Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 163 of 168
Found at i:48986765 original size:11 final size:11
Alignment explanation
Indices: 48986749--48986774 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
48986739 TAAAAATTAA
48986749 AAAAGTATTTT
1 AAAAGTATTTT
48986760 AAAAGTATTTT
1 AAAAGTATTTT
48986771 AAAA
1 AAAA
48986775 ATAAAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:49009368 original size:23 final size:23
Alignment explanation
Indices: 49009342--49009387 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
49009332 CTTGGTATTT
*
49009342 CAAGTGGCAGCGATCAGACAACC
1 CAAGTGACAGCGATCAGACAACC
49009365 CAAGTGACAGCGATCAGACAACC
1 CAAGTGACAGCGATCAGACAACC
49009388 GGTTCGAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.30, G:0.24, T:0.09
Consensus pattern (23 bp):
CAAGTGACAGCGATCAGACAACC
Found at i:49011498 original size:50 final size:50
Alignment explanation
Indices: 49011379--49011617 Score: 255
Period size: 50 Copynumber: 4.6 Consensus size: 50
49011369 GGTAAAAACA
* * * ** *
49011379 TGCCAAAGCCATGTCCCATACATGGTCTTACATGGGATGTTCTCATGTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATCTCGG
* * *
49011430 TTTCC-ATGCCATGTCCCAGACATGGTCTTACGGGGGACCTTTCATCTCGG
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
49011480 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
49011530 TGCCCATGCCATGTCCCAGACATGGTTTTACAGGGGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATCTC--GG
* * *
49011585 ATGCCAATGTCATGTCCCAAACATGGTTTTACA
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACA
49011618 TGAGATCTCT
Statistics
Matches: 159, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
49 3 0.02
50 89 0.56
51 28 0.18
52 3 0.02
53 5 0.03
55 2 0.01
56 29 0.18
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:49011566 original size:100 final size:105
Alignment explanation
Indices: 49011378--49011624 Score: 306
Period size: 100 Copynumber: 2.4 Consensus size: 105
49011368 TGGTAAAAAC
* ** * **
49011378 ATGCCAAAGCCATGTCCCATACATGGTCTTACATGGGATGTTCTCATGTCGGTTTCCATGCCATG
1 ATGCCAAAGCCATGTCCCAAACATGGTCTTACATGGGATCCTCTCATCTCGGTGCCCATGCCATG
*
49011443 TCCCAGACATGGTCTTACGGGGGACCT-T-TCATCTC-GG
66 TCCCAGACATGGTCTTACAGGGGACCTCTATCATCTCAGG
* *
49011480 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAAACATGGTCTTACATGGGATCCTCTCATCTCGGTGCCCATGCCATG
* *
49011543 TCCCAGACATGGTTTTACAGGGGACCTCTCATGATCTCAAGG
66 TCCCAGACATGGTCTTACAGGGGACCTCT-ATCATCTC-AGG
* * * *
49011585 ATGCCAATGTCATGTCCCAAACATGGTTTTACATGAGATC
1 ATGCCAAAGCCATGTCCCAAACATGGTCTTACATGGGATC
49011625 TCTTTACCCA
Statistics
Matches: 123, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
100 46 0.37
101 36 0.29
103 6 0.05
105 2 0.02
106 32 0.26
107 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (105 bp):
ATGCCAAAGCCATGTCCCAAACATGGTCTTACATGGGATCCTCTCATCTCGGTGCCCATGCCATG
TCCCAGACATGGTCTTACAGGGGACCTCTATCATCTCAGG
Found at i:49012015 original size:29 final size:31
Alignment explanation
Indices: 49011965--49012022 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
49011955 CCTCGACTCT
* *
49011965 AACTTTTTCAAAATTATGA-TTTTGCCCCTA
1 AACTTTTACAAAATTATCATTTTTGCCCCTA
*
49011995 AACTTTTACATAATTA-CATTTTTGCCCC
1 AACTTTTACAAAATTATCATTTTTGCCCC
49012023 CAAGGCTCGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.29, C:0.22, G:0.05, T:0.43
Consensus pattern (31 bp):
AACTTTTACAAAATTATCATTTTTGCCCCTA
Found at i:49014494 original size:6 final size:6
Alignment explanation
Indices: 49014483--49014516 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
49014473 TATAACACTA
* *
49014483 AAAATT AAAATT AAAATT AAAATG AAAATG AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAA
49014517 ATGATATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (6 bp):
AAAATT
Found at i:49014527 original size:2 final size:2
Alignment explanation
Indices: 49014520--49014549 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
49014510 ATGAAAAATG
49014520 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
49014550 CTACTACTAG
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:49021916 original size:15 final size:15
Alignment explanation
Indices: 49021896--49021950 Score: 65
Period size: 15 Copynumber: 3.4 Consensus size: 15
49021886 GGGGAAATTC
49021896 GAGTTAAGTACTAAT
1 GAGTTAAGTACTAAT
49021911 GAGTTAAGTACGACTAAAT
1 GAGTTAAGT---ACT-AAT
*
49021930 GAGTTAAATACTAAT
1 GAGTTAAGTACTAAT
49021945 GAGTTA
1 GAGTTA
49021951 CCCATTAGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
15 18 0.51
16 3 0.09
18 3 0.09
19 11 0.31
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.31
Consensus pattern (15 bp):
GAGTTAAGTACTAAT
Found at i:49033314 original size:2 final size:2
Alignment explanation
Indices: 49033307--49033338 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
49033297 ATTTGTTATT
*
49033307 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
49033339 AATGTATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:49034045 original size:2 final size:2
Alignment explanation
Indices: 49034038--49034073 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
49034028 TTGTTATTAA
49034038 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49034074 TTCCTTGTCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49034529 original size:24 final size:24
Alignment explanation
Indices: 49034490--49034542 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
49034480 AATACTTCTA
49034490 TATTTAGTTTTTAAAAATA-TTTT
1 TATTTAGTTTTTAAAAATAGTTTT
* *
49034513 TTTTTATTTTTTAAAAATAGTTTT
1 TATTTAGTTTTTAAAAATAGTTTT
49034537 TATTTA
1 TATTTA
49034543 AAAAAAACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 17 0.65
24 9 0.35
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (24 bp):
TATTTAGTTTTTAAAAATAGTTTT
Found at i:49046052 original size:24 final size:25
Alignment explanation
Indices: 49045999--49046052 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
49045989 ATTGTAAAAT
* *
49045999 ATAATTTTATTTTACTTATTTTTTT
1 ATAATATTATTTTACTTATTTTTTA
49046024 A-AATATTATTTTA-TT-TTTATTTA
1 ATAATATTATTTTACTTATTT-TTTA
49046047 ATAATA
1 ATAATA
49046053 ATTCTAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 3 0.12
23 6 0.24
24 15 0.60
25 1 0.04
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (25 bp):
ATAATATTATTTTACTTATTTTTTA
Found at i:49050330 original size:6 final size:6
Alignment explanation
Indices: 49050319--49050353 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
49050309 AAATATCGTA
49050319 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
49050354 ATATATATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:49055494 original size:19 final size:19
Alignment explanation
Indices: 49055470--49055538 Score: 81
Period size: 19 Copynumber: 3.6 Consensus size: 19
49055460 AAAATATAAA
49055470 ATTTAGAATTTTTATAAA-T
1 ATTTAGAATTTTTA-AAATT
49055489 ATTTAGAA-TTTTAAAATT
1 ATTTAGAATTTTTAAAATT
49055507 ATTTTA-AATTTTTGAAAATT
1 A-TTTAGAATTTTT-AAAATT
*
49055527 ATTTTGAATTTT
1 ATTTAGAATTTT
49055539 GGTTGAGAGA
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
17 3 0.07
18 9 0.20
19 19 0.43
20 13 0.30
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (19 bp):
ATTTAGAATTTTTAAAATT
Found at i:49055526 original size:20 final size:19
Alignment explanation
Indices: 49055430--49055538 Score: 71
Period size: 19 Copynumber: 5.5 Consensus size: 19
49055420 TTATATGTTG
* * *
49055430 TTTAGATTTTTTAGATTAT
1 TTTAAATTTTTAAAATTAT
* * *
49055449 TATAATTTTTTAAAATATAAAA
1 TTTAAATTTTTAAAAT-T--AT
49055471 TTTAGAATTTTTATAAA-TA-
1 TTTA-AATTTTTA-AAATTAT
49055490 TTTAGAA-TTTTAAAATTAT
1 TTTA-AATTTTTAAAATTAT
49055509 TTTAAATTTTTGAAAATTAT
1 TTTAAATTTTT-AAAATTAT
*
49055529 TTTGAATTTT
1 TTTAAATTTT
49055539 GGTTGAGAGA
Statistics
Matches: 72, Mismatches: 9, Indels: 17
0.73 0.09 0.17
Matches are distributed among these distances:
17 3 0.04
18 9 0.12
19 26 0.36
20 19 0.26
22 5 0.07
23 7 0.10
24 3 0.04
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (19 bp):
TTTAAATTTTTAAAATTAT
Found at i:49062962 original size:21 final size:21
Alignment explanation
Indices: 49062898--49063062 Score: 120
Period size: 21 Copynumber: 7.9 Consensus size: 21
49062888 CCGTGTTTGC
* * *
49062898 TTTCCGTTTAGCTCTCATGAGC
1 TTTCAGTTTAGCTCTTATG-GG
* * *
49062920 TTT-AG-TTAACTCATATGAG
1 TTTCAGTTTAGCTCTTATGGG
*
49062939 TTTCAGTTTAGCCCTTATGGG
1 TTTCAGTTTAGCTCTTATGGG
* *
49062960 TTTCAGTTTAGCTCTTTTGAG
1 TTTCAGTTTAGCTCTTATGGG
* *
49062981 CTTCAGTTTAACTCTTATGGG
1 TTTCAGTTTAGCTCTTATGGG
* *
49063002 TTTCCGTTTAGCTCTTATGAGC
1 TTTCAGTTTAGCTCTTATG-GG
* * * *
49063024 TTTC-GTTTAACCCTTACGGA
1 TTTCAGTTTAGCTCTTATGGG
* *
49063044 TTTCCGTTTAGCACTTATG
1 TTTCAGTTTAGCTCTTATG
49063063 TGCTTCTGTG
Statistics
Matches: 111, Mismatches: 28, Indels: 9
0.75 0.19 0.06
Matches are distributed among these distances:
19 3 0.03
20 16 0.14
21 84 0.76
22 8 0.07
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.44
Consensus pattern (21 bp):
TTTCAGTTTAGCTCTTATGGG
Found at i:49062988 original size:42 final size:42
Alignment explanation
Indices: 49062933--49063068 Score: 175
Period size: 42 Copynumber: 3.2 Consensus size: 42
49062923 AGTTAACTCA
* * *
49062933 TATGAGTTTCAGTTTAGCCCTTATGGGTTTCAGTTTAGCTCT
1 TATGAGCTTCAGTTTAACCCTTATGGGTTTCCGTTTAGCTCT
* *
49062975 TTTGAGCTTCAGTTTAACTCTTATGGGTTTCCGTTTAGCTCT
1 TATGAGCTTCAGTTTAACCCTTATGGGTTTCCGTTTAGCTCT
* * *
49063017 TATGAGCTTTC-GTTTAACCCTTACGGATTTCCGTTTAGCACT
1 TATGAGC-TTCAGTTTAACCCTTATGGGTTTCCGTTTAGCTCT
*
49063059 TATGTGCTTC
1 TATGAGCTTC
49063069 TGTGCAGCCT
Statistics
Matches: 82, Mismatches: 11, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
41 3 0.04
42 76 0.93
43 3 0.04
ACGTcount: A:0.16, C:0.20, G:0.19, T:0.45
Consensus pattern (42 bp):
TATGAGCTTCAGTTTAACCCTTATGGGTTTCCGTTTAGCTCT
Found at i:49063032 original size:63 final size:61
Alignment explanation
Indices: 49062896--49063032 Score: 166
Period size: 63 Copynumber: 2.2 Consensus size: 61
49062886 TTCCGTGTTT
*
49062896 GCTTTCCGTTTAGCTCTCATGAGCTTTAGTTAACTCATATGAGTTTCAGTTTAGCCCTTATG
1 GCTTT-CGTTTAGCTCTCATGAGCTTCAGTTAACTCATATGAGTTTCAGTTTAGCCCTTATG
* ** * * * *
49062958 GGTTTCAGTTTAGCTCTTTTGAGCTTCAGTTTAACTCTTATGGGTTTCCGTTTAGCTCTTATG
1 GCTTTC-GTTTAGCTCTCATGAGCTTCAG-TTAACTCATATGAGTTTCAGTTTAGCCCTTATG
49063021 AGCTTTCGTTTA
1 -GCTTTCGTTTA
49063033 ACCCTTACGG
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
61 1 0.02
62 23 0.37
63 34 0.54
64 5 0.08
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.45
Consensus pattern (61 bp):
GCTTTCGTTTAGCTCTCATGAGCTTCAGTTAACTCATATGAGTTTCAGTTTAGCCCTTATG
Found at i:49082267 original size:52 final size:52
Alignment explanation
Indices: 49082189--49082293 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
49082179 TTTATTGCCT
49082189 AATAAATTTTCTCAATTATGATATTATTAGACATAGCACCTGTGGAAGTTCA
1 AATAAATTTTCTCAATTATGATATTATTAGACATAGCACCTGTGGAAGTTCA
49082241 AATAAATTTTCTCAATTATGATATTATTAGACATAGCACCTGTGGAAGTTCA
1 AATAAATTTTCTCAATTATGATATTATTAGACATAGCACCTGTGGAAGTTCA
49082293 A
1 A
49082294 TTGCCTGATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.36
Consensus pattern (52 bp):
AATAAATTTTCTCAATTATGATATTATTAGACATAGCACCTGTGGAAGTTCA
Found at i:49087464 original size:2 final size:2
Alignment explanation
Indices: 49087457--49087483 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
49087447 TCCTGCTGGC
49087457 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
49087484 GGTATCCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49088067 original size:18 final size:18
Alignment explanation
Indices: 49088046--49088087 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
49088036 TCATGCAATC
*
49088046 CATTTT-TTTACAATTGTT
1 CATTTTCTTTAAAATT-TT
49088064 CATTTTCTTTAAAATTTT
1 CATTTTCTTTAAAATTTT
49088082 CATTTT
1 CATTTT
49088088 GAGCTATACC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.24, C:0.12, G:0.02, T:0.62
Consensus pattern (18 bp):
CATTTTCTTTAAAATTTT
Found at i:49090124 original size:2 final size:2
Alignment explanation
Indices: 49090119--49090145 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
49090109 TATATATATA
49090119 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
49090146 TTGGTCGATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:49090995 original size:14 final size:14
Alignment explanation
Indices: 49090976--49091006 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
49090966 AAAATTGTTG
49090976 TATATACATACATA
1 TATATACATACATA
*
49090990 TATATACATATATA
1 TATATACATACATA
49091004 TAT
1 TAT
49091007 GATGACTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (14 bp):
TATATACATACATA
Found at i:49094436 original size:24 final size:24
Alignment explanation
Indices: 49094391--49094436 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
49094381 TCCCCTTAAC
*
49094391 AAATAAACTCAATTTTATAAATAA
1 AAATAAACTAAATTTTATAAATAA
49094415 AAATAAAACTAAATTTTA-AAAT
1 AAAT-AAACTAAATTTTATAAAT
49094437 TTCCACAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.33
Consensus pattern (24 bp):
AAATAAACTAAATTTTATAAATAA
Found at i:49098038 original size:44 final size:47
Alignment explanation
Indices: 49097974--49098065 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 47
49097964 TGCACTAATG
*
49097974 AACAGAGAGCACTGAAGTGCTA-T-A-CAGAGAGCACAAATGTGCTA
1 AACAGAGAGCACTGAAGTGCTAGTAATCAGAGAGCACAAACGTGCTA
* *
49098018 AACAGAGAGCACTGACGTGCTAGTAATCAGAGAGCACTAACGTGCTA
1 AACAGAGAGCACTGAAGTGCTAGTAATCAGAGAGCACAAACGTGCTA
49098065 A
1 A
49098066 TAATCAGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
44 21 0.50
45 1 0.02
46 1 0.02
47 19 0.45
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.16
Consensus pattern (47 bp):
AACAGAGAGCACTGAAGTGCTAGTAATCAGAGAGCACAAACGTGCTA
Found at i:49098051 original size:25 final size:23
Alignment explanation
Indices: 49097974--49098073 Score: 107
Period size: 22 Copynumber: 4.3 Consensus size: 23
49097964 TGCACTAATG
49097974 AACAGAGAGCACTGAA-GTGCTAT
1 AACAGAGAGCACT-AACGTGCTAT
* *
49097997 -ACAGAGAGCACAAATGTGCTA-
1 AACAGAGAGCACTAACGTGCTAT
*
49098018 AACAGAGAGCACTGACGTGCTAGT
1 AACAGAGAGCACTAACGTGCTA-T
49098042 AATCAGAGAGCACTAACGTGCTAAT
1 AA-CAGAGAGCACTAACGTGCT-AT
49098067 AATCAGA
1 AA-CAGA
49098074 AAGCGCGCTA
Statistics
Matches: 66, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
21 2 0.03
22 35 0.53
24 2 0.03
25 26 0.39
26 1 0.02
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.17
Consensus pattern (23 bp):
AACAGAGAGCACTAACGTGCTAT
Found at i:49099109 original size:21 final size:22
Alignment explanation
Indices: 49099083--49099125 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
49099073 ATTAATAAGT
49099083 ATGTAT-ATATATTAATTACAA
1 ATGTATAATATATTAATTACAA
*
49099104 ATGTATACATATATTTATTACA
1 ATGTATA-ATATATTAATTACA
49099126 CTTGTCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
23 13 0.68
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (22 bp):
ATGTATAATATATTAATTACAA
Found at i:49109326 original size:20 final size:21
Alignment explanation
Indices: 49109286--49109329 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
49109276 TAATACTCTC
49109286 AAAATAATATTTATTTATTTAT
1 AAAATAATA-TTATTTATTTAT
*
49109308 AAAATAATA-TATTTTTTTAT
1 AAAATAATATTATTTATTTAT
49109328 AA
1 AA
49109330 TTTCACAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.57
22 9 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AAAATAATATTATTTATTTAT
Found at i:49114115 original size:3 final size:3
Alignment explanation
Indices: 49114107--49114136 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
49114097 AAAAAATGTC
49114107 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
49114137 GATTCTTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:49122623 original size:18 final size:21
Alignment explanation
Indices: 49122602--49122648 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 21
49122592 ATTTCTTTAT
*
49122602 TTTTCTTTTT-T-TCTTC-CC
1 TTTTCTTTTTCTCTCTTCTCA
*
49122620 TTTTATTTTTCTCTCTTCTCA
1 TTTTCTTTTTCTCTCTTCTCA
49122641 TTTTCTTT
1 TTTTCTTT
49122649 ACTGAAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 9 0.39
19 1 0.04
20 5 0.22
21 8 0.35
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTCTTTTTCTCTCTTCTCA
Found at i:49123774 original size:15 final size:16
Alignment explanation
Indices: 49123746--49123777 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
49123736 CTGTTTTAGT
49123746 AATTTAACCAAAATAA
1 AATTTAACCAAAATAA
49123762 AATTTAA-CAAAATAA
1 AATTTAACCAAAATAA
49123777 A
1 A
49123778 TCATTAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25
Consensus pattern (16 bp):
AATTTAACCAAAATAA
Found at i:49126289 original size:16 final size:16
Alignment explanation
Indices: 49126270--49126314 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
49126260 TATATATGTA
49126270 TAATAATATTTAAAAT
1 TAATAATATTTAAAAT
49126286 TAATAAT-TATTAAAAT
1 TAATAATAT-TTAAAAT
*
49126302 TTATAA-ATTTAAA
1 TAATAATATTTAAA
49126315 CTTTAATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 6 0.23
16 20 0.77
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATAATATTTAAAAT
Found at i:49128448 original size:14 final size:13
Alignment explanation
Indices: 49128431--49128484 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 13
49128421 ATAATATAAT
49128431 ATTTATAAATATGA
1 ATTTATAAATAT-A
49128445 ATTTATAACATATAA
1 ATTTATAA-ATAT-A
*
49128460 TATTTATAAAAATA
1 -ATTTATAAATATA
49128474 ATTTTATAAAT
1 A-TTTATAAAT
49128485 TGTCCAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 1 0.03
14 17 0.50
15 8 0.24
16 8 0.24
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (13 bp):
ATTTATAAATATA
Found at i:49128458 original size:30 final size:30
Alignment explanation
Indices: 49128424--49128482 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
49128414 TTTGTAGATA
*
49128424 ATATAATATTTATAAATATGAA-TTTATAAC
1 ATATAATATTTATAAAAAT-AATTTTATAAC
49128454 ATATAATATTTATAAAAATAATTTTATAA
1 ATATAATATTTATAAAAATAATTTTATAA
49128483 ATTGTCCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 2 0.07
30 25 0.93
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (30 bp):
ATATAATATTTATAAAAATAATTTTATAAC
Found at i:49131238 original size:3 final size:3
Alignment explanation
Indices: 49131230--49131255 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
49131220 GTTTGCTTTT
49131230 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
49131256 TTTTGTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:49133072 original size:16 final size:18
Alignment explanation
Indices: 49133051--49133083 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
49133041 AACATTAAAA
49133051 TAATATT-TAA-ATTCAT
1 TAATATTATAAGATTCAT
49133067 TAATATTATAAGATTCA
1 TAATATTATAAGATTCA
49133084 ATAAAAATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (18 bp):
TAATATTATAAGATTCAT
Found at i:49138884 original size:17 final size:18
Alignment explanation
Indices: 49138843--49138885 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
49138833 GTATAAGATA
49138843 ATATAATTATATTAACTT
1 ATATAATTATATTAACTT
**
49138861 ATA-AATTATA-TATTTT
1 ATATAATTATATTAACTT
49138877 ATATAATTA
1 ATATAATTA
49138886 ATAAAATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 7 0.32
17 12 0.55
18 3 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATAATTATATTAACTT
Found at i:49139903 original size:37 final size:36
Alignment explanation
Indices: 49139844--49139916 Score: 87
Period size: 35 Copynumber: 2.0 Consensus size: 36
49139834 CAATTCACCA
*
49139844 AAAAAAAAACATACATATATAAACATGTTTTAAAATAT
1 AAAAAAAAACATACATATATAAA-A-GTTTGAAAATAT
*
49139882 AAAAAAAAAC-TA-ATGTAATAAAAGTTTGAAAATAT
1 AAAAAAAAACATACATAT-ATAAAAGTTTGAAAATAT
49139917 TTCTCTGATG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
35 11 0.34
36 4 0.12
37 7 0.22
38 10 0.31
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.27
Consensus pattern (36 bp):
AAAAAAAAACATACATATATAAAAGTTTGAAAATAT
Found at i:49140718 original size:2 final size:2
Alignment explanation
Indices: 49140711--49140740 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
49140701 GATTTTGTTC
49140711 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 A
49140741 CCTGGCTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49152784 original size:2 final size:2
Alignment explanation
Indices: 49152777--49152831 Score: 94
Period size: 2 Copynumber: 27.5 Consensus size: 2
49152767 CAAAATTTAG
49152777 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49152819 AT AT -T AGT AT AT A
1 AT AT AT A-T AT AT A
49152832 ANNNNNNNNN
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.02
2 48 0.94
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:49156346 original size:2 final size:2
Alignment explanation
Indices: 49156341--49156371 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
49156331 AAAAAAAGGG
49156341 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49156372 TTTTAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49158190 original size:4 final size:4
Alignment explanation
Indices: 49158176--49158207 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
49158166 TTGAAGACTT
49158176 AGAA AGAAA AGAA AGAA AGAA AGAA AGAA AGA
1 AGAA AG-AA AGAA AGAA AGAA AGAA AGAA AGA
49158208 GGGCAGAGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:49167429 original size:27 final size:28
Alignment explanation
Indices: 49167385--49167438 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
49167375 ATCAATTTTT
* *
49167385 TTTATTAAAATATTTTATTTATTTTTTCG
1 TTTAATAAAATA-TTTATTAATTTTTTCG
49167414 TTTAATAAAATA-TTATTAATTTTTT
1 TTTAATAAAATATTTATTAATTTTTT
49167439 TCTGGATCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 12 0.52
29 11 0.48
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (28 bp):
TTTAATAAAATATTTATTAATTTTTTCG
Found at i:49167556 original size:27 final size:27
Alignment explanation
Indices: 49167496--49167557 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
49167486 GCTATTTCAT
* *
49167496 AGGCGCGACTAGTTGAGCCTATCTGAC
1 AGGCGCGACTAGTTGAGCCTAACTCAC
* * *
49167523 AGCCGCGACTAGTTGTGCCTAACTCAG
1 AGGCGCGACTAGTTGAGCCTAACTCAC
49167550 AGGCGCGA
1 AGGCGCGA
49167558 ATGGTGGTGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.23, C:0.27, G:0.31, T:0.19
Consensus pattern (27 bp):
AGGCGCGACTAGTTGAGCCTAACTCAC
Found at i:49168620 original size:33 final size:33
Alignment explanation
Indices: 49168572--49168653 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 33
49168562 CCGGGAGGAG
* * *
49168572 TGGAGTACGGCGGTGGATACGGGCT-GGAAAGAGC
1 TGGAGTACTGAGGTGGATACGAGCTAGG-AAGA-C
* *
49168606 -GGAGTACTGAGGTGGATATGAGCTAGGATGAC
1 TGGAGTACTGAGGTGGATACGAGCTAGGAAGAC
49168638 TGGAGTACTGAGGTGG
1 TGGAGTACTGAGGTGG
49168654 TAATGGGCTG
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
32 1 0.02
33 38 0.93
34 2 0.05
ACGTcount: A:0.24, C:0.11, G:0.45, T:0.20
Consensus pattern (33 bp):
TGGAGTACTGAGGTGGATACGAGCTAGGAAGAC
Found at i:49171603 original size:60 final size:60
Alignment explanation
Indices: 49171530--49171648 Score: 211
Period size: 60 Copynumber: 2.0 Consensus size: 60
49171520 ATACTAAACT
* * *
49171530 AAACACAACAATTTATAACTTAATCCTAAATTACTAATAAATTAATTTTAAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
49171590 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
49171649 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:0.13, G:0.00, T:0.34
Consensus pattern (60 bp):
AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
Found at i:49171847 original size:20 final size:20
Alignment explanation
Indices: 49171803--49171848 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
49171793 AATACATTAC
*
49171803 TTTT-TCCTTTCTTTCTTCT
1 TTTTCTCCTTTCTCTCTTCT
* *
49171822 TCTTCTCCTTTCTCTCTTTT
1 TTTTCTCCTTTCTCTCTTCT
49171842 TTTTCTC
1 TTTTCTC
49171849 TCCTCCGGTG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTCTCCTTTCTCTCTTCT
Found at i:49172044 original size:27 final size:27
Alignment explanation
Indices: 49172000--49172072 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 27
49171990 AACAGACCAT
* * *
49172000 TCGCGCCTACCTGTCAGGCTTGATTAG
1 TCGCGCCTATCTGACAGGCTCGATTAG
*
49172027 TCGCGCCTGTCTGACAGGCTCGATTAG
1 TCGCGCCTATCTGACAGGCTCGATTAG
49172054 TCGCGCCTATCTGACAGGC
1 TCGCGCCTATCTGACAGGC
49172073 ACGACCCGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.15, C:0.32, G:0.27, T:0.26
Consensus pattern (27 bp):
TCGCGCCTATCTGACAGGCTCGATTAG
Found at i:49172193 original size:21 final size:22
Alignment explanation
Indices: 49172160--49172205 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
49172150 ATAAAAAAGT
49172160 AATATTTTATTTAA-ACAAAAA
1 AATATTTTATTTAATACAAAAA
*
49172181 AATATATTT-TTTAATATAAAAA
1 AATAT-TTTATTTAATACAAAAA
49172203 AAT
1 AAT
49172206 TCATTTGCGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
AATATTTTATTTAATACAAAAA
Found at i:49172200 original size:26 final size:25
Alignment explanation
Indices: 49172135--49172204 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 25
49172125 ATATATTTAA
49172135 ATATTTTTTAA-A-AAAATAAAAAAGT
1 ATATTTTTTAATATAAAA-AAAAAA-T
* *
49172160 A-ATATTTT-ATTTAAACAAAAAAAT
1 ATATTTTTTAATATAAA-AAAAAAAT
49172184 ATATTTTTTAATATAAAAAAA
1 ATATTTTTTAATATAAAAAAA
49172205 TTCATTTGCG
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
23 1 0.03
24 8 0.22
25 20 0.56
26 7 0.19
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (25 bp):
ATATTTTTTAATATAAAAAAAAAAT
Found at i:49172966 original size:19 final size:17
Alignment explanation
Indices: 49172930--49172976 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
49172920 AAATAAAATT
49172930 CTAAAACCAAAACTAAAA
1 CTAAAA-CAAAACTAAAA
49172948 CTAAAACAAAAGTCTAAAA
1 CTAAAACAAAA--CTAAAA
*
49172967 ATAAAA-AAAA
1 CTAAAACAAAA
49172977 AAACATATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
18 10 0.38
19 11 0.42
ACGTcount: A:0.70, C:0.15, G:0.02, T:0.13
Consensus pattern (17 bp):
CTAAAACAAAACTAAAA
Found at i:49175723 original size:23 final size:23
Alignment explanation
Indices: 49175697--49175740 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
49175687 CCAATTCGAA
*
49175697 AAATACAAAGACAAAAATTAATC
1 AAATAAAAAGACAAAAATTAATC
* *
49175720 AAATAAAAATATAAAAATTAA
1 AAATAAAAAGACAAAAATTAA
49175741 ATTCACAACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.70, C:0.07, G:0.02, T:0.20
Consensus pattern (23 bp):
AAATAAAAAGACAAAAATTAATC
Found at i:49182818 original size:69 final size:69
Alignment explanation
Indices: 49182706--49182882 Score: 300
Period size: 69 Copynumber: 2.6 Consensus size: 69
49182696 CCAACAATAC
*
49182706 TAACTACGATTATAAGTAATTTCTAGACATCAGAGACCACTCAGTCGCATTCCAAAATGCAGTCA
1 TAACTACGATTATAAGTAATTTCTAGACATCAGAGACCACTCAGTCGCATTCCAAAATGCAATCA
49182771 ATTA
66 ATTA
* * *
49182775 TAACTATGATTATAAGTAATTTCTAGACATCAGAGACCCCTCAGTTGCATTCCAAAATGCAATCA
1 TAACTACGATTATAAGTAATTTCTAGACATCAGAGACCACTCAGTCGCATTCCAAAATGCAATCA
*
49182840 GTTA
66 ATTA
*
49182844 TAACTACGATTTTAAGTAATTTCTAGACATCAGAGACCA
1 TAACTACGATTATAAGTAATTTCTAGACATCAGAGACCA
49182883 TCAATCACAT
Statistics
Matches: 100, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 100 1.00
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.29
Consensus pattern (69 bp):
TAACTACGATTATAAGTAATTTCTAGACATCAGAGACCACTCAGTCGCATTCCAAAATGCAATCA
ATTA
Found at i:49183847 original size:3 final size:3
Alignment explanation
Indices: 49183839--49183879 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
49183829 ACAAATTTGA
49183839 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
49183880 AGGGCCTAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:49185546 original size:84 final size:84
Alignment explanation
Indices: 49185299--49185530 Score: 392
Period size: 84 Copynumber: 2.8 Consensus size: 84
49185289 GTTATAATAT
* * **
49185299 TTGGATAAATCATTTTATTATTCTTCTCAATAAAGCTTTGATCTAATGATCGTCTAAACTTGATC
1 TTGGATAAATCATTTTATTTTTCTCCTTGATAAAGCTTTGATCTAATGATCGTCTAAACTTGATC
*
49185364 TTAGATAAATGTGGGTCGA
66 TTAGATAAATGTGGGCCGA
*
49185383 TTGGATAAATCATTTTATTTTTCTCCTTGATAAAGCTTTGATCTAATGATTGTCTAAACTTGATC
1 TTGGATAAATCATTTTATTTTTCTCCTTGATAAAGCTTTGATCTAATGATCGTCTAAACTTGATC
49185448 TTAGATAAATGTGGGCCGA
66 TTAGATAAATGTGGGCCGA
* *
49185467 TTGGATAAATCATTTTATTTTTCTCCTTGATAAAGCTTTGATCTAATGGTCGTATAAACTTGAT
1 TTGGATAAATCATTTTATTTTTCTCCTTGATAAAGCTTTGATCTAATGATCGTCTAAACTTGAT
49185531 ATTGGATAGA
Statistics
Matches: 139, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 139 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (84 bp):
TTGGATAAATCATTTTATTTTTCTCCTTGATAAAGCTTTGATCTAATGATCGTCTAAACTTGATC
TTAGATAAATGTGGGCCGA
Found at i:49187762 original size:26 final size:26
Alignment explanation
Indices: 49187719--49187768 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
49187709 TAATAACGGA
* *
49187719 TTGCTCTATTCTTATTATTTTGTTAC
1 TTGCTCTATTATTATTATTATGTTAC
*
49187745 TTGCTCTATTATTTTTATTATGTT
1 TTGCTCTATTATTATTATTATGTT
49187769 TTTATAGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.16, C:0.12, G:0.08, T:0.64
Consensus pattern (26 bp):
TTGCTCTATTATTATTATTATGTTAC
Found at i:49192052 original size:25 final size:24
Alignment explanation
Indices: 49192024--49192078 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 24
49192014 TCCCGATATT
49192024 TGGCTATCTTGAGCTTCCCGATTAA
1 TGGCTATCTTGAGCTTCCCG-TTAA
* *
49192049 TGGCTCTCTTGAGCTTCCCGTTTA
1 TGGCTATCTTGAGCTTCCCGTTAA
49192073 TGGCTA
1 TGGCTA
49192079 GTATGAGCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 8 0.30
25 19 0.70
ACGTcount: A:0.15, C:0.25, G:0.22, T:0.38
Consensus pattern (24 bp):
TGGCTATCTTGAGCTTCCCGTTAA
Found at i:49195679 original size:22 final size:22
Alignment explanation
Indices: 49195638--49195704 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
49195628 TGCACTAATG
* *
49195638 AACAAAGAGCACTGAGGTGCTA
1 AACAAAGAGCACTAATGTGCTA
* *
49195660 TACAAAGAGCACAAATGTGCTA
1 AACAAAGAGCACTAATGTGCTA
**
49195682 AACGGAGAGCACTAATGTGCTA
1 AACAAAGAGCACTAATGTGCTA
49195704 A
1 A
49195705 TAATCGGATA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (22 bp):
AACAAAGAGCACTAATGTGCTA
Found at i:49197128 original size:14 final size:14
Alignment explanation
Indices: 49197109--49197147 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
49197099 TTGTTTCACT
*
49197109 GAAAATGGCTTCCG
1 GAAAATGACTTCCG
* *
49197123 GAAAATGATTTCTG
1 GAAAATGACTTCCG
49197137 GAAAATGACTT
1 GAAAATGACTT
49197148 ACTTTTCTGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (14 bp):
GAAAATGACTTCCG
Found at i:49197714 original size:8 final size:9
Alignment explanation
Indices: 49197696--49197720 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
49197686 AAAATATTTT
49197696 AAAAATAAA
1 AAAAATAAA
49197705 AAAAATAAA
1 AAAAATAAA
49197714 AAAAATA
1 AAAAATA
49197721 TTTTTTAAAG
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAATAAA
Found at i:49198131 original size:18 final size:18
Alignment explanation
Indices: 49198093--49198128 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
49198083 TTATTATTTT
*
49198093 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
49198111 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
49198129 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:49205877 original size:29 final size:31
Alignment explanation
Indices: 49205842--49205909 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 31
49205832 TAATAAATAT
49205842 ATATTTTTATTTTTA-TTTTTAAATTTTAAA
1 ATATTTTTATTTTTATTTTTTAAATTTTAAA
* *
49205872 A-ATTTTTATTTTTATTTTTTTACTTTTAAA
1 ATATTTTTATTTTTATTTTTTAAATTTTAAA
49205902 ATATTTTT
1 ATATTTTT
49205910 TGTGTTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 13 0.38
30 15 0.44
31 6 0.18
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.69
Consensus pattern (31 bp):
ATATTTTTATTTTTATTTTTTAAATTTTAAA
Found at i:49210532 original size:5 final size:6
Alignment explanation
Indices: 49210507--49210531 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
49210497 GATAAAATCT
49210507 AATAAA AATAAA AATAAA AATAAA A
1 AATAAA AATAAA AATAAA AATAAA A
49210532 TCCATGTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:49212622 original size:39 final size:39
Alignment explanation
Indices: 49212572--49212650 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
49212562 AAACCCTCTC
49212572 AAAATTTGGGTGAGCCTTCGGGTTTGGATAAATAACTCA
1 AAAATTTGGGTGAGCCTTCGGGTTTGGATAAATAACTCA
* *
49212611 AAAATTTGGGTGGGTCTTCGGGTTTGGATAAATAACTCA
1 AAAATTTGGGTGAGCCTTCGGGTTTGGATAAATAACTCA
49212650 A
1 A
49212651 CCATTGAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.30, C:0.11, G:0.27, T:0.32
Consensus pattern (39 bp):
AAAATTTGGGTGAGCCTTCGGGTTTGGATAAATAACTCA
Found at i:49215887 original size:43 final size:43
Alignment explanation
Indices: 49215839--49216019 Score: 228
Period size: 43 Copynumber: 4.3 Consensus size: 43
49215829 TTTTAGCAAT
*
49215839 AAACGCCGCTATAGAACAAGATCTTTAGCG-GCTTATTTCACAC
1 AAACGCCGCTATAGAACAAGACCTTTAGCGCGCTT-TTTCACAC
49215882 AAACGCCGCTATAGAACAAGACCTTTAGCGCGC-TTTTC-CAC
1 AAACGCCGCTATAGAACAAGACCTTTAGCGCGCTTTTTCACAC
* * * * * *
49215923 CAACGCCGCTAAAGATCATGACTTTTAACGGCGCTTTTT-ACAC
1 AAACGCCGCTATAGAACAAGACCTTTAGC-GCGCTTTTTCACAC
*
49215966 AAACGCCGCTATAGAACAAGACCTTTAGCGGCGC-TTTTCCCAC
1 AAACGCCGCTATAGAACAAGACCTTTAGC-GCGCTTTTTCACAC
49216009 AAACGCCGCTA
1 AAACGCCGCTA
49216020 AAAACATATC
Statistics
Matches: 119, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
41 26 0.22
42 12 0.10
43 79 0.66
44 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTATAGAACAAGACCTTTAGCGCGCTTTTTCACAC
Found at i:49216034 original size:84 final size:82
Alignment explanation
Indices: 49215839--49216034 Score: 245
Period size: 84 Copynumber: 2.3 Consensus size: 82
49215829 TTTTAGCAAT
* * *
49215839 AAACGCCGCTATAGAACAAGATCTTTAGCGGCTTATTTCACACAAACGCCGCTATAGAACAAGAC
1 AAACGCCGCTA-AAAAC-ATATCTTTAACGGCTTATTTCACACAAACGCCGCTATAGAACAAGAC
49215904 CTTTAGCGCGCTTTTCCAC
64 CTTTAGCGCGCTTTTCCAC
* *
49215923 CAACGCCGCTAAAGATCATGA-CTTTTAACGGCGCTT-TTT-ACACAAACGCCGCTATAGAACAA
1 AAACGCCGCTAAA-AACAT-ATC-TTTAAC-G-GCTTATTTCACACAAACGCCGCTATAGAACAA
49215985 GACCTTTAGCGGCGCTTTTCCCAC
61 GACCTTTAGC-GCGCTTTT-CCAC
49216009 AAACGCCGCTAAAAACATATCTTTAA
1 AAACGCCGCTAAAAACATATCTTTAA
49216035 AAAAATAATT
Statistics
Matches: 97, Mismatches: 7, Indels: 16
0.81 0.06 0.13
Matches are distributed among these distances:
83 3 0.03
84 57 0.59
85 17 0.18
86 20 0.21
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.24
Consensus pattern (82 bp):
AAACGCCGCTAAAAACATATCTTTAACGGCTTATTTCACACAAACGCCGCTATAGAACAAGACCT
TTAGCGCGCTTTTCCAC
Found at i:49221935 original size:19 final size:20
Alignment explanation
Indices: 49221899--49221938 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
49221889 TGTATTTATG
* *
49221899 TTTTTAATATATATTATTTT
1 TTTTTAAAATATAATATTTT
49221919 TTTTTAAAAT-TAATATTTT
1 TTTTTAAAATATAATATTTT
49221938 T
1 T
49221939 AGATGGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTTAAAATATAATATTTT
Found at i:49221959 original size:2 final size:2
Alignment explanation
Indices: 49221952--49221982 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
49221942 TGGATTTTAA
49221952 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
49221983 AAAGCTTGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49230759 original size:14 final size:15
Alignment explanation
Indices: 49230737--49230774 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
49230727 CAATCAAACA
49230737 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
49230751 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
49230766 ACAGAAAAT
1 CCAGAAAAT
49230775 TAAAAAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:49230948 original size:16 final size:17
Alignment explanation
Indices: 49230913--49230950 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
49230903 ATTAAACCCG
*
49230913 AATAACCCAGAACCCCA
1 AATAACCCAGAACCCAA
*
49230930 AATAACCCA-AACCGAA
1 AATAACCCAGAACCCAA
49230946 AATAA
1 AATAA
49230951 TTGGACCCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.55, C:0.32, G:0.05, T:0.08
Consensus pattern (17 bp):
AATAACCCAGAACCCAA
Found at i:49241448 original size:26 final size:26
Alignment explanation
Indices: 49241419--49241488 Score: 70
Period size: 28 Copynumber: 2.6 Consensus size: 26
49241409 GAAATTTGTA
* *
49241419 ATTTATGTATTTATATA-ATTTTTGAT
1 ATTTATATATTTATATATATTTAT-AT
*
49241445 ATTTTAATATATATATATATATTTATAT
1 A-TTT-ATATATTTATATATATTTATAT
*
49241473 ATTTATATATTCATAT
1 ATTTATATATTTATAT
49241489 TTAATATTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
26 11 0.31
27 6 0.17
28 14 0.39
29 5 0.14
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (26 bp):
ATTTATATATTTATATATATTTATAT
Found at i:49241471 original size:16 final size:16
Alignment explanation
Indices: 49241452--49241488 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
49241442 GATATTTTAA
49241452 TATATATATATATATT
1 TATATATATATATATT
*
49241468 TATATATTTATATATT
1 TATATATATATATATT
*
49241484 CATAT
1 TATAT
49241489 TTAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATATATATATATT
Found at i:49241488 original size:28 final size:27
Alignment explanation
Indices: 49241419--49241498 Score: 67
Period size: 27 Copynumber: 2.9 Consensus size: 27
49241409 GAAATTTGTA
* *
49241419 ATTTATGTATT-TATATAATTTTTGATAT
1 ATTTATATATTATATAT-ATATTT-ATAT
49241447 -TTTA-ATATATATATATATATTTATAT
1 ATTTATATAT-TATATATATATTTATAT
*
49241473 ATTTATATATTCATATTTAATATTTA
1 ATTTATATATT-ATATAT-ATATTTA
49241499 CAAACATTGA
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
26 7 0.16
27 15 0.35
28 14 0.33
29 7 0.16
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.59
Consensus pattern (27 bp):
ATTTATATATTATATATATATTTATAT
Found at i:49244460 original size:22 final size:22
Alignment explanation
Indices: 49244410--49244453 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
49244400 TTGCAAAGGT
* *
49244410 AATTTATGTTTCTTCTTCCATC
1 AATTTCTGCTTCTTCTTCCATC
49244432 AATTTCTGCTTCTTCTTCCATC
1 AATTTCTGCTTCTTCTTCCATC
49244454 GTTTTCTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.16, C:0.27, G:0.05, T:0.52
Consensus pattern (22 bp):
AATTTCTGCTTCTTCTTCCATC
Found at i:49248205 original size:49 final size:49
Alignment explanation
Indices: 49248148--49248251 Score: 163
Period size: 49 Copynumber: 2.1 Consensus size: 49
49248138 TCATGTGTTA
* * * * *
49248148 TAATTTTATAAAGTGTTGAGCTTTTGATTCATGATATTGAACTTGATTT
1 TAATTTTATAAAGCGTTCACCTTTTGATTCATGATATTAAACTTAATTT
49248197 TAATTTTATAAAGCGTTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGCGTTCACCTTTTGATTCATGATATTAAACTTAATTT
49248246 TAATTT
1 TAATTT
49248252 GTTTTTTTTG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.49
Consensus pattern (49 bp):
TAATTTTATAAAGCGTTCACCTTTTGATTCATGATATTAAACTTAATTT
Found at i:49249964 original size:61 final size:59
Alignment explanation
Indices: 49249895--49250085 Score: 174
Period size: 61 Copynumber: 3.2 Consensus size: 59
49249885 ATTTTATAGT
49249895 ATTATATATTATGATTTTAGTAAATTTGTATAAGAATTTTTAATACTAAGAATTTTATTAA
1 ATTATATATTATGATTTTAGTAAATTT-TATAAGAATTTTTAATA-TAAGAATTTTATTAA
** * * * * * *
49249956 ATTATATATT-TGTATTAAATTATATTTAATAATAATTATGTTAA-ATTA-TATTTTA-TAA
1 ATTATATATTATG-ATTTTAGTAAATTTTATAAGAATT-T-TTAATATAAGAATTTTATTAA
* * * *
49250014 TATTTTATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
1 -ATTATATATTATGATTTTAGTAAATT-TTATAAGAATTTTTAATA-TAAGAATTTTATTAA
49250076 ATTATATATT
1 ATTATATATT
49250086 TTTATTAAAT
Statistics
Matches: 99, Mismatches: 21, Indels: 20
0.71 0.15 0.14
Matches are distributed among these distances:
58 7 0.07
59 25 0.25
60 23 0.23
61 37 0.37
62 7 0.07
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.51
Consensus pattern (59 bp):
ATTATATATTATGATTTTAGTAAATTTTATAAGAATTTTTAATATAAGAATTTTATTAA
Found at i:49249971 original size:18 final size:17
Alignment explanation
Indices: 49249946--49249980 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
49249936 AATACTAAGA
49249946 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
49249963 ATTTGTATTAAATTATAT
1 ATTT-TATTAAATTATAT
49249981 TTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:49250074 original size:120 final size:120
Alignment explanation
Indices: 49249861--49250120 Score: 421
Period size: 120 Copynumber: 2.2 Consensus size: 120
49249851 NNNNNNNNNN
* * * **
49249861 TTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTTGTAT
1 TTAATAATAATTATATTAAATTATATTTTATAATATTATATATTATGATTTTAGAAAATTCATAT
*
49249926 AAGAATTTTTAATACTAAGAATTTTATTAAATTATATATTTGTATTAAATTATAT
66 AAGAATATTTAATACTAAGAATTTTATTAAATTATATATTTGTATTAAATTATAT
* *
49249981 TTAATAATAATTATGTTAAATTATATTTTATAATATTTTATATTATGATTTTAGAAAATTCATAT
1 TTAATAATAATTATATTAAATTATATTTTATAATATTATATATTATGATTTTAGAAAATTCATAT
* * *
49250046 AAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTGTAT
66 AAGAATATTTAATACTAAGAATTTTATTAAATTATATATTTGTATTAAATTATAT
49250101 TTAATAATAATTATATTAAA
1 TTAATAATAATTATATTAAA
49250121 ATATGATTAA
Statistics
Matches: 129, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
120 129 1.00
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.52
Consensus pattern (120 bp):
TTAATAATAATTATATTAAATTATATTTTATAATATTATATATTATGATTTTAGAAAATTCATAT
AAGAATATTTAATACTAAGAATTTTATTAAATTATATATTTGTATTAAATTATAT
Found at i:49250317 original size:45 final size:44
Alignment explanation
Indices: 49250225--49250320 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 44
49250215 ATTACAACAT
* *
49250225 CATTCCATTCAACCAAACACAAGAATAGTATTACGCCTCTATTC
1 CATTACATTCAACCAAACACAAGAATACTATTACGCCTCTATTC
*
49250269 CATTACATTCAACCAAACA-ATTGAATTACTATT-CTGCCTCTATTC
1 CATTACATTCAACCAAACACA-AGAA-TACTATTAC-GCCTCTATTC
49250314 CATTACA
1 CATTACA
49250321 GCTCTATTTC
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
43 1 0.02
44 22 0.48
45 23 0.50
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.31
Consensus pattern (44 bp):
CATTACATTCAACCAAACACAAGAATACTATTACGCCTCTATTC
Found at i:49250327 original size:16 final size:16
Alignment explanation
Indices: 49250306--49250338 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
49250296 ACTATTCTGC
49250306 CTCTATTCCATTACAG
1 CTCTATTCCATTACAG
*
49250322 CTCTATTTCATTACAG
1 CTCTATTCCATTACAG
49250338 C
1 C
49250339 GAACCAAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.30, G:0.06, T:0.39
Consensus pattern (16 bp):
CTCTATTCCATTACAG
Found at i:49264420 original size:2 final size:2
Alignment explanation
Indices: 49264415--49264445 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
49264405 TCTCAAGCTA
*
49264415 AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
49264446 CGTATATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49267226 original size:26 final size:28
Alignment explanation
Indices: 49267195--49267259 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 28
49267185 TCTAAGATAA
* * *
49267195 AAATTAAACCCCATGCTCAAT-C-TAAT
1 AAATTAAACCCAATGCCCAATACACAAT
49267221 AAATTAAACCCAATGCCCAATACACAAT
1 AAATTAAACCCAATGCCCAATACACAAT
*
49267249 AAACTAAACCC
1 AAATTAAACCC
49267260 TAGCCCCATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 19 0.58
27 1 0.03
28 13 0.39
ACGTcount: A:0.48, C:0.29, G:0.03, T:0.20
Consensus pattern (28 bp):
AAATTAAACCCAATGCCCAATACACAAT
Found at i:49273345 original size:21 final size:21
Alignment explanation
Indices: 49273309--49273359 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
49273299 TATATATTTA
*
49273309 AAATTTAATCTTATTACAATTC
1 AAATTTTATCTTATTA-AATTC
*
49273331 AAATTTTAT-TTATTAAATTT
1 AAATTTTATCTTATTAAATTC
49273351 AAATATTTA
1 AAAT-TTTA
49273360 GACATTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 8 0.31
21 10 0.38
22 8 0.31
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATTTTATCTTATTAAATTC
Found at i:49275853 original size:30 final size:30
Alignment explanation
Indices: 49275817--49275934 Score: 209
Period size: 30 Copynumber: 3.9 Consensus size: 30
49275807 AGGACATATG
* *
49275817 CCCATGTGCTAGGTCGCGTGTCACACACGA
1 CCCATGTGCTAGGCCGTGTGTCACACACGA
49275847 CCCATGTGCTAGGCCGTGTGTCACACACGA
1 CCCATGTGCTAGGCCGTGTGTCACACACGA
49275877 CCCATGTGCTAGGCCGTGTGTCACACACGA
1 CCCATGTGCTAGGCCGTGTGTCACACACGA
*
49275907 CCTATGTGCTAGGCCGTGTGTCACACAC
1 CCCATGTGCTAGGCCGTGTGTCACACAC
49275935 AGCTGAGACA
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 85 1.00
ACGTcount: A:0.19, C:0.33, G:0.26, T:0.21
Consensus pattern (30 bp):
CCCATGTGCTAGGCCGTGTGTCACACACGA
Found at i:49276927 original size:24 final size:25
Alignment explanation
Indices: 49276867--49276928 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 25
49276857 TCAGGCTTAG
*
49276867 TAACAGGAAGCTCACAAATAGCCTA
1 TAACAGGAAGCTCACAAAGAGCCTA
* * *
49276892 TATCGGGTAGCTC-CAAAGAGCACT-
1 TAACAGGAAGCTCACAAAGAGC-CTA
49276916 TAACAGGAAGCTC
1 TAACAGGAAGCTC
49276929 TGGAGAGCAG
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
24 17 0.59
25 12 0.41
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (25 bp):
TAACAGGAAGCTCACAAAGAGCCTA
Found at i:49277529 original size:21 final size:21
Alignment explanation
Indices: 49277503--49277553 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
49277493 TATATGAGTA
49277503 AATTTA-ACTTCAATTTAATAC
1 AATTTACA-TTCAATTTAATAC
* *
49277524 AATTTACATTCAATTTTATCC
1 AATTTACATTCAATTTAATAC
*
49277545 AATTCACAT
1 AATTTACAT
49277554 CTCAGGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.43
Consensus pattern (21 bp):
AATTTACATTCAATTTAATAC
Found at i:49282404 original size:2 final size:2
Alignment explanation
Indices: 49282399--49282423 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
49282389 AAAAAGTGTG
49282399 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 T
49282424 TATGTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:49293099 original size:22 final size:23
Alignment explanation
Indices: 49293057--49293099 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
49293047 AGTGGGGGCA
49293057 TAAATCAAAATAACATTTGGAAT
1 TAAATCAAAATAACATTTGGAAT
49293080 TAAATCAAAATAA-ATTTGGA
1 TAAATCAAAATAACATTTGGA
49293100 TATATAGAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.30
Consensus pattern (23 bp):
TAAATCAAAATAACATTTGGAAT
Found at i:49295934 original size:24 final size:24
Alignment explanation
Indices: 49295906--49295960 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
49295896 TAATATTGAT
*
49295906 CTTTTATAAATAATAAATACTTTTA
1 CTTTTA-AAATAATAAATAATTTTA
* *
49295931 -TTTTGAACATAATAATTAATTTTA
1 CTTTT-AAAATAATAAATAATTTTA
49295955 CTTTTA
1 CTTTTA
49295961 CATATGATAC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (24 bp):
CTTTTAAAATAATAAATAATTTTA
Found at i:49297310 original size:7 final size:7
Alignment explanation
Indices: 49297298--49297324 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
49297288 AAATTCTAAA
49297298 AAATATT
1 AAATATT
49297305 AAATATT
1 AAATATT
49297312 AAATATT
1 AAATATT
49297319 AAATAT
1 AAATAT
49297325 GATTTAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AAATATT
Found at i:49306979 original size:19 final size:19
Alignment explanation
Indices: 49306955--49307018 Score: 67
Period size: 19 Copynumber: 3.2 Consensus size: 19
49306945 AAATTTTCAG
49306955 AAATTTAAAATAATTTTTA
1 AAATTTAAAATAATTTTTA
*
49306974 AAATTTAAAAT-ATTTATAA
1 AAATTTAAAATAATTT-TTA
49306993 AAATTTCAAAATTTATATTTTTA
1 AAATTT-AAAA--TA-ATTTTTA
49307016 AAA
1 AAA
49307019 AAATCTAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
18 4 0.11
19 19 0.51
20 4 0.11
22 1 0.03
23 5 0.14
24 4 0.11
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
AAATTTAAAATAATTTTTA
Found at i:49308018 original size:57 final size:60
Alignment explanation
Indices: 49307891--49308030 Score: 155
Period size: 61 Copynumber: 2.4 Consensus size: 60
49307881 TTATTAAATT
* * * * *
49307891 TTAATAAAATTATTGTTAAATATATTTTTATTAAAATAATAATAAATAATTTAATCATATT
1 TTAATATAATTATTATTAAATATATATTTAATAAAATAATAATAAAT-ATTTAATCATATC
*
49307952 TTAACATAATTATTATTAAATATA-ATTTAATAAAATAAT-ATACAAT-TTATAA-CAT-TC
1 TTAATATAATTATTATTAAATATATATTTAATAAAATAATAATA-AATATT-TAATCATATC
49308009 TTAATATAATTATTATATAAAT
1 TTAATATAATTATTAT-TAAAT
49308031 TTAAAAAATT
Statistics
Matches: 69, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
57 16 0.23
58 10 0.14
59 6 0.09
60 16 0.23
61 21 0.30
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.46
Consensus pattern (60 bp):
TTAATATAATTATTATTAAATATATATTTAATAAAATAATAATAAATATTTAATCATATC
Found at i:49312112 original size:82 final size:82
Alignment explanation
Indices: 49312026--49312190 Score: 330
Period size: 82 Copynumber: 2.0 Consensus size: 82
49312016 TAAAATAATT
49312026 TTACATGAAATCATTATATTTTATCATCTATTTGATATAACTAGAAAAGGACATAAAGCCCAAAA
1 TTACATGAAATCATTATATTTTATCATCTATTTGATATAACTAGAAAAGGACATAAAGCCCAAAA
49312091 GGAAAAACAAACCCAAG
66 GGAAAAACAAACCCAAG
49312108 TTACATGAAATCATTATATTTTATCATCTATTTGATATAACTAGAAAAGGACATAAAGCCCAAAA
1 TTACATGAAATCATTATATTTTATCATCTATTTGATATAACTAGAAAAGGACATAAAGCCCAAAA
49312173 GGAAAAACAAACCCAAG
66 GGAAAAACAAACCCAAG
49312190 T
1 T
49312191 CCCATACTCC
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 83 1.00
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (82 bp):
TTACATGAAATCATTATATTTTATCATCTATTTGATATAACTAGAAAAGGACATAAAGCCCAAAA
GGAAAAACAAACCCAAG
Found at i:49313833 original size:4 final size:4
Alignment explanation
Indices: 49313824--49313871 Score: 80
Period size: 4 Copynumber: 12.0 Consensus size: 4
49313814 TTCCAAGGTA
49313824 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG- ATTGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-TGT ATGT ATGT ATGT
49313872 GCTTGATTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 1 0.02
4 40 0.95
5 1 0.02
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:49315351 original size:26 final size:28
Alignment explanation
Indices: 49315298--49315351 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 28
49315288 ATTTTCAATG
*
49315298 ATCATTTCAATTTTTATGAAATTATAAT
1 ATCATTTCAATTTTTATGAAAATATAAT
*
49315326 ATCATTTTAA-TTTTA-GAAAATATAAT
1 ATCATTTCAATTTTTATGAAAATATAAT
49315352 TTAATTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 10 0.42
27 5 0.21
28 9 0.38
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.48
Consensus pattern (28 bp):
ATCATTTCAATTTTTATGAAAATATAAT
Found at i:49315524 original size:14 final size:14
Alignment explanation
Indices: 49315480--49315528 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
49315470 AAATCTCAAC
*
49315480 AAATATTAAATATT
1 AAATATTAAATATA
*
49315494 AAATAATTAAGTA-A
1 AAAT-ATTAAATATA
*
49315508 AAATATAAAATATA
1 AAATATTAAATATA
49315522 AAATATT
1 AAATATT
49315529 TATTTTTCTA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
13 6 0.21
14 15 0.54
15 7 0.25
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (14 bp):
AAATATTAAATATA
Found at i:49323335 original size:3 final size:3
Alignment explanation
Indices: 49323327--49323360 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
49323317 AACTTAACAC
*
49323327 AGA AGA AGA AGA AGA AGA AGA AGA AGA AAA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
49323361 ATAACTGAGA
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:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:49324302 original size:3 final size:3
Alignment explanation
Indices: 49324294--49324332 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
49324284 TGATTCACCG
* * *
49324294 TCA TCA TCA CCA TCA TCA TCG TCA TCG TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
49324333 CTTTCTCGAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.28, C:0.36, G:0.05, T:0.31
Consensus pattern (3 bp):
TCA
Found at i:49339205 original size:4 final size:4
Alignment explanation
Indices: 49339196--49339248 Score: 106
Period size: 4 Copynumber: 13.2 Consensus size: 4
49339186 TATCTAGTGG
49339196 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
49339244 TGTA T
1 TGTA T
49339249 ATTCAAGTGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:49342456 original size:29 final size:31
Alignment explanation
Indices: 49342409--49342477 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 31
49342399 ATGGGAAAAG
*
49342409 TTTGATTTAATGTGTAATTTTATACAT-AAAT
1 TTTGATTT-ATGTGCAATTTTATACATGAAAT
*
49342440 TTTGATTT-TGTGCAATTTTATATATGAAAT
1 TTTGATTTATGTGCAATTTTATACATGAAAT
*
49342470 TTTAATTT
1 TTTGATTT
49342478 GATCTAATTC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 15 0.44
30 11 0.32
31 8 0.24
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.55
Consensus pattern (31 bp):
TTTGATTTATGTGCAATTTTATACATGAAAT
Found at i:49345075 original size:23 final size:24
Alignment explanation
Indices: 49345049--49345093 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
49345039 TAGGAATACC
*
49345049 TCATCTAA-ATATT-TTAGTATTTA
1 TCATATAACATATTGTTA-TATTTA
49345072 TCATATAACATATTGTTATATT
1 TCATATAACATATTGTTATATT
49345094 CTTCTATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 9 0.47
25 3 0.16
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (24 bp):
TCATATAACATATTGTTATATTTA
Found at i:49346075 original size:3 final size:3
Alignment explanation
Indices: 49346064--49346101 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
49346054 AATTAAATAA
*
49346064 TAT TA- TAT TAT TAT TAT ATAT TGT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TA
49346102 ACTAATACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:49346138 original size:9 final size:9
Alignment explanation
Indices: 49346126--49346161 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
49346116 GAAATAAAAT
49346126 AAAAGAAAC
1 AAAAGAAAC
49346135 AAAAGAAAC
1 AAAAGAAAC
*
49346144 AAAAG-AAG
1 AAAAGAAAC
49346152 AAAAGAAAC
1 AAAAGAAAC
49346161 A
1 A
49346162 GAGACCATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.78, C:0.08, G:0.14, T:0.00
Consensus pattern (9 bp):
AAAAGAAAC
Found at i:49347916 original size:57 final size:57
Alignment explanation
Indices: 49347828--49347983 Score: 267
Period size: 57 Copynumber: 2.7 Consensus size: 57
49347818 TATGGTCTTA
* *
49347828 CACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTATCATTTATCTCTTGT
1 CACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTATCAATTATCACTTGT
*
49347885 CACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTATCAATTGTCACTTGT
1 CACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTATCAATTATCACTTGT
*
49347942 CACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTT
1 CACTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTT
49347984 GTCACTGATC
Statistics
Matches: 94, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
57 76 0.81
58 18 0.19
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (57 bp):
CACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTATCAATTATCACTTGT
Found at i:49349686 original size:16 final size:16
Alignment explanation
Indices: 49349665--49349703 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
49349655 TTATGTGTAT
49349665 GGTAAG-CAAATAATAA
1 GGTAAGTCAAAT-ATAA
*
49349681 GGTAAGTGAAATATAA
1 GGTAAGTCAAATATAA
49349697 GGTAAGT
1 GGTAAGT
49349704 ATTATTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.49, C:0.03, G:0.26, T:0.23
Consensus pattern (16 bp):
GGTAAGTCAAATATAA
Found at i:49350049 original size:21 final size:21
Alignment explanation
Indices: 49349976--49350085 Score: 141
Period size: 23 Copynumber: 5.1 Consensus size: 21
49349966 GGCTTTGCCG
49349976 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
49349997 ACATCAGGCACTTTATGTGTCGT
1 --ATCAGGCACTTTATGTGTCGT
49350020 ATCTCAGGCACTTTATGTGTCGT
1 A--TCAGGCACTTTATGTGTCGT
* *
49350043 ATCAGGCACCTCATGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
* *
49350064 TTCAGGCAC-TTATGTATCGT
1 ATCAGGCACTTTATGTGTCGT
49350084 AT
1 AT
49350086 ACTGATCAGG
Statistics
Matches: 79, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
20 10 0.13
21 27 0.34
23 42 0.53
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (21 bp):
ATCAGGCACTTTATGTGTCGT
Found at i:49364263 original size:6 final size:6
Alignment explanation
Indices: 49364254--49364281 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
49364244 ATTCTTAATC
49364254 TATTAA TATTAA TATTAA TATTAA TATT
1 TATTAA TATTAA TATTAA TATTAA TATT
49364282 TATCTTATTT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TATTAA
Found at i:49364818 original size:22 final size:23
Alignment explanation
Indices: 49364780--49364823 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
49364770 ATAATTTGTC
*
49364780 ATTATTTTGTATAATGTGAATTA
1 ATTAGTTTGTATAATGTGAATTA
49364803 ATTAGTTTG-ATAATGTGAATT
1 ATTAGTTTGTATAATGTGAATT
49364824 TGTCAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (23 bp):
ATTAGTTTGTATAATGTGAATTA
Found at i:49367761 original size:27 final size:27
Alignment explanation
Indices: 49367730--49367793 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 27
49367720 AGTGGTCTAT
* *
49367730 ATATAATTTTTTAATAAATTAAAAGGC
1 ATATAATTTTTTAATAAATTAAAAAGA
* * *
49367757 ATATAA--ATTTATTAAATTAAAAATA
1 ATATAATTTTTTAATAAATTAAAAAGA
49367782 ATATAATTTTTT
1 ATATAATTTTTT
49367794 TTCAAAATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
25 20 0.69
27 9 0.31
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (27 bp):
ATATAATTTTTTAATAAATTAAAAAGA
Found at i:49372634 original size:91 final size:91
Alignment explanation
Indices: 49372539--49372901 Score: 561
Period size: 91 Copynumber: 4.0 Consensus size: 91
49372529 TGATTTTAGT
*
49372539 AAATTCATATAAGAAAATTTATTAGTAAGAATTTTGTGAAATTATATATTATTATTAAATTATAT
1 AAATTCATATAAGAAAATTTATTAGTAAGAATTTTATGAAATTATATATTATTATTAAATTATAT
*
49372604 TTAATAATAATAATTTTTAATTATAC
66 TTAATAATAATAATTTTAAATTATAC
* *
49372630 AAATTCGTATAAGAAAATTTATTAGTAAGAATTTTATGAAATTATATATTATTATTAAAATATAT
1 AAATTCATATAAGAAAATTTATTAGTAAGAATTTTATGAAATTATATATTATTATTAAATTATAT
*
49372695 TTAATAATAATTATTTTAAATTATAC
66 TTAATAATAATAATTTTAAATTATAC
* *
49372721 AATTTCGTATAAGAAAATTTATTAGTAAGAATTTTATGAAATTATATATTATTATTAAATTATAT
1 AAATTCATATAAGAAAATTTATTAGTAAGAATTTTATGAAATTATATATTATTATTAAATTATAT
49372786 TTAATAATAATAATTTTAAATTATAC
66 TTAATAATAATAATTTTAAATTATAC
* * * * *
49372812 AAATTCACATAAGAATATTTATTACTAA-AATTTTTTATTAAATTATATATTTTTATTAAATTAT
1 AAATTCATATAAGAAAATTTATTAGTAAGAA--TTTTATGAAATTATATATTATTATTAAATTAT
*
49372876 ATTTAATAAAAACTAA--TTAAATTATA
64 ATTTAATAATAA-TAATTTTAAATTATA
49372902 TTTTATAGTA
Statistics
Matches: 253, Mismatches: 16, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
90 2 0.01
91 207 0.82
92 41 0.16
93 3 0.01
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (91 bp):
AAATTCATATAAGAAAATTTATTAGTAAGAATTTTATGAAATTATATATTATTATTAAATTATAT
TTAATAATAATAATTTTAAATTATAC
Found at i:49372650 original size:44 final size:44
Alignment explanation
Indices: 49372602--49372851 Score: 141
Period size: 44 Copynumber: 5.6 Consensus size: 44
49372592 ATTAAATTAT
49372602 ATTTAATAATAATAATTTTTAATTATACAAATTCGTATAAGAAA
1 ATTTAATAATAATAATTTTTAATTATACAAATTCGTATAAGAAA
* * * * **
49372646 ATTTATTAGTAAGAATTTTATGAAATTAT--ATATTATTATTAA-AATA
1 ATTTAATAATAATAATTTT-T--AATTATACAAATTCGTA-TAAGAA-A
* * *
49372692 TATTTAATAATAATTATTTTAAATTATACAATTTCGTATAAGAAA
1 -ATTTAATAATAATAATTTTTAATTATACAAATTCGTATAAGAAA
* * * * * ** ** *
49372737 ATTTATTAGTAAGAATTTTATGAAATTATATATTATTATTA-AATTAT
1 ATTTAATAATAATAATTTT-T--AATTATACA-AATTCGTATAAGAAA
* ** *
49372784 ATTTAATAATAATAATTTTAAATTATACAAATTCACATAAGAAT
1 ATTTAATAATAATAATTTTTAATTATACAAATTCGTATAAGAAA
* * *
49372828 ATTTATTACTAA-AATTTTTTATTA
1 ATTTAATAATAATAATTTTTAATTA
49372852 AATTATATAT
Statistics
Matches: 149, Mismatches: 43, Indels: 29
0.67 0.19 0.13
Matches are distributed among these distances:
43 14 0.09
44 59 0.40
45 13 0.09
46 11 0.07
47 48 0.32
48 4 0.03
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (44 bp):
ATTTAATAATAATAATTTTTAATTATACAAATTCGTATAAGAAA
Found at i:49372866 original size:18 final size:18
Alignment explanation
Indices: 49372843--49372877 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
49372833 TTACTAAAAT
49372843 TTTTTATTAAATTATATA
1 TTTTTATTAAATTATATA
49372861 TTTTTATTAAATTATAT
1 TTTTTATTAAATTATAT
49372878 TTAATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTTATTAAATTATATA
Found at i:49373074 original size:121 final size:121
Alignment explanation
Indices: 49372812--49373156 Score: 543
Period size: 120 Copynumber: 2.9 Consensus size: 121
49372802 TAAATTATAC
* **
49372812 AAATTCACATAAGAATATTTATTACTAAAATTTTTTATTAAATTATATATTTTTATTAAATTATA
1 AAATTCATATAAGAATATTTATTACTAAAAAATTTTATTAAATTATATATTTTTATTAAATTATA
49372877 TTTAATAAAAACT-AATTAAATTATATTTTATAGTATTATATAATATGATTTTAGT
66 TTTAATAAAAACTAAATTAAATTATATTTTATAGTATTATATAATATGATTTTAGT
* *
49372932 AAATTCATATAAGAATATTTATGACTAAAAAATTTTATGAAATTATATATTTTTATTAAATTATA
1 AAATTCATATAAGAATATTTATTACTAAAAAATTTTATTAAATTATATATTTTTATTAAATTATA
*
49372997 TTTAATAAAAACTAAATTAAATTATATTTTATAGTATTATATATTATGATTTTAGT
66 TTTAATAAAAACTAAATTAAATTATATTTTATAGTATTATATAATATGATTTTAGT
* * * * *
49373053 AAATTCGTATAAGAATCTTTATTA-TTAAGAATTTTATTAAATCATATATTTTTATTAAATTATA
1 AAATTCATATAAGAATATTTATTACTAAAAAATTTTATTAAATTATATATTTTTATTAAATTATA
*
49373117 TTTAATAAATAA-TAATTTTAAATTATATTTTATAGTATTA
66 TTTAATAAA-AACTAA-ATTAAATTATATTTTATAGTATTA
49373157 GTAAATTCAT
Statistics
Matches: 208, Mismatches: 14, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
120 121 0.58
121 87 0.42
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (121 bp):
AAATTCATATAAGAATATTTATTACTAAAAAATTTTATTAAATTATATATTTTTATTAAATTATA
TTTAATAAAAACTAAATTAAATTATATTTTATAGTATTATATAATATGATTTTAGT
Found at i:49373090 original size:15 final size:16
Alignment explanation
Indices: 49373062--49373091 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
49373052 TAAATTCGTA
49373062 TAAGAATCTTTATTAT
1 TAAGAATCTTTATTAT
49373078 TAAGAAT-TTTATTA
1 TAAGAATCTTTATTA
49373092 AATCATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (16 bp):
TAAGAATCTTTATTAT
Found at i:49373118 original size:16 final size:17
Alignment explanation
Indices: 49373084--49373119 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
49373074 TTATTAAGAA
49373084 TTTTATTAAATCATATAT
1 TTTTATTAAAT-ATATAT
49373102 TTTTATTAAAT-TATAT
1 TTTTATTAAATATATAT
49373118 TT
1 TT
49373120 AATAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
18 11 0.61
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTATTAAATATATAT
Found at i:49373159 original size:106 final size:105
Alignment explanation
Indices: 49373048--49373243 Score: 329
Period size: 106 Copynumber: 1.9 Consensus size: 105
49373038 TATTATGATT
* * *
49373048 TTAGTAAATTCGTATAAGAATCTTTATTATTAAGAATTTTATTAAATCATATATTTTTATTAAAT
1 TTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATCATATATTTTTATTAAAT
*
49373113 TATATTTAATAAATAATAATTTTAAATTATATTTTATAGTA
66 TATATTTAAT-AATAATAATGTTAAATTATATTTTATAGTA
*
49373154 TTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTTATTAAAT
1 TTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATCATATATTTTTATTAAAT
*
49373219 TATATTTAATAATAATTATGTTAAA
66 TATATTTAATAATAATAATGTTAAA
49373244 ATATGATTAA
Statistics
Matches: 84, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
105 13 0.15
106 71 0.85
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (105 bp):
TTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATCATATATTTTTATTAAAT
TATATTTAATAATAATAATGTTAAATTATATTTTATAGTA
Found at i:49373237 original size:24 final size:22
Alignment explanation
Indices: 49373209--49373287 Score: 63
Period size: 27 Copynumber: 3.4 Consensus size: 22
49373199 ATTATATATT
49373209 TTTATTAAATTATATTTAATAA
1 TTTATTAAATTATATTTAATAA
* *
49373231 TAATTATGTTAAAATATGATTAAATAA
1 T--TTA--TTAAATTAT-ATTTAATAA
*
49373258 TTTATT-ATTTATA-TTAATAA
1 TTTATTAAATTATATTTAATAA
49373278 TCTTATTAAA
1 T-TTATTAAA
49373288 ATTTAATAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
20 7 0.16
21 6 0.14
22 6 0.14
23 2 0.05
24 3 0.07
25 3 0.07
26 8 0.18
27 9 0.20
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.51
Consensus pattern (22 bp):
TTTATTAAATTATATTTAATAA
Found at i:49373484 original size:16 final size:16
Alignment explanation
Indices: 49373465--49373509 Score: 90
Period size: 16 Copynumber: 2.8 Consensus size: 16
49373455 CTATTATGCC
49373465 TCTATTCCATTACGTA
1 TCTATTCCATTACGTA
49373481 TCTATTCCATTACGTA
1 TCTATTCCATTACGTA
49373497 TCTATTCCATTAC
1 TCTATTCCATTAC
49373510 AGCGACCCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.24, C:0.27, G:0.04, T:0.44
Consensus pattern (16 bp):
TCTATTCCATTACGTA
Found at i:49381531 original size:6 final size:6
Alignment explanation
Indices: 49381517--49381546 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
49381507 TTCAAATAAA
*
49381517 TAAATT TAAAGT TAAATT TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT
49381547 ATATAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (6 bp):
TAAATT
Found at i:49386585 original size:51 final size:51
Alignment explanation
Indices: 49386530--49387023 Score: 466
Period size: 51 Copynumber: 9.7 Consensus size: 51
49386520 GTGAAAGTGT
* *
49386530 TGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATAA
* * * * * * * *
49386581 TGGTCACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT-T
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAA-ATAA
* *
49386632 TGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATAA
* * * * ** * * * *
49386683 TGGTCACATGTGTAGCACTAAGTGAAGGCTACAATATGTACCGAGAAGCT-T
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAA-ATAA
* ** *
49386734 TGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATTGATAAATGA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATAA
* * * * * *
49386785 TGGTCACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGAAAAACT-T
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAA-TAA
* * * * *
49386836 TAGCCACGTATGTAGTACTATGTGAAGGCTACTACGTGAATCG-TAAA-ACT
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATA-A
* * * *
49386886 TGATCACGTGTATAGTACTATGTGAAGGCTATTATGTGAACCG-TAAA-AA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATAA
* * *
49386935 TTGATCACGTGTGTAGTACTATGTGAAGGCTATTATGTGAACCG-TAAA-AA
1 -TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATAA
*
49386985 TTGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 -TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTG
49387024 TATCGAATGA
Statistics
Matches: 360, Mismatches: 75, Indels: 17
0.80 0.17 0.04
Matches are distributed among these distances:
50 131 0.36
51 226 0.63
52 3 0.01
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (51 bp):
TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATAA
Done.