCTTTT-CAAACATAGCCTAAAGGTTTTCT
323 ATCCACCAATTACACCCAAATTCAATTACTAAGTTG-TTTTCCAAACATAGCCAAAAGGTTTTCC
*
5213838 CAGTTCACTAATTGGCATCTTTCAAGGACAAGG
387 CAGTTCACTAATTGGCATCTTTCAAGAACAAGG
* *
5213871 -TAACATTCACAACTATCTATTATTTACTTGGGTTAAGGTAGAACCATTTCATAATTTTTGTAGC
1 ATAACATTCACAACTATCTATTATTTACTTGGGTTAAGATAGAACCATTTCATAGTTTTTGTAGC
* * *
5213935 TTAACTAGAACCTTGTAATTTTTCGAAGGCCCAACTAAAAA-TCTCTCTAGTTTTTATGGTTCAA
66 TTAACTAGAACCTTCTAACTTTTCGAAGGCCCAACTAAAAACT-TCTCTAGTTTTTATGGCTCAA
*
5213999 TTAGTAATCCTCTGAATATACAAATTGGTGATTTGTGTAAAAAAATGAAAATCCTCTAAAATGTA
130 TTAGTAATCCTCTGAATATACAAATTGGTGATTTGTGT-AAAAAATGAAAAACCTCTAAAATGTA
*
5214064 -G-GTGTTTACAAAG
194 TGAGTGTTTGCAAAG
5214077 TTTAGCTTAT
Statistics
Matches: 577, Mismatches: 41, Indels: 20
0.90 0.06 0.03
Matches are distributed among these distances:
416 10 0.02
417 2 0.00
418 176 0.31
419 3 0.01
420 112 0.19
421 247 0.43
422 27 0.05
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (419 bp):
ATAACATTCACAACTATCTATTATTTACTTGGGTTAAGATAGAACCATTTCATAGTTTTTGTAGC
TTAACTAGAACCTTCTAACTTTTCGAAGGCCCAACTAAAAACTTCTCTAGTTTTTATGGCTCAAT
TAGTAATCCTCTGAATATACAAATTGGTGATTTGTGTAAAAAATGAAAAACCTCTAAAATGTATG
AGTGTTTGCAAAGCCATATAGTAATTGGATTTTGGTGTAATTACTTGCGTAATTACTCCAATTCT
CACCCTCACCGAAGAGTTGGAAAGTGTAATTGGGGTGCTTCAATTATACACAATTTAATGGGATC
CACCAATTACACCCAAATTCAATTACTAAGTTGTTTTCCAAACATAGCCAAAAGGTTTTCCCAGT
TCACTAATTGGCATCTTTCAAGAACAAGG
Found at i:5216472 original size:3 final size:3
Alignment explanation
Indices: 5216457--5216495 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
5216447 GCTGTTGTAA
* *
5216457 AAG AAG GAG AAG AAG AAG GAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
5216496 CAGAGTGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:5216474 original size:12 final size:12
Alignment explanation
Indices: 5216457--5216495 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
5216447 GCTGTTGTAA
5216457 AAGAAGGAGAAG
1 AAGAAGGAGAAG
5216469 AAGAAGGAGAAG
1 AAGAAGGAGAAG
*
5216481 AAGAAGAAGAAG
1 AAGAAGGAGAAG
5216493 AAG
1 AAG
5216496 CAGAGTGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (12 bp):
AAGAAGGAGAAG
Found at i:5229083 original size:9 final size:9
Alignment explanation
Indices: 5229069--5229144 Score: 82
Period size: 9 Copynumber: 8.4 Consensus size: 9
5229059 TTTGGTTAAA
5229069 AATTAACCG
1 AATTAACCG
5229078 AATTAACCG
1 AATTAACCG
*
5229087 AATTACCCG
1 AATTAACCG
*
5229096 AATTAACTG
1 AATTAACCG
* *
5229105 AATTAGCCA
1 AATTAACCG
*
5229114 AATTACCCG
1 AATTAACCG
5229123 AATT-ACCTG
1 AATTAACC-G
*
5229132 AATTACCCG
1 AATTAACCG
5229141 AATT
1 AATT
5229145 GAATCACTAC
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
8 2 0.04
9 51 0.93
10 2 0.04
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:5229107 original size:27 final size:27
Alignment explanation
Indices: 5229069--5229144 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
5229059 TTTGGTTAAA
*
5229069 AATTAACCGAATTAACCGAATTACCCG
1 AATTAACTGAATTAACCGAATTACCCG
* *
5229096 AATTAACTGAATTAGCCAAATTACCCG
1 AATTAACTGAATTAACCGAATTACCCG
* *
5229123 AATTACCTGAATTACCCGAATT
1 AATTAACTGAATTAACCGAATT
5229145 GAATCACTAC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (27 bp):
AATTAACTGAATTAACCGAATTACCCG
Found at i:5229320 original size:18 final size:18
Alignment explanation
Indices: 5229294--5229333 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5229284 TTTATGATTA
*
5229294 GGTTGGGTTCGATAATTG
1 GGTTAGGTTCGATAATTG
* *
5229312 GGTTAGGTTGGATACTTG
1 GGTTAGGTTCGATAATTG
5229330 GGTT
1 GGTT
5229334 TGGATTGGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.15, C:0.05, G:0.40, T:0.40
Consensus pattern (18 bp):
GGTTAGGTTCGATAATTG
Found at i:5231294 original size:24 final size:24
Alignment explanation
Indices: 5231244--5231296 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
5231234 CAAAGAATAG
* * * * *
5231244 AAAAGAATATATTTAAATTGTGTA
1 AAAAGAAAATAATTAAATAGGGAA
5231268 AAAAGAAAATAATTAAATAGGGAA
1 AAAAGAAAATAATTAAATAGGGAA
5231292 AAAAG
1 AAAAG
5231297 GGGAATCAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.60, C:0.00, G:0.15, T:0.25
Consensus pattern (24 bp):
AAAAGAAAATAATTAAATAGGGAA
Found at i:5238874 original size:29 final size:28
Alignment explanation
Indices: 5238820--5238875 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 28
5238810 ATAGGGAGTT
5238820 AAATTTGGCTTAAAGTGAAATTGTTATAA
1 AAATTTGGCTTAAAGTGAAA-TGTTATAA
*
5238849 AAATTTGTGGTTAAATGTGAAA-GTTAT
1 AAATTTG-GCTTAAA-GTGAAATGTTAT
5238876 GTTAGTATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 12 0.50
30 6 0.25
31 6 0.25
ACGTcount: A:0.39, C:0.02, G:0.20, T:0.39
Consensus pattern (28 bp):
AAATTTGGCTTAAAGTGAAATGTTATAA
Found at i:5241254 original size:46 final size:46
Alignment explanation
Indices: 5241187--5241325 Score: 251
Period size: 46 Copynumber: 3.0 Consensus size: 46
5241177 CATGGTAAAG
**
5241187 TGTGAAAAGTAGGTATGGTGTTTCGGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAGT
5241233 TGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAGT
*
5241279 TGTGAAAAGTAAGTATGGTGTTTCAATGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAGT
5241325 T
1 T
5241326 ATAGCAATGT
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 90 1.00
ACGTcount: A:0.36, C:0.09, G:0.27, T:0.29
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAGT
Found at i:5249646 original size:2 final size:2
Alignment explanation
Indices: 5249639--5249668 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5249629 TATTTTGCAA
5249639 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
5249669 GTTTAGGCAG
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:5257991 original size:24 final size:24
Alignment explanation
Indices: 5257964--5258106 Score: 223
Period size: 24 Copynumber: 6.0 Consensus size: 24
5257954 TGGTACTCCA
* *
5257964 CCATCATCTGGAGGTGGTAGTCCC
1 CCATCATATGGAGGTGGCAGTCCC
* *
5257988 CCATCGTATGGAGGAGGCAGTCCC
1 CCATCATATGGAGGTGGCAGTCCC
* *
5258012 CCATCGTATGGAGGAGGCAGTCCC
1 CCATCATATGGAGGTGGCAGTCCC
*
5258036 CCATCATACGGAGGTGGCAGTCCC
1 CCATCATATGGAGGTGGCAGTCCC
5258060 CCATCATATGGAGGTGGCAGTCCC
1 CCATCATATGGAGGTGGCAGTCCC
5258084 CCATCATATGGAGGTGGCAGTCC
1 CCATCATATGGAGGTGGCAGTCC
5258107 ACCAACTACT
Statistics
Matches: 111, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 111 1.00
ACGTcount: A:0.20, C:0.29, G:0.31, T:0.20
Consensus pattern (24 bp):
CCATCATATGGAGGTGGCAGTCCC
Found at i:5265899 original size:14 final size:14
Alignment explanation
Indices: 5265882--5265914 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
5265872 TATTAAATTG
5265882 TAGAACTAAAATGC
1 TAGAACTAAAATGC
5265896 TAGAACTAAAATGC
1 TAGAACTAAAATGC
*
5265910 CAGAA
1 TAGAA
5265915 ATTGTTCGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.52, C:0.15, G:0.15, T:0.18
Consensus pattern (14 bp):
TAGAACTAAAATGC
Done.