Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008480.1 Hibiscus syriacus cultivar Beakdansim tig00111311_pilon, whole genome shotgun sequence
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: 2515485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 13
Found at i:1530864 original size:14 final size:12
Alignment explanation
Indices: 1530845--1530914 Score: 52
Period size: 14 Copynumber: 5.3 Consensus size: 12
1530835 TATTAATATT
1530845 TAATGATTTGATAC
1 TAATGA-TT-ATAC
1530859 TAATGATT-TAC
1 TAATGATTATAC
*
1530870 TAATGATTACTAA
1 TAATGATTA-TAC
*
1530883 TAATGAAATTATAA
1 TAATG--ATTATAC
1530897 TAATGATTTGATAC
1 TAATGA-TT-ATAC
1530911 TAAT
1 TAAT
1530915 AATCATAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
11 11 0.23
12 1 0.02
13 11 0.23
14 21 0.44
15 4 0.08
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.41
Consensus pattern (12 bp):
TAATGATTATAC
Found at i:1531207 original size:49 final size:49
Alignment explanation
Indices: 1531127--1531362 Score: 375
Period size: 49 Copynumber: 4.7 Consensus size: 49
1531117 CAACTAATAT
*
1531127 TTAATGATTTAAT-ATTATGATTTAGTAATGATTAGTAATAATAAAATTATTA
1 TTAAT-ATTTAATGATT-TGA--TAGTAATGATTAGTAATAATGAAATTATTA
*
1531179 TTATTATTTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTA
1 TTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTA
*
1531228 TTAATATTTAATGATTTGATAATAATGATTAGTAATAATGAAATTATTA
1 TTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTA
*
1531277 TTAATATATAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTA
1 TTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTA
*
1531326 TTAATATTTAATGATATGATAGTAATGATTTAGTAAT
1 TTAATATTTAATGATTTGATAGTAATGA-TTAGTAAT
1531363 GATTAGTAAT
Statistics
Matches: 174, Mismatches: 8, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
49 149 0.86
50 8 0.05
51 10 0.06
52 7 0.04
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.45
Consensus pattern (49 bp):
TTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTA
Found at i:1531265 original size:13 final size:14
Alignment explanation
Indices: 1531236--1531317 Score: 56
Period size: 14 Copynumber: 6.4 Consensus size: 14
1531226 TATTAATATT
*
1531236 TAATGATTTGATAA
1 TAATGATTAGATAA
1531250 TAATGATTAG-TAA
1 TAATGATTAGATAA
1531263 TAATGA--A-AT--
1 TAATGATTAGATAA
*
1531272 T-ATTATTA-ATATA
1 TAATGATTAGATA-A
* *
1531285 TAATGATTTGATAG
1 TAATGATTAGATAA
1531299 TAATGATTAG-TAA
1 TAATGATTAGATAA
1531312 TAATGA
1 TAATGA
1531318 AATTATTATT
Statistics
Matches: 53, Mismatches: 7, Indels: 17
0.69 0.09 0.22
Matches are distributed among these distances:
8 3 0.06
9 1 0.02
10 3 0.06
11 2 0.04
13 18 0.34
14 23 0.43
15 3 0.06
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.41
Consensus pattern (14 bp):
TAATGATTAGATAA
Found at i:1531385 original size:98 final size:97
Alignment explanation
Indices: 1531152--1531414 Score: 316
Period size: 98 Copynumber: 2.7 Consensus size: 97
1531142 TATGATTTAG
* * * * *
1531152 TAATGATTAGTAATAATAAAATTATTATTATTATTTAATGATTTGATAGTAATGATTAGTAATAA
1 TAATGATTAGTAATAATGAAATCATGA-TAATATATAATGATTTGATAGTAATGATTAGTAATAA
*
1531217 TGAAATTATTATTAATATTTAATGATTTGATAA
65 TGAAATTATTATTAATATTTAATGATATGATAA
* *
1531250 TAATGATTAGTAATAATGAAATTATTATTAATATATAATGATTTGATAGTAATGATTAGTAATAA
1 TAATGATTAGTAATAATGAAATCATGA-TAATATATAATGATTTGATAGTAATGATTAGTAATAA
*
1531315 TGAAATTATTATTAATATTTAATGATATGATAG
65 TGAAATTATTATTAATATTTAATGATATGATAA
* * * * *
1531348 TAATGATTTAGTAATGATTAGTAATCATGA-AATTATAATAATAATTTAATACTAATGATT--TA
1 TAATGA-TTAGTAAT-AAT-GAAATCATGATAA-TAT-ATAATGATTTGATAGTAATGATTAGTA
1531410 ATAAT
61 ATAAT
1531415 TTTTTCGATA
Statistics
Matches: 148, Mismatches: 12, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
98 99 0.67
99 17 0.11
100 5 0.03
101 27 0.18
ACGTcount: A:0.45, C:0.01, G:0.11, T:0.44
Consensus pattern (97 bp):
TAATGATTAGTAATAATGAAATCATGATAATATATAATGATTTGATAGTAATGATTAGTAATAAT
GAAATTATTATTAATATTTAATGATATGATAA
Found at i:1531543 original size:11 final size:12
Alignment explanation
Indices: 1531526--1531581 Score: 71
Period size: 11 Copynumber: 4.7 Consensus size: 12
1531516 TCAATTTACC
1531526 ATAATAATGATT
1 ATAATAATGATT
1531538 -TAATAATGATTT
1 ATAATAATGA-TT
*
1531550 AGTAATAATTATT
1 A-TAATAATGATT
1531563 ATAATAATGATT
1 ATAATAATGATT
1531575 -TAATAAT
1 ATAATAAT
1531582 CAAGTCGATA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
11 16 0.41
12 12 0.31
13 3 0.08
14 8 0.21
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (12 bp):
ATAATAATGATT
Found at i:1531616 original size:14 final size:13
Alignment explanation
Indices: 1531597--1531671 Score: 60
Period size: 14 Copynumber: 5.2 Consensus size: 13
1531587 CGATAAATTA
1531597 TTATTATTAATGAT
1 TTATTATTAAT-AT
1531611 TTATTATTAATAT
1 TTATTATTAATAT
* *
1531624 TTAATGATTTAGTAATT
1 TT-ATTA-TTAAT-A-T
*
1531641 ATTATTAATAATGAT
1 -TTATTATTAAT-AT
1531656 TTATTATTAATAT
1 TTATTATTAATAT
1531669 TTA
1 TTA
1531672 ATGATTTGAT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
13 9 0.18
14 24 0.49
15 5 0.10
16 5 0.10
17 4 0.08
18 2 0.04
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (13 bp):
TTATTATTAATAT
Found at i:1531629 original size:21 final size:21
Alignment explanation
Indices: 1531593--1531687 Score: 113
Period size: 21 Copynumber: 4.4 Consensus size: 21
1531583 AAGTCGATAA
*
1531593 ATTATTATTA-TTAATGATTT
1 ATTATTAATATTTAATGATTT
1531613 ATTATTAATATTTAATGATTT
1 ATTATTAATATTTAATGATTT
* *
1531634 AGTAATTATTATTAATAATGATTT
1 A-TTATTAATATT--TAATGATTT
1531658 ATTATTAATATTTAATGATTT
1 ATTATTAATATTTAATGATTT
1531679 GA-TATTAAT
1 -ATTATTAAT
1531688 GATTAAGTAA
Statistics
Matches: 65, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
20 9 0.14
21 27 0.42
22 10 0.15
23 9 0.14
24 10 0.15
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (21 bp):
ATTATTAATATTTAATGATTT
Found at i:1531647 original size:45 final size:45
Alignment explanation
Indices: 1531592--1531678 Score: 165
Period size: 45 Copynumber: 1.9 Consensus size: 45
1531582 CAAGTCGATA
*
1531592 AATTATTATTATTAATGATTTATTATTAATATTTAATGATTTAGT
1 AATTATTATTAATAATGATTTATTATTAATATTTAATGATTTAGT
1531637 AATTATTATTAATAATGATTTATTATTAATATTTAATGATTT
1 AATTATTATTAATAATGATTTATTATTAATATTTAATGATTT
1531679 GATATTAATG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (45 bp):
AATTATTATTAATAATGATTTATTATTAATATTTAATGATTTAGT
Found at i:1531687 original size:59 final size:59
Alignment explanation
Indices: 1531597--1531711 Score: 153
Period size: 59 Copynumber: 1.9 Consensus size: 59
1531587 CGATAAATTA
* * * *
1531597 TTATTATTAATGATTTATTATTAATATTTAATGATTTAGTAATTATTATTAATAATGAT
1 TTATTATTAATGATTTATGATTAATATTTAATGATTAAGTAATGATTAGTAATAATGAT
*
1531656 TTATTATTAAT-ATTTAATGATTTGATA-TTAATGATTAAGTAATGATTAGTAATAAT
1 TTATTATTAATGATTT-ATGA-TTAATATTTAATGATTAAGTAATGATTAGTAATAAT
1531712 AAAATTGTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
58 4 0.08
59 40 0.82
60 5 0.10
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (59 bp):
TTATTATTAATGATTTATGATTAATATTTAATGATTAAGTAATGATTAGTAATAATGAT
Found at i:1531712 original size:45 final size:45
Alignment explanation
Indices: 1531592--1531702 Score: 154
Period size: 45 Copynumber: 2.4 Consensus size: 45
1531582 CAAGTCGATA
* *
1531592 AATTATTATTATTAATGATTTATTATTAATATTTAATGATTTAGT
1 AATTATGATTAATAATGATTTATTATTAATATTTAATGATTTAGT
*
1531637 AATTATTATTAATAATGATTTATTATTAATATTTAATGATTT-G-
1 AATTATGATTAATAATGATTTATTATTAATATTTAATGATTTAGT
1531680 ATATTAATGATTAAGTAATGATT
1 A-ATT-ATGATTAA-TAATGATT
1531703 AGTAATAATA
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
43 1 0.02
44 4 0.07
45 48 0.79
46 8 0.13
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (45 bp):
AATTATGATTAATAATGATTTATTATTAATATTTAATGATTTAGT
Found at i:1532011 original size:14 final size:12
Alignment explanation
Indices: 1531983--1532124 Score: 94
Period size: 12 Copynumber: 11.6 Consensus size: 12
1531973 TAATAATTAT
*
1531983 ATGA-TTTAGTA
1 ATGATTTTAATA
1531994 ATGATTTGATAATA
1 ATGATTT--TAATA
1532008 ATGA-TTTAATA
1 ATGATTTTAATA
1532019 ATGATTTTAATA
1 ATGATTTTAATA
* * * * *
1532031 TTTAATGTAATG
1 ATGATTTTAATA
*
1532043 ATGA-TTTAGTA
1 ATGATTTTAATA
1532054 ATGATTTGATAATA
1 ATGATTT--TAATA
* *
1532068 ATCATTATAATA
1 ATGATTTTAATA
1532080 ATGATTTGATAATA
1 ATGATTT--TAATA
*
1532094 ATGA-TTTAGTA
1 ATGATTTTAATA
*
1532105 ATTATTATTAATA
1 ATGATT-TTAATA
1532118 ATGATTT
1 ATGATTT
1532125 ATTATTAATA
Statistics
Matches: 100, Mismatches: 20, Indels: 21
0.71 0.14 0.15
Matches are distributed among these distances:
11 28 0.28
12 32 0.32
13 14 0.14
14 26 0.26
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.46
Consensus pattern (12 bp):
ATGATTTTAATA
Found at i:1532128 original size:14 final size:13
Alignment explanation
Indices: 1531992--1532126 Score: 85
Period size: 14 Copynumber: 10.8 Consensus size: 13
1531982 TATGATTTAG
1531992 TAATGATTTGATAA
1 TAATGATTT-ATAA
1532006 TAATGA-TT-TAA
1 TAATGATTTATAA
1532017 TAATGATTT-TAA
1 TAATGATTTATAA
* * * *
1532029 TATTTA-ATGTAA
1 TAATGATTTATAA
* *
1532041 TGATGA-TT-TAG
1 TAATGATTTATAA
1532052 TAATGATTTGATAA
1 TAATGATTT-ATAA
*
1532066 TAATCA-TTATAA
1 TAATGATTTATAA
1532078 TAATGATTTGATAA
1 TAATGATTT-ATAA
1532092 TAATGATTTAGTAA
1 TAATGATTTA-TAA
1532106 T--T-A-TTATTAA
1 TAATGATTTA-TAA
1532116 TAATGATTTAT
1 TAATGATTTAT
1532127 TATTAATATT
Statistics
Matches: 96, Mismatches: 13, Indels: 25
0.72 0.10 0.19
Matches are distributed among these distances:
10 7 0.07
11 18 0.19
12 29 0.30
13 9 0.09
14 33 0.34
ACGTcount: A:0.41, C:0.01, G:0.11, T:0.47
Consensus pattern (13 bp):
TAATGATTTATAA
Found at i:1532140 original size:24 final size:24
Alignment explanation
Indices: 1532089--1532136 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1532079 AATGATTTGA
*
1532089 TAATAATGATTTAGTAATTATTAT
1 TAATAATGATTTAGTAATTAATAT
*
1532113 TAATAATGATTTA-TTATTAATAT
1 TAATAATGATTTAGTAATTAATAT
1532136 T
1 T
1532137 TAATTATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (24 bp):
TAATAATGATTTAGTAATTAATAT
Found at i:1532143 original size:17 final size:17
Alignment explanation
Indices: 1532103--1532144 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1532093 AATGATTTAG
1532103 TAATTATTATTAATAAT
1 TAATTATTATTAATAAT
* * *
1532120 GATTTATTATTAATATT
1 TAATTATTATTAATAAT
1532137 TAATTATT
1 TAATTATT
1532145 TGATACTAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TAATTATTATTAATAAT
Found at i:1532168 original size:86 final size:85
Alignment explanation
Indices: 1531989--1532186 Score: 208
Period size: 86 Copynumber: 2.3 Consensus size: 85
1531979 TTATATGATT
*
1531989 TAGTAATGATTTGATAATAATGATTTAATAATGATTTTAATATTTAATGTAATGATGATTTAGTA
1 TAGTAATGATTTGATAATAATGATTTAATAATGATTTTAATATTTAATGTAATAATGATTTA-TA
1532054 ATGATTTGATAATAATCATTA
65 ATGATTTGATAATAATCATTA
* * * * *
1532075 TAATAATGATTTGATAATAATGATTTAGTAATTATTATTAATAATGATTTAT-TATTAAT-A-TT
1 TAGTAATGATTTGATAATAATGATTTAATAATGATT-TTAAT-AT--TTAATGTAATAATGATTT
* * *
1532137 -TAATTATTTGATACTAATGATTA
62 ATAATGATTTGATAATAATCATTA
*
1532160 CTAGTAATGAAATT-ATAATAATGATTT
1 -TAGTAATG-ATTTGATAATAATGATTT
1532187 GATACTAAAA
Statistics
Matches: 95, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
85 20 0.21
86 53 0.56
87 10 0.11
88 3 0.03
89 5 0.05
90 4 0.04
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (85 bp):
TAGTAATGATTTGATAATAATGATTTAATAATGATTTTAATATTTAATGTAATAATGATTTATAA
TGATTTGATAATAATCATTA
Found at i:1534737 original size:4 final size:4
Alignment explanation
Indices: 1534728--1534752 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1534718 AACTATGTCC
1534728 ACTA ACTA ACTA ACTA ACTA ACTA A
1 ACTA ACTA ACTA ACTA ACTA ACTA A
1534753 TAATTTAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACTA
Found at i:1535119 original size:29 final size:29
Alignment explanation
Indices: 1535076--1535178 Score: 136
Period size: 29 Copynumber: 3.6 Consensus size: 29
1535066 TTATAGCTGC
* * *
1535076 ATGGCATGGCAACCTACAAGTTCACCCAG
1 ATGGCATGGCGACCTACAAGGTCACCCGG
*
1535105 ATGGCATGGCGACCTACAAGGTCGCCCGG
1 ATGGCATGGCGACCTACAAGGTCACCCGG
* *
1535134 AGGGCATGGCGACCTACAAGGTCTCCCGG
1 ATGGCATGGCGACCTACAAGGTCACCCGG
1535163 A-GAGCATGGCGACCTA
1 ATG-GCATGGCGACCTA
1535179 TGTGTTGGGG
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
28 1 0.01
29 66 0.99
ACGTcount: A:0.25, C:0.30, G:0.30, T:0.15
Consensus pattern (29 bp):
ATGGCATGGCGACCTACAAGGTCACCCGG
Found at i:1536190 original size:41 final size:41
Alignment explanation
Indices: 1536129--1536389 Score: 258
Period size: 41 Copynumber: 6.3 Consensus size: 41
1536119 TGTTTTAAAA
* *
1536129 AAACGCCGCTAAAGAA-TCATACTTTCATGGCGTTTATATAC
1 AAACGCCGCTAAA-AACTCATACTTTAATGGCGTTTTTATAC
* *
1536170 AAACGCCGCTAAAAACTCATACTTTCATGGCATTTTTATAC
1 AAACGCCGCTAAAAACTCATACTTTAATGGCGTTTTTATAC
* * *** *
1536211 AAACGCCGCTATAAACT-AGTACTTTAGTGTTATTTTGATAC
1 AAACGCCGCTAAAAACTCA-TACTTTAATGGCGTTTTTATAC
* * * * *
1536252 AAACGCCGCTAAAGATTCTTACTTTAATGGGGTTTATGTTTAC
1 AAACGCCGCTAAAAACTCATACTTTAATGGCGTTT-T-TATAC
* *
1536295 AAACGCCGCTATAAACTCATACTTTAATGGCGTTTTTATAA
1 AAACGCCGCTAAAAACTCATACTTTAATGGCGTTTTTATAC
* * * **
1536336 AAACACCGCTATAAAGT-AGTACTTTGGTGGCGTTTTTATAC
1 AAACGCCGCTAAAAACTCA-TACTTTAATGGCGTTTTTATAC
1536377 AAACGCCGCTAAA
1 AAACGCCGCTAAA
1536390 GAGTTTTTAT
Statistics
Matches: 182, Mismatches: 32, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
40 4 0.02
41 143 0.79
42 2 0.01
43 33 0.18
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (41 bp):
AAACGCCGCTAAAAACTCATACTTTAATGGCGTTTTTATAC
Found at i:1536349 original size:125 final size:123
Alignment explanation
Indices: 1536129--1536391 Score: 364
Period size: 125 Copynumber: 2.1 Consensus size: 123
1536119 TGTTTTAAAA
*
1536129 AAACGCCGCTAAAGAATCATACTTTCATGGCGTTTATATACAAACGCCGCTAAAAACTCATACTT
1 AAACGCCGCTAAAGAATCATACTTTAATGGCGTTTATATACAAACGCCGCTAAAAACTCATACTT
* * * **
1536194 TCATGGCATTTTTATACAAACGCCGCTATAAACTAGTACTTTAGTGTTATTTTGATAC
66 TAATGGCATTTTTATAAAAACACCGCTATAAACTAGTACTTTAGTGGCATTTTGATAC
* * * * *
1536252 AAACGCCGCTAAAGATTCTTACTTTAATGGGGTTTATGTTTACAAACGCCGCTATAAACTCATAC
1 AAACGCCGCTAAAGAATCATACTTTAATGGCGTTTA--TATACAAACGCCGCTAAAAACTCATAC
* * * * *
1536317 TTTAATGGCGTTTTTATAAAAACACCGCTATAAAGTAGTACTTTGGTGGCGTTTTTATAC
64 TTTAATGGCATTTTTATAAAAACACCGCTATAAACTAGTACTTTAGTGGCATTTTGATAC
1536377 AAACGCCGCTAAAGA
1 AAACGCCGCTAAAGA
1536392 GTTTTTATAT
Statistics
Matches: 122, Mismatches: 16, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
123 32 0.26
125 90 0.74
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (123 bp):
AAACGCCGCTAAAGAATCATACTTTAATGGCGTTTATATACAAACGCCGCTAAAAACTCATACTT
TAATGGCATTTTTATAAAAACACCGCTATAAACTAGTACTTTAGTGGCATTTTGATAC
Found at i:1536395 original size:25 final size:25
Alignment explanation
Indices: 1536367--1536416 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
1536357 CTTTGGTGGC
*
1536367 GTTTTTATACAAACGCCGCTAAAGA
1 GTTTTTATACAAACGCCACTAAAGA
*
1536392 GTTTTTATATAAACGCCACTAAAGA
1 GTTTTTATACAAACGCCACTAAAGA
1536417 TTCGTACGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (25 bp):
GTTTTTATACAAACGCCACTAAAGA
Found at i:1537062 original size:43 final size:43
Alignment explanation
Indices: 1537014--1537096 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
1537004 AGCTTTCATT
* **
1537014 TTTTTTCTGTGATTTATTTAATTTTTCTTTGGGGTTGTTTTTA
1 TTTTTTCTGGGATTTATTTAATTTTTCTCCGGGGTTGTTTTTA
* *
1537057 TTTTTTTTGGGATTTATTTTATTTTTCTCCGGGGTTGTTT
1 TTTTTTCTGGGATTTATTTAATTTTTCTCCGGGGTTGTTT
1537097 AACCAGGACT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.10, C:0.06, G:0.18, T:0.66
Consensus pattern (43 bp):
TTTTTTCTGGGATTTATTTAATTTTTCTCCGGGGTTGTTTTTA
Found at i:1537065 original size:21 final size:22
Alignment explanation
Indices: 1537034--1537096 Score: 76
Period size: 21 Copynumber: 2.9 Consensus size: 22
1537024 GATTTATTTA
1537034 ATTTTTCTTTGGGGTTGTTTTT
1 ATTTTTCTTTGGGGTTGTTTTT
*
1537056 ATTTTT-TTTGGGATT-TATTTT
1 ATTTTTCTTTGGGGTTGT-TTTT
**
1537077 ATTTTTCTCCGGGGTTGTTT
1 ATTTTTCTTTGGGGTTGTTT
1537097 AACCAGGACT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 1 0.03
21 18 0.53
22 14 0.41
23 1 0.03
ACGTcount: A:0.08, C:0.06, G:0.21, T:0.65
Consensus pattern (22 bp):
ATTTTTCTTTGGGGTTGTTTTT
Found at i:1539346 original size:43 final size:42
Alignment explanation
Indices: 1539283--1539527 Score: 244
Period size: 43 Copynumber: 5.8 Consensus size: 42
1539273 CGTTTGTAAA
* * *
1539283 AAAAACACTGCTATATATCTGACCTTTTGCGGCGTTTATATCC
1 AAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTAT-TCC
* * * *
1539326 AACAACGCCGCTATAGATCTGACTTTTTGCGACGTTTGTATCC
1 AAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTAT-TCC
* * * * *
1539369 AAAAATGCCGCTAAAGATATGAACTTTTGCGGCGTTTGTTCC
1 AAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTATTCC
*
1539411 AAAAACGCCGCTATAGATCTGACCTTTT-AGGCAGTTTATT-C
1 AAAAACGCCGCTATAGATCTGACCTTTTGCGGC-GTTTATTCC
** * *
1539452 AAAAAAACAG-TGATAGATCTGACCTTTTGCGGCGTTTATTCT
1 AAAAACGCCGCT-ATAGATCTGACCTTTTGCGGCGTTTATTCC
* * *
1539494 AAAAATGCCGCTATTGATCTCGACCTCTTGCGGC
1 AAAAACGCCGCTATAGATCT-GACCTTTTGCGGC
1539528 CCCGCAATAG
Statistics
Matches: 166, Mismatches: 30, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
40 1 0.01
41 34 0.20
42 50 0.30
43 81 0.49
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.32
Consensus pattern (42 bp):
AAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTATTCC
Found at i:1539498 original size:83 final size:86
Alignment explanation
Indices: 1539281--1539519 Score: 247
Period size: 83 Copynumber: 2.8 Consensus size: 86
1539271 GTCGTTTGTA
* * *
1539281 AAAAAAACACTGCTATATATCTGACCTTTTGCGGCGTTTATATCCAACAACGCCGCTATAGATCT
1 AAAAAAACAGTG--ATAGATCTGACCTTTTGCGGCGTTTAT-TCCAAAAACGCCGCTATAGATCT
*
1539346 GA-CTTTTTGCGACGTTTGTATCC
63 GACCTTTTGGCGACGTTTGTATCC
** * * * * *
1539369 AAAAATGCCGCT-AAAGATATGAACTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGA
1 AAAAAAACAG-TGATAGATCTGACCTTTTGCGGCGTTTATTCCAAAAACGCCGCTATAGATCTGA
*
1539433 CCTTTTAGGC-A-G-TT-TATTC
65 CCTTTT-GGCGACGTTTGTATCC
* * *
1539452 AAAAAAACAGTGATAGATCTGACCTTTTGCGGCGTTTATTCTAAAAATGCCGCTATTGATCTCGA
1 AAAAAAACAGTGATAGATCTGACCTTTTGCGGCGTTTATTCCAAAAACGCCGCTATAGATCT-GA
1539517 CCT
65 CCT
1539520 CTTGCGGCCC
Statistics
Matches: 124, Mismatches: 22, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
82 1 0.01
83 54 0.44
84 7 0.06
85 25 0.20
86 28 0.23
87 2 0.02
88 6 0.05
89 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.32
Consensus pattern (86 bp):
AAAAAAACAGTGATAGATCTGACCTTTTGCGGCGTTTATTCCAAAAACGCCGCTATAGATCTGAC
CTTTTGGCGACGTTTGTATCC
Found at i:1539562 original size:17 final size:17
Alignment explanation
Indices: 1539540--1539586 Score: 94
Period size: 17 Copynumber: 2.8 Consensus size: 17
1539530 CGCAATAGAA
1539540 ATCGACCTTTTGCAGAT
1 ATCGACCTTTTGCAGAT
1539557 ATCGACCTTTTGCAGAT
1 ATCGACCTTTTGCAGAT
1539574 ATCGACCTTTTGC
1 ATCGACCTTTTGC
1539587 GGCGTTTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (17 bp):
ATCGACCTTTTGCAGAT
Found at i:1541843 original size:3 final size:3
Alignment explanation
Indices: 1541835--1541884 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
1541825 CTAAGGCTTT
*
1541835 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1541883 TT
1 TT
1541885 TCAAGTCTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1543830 original size:33 final size:33
Alignment explanation
Indices: 1543775--1543851 Score: 79
Period size: 33 Copynumber: 2.4 Consensus size: 33
1543765 ATATGTCAAC
* * *
1543775 ATTTAACTAAATAAATTAAATTTATTAAATAA-A
1 ATTTGACTAAATTAATTAAATTT-GTAAATAATA
* *
1543808 ATTTGACTAAATTGATTGAATTTGTAAATAATA
1 ATTTGACTAAATTAATTAAATTTGTAAATAATA
1543841 A--TGACTAAATT
1 ATTTGACTAAATT
1543852 TGAAACTATA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
31 10 0.26
32 7 0.18
33 21 0.55
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.40
Consensus pattern (33 bp):
ATTTGACTAAATTAATTAAATTTGTAAATAATA
Found at i:1550975 original size:15 final size:15
Alignment explanation
Indices: 1550953--1550994 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1550943 AATTAAAAAA
1550953 TATATATATATAATAT
1 TATATATATATAAT-T
*
1550969 T-TATATATTTAATT
1 TATATATATATAATT
*
1550983 TAAATATATATA
1 TATATATATATA
1550995 CCTGGCCCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 2 0.09
15 19 0.86
16 1 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATATATATATAATT
Found at i:1552909 original size:2 final size:2
Alignment explanation
Indices: 1552881--1552942 Score: 83
Period size: 2 Copynumber: 31.5 Consensus size: 2
1552871 TCATATAAGC
* *
1552881 AT AT AA AT A- AT A- AT AT AT GAT AA 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
1552922 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
1552943 AACTCACACA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
1 2 0.04
2 49 0.92
3 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1556147 original size:13 final size:13
Alignment explanation
Indices: 1556131--1556166 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
1556121 ATAAATAGTA
1556131 AATTAAAATTCCT
1 AATTAAAATTCCT
1556144 AATTAAAA-TCCT
1 AATTAAAATTCCT
*
1556156 AATTGAAATTC
1 AATTAAAATTC
1556167 TAAGCAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.47, C:0.14, G:0.03, T:0.36
Consensus pattern (13 bp):
AATTAAAATTCCT
Found at i:1565191 original size:264 final size:262
Alignment explanation
Indices: 1564715--1565190 Score: 746
Period size: 265 Copynumber: 1.8 Consensus size: 262
1564705 TTATTTTGGG
* * *
1564715 TCGGGTCGGGTCGAGTTCGAGTTTAGGGTGAAAAATACCTGACCCGAAAATATATATAATTTTAC
1 TCGGGTCGGGTCGAGTTCGAGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAAGTTTAC
* * *
1564780 CTTATATATTTAGGAATAATTACAATAATGCCCCTCTATATATAATTTTTTTTAATTAAGTCATT
66 CTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCACT
1564845 GTTTTTATTGAATAAAAATAATTTTTTTTATTATTTCGGGTCGGGTCGGGTCGGATTTCTAATTC
131 GTTTTTATTGAATAAAAATAATTTTTTTTATTATTTCGGGTCGGGT---GTCGGATTTCTAATTC
1564910 ATAAATTCGGATCGGGTCGGGTGAAACTTTATTTTGGTCGGTTCGAGTCGGGTTTTTTTAAGTGT
193 ATAAATTCGGATCGGGTCGGGTGAAACTTTATTTTGGTCGGTTCGAGTCGGGTTTTTTTAAGTGT
1564975 GATAT
258 GATAT
* * *
1564980 TCGGGTCGGGTCGGGTTCGGGTTTAGGGTGGAAAATACCCGACCC-AAAAAATATATAAGTTTAC
1 TCGGGTCGGGTCGAGTTCGAGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAAGTTTAC
*
1565044 CTTATATATTTAGGAATAATTACAATAATACCTCTCTCTCTATAT-ATTTTTTTCAATTAAGTCA
66 CTTATATATTTAGGAATAATTACAATAATACC-C-CTCTATATATAATTTTTTTCAATTAAGTCA
*
1565108 CTGTTTTTATTGAATAAAAATAA-TTTTTTTATTATTTCGGGTC-GGT-TCGGGTTTCTAATTCA
129 CTGTTTTTATTGAATAAAAATAATTTTTTTTATTATTTCGGGTCGGGTGTCGGATTTCTAATTCA
* * *
1565170 TATATTTGGGTCGGGTCGGGT
194 TAAATTCGGATCGGGTCGGGT
1565191 CTCGAATGGA
Statistics
Matches: 195, Mismatches: 14, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
259 33 0.17
263 3 0.02
264 68 0.35
265 82 0.42
266 9 0.05
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (262 bp):
TCGGGTCGGGTCGAGTTCGAGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAAGTTTAC
CTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCACT
GTTTTTATTGAATAAAAATAATTTTTTTTATTATTTCGGGTCGGGTGTCGGATTTCTAATTCATA
AATTCGGATCGGGTCGGGTGAAACTTTATTTTGGTCGGTTCGAGTCGGGTTTTTTTAAGTGTGAT
AT
Found at i:1565609 original size:18 final size:17
Alignment explanation
Indices: 1565564--1565610 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
1565554 TATGAAATTG
*
1565564 GATTCCAATTCCTGACA
1 GATTCCAATTCCTCACA
*
1565581 GATTTCAATTCCTTCACA
1 GATTCCAATTCC-TCACA
*
1565599 TATTCCAATTCC
1 GATTCCAATTCC
1565611 CTCAGAAGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.28, C:0.30, G:0.06, T:0.36
Consensus pattern (17 bp):
GATTCCAATTCCTCACA
Found at i:1584321 original size:35 final size:35
Alignment explanation
Indices: 1584277--1584345 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
1584267 TTTCATTTTT
* *
1584277 CTTTCTCATATTCGTAAAAGAATTATTGTTATTTC
1 CTTTCTCATATTCATAAAAGAATTATTATTATTTC
*
1584312 CTTTTTCATATTCATAAAAGAATTATTATTATTT
1 CTTTCTCATATTCATAAAAGAATTATTATTATTT
1584346 TTTAAGGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.32, C:0.12, G:0.06, T:0.51
Consensus pattern (35 bp):
CTTTCTCATATTCATAAAAGAATTATTATTATTTC
Found at i:1584456 original size:17 final size:17
Alignment explanation
Indices: 1584436--1584474 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
1584426 AAATATTATA
1584436 TTATATTTATCACATAT
1 TTATATTTATCACATAT
*
1584453 TTATATTTATTACATAT
1 TTATATTTATCACATAT
1584470 TTATA
1 TTATA
1584475 AATGAGTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATATTTATCACATAT
Found at i:1584778 original size:33 final size:33
Alignment explanation
Indices: 1584735--1584806 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
1584725 ATCATAAAAA
* * * *
1584735 TAAGAATTTTATGCCTTTTTATTATTATTAGAT
1 TAAGAGTTTTATACCTTTTTAATATTATTACAT
**
1584768 TAAGAGTTTTATATTTTTTTAATATTATTACAT
1 TAAGAGTTTTATACCTTTTTAATATTATTACAT
*
1584801 TGAGAG
1 TAAGAG
1584807 AAATTATATG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.32, C:0.04, G:0.11, T:0.53
Consensus pattern (33 bp):
TAAGAGTTTTATACCTTTTTAATATTATTACAT
Found at i:1584862 original size:2 final size:2
Alignment explanation
Indices: 1584857--1584888 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1584847 TGAGAGAAAT
1584857 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
1584889 GAGAGAGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1584893 original size:2 final size:2
Alignment explanation
Indices: 1584888--1584932 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1584878 ATATATATAT
1584888 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1584930 AG A
1 AG A
1584933 ATTGAACTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1587057 original size:35 final size:35
Alignment explanation
Indices: 1586991--1587057 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
1586981 TTATTCATTC
* * *
1586991 AGGTAATTAACGTTATAAATATTGCCGCTTTAGGT
1 AGGTAATTAACGTCATAAACATTGCCACTTTAGGT
*
1587026 AGGTAATTAACGTCATAAACATTGTCACTTTA
1 AGGTAATTAACGTCATAAACATTGCCACTTTA
1587058 TGTGTTGTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.36
Consensus pattern (35 bp):
AGGTAATTAACGTCATAAACATTGCCACTTTAGGT
Found at i:1588571 original size:25 final size:25
Alignment explanation
Indices: 1588521--1588574 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
1588511 TTGCTAGAAA
*
1588521 ATTAAGATAAGAACACAATATTAAG
1 ATTAAGATAAGAACACAATATAAAG
* *
1588546 ATTAAGATAATGAAGATAA-ATAAAG
1 ATTAAGATAA-GAACACAATATAAAG
1588571 ATTA
1 ATTA
1588575 TGATTGAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 19 0.76
26 6 0.24
ACGTcount: A:0.57, C:0.04, G:0.13, T:0.26
Consensus pattern (25 bp):
ATTAAGATAAGAACACAATATAAAG
Found at i:1590314 original size:17 final size:19
Alignment explanation
Indices: 1590286--1590334 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1590276 TATTTTGAAA
1590286 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
1590304 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
1590323 CACCGATGCACT
1 CATCGATGCACT
1590335 AAAGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:1590314 original size:64 final size:64
Alignment explanation
Indices: 1590155--1590336 Score: 192
Period size: 65 Copynumber: 2.8 Consensus size: 64
1590145 AATTAAAGTG
* *
1590155 AACATCGAATGCATTTCATGCATCGATGCA-CATACCATGCACCGATGCACTAAGGATGTTATCA
1 AACATCGAATGCA-TTGATGCATCGATGCACCATA-CATGCACCGATGCACTAAGGATATTATCA
1590219 A
64 A
* ** * **
1590220 AACATCGAATGCATTCGATGCATCGATGCACCAGT-CATGCATCGATGCACTCTGGCTATT-TTG
1 AACATCGAATGCATT-GATGCATCGATGCACCA-TACATGCACCGATGCACTAAGGATATTATCA
1590283 A
64 A
* *
1590284 AACATCGAATGCACTTGATGCATCGATGCACTCTTA-GTGCACCGATGCACTAA
1 AACATCGAATGCA-TTGATGCATCGATGCAC-CATACATGCACCGATGCACTAA
1590337 AGGTCCAACG
Statistics
Matches: 98, Mismatches: 13, Indels: 13
0.79 0.10 0.10
Matches are distributed among these distances:
64 46 0.47
65 49 0.50
66 2 0.02
67 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (64 bp):
AACATCGAATGCATTGATGCATCGATGCACCATACATGCACCGATGCACTAAGGATATTATCAA
Found at i:1590790 original size:17 final size:16
Alignment explanation
Indices: 1590768--1590801 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1590758 TAAAGATAGT
1590768 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
1590785 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
1590801 A
1 A
1590802 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:1594654 original size:19 final size:20
Alignment explanation
Indices: 1594632--1594675 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1594622 GAGAAAAGGT
1594632 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
* *
1594651 AAAAATTAATAATGAAAGAT
1 AAAAGTTAATAATGAAAGAG
1594671 AAAAG
1 AAAAG
1594676 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Found at i:1600994 original size:17 final size:16
Alignment explanation
Indices: 1600972--1601005 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1600962 TAAAGACAGT
1600972 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
1600989 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
1601005 A
1 A
1601006 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:1610926 original size:64 final size:64
Alignment explanation
Indices: 1610768--1610951 Score: 196
Period size: 65 Copynumber: 2.8 Consensus size: 64
1610758 AATTAAAGTG
* * *
1610768 AACATCGAATGCATTTCATGCAGCGATGCA-CATACCATGCACCGATGCACTAAGGATGTTATGA
1 AACATCGAATGCA-TTGATGCATCGATGCACCATA-CATGCACCGATGCACTAAGGATATTATGA
1610832 A
64 A
* ** * *
1610833 AACATCGAATGCATTCGATGCATCGATGCACCAGT-CATGCATCGATGCACTCTGGCTATTTTG-
1 AACATCGAATGCATT-GATGCATCGATGCACCA-TACATGCACCGATGCACTAAGGATATTATGA
1610896 A
64 A
* *
1610897 AACATCGAATGCACTTGATGCATCGATGCACTCTTA-GTGCACCGATGCACTAAGG
1 AACATCGAATGCA-TTGATGCATCGATGCAC-CATACATGCACCGATGCACTAAGG
1610952 GTCCAACGAT
Statistics
Matches: 100, Mismatches: 13, Indels: 13
0.79 0.10 0.10
Matches are distributed among these distances:
64 47 0.47
65 50 0.50
66 2 0.02
67 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (64 bp):
AACATCGAATGCATTGATGCATCGATGCACCATACATGCACCGATGCACTAAGGATATTATGAA
Found at i:1610927 original size:17 final size:19
Alignment explanation
Indices: 1610899--1610947 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1610889 TATTTTGAAA
1610899 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
1610917 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
1610936 CACCGATGCACT
1 CATCGATGCACT
1610948 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:1611847 original size:2 final size:2
Alignment explanation
Indices: 1611842--1611879 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1611832 AAATAGAATT
1611842 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
1611880 ACAGCAACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1614069 original size:20 final size:20
Alignment explanation
Indices: 1614044--1614090 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
1614034 ATATGATTTT
*
1614044 GACCCGGTCTGATTTGACTC
1 GACCCGATCTGATTTGACTC
1614064 GACCCGATCTGATTTGACTC
1 GACCCGATCTGATTTGACTC
1614084 GACCCGA
1 GACCCGA
1614091 GACCCGACCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.19, C:0.32, G:0.23, T:0.26
Consensus pattern (20 bp):
GACCCGATCTGATTTGACTC
Found at i:1615330 original size:25 final size:25
Alignment explanation
Indices: 1615312--1615358 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
1615302 AAAATTTGTG
*
1615312 TTTTATTTTTTAAAA-AAAATATAA
1 TTTTATTTTTTAAAATAAAATTTAA
1615336 TTTTATTTTTTAAAATAAAATTT
1 TTTTATTTTTTAAAATAAAATTT
1615359 TTAAAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TTTTATTTTTTAAAATAAAATTTAA
Found at i:1616619 original size:15 final size:13
Alignment explanation
Indices: 1616588--1616622 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
1616578 ATATTTTATC
1616588 TTTTTAAAATTAA
1 TTTTTAAAATTAA
1616601 TTTTTAACAATTAA
1 TTTTTAA-AATTAA
*
1616615 ATTTTAAA
1 TTTTTAAA
1616623 CTGTATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (13 bp):
TTTTTAAAATTAA
Found at i:1616905 original size:38 final size:39
Alignment explanation
Indices: 1616851--1616927 Score: 129
Period size: 38 Copynumber: 2.0 Consensus size: 39
1616841 GAAATCTGTA
*
1616851 GAAATTGGAATACAATTCCATATTCTGTTTGGTTGGCAG
1 GAAATTGGAATACAATTCCATATTCTGTTTGGTTCGCAG
*
1616890 GAAA-TGGAATCCAATTCCATATTCTGTTTGGTTCGCAG
1 GAAATTGGAATACAATTCCATATTCTGTTTGGTTCGCAG
1616928 ACATTTCAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 32 0.89
39 4 0.11
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (39 bp):
GAAATTGGAATACAATTCCATATTCTGTTTGGTTCGCAG
Found at i:1617475 original size:38 final size:37
Alignment explanation
Indices: 1617422--1617510 Score: 133
Period size: 38 Copynumber: 2.4 Consensus size: 37
1617412 TTTTCACCCT
*
1617422 AAACCCGAAACCGACCCGACCCGAATAACACACTTAAA
1 AAACCCG-ACCCGACCCGACCCGAATAACACACTTAAA
* *
1617460 AACCCTCGACCCGACCCGACCCGAATATCACACTTAAA
1 AAACC-CGACCCGACCCGACCCGAATAACACACTTAAA
1617498 AAACCCGACCCGA
1 AAACCCGACCCGA
1617511 ACAAAATAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
37 8 0.17
38 36 0.78
39 2 0.04
ACGTcount: A:0.39, C:0.40, G:0.11, T:0.09
Consensus pattern (37 bp):
AAACCCGACCCGACCCGACCCGAATAACACACTTAAA
Found at i:1617757 original size:37 final size:38
Alignment explanation
Indices: 1617678--1617764 Score: 131
Period size: 38 Copynumber: 2.3 Consensus size: 38
1617668 TTCACCCTAA
*
1617678 ACCCGGACCCGACCCAAATATTACACTTAAAAAACCCCG
1 ACCC-GACCCGACCCAAATATCACACTTAAAAAACCCCG
* *
1617717 ACCCGACTCGACCCGAATATCACACTTAAAAAA-CCCG
1 ACCCGACCCGACCCAAATATCACACTTAAAAAACCCCG
1617754 ACCCGACCCGA
1 ACCCGACCCGA
1617765 ACAAAATAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
37 14 0.32
38 26 0.59
39 4 0.09
ACGTcount: A:0.37, C:0.40, G:0.11, T:0.11
Consensus pattern (38 bp):
ACCCGACCCGACCCAAATATCACACTTAAAAAACCCCG
Found at i:1618017 original size:254 final size:252
Alignment explanation
Indices: 1617379--1618028 Score: 898
Period size: 255 Copynumber: 2.6 Consensus size: 252
1617369 ATATAAGGTA
* *
1617379 AAATTATATATTTTTTTCGGGTCAGTCCGGTTTTTTTCACCCTAAACCCGAAACCGACCCGACCC
1 AAATTATATA-TATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCC--AA---ACCCGACCC
*
1617444 GAATAACACACTT-AAAAACCCTCGACCCGACCCGACCCGAATATCACACTTAAAA--A-ACCCG
60 GAATATCACACTTAAAAAACCC-CGACCCGACCCGACCCGAATATCACACTTAAAACCAGACCCG
1617505 ACCCGAACAAAATAAAATTTCATACGACCCGACCCGAATATATAAATTAGAAATCCAACCCGACC
124 ACCCGAACAAAATAAAATTTCATACGACCCGACCCGAATATATAAATTAGAAATCCAACCCGACC
* *
1617570 CGACCTGAAATAATAAAAACATATTTTTATTTAATAAAAACAATGACTTAATCCGACCCGACCT
189 CGACCTGAAATAATAAAAAAATATTTTTATTTAATAAAAACAATAACTTAATCCGACCCGACCT
* ** *
1617634 GAATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGGACCCGACCCAAATAT
1 AAATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCAAACCCGACCCGAATAT
* * *
1617699 TACACTTAAAAAACCCCGACCCGACTCGACCCGAATATCACACTTAAAAAACCCGACCCGACCCG
66 CACACTTAAAAAACCCCGACCCGACCCGACCCGAATATCACACTT--AAAACCAGACCCGACCCG
* * * * * * *
1617764 AACAAAATAAAGTTTCATCCGACTCGACCTGAATATATGAATTAGAAATTCAACCCGGCCCGACC
129 AACAAAATAAAATTTCATACGACCCGACCCGAATATATAAATTAGAAATCCAACCCGACCCGACC
*
1617829 TGAAATAATAAAAAAAATATTTTTATTTAATAAAAACAGTAACTTAATCCGACCCGACCT
194 TGAAATAAT-AAAAAAATATTTTTATTTAATAAAAACAATAACTTAATCCGACCCGACCT
* *
1617889 AAATTATATATATTTTCGGGTCGGTTCGATTTTTTTCACCCTAAACCCAAACCCGACCCGAATAT
1 AAATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCAAACCCGACCCGAATAT
* * * * *
1617954 CACACTTAAAAAAACCCGATCCTACCCGACCCGAATAT-ATGAATTAGAAACCAGACCCGACCCG
66 CACACTTAAAAAACCCCGACCCGACCCGACCCGAATATCA-CACTTA-AAACCAGACCCGACCCG
*
1618018 AA-ATAATAAAA
129 AACAAAATAAAA
1618029 AAATATTTTT
Statistics
Matches: 350, Mismatches: 36, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
249 47 0.13
250 8 0.02
251 4 0.01
253 8 0.02
254 132 0.38
255 151 0.43
ACGTcount: A:0.38, C:0.28, G:0.11, T:0.23
Consensus pattern (252 bp):
AAATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCAAACCCGACCCGAATAT
CACACTTAAAAAACCCCGACCCGACCCGACCCGAATATCACACTTAAAACCAGACCCGACCCGAA
CAAAATAAAATTTCATACGACCCGACCCGAATATATAAATTAGAAATCCAACCCGACCCGACCTG
AAATAATAAAAAAATATTTTTATTTAATAAAAACAATAACTTAATCCGACCCGACCT
Found at i:1619171 original size:19 final size:19
Alignment explanation
Indices: 1619139--1619175 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1619129 ATGACCAACA
*
1619139 AAATCACAATGCGATCTCT
1 AAATCACAACGCGATCTCT
*
1619158 AAATCGCAACGCGATCTC
1 AAATCACAACGCGATCTC
1619176 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.22
Consensus pattern (19 bp):
AAATCACAACGCGATCTCT
Found at i:1620325 original size:12 final size:13
Alignment explanation
Indices: 1620310--1620343 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
1620300 AAAAGAAAAA
1620310 GAAGAAA-TCCCC
1 GAAGAAAGTCCCC
1620322 GAAGAAAAGTCCCC
1 GAAG-AAAGTCCCC
1620336 GAAGAAAG
1 GAAGAAAG
1620344 AAAATTCCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 7 0.35
14 9 0.45
ACGTcount: A:0.47, C:0.24, G:0.24, T:0.06
Consensus pattern (13 bp):
GAAGAAAGTCCCC
Found at i:1622712 original size:140 final size:140
Alignment explanation
Indices: 1622460--1622729 Score: 486
Period size: 140 Copynumber: 1.9 Consensus size: 140
1622450 AAACGTTGTA
* *
1622460 TTATGTGTAAACTTTTAATATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTATAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
* *
1622525 TGATCTATTTAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATCTATTCAGATGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
1622590 TATGTGTATT
131 TATGTGTATT
*
1622600 TTATGTATAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTTCTA
1 TTATGTATAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
*
1622665 TGATCTGTTCAGATGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATCTATTCAGATGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
1622730 CGCAACGCGA
Statistics
Matches: 124, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
140 124 1.00
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.43
Consensus pattern (140 bp):
TTATGTATAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATCTATTCAGATGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:1622725 original size:20 final size:20
Alignment explanation
Indices: 1622700--1622876 Score: 237
Period size: 20 Copynumber: 8.8 Consensus size: 20
1622690 TTACACATTC
*
1622700 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1622720 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
1622740 ATTTAACTATCGCAACGCAA
1 ATTTGACTATCGCAACGCGA
*
1622760 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
1622780 ATATGACTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
*
1622800 ATTTTACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
1622820 ATTTTACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* * *
1622840 ATTTGATTATCACAACGGGA
1 ATTTGACTATCGCAACGCGA
*
1622860 ATTTGACTATCACAACG
1 ATTTGACTATCGCAACG
1622877 AGAAAATCGC
Statistics
Matches: 140, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 140 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:1622950 original size:20 final size:20
Alignment explanation
Indices: 1622927--1622992 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
1622917 AACTTTTGCG
*
1622927 TTGCGATTTTGGCTTTCGCA
1 TTGCGATTTTGACTTTCGCA
* *
1622947 TTGCAATCTTGACTTTCGCA
1 TTGCGATTTTGACTTTCGCA
* * *
1622967 TTGCGATTTTGAGTTTAGCG
1 TTGCGATTTTGACTTTCGCA
1622987 TTGCGA
1 TTGCGA
1622993 AAGTGTACAT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.15, C:0.18, G:0.24, T:0.42
Consensus pattern (20 bp):
TTGCGATTTTGACTTTCGCA
Found at i:1623128 original size:27 final size:26
Alignment explanation
Indices: 1623096--1623219 Score: 78
Period size: 27 Copynumber: 4.8 Consensus size: 26
1623086 ATAAGAATTA
1623096 TTTACACATCAATTAAACAAATCAACT
1 TTTACACATCAATTAAACAAATCAA-T
* ** *
1623123 TTTACAAATCAACTTTTATAAATCAAT
1 TTTACACATCAA-TTAAACAAATCAAT
** * * *
1623150 TAAACAAGCA-CAAAT-AA-GAAT-TA-
1 TTTAC-A-CATCAATTAAACAAATCAAT
1623173 TTTACACATCAATTAAACAAATCAACT
1 TTTACACATCAATTAAACAAATCAA-T
*
1623200 TTTACAAATCAATTAAACAA
1 TTTACACATCAATTAAACAA
1623220 GAAAAAAATG
Statistics
Matches: 71, Mismatches: 17, Indels: 18
0.67 0.16 0.17
Matches are distributed among these distances:
21 2 0.03
22 5 0.07
23 5 0.07
24 4 0.06
25 4 0.06
26 1 0.01
27 35 0.49
28 14 0.20
29 1 0.01
ACGTcount: A:0.51, C:0.18, G:0.02, T:0.30
Consensus pattern (26 bp):
TTTACACATCAATTAAACAAATCAAT
Found at i:1623131 original size:14 final size:14
Alignment explanation
Indices: 1623112--1623148 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1623102 CATCAATTAA
1623112 ACAAATCAACTTTT
1 ACAAATCAACTTTT
1623126 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1623140 ATAAATCAA
1 ACAAATCAA
1623149 TTAAACAAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1623164 original size:77 final size:77
Alignment explanation
Indices: 1623066--1623211 Score: 283
Period size: 77 Copynumber: 1.9 Consensus size: 77
1623056 TTTACATTTC
*
1623066 AATCAATTAAATAAGCACAAATAAGAATTATTTACACATCAATTAAACAAATCAACTTTTACAAA
1 AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTAAACAAATCAACTTTTACAAA
1623131 TCAACTTTTATA
66 TCAACTTTTATA
1623143 AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTAAACAAATCAACTTTTACAAA
1 AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTAAACAAATCAACTTTTACAAA
1623208 TCAA
66 TCAA
1623212 TTAAACAAGA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 68 1.00
ACGTcount: A:0.52, C:0.16, G:0.03, T:0.29
Consensus pattern (77 bp):
AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTAAACAAATCAACTTTTACAAA
TCAACTTTTATA
Found at i:1623190 original size:36 final size:36
Alignment explanation
Indices: 1623067--1623192 Score: 119
Period size: 36 Copynumber: 3.4 Consensus size: 36
1623057 TTACATTTCA
*
1623067 ATCAATTAAATAAGCACAAATAAGAATTATTTACAC
1 ATCAATTAAACAAGCACAAATAAGAATTATTTACAC
* *** * * *
1623103 ATCAATTAAACAAATCAACTTTTACA-AATCAACTTTTATAA
1 ATCAATTAAAC-AAGC-ACAAATA-AGAAT-TA--TTTACAC
1623144 ATCAATTAAACAAGCACAAATAAGAATTATTTACAC
1 ATCAATTAAACAAGCACAAATAAGAATTATTTACAC
1623180 ATCAATTAAACAA
1 ATCAATTAAACAA
1623193 ATCAACTTTT
Statistics
Matches: 68, Mismatches: 15, Indels: 14
0.70 0.15 0.14
Matches are distributed among these distances:
36 28 0.41
37 3 0.04
38 9 0.13
39 9 0.13
40 3 0.04
41 16 0.24
ACGTcount: A:0.52, C:0.16, G:0.03, T:0.29
Consensus pattern (36 bp):
ATCAATTAAACAAGCACAAATAAGAATTATTTACAC
Found at i:1624652 original size:21 final size:21
Alignment explanation
Indices: 1624616--1624719 Score: 75
Period size: 21 Copynumber: 5.0 Consensus size: 21
1624606 GAATGGTGGG
* *
1624616 AGGGACCTCTTCAACGATGAT
1 AGGGGCCTCTTGAACGATGAT
* * **
1624637 AGGGGCCTATTGAACGGTGGG
1 AGGGGCCTCTTGAACGATGAT
* **
1624658 AGGGGACTCTTGAGGGATGAT
1 AGGGGCCTCTTGAACGATGAT
* *
1624679 AGGGCCCTCTTGAACGAT-AGG
1 AGGGGCCTCTTGAACGATGA-T
* *
1624700 AGAGGCCTCTTGAATGATGA
1 AGGGGCCTCTTGAACGATGA
1624720 CAGGTGAGTC
Statistics
Matches: 60, Mismatches: 21, Indels: 3
0.71 0.25 0.04
Matches are distributed among these distances:
20 1 0.02
21 58 0.97
22 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.36, T:0.22
Consensus pattern (21 bp):
AGGGGCCTCTTGAACGATGAT
Found at i:1624668 original size:42 final size:42
Alignment explanation
Indices: 1624604--1624694 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 42
1624594 AATCGGGCTC
* *
1624604 TTGAATGGTGGGAGGGACCTCTTCAACGATGATAGGGGCCTA
1 TTGAACGGTGGGAGGGACCTCTTCAACGATGATAGGGCCCTA
* ** *
1624646 TTGAACGGTGGGAGGGGA-CTCTTGAGGGATGATAGGGCCCTC
1 TTGAACGGTGGGA-GGGACCTCTTCAACGATGATAGGGCCCTA
1624688 TTGAACG
1 TTGAACG
1624695 ATAGGAGAGG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 38 0.90
43 4 0.10
ACGTcount: A:0.22, C:0.16, G:0.38, T:0.23
Consensus pattern (42 bp):
TTGAACGGTGGGAGGGACCTCTTCAACGATGATAGGGCCCTA
Found at i:1624710 original size:42 final size:42
Alignment explanation
Indices: 1624631--1624712 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
1624621 CCTCTTCAAC
* * * *
1624631 GATGATAGGGGCCTATTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGATAGGGCCCTATTGAACGATAGGAGAGGACTCTTGAGG
* *
1624673 GATGATAGGGCCCTCTTGAACGATAGGAGAGGCCTCTTGA
1 GATGATAGGGCCCTATTGAACGATAGGAGAGGACTCTTGA
1624713 ATGATGACAG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.23, C:0.16, G:0.39, T:0.22
Consensus pattern (42 bp):
GATGATAGGGCCCTATTGAACGATAGGAGAGGACTCTTGAGG
Found at i:1624719 original size:42 final size:42
Alignment explanation
Indices: 1624621--1624719 Score: 108
Period size: 42 Copynumber: 2.4 Consensus size: 42
1624611 GTGGGAGGGA
* * * * *
1624621 CCTCTTCAACGATGATAGGGGCCTATTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGATAGGGCCCTATTGAACGATAGGAGAGG
* ** *
1624663 ACTCTTGAGGGATGATAGGGCCCTCTTGAACGATAGGAGAGG
1 CCTCTTGAACGATGATAGGGCCCTATTGAACGATAGGAGAGG
*
1624705 CCTCTTGAATGATGA
1 CCTCTTGAACGATGA
1624720 CAGGTGAGTC
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.24, C:0.18, G:0.34, T:0.23
Consensus pattern (42 bp):
CCTCTTGAACGATGATAGGGCCCTATTGAACGATAGGAGAGG
Found at i:1625233 original size:20 final size:20
Alignment explanation
Indices: 1625208--1625250 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1625198 ATAGTTTCTA
1625208 AAACTTAAAATCGCAACACG
1 AAACTTAAAATCGCAACACG
*
1625228 AAACTTAAAATCGCAACGCG
1 AAACTTAAAATCGCAACACG
1625248 AAA
1 AAA
1625251 TTGACTATCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.51, C:0.23, G:0.12, T:0.14
Consensus pattern (20 bp):
AAACTTAAAATCGCAACACG
Found at i:1625332 original size:19 final size:19
Alignment explanation
Indices: 1625208--1625332 Score: 91
Period size: 19 Copynumber: 6.7 Consensus size: 19
1625198 ATAGTTTCTA
*
1625208 AAACTTAAAATCGCAACACG
1 AAAC-TAAAATCGCAACGCG
1625228 AAACTTAAAATCGCAACGCG
1 AAAC-TAAAATCGCAACGCG
* **
1625248 AAATTGACTATCGCAACG-G
1 AAACT-AAAATCGCAACGCG
* *
1625267 -GA-T--AATCGCAATGCG
1 AAACTAAAATCGCAACGCG
*
1625282 AAA-TAAAAATCGCAACGAG
1 AAACT-AAAATCGCAACGCG
*
1625301 AAACCAAAATCGCAACGCG
1 AAACTAAAATCGCAACGCG
*
1625320 AAACTAAATTCGC
1 AAACTAAAATCGC
1625333 GTTGCGATTT
Statistics
Matches: 84, Mismatches: 14, Indels: 15
0.74 0.12 0.13
Matches are distributed among these distances:
14 8 0.10
15 1 0.01
16 2 0.02
17 1 0.01
18 1 0.01
19 39 0.46
20 32 0.38
ACGTcount: A:0.46, C:0.23, G:0.16, T:0.15
Consensus pattern (19 bp):
AAACTAAAATCGCAACGCG
Found at i:1625427 original size:20 final size:20
Alignment explanation
Indices: 1625399--1625447 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
1625389 GCGATTATCC
* *
1625399 CGTTACGATAGTCAAATTCG
1 CGTTGCGATAATCAAATTCG
***
1625419 CGTTGCGATAATCCTTTTCG
1 CGTTGCGATAATCAAATTCG
1625439 CGTTGCGAT
1 CGTTGCGAT
1625448 TTTTAAGTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAATCAAATTCG
Found at i:1627361 original size:20 final size:20
Alignment explanation
Indices: 1627338--1627378 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1627328 TCTGAAACTT
*
1627338 AAAATCGCAACACGAAAATG
1 AAAATCACAACACGAAAATG
1627358 AAAATCACAACACGAAAATG
1 AAAATCACAACACGAAAATG
1627378 A
1 A
1627379 CTATCGCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.59, C:0.20, G:0.12, T:0.10
Consensus pattern (20 bp):
AAAATCACAACACGAAAATG
Found at i:1627441 original size:19 final size:19
Alignment explanation
Indices: 1627414--1627466 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
1627404 GCAACGAGAT
*
1627414 AATCACAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* * *
1627433 AATCGCAACACAAAAATGAC
1 AATCGCAACGC-GAAATGAA
*
1627453 TATCGCAACGCGAA
1 AATCGCAACGCGAA
1627467 TTTGACTATC
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.49, C:0.25, G:0.15, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1627453 original size:53 final size:54
Alignment explanation
Indices: 1627360--1627462 Score: 136
Period size: 53 Copynumber: 1.9 Consensus size: 54
1627350 CGAAAATGAA
** ** **
1627360 AATCACAACACGAAAATGACTATCGCAATGCAAATTTGACTATCGCAACGAGAT
1 AATCACAACACGAAAATGAAAATCGCAACACAAAAATGACTATCGCAACGAGAT
*
1627414 AATCACAACGCG-AAATGAAAATCGCAACACAAAAATGACTATCGCAACG
1 AATCACAACACGAAAATGAAAATCGCAACACAAAAATGACTATCGCAACG
1627463 CGAATTTGAC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
53 31 0.74
54 11 0.26
ACGTcount: A:0.46, C:0.23, G:0.15, T:0.17
Consensus pattern (54 bp):
AATCACAACACGAAAATGAAAATCGCAACACAAAAATGACTATCGCAACGAGAT
Found at i:1627868 original size:20 final size:21
Alignment explanation
Indices: 1627843--1627900 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
1627833 GCTCTGAGAT
1627843 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
* *
1627863 GGAGATGGGGACGGATTTCGTC
1 GGAGAT-GAGACGGATTTCGCC
*
1627885 GAAGATGAGGACGGAT
1 GGAGATGA-GACGGAT
1627901 GTCGAGAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 6 0.19
21 1 0.03
22 24 0.77
ACGTcount: A:0.26, C:0.14, G:0.41, T:0.19
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:1627877 original size:22 final size:22
Alignment explanation
Indices: 1627850--1627900 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1627840 GATGGAGATA
* *
1627850 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGAAGATGAG
*
1627872 GACGGATTTCGTCGAAGATGAG
1 GACGGATTTCGCCGAAGATGAG
1627894 GACGGAT
1 GACGGAT
1627901 GTCGAGAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.24, C:0.16, G:0.41, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGAAGATGAG
Found at i:1628184 original size:20 final size:19
Alignment explanation
Indices: 1628161--1628206 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1628151 GGAAACTGAT
* *
1628161 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
1628181 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
1628200 TTGCGAT
1 TTGCGAT
1628207 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:1628196 original size:19 final size:19
Alignment explanation
Indices: 1628172--1628208 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1628162 TGCGATACTG
*
1628172 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
1628191 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
1628209 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:1633648 original size:3 final size:3
Alignment explanation
Indices: 1633640--1633664 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1633630 GTTAACTTTC
1633640 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
1633665 TTTTTTGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:1637172 original size:20 final size:20
Alignment explanation
Indices: 1637118--1637172 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
1637108 TTTGGTTCAC
*
1637118 GGAATGTAAGATTAATAGTG
1 GGAATGTAAGATTACTAGTG
*
1637138 AGAATGTAAGATTACTAGTG
1 GGAATGTAAGATTACTAGTG
*
1637158 GGAATATAAGATTAC
1 GGAATGTAAGATTAC
1637173 CAGGGAATAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.42, C:0.04, G:0.25, T:0.29
Consensus pattern (20 bp):
GGAATGTAAGATTACTAGTG
Found at i:1637933 original size:15 final size:14
Alignment explanation
Indices: 1637913--1637942 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1637903 CCAACTATCT
1637913 CTCCCCCACCCCCCC
1 CTCCCCC-CCCCCCC
1637928 CTCCCCCCCCCCCC
1 CTCCCCCCCCCCCC
1637942 C
1 C
1637943 AAAAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.03, C:0.90, G:0.00, T:0.07
Consensus pattern (14 bp):
CTCCCCCCCCCCCC
Found at i:1639254 original size:9 final size:9
Alignment explanation
Indices: 1639240--1639265 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1639230 GCAGAGTTGA
1639240 TGATGATGG
1 TGATGATGG
1639249 TGATGATGG
1 TGATGATGG
1639258 TGATGATG
1 TGATGATG
1639266 ATGGAAGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.42, T:0.35
Consensus pattern (9 bp):
TGATGATGG
Found at i:1643127 original size:20 final size:20
Alignment explanation
Indices: 1643102--1643149 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1643092 GCGAAATAAA
1643102 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATCTCCAG
*
1643122 AATCGCAACGCGATCTCTAG
1 AATCGCAACGCGATCTCCAG
1643142 AATCGCAA
1 AATCGCAA
1643150 ATTAGTTCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (20 bp):
AATCGCAACGCGATCTCCAG
Found at i:1643186 original size:21 final size:20
Alignment explanation
Indices: 1643162--1643375 Score: 93
Period size: 20 Copynumber: 10.5 Consensus size: 20
1643152 TAGTTCCTAG
1643162 AATCGCAACGCGATTATGAA
1 AATCGCAACGCGATTATGAA
*
1643182 GAATCGCAATGCGA-TA-GTACA
1 -AATCGCAACGCGATTATG-A-A
** * * *
1643203 AATTCGCATTGCGATTTTCCAT
1 AA-TCGCAACGCGATTAT-GAA
*
1643225 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGATTATGAA
**
1643245 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGATTATGA-A
*
1643265 AATCGCAACGCGATTATGAC
1 AATCGCAACGCGATTATGAA
* *
1643285 TATCGCAA--CGAGTATCCGTAA
1 AATCGCAACGCGATTAT--G-AA
*
1643306 AATCGCAACGCG--TATCCGTA
1 AATCGCAACGCGATTAT--GAA
* * * *
1643326 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGATTATGAA
* *
1643346 AATCGCAACGCG-TATCTGTA
1 AATCGCAACGCGAT-TATGAA
1643366 AATCGCAACG
1 AATCGCAACG
1643376 AGAATACGTA
Statistics
Matches: 151, Mismatches: 26, Indels: 33
0.72 0.12 0.16
Matches are distributed among these distances:
18 6 0.04
19 2 0.01
20 86 0.57
21 49 0.32
22 5 0.03
23 3 0.02
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGATTATGAA
Found at i:1643250 original size:20 final size:20
Alignment explanation
Indices: 1643225--1643455 Score: 162
Period size: 20 Copynumber: 11.4 Consensus size: 20
1643215 GATTTTCCAT
*
1643225 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
* *
1643245 AATCGCAACGCGAACA-TATA
1 AATCGCAACGCGAATACGA-A
* * *
1643265 AATCGCAACGCGATTATGAC
1 AATCGCAACGCGAATACGAA
* * * *
1643285 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATACG-AA
* * *
1643306 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* *
1643326 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* *
1643346 AATCGCAACGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GAA
* *
1643366 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * * *
1643386 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
1643406 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
1643427 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
1643447 AATCGCAAC
1 AATCGCAAC
1643456 ACGATTTTTA
Statistics
Matches: 169, Mismatches: 34, Indels: 16
0.77 0.16 0.07
Matches are distributed among these distances:
19 2 0.01
20 132 0.78
21 35 0.21
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:1643272 original size:40 final size:40
Alignment explanation
Indices: 1643225--1643455 Score: 200
Period size: 40 Copynumber: 5.7 Consensus size: 40
1643215 GATTTTCCAT
* * * *
1643225 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATA
1 AATCGCAACGCGTATCTGTAAATCGCAACGAGAACATATA
* * * *
1643265 AATCGCAACGCG-AT-TATGACTATCGCAACGAGTATCCGTA-A
1 AATCGCAACGCGTATCTGT-A-AATCGCAACGAG-A-ACATATA
* * **
1643306 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
1 AATCGCAACGCGTATCTGTAAATCGCAACGAGAACATATA
* **
1643346 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTA
1 AATCGCAACGCGTATCTGTAAATCGCAACGAGAACATATA
* * * *
1643386 AATCGCAATGCGTATCCGTAAATCGCAACGACAATACGTA-A
1 AATCGCAACGCGTATCTGTAAATCGCAACGA-GA-ACATATA
*
1643427 AATCGCAACGCGTATCCGTAAATCGCAAC
1 AATCGCAACGCGTATCTGTAAATCGCAAC
1643456 ACGATTTTTA
Statistics
Matches: 159, Mismatches: 23, Indels: 17
0.80 0.12 0.09
Matches are distributed among these distances:
38 1 0.01
39 3 0.02
40 92 0.58
41 55 0.35
42 7 0.04
43 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (40 bp):
AATCGCAACGCGTATCTGTAAATCGCAACGAGAACATATA
Found at i:1643388 original size:121 final size:120
Alignment explanation
Indices: 1643225--1643455 Score: 304
Period size: 121 Copynumber: 1.9 Consensus size: 120
1643215 GATTTTCCAT
* * *
1643225 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATAAATCGCAACGCGATTAT-G-ACTAT
1 AATCGCAACGCGAATATGAAAATCGCAACGAGAACACATAAATCGCAACGCG--TATCGTA-AAT
** *
1643288 CGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
63 CGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
* * * * * *
1643346 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAAATCG
1 AATCGCAACGCGAATATGAAAATCGCAACGAGAACACATAAATCGCAACGCGTAT-CGTAAATCG
1643411 CAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAAC
65 CAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAAC
1643456 ACGATTTTTA
Statistics
Matches: 95, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
119 3 0.03
121 91 0.96
122 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (120 bp):
AATCGCAACGCGAATATGAAAATCGCAACGAGAACACATAAATCGCAACGCGTATCGTAAATCGC
AACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
Found at i:1644080 original size:21 final size:20
Alignment explanation
Indices: 1644020--1644095 Score: 91
Period size: 20 Copynumber: 3.8 Consensus size: 20
1644010 TTCTAAACTT
1644020 AAAATCGCAAC-ATGAAAATG
1 AAAATCGCAACGA-GAAAATG
*
1644040 AAAATCGCAACAAGAAAATG
1 AAAATCGCAACGAGAAAATG
** *
1644060 ACTATTGCAACGAGAGAAATG
1 AAAATCGCAACGAGA-AAATG
1644081 AAAATCGCAACGAGA
1 AAAATCGCAACGAGA
1644096 TAATCGCAAC
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
20 29 0.62
21 18 0.38
ACGTcount: A:0.53, C:0.16, G:0.18, T:0.13
Consensus pattern (20 bp):
AAAATCGCAACGAGAAAATG
Found at i:1644146 original size:19 final size:19
Alignment explanation
Indices: 1644124--1644230 Score: 90
Period size: 19 Copynumber: 6.1 Consensus size: 19
1644114 GAAACCAAAA
*
1644124 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1644143 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1644157 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1644176 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1644190 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1644209 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
1644229 TC
1 TC
1644231 AACCAAAAGA
Statistics
Matches: 69, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
14 20 0.29
16 5 0.07
17 6 0.09
19 22 0.32
20 16 0.23
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1644165 original size:14 final size:14
Alignment explanation
Indices: 1644146--1644201 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
1644136 TTTCATTTCG
1644146 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1644160 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1644179 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1644193 CGTTGCGAT
1 CGTTGCGAT
1644202 AGTCATTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1644171 original size:33 final size:33
Alignment explanation
Indices: 1644129--1644222 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
1644119 CAAAATCGCA
1644129 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1644162 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
1644195 TTGCGATAGTCATTTCCGCGTTGCGATT
1 TTGCGATTTTCATTT-CGCGTTGCGATT
1644223 TTCATTTCAA
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 46 0.79
34 12 0.21
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.44
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1646245 original size:21 final size:21
Alignment explanation
Indices: 1646221--1646287 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1646211 TCATTCCTTG
1646221 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1646242 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1646263 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1646284 AGAG
1 AGAG
1646288 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1646245 original size:42 final size:42
Alignment explanation
Indices: 1646169--1646287 Score: 116
Period size: 42 Copynumber: 2.8 Consensus size: 42
1646159 GACTCGCCTG
* * * * * * *
1646169 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCTCTA
1 TCATCCTTGAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
1646211 TCATTCCTTG-AGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCA-TCCTTGAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* *
1646253 TCATCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATCCTTGAAGA-GTCCCCTCCCACCGTTCAAGAG
1646288 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
41 5 0.08
42 53 0.83
43 6 0.09
ACGTcount: A:0.23, C:0.34, G:0.18, T:0.24
Consensus pattern (42 bp):
TCATCCTTGAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:1647882 original size:19 final size:19
Alignment explanation
Indices: 1647803--1647875 Score: 75
Period size: 19 Copynumber: 4.1 Consensus size: 19
1647793 CAAGAGAATT
* *
1647803 GCAATGCGAAATTAAAATC
1 GCAACGCGAAACTAAAATC
1647822 GCAA--CG--AC-AAAATC
1 GCAACGCGAAACTAAAATC
*
1647836 ACAACGCGAAACTAAAATC
1 GCAACGCGAAACTAAAATC
*
1647855 GCAACGCGAAACTAAATTC
1 GCAACGCGAAACTAAAATC
1647874 GC
1 GC
1647876 GTTGCGATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
14 9 0.20
15 1 0.02
16 2 0.04
17 2 0.04
18 2 0.04
19 29 0.64
ACGTcount: A:0.47, C:0.25, G:0.15, T:0.14
Consensus pattern (19 bp):
GCAACGCGAAACTAAAATC
Found at i:1647987 original size:20 final size:19
Alignment explanation
Indices: 1647871--1648008 Score: 116
Period size: 19 Copynumber: 7.7 Consensus size: 19
1647861 CGAAACTAAA
*
1647871 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
1647890 TTCACATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
1647906 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
1647923 TTCGCATTACGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
1647939 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
**
1647956 TTCGCATTGCGATAGTCAT
1 TTCGCATTGCGATTTTCAT
*
1647975 TTCCGCGTTGCGATTTTCAT
1 TT-CGCATTGCGATTTTCAT
1647995 TTCGCATTGCGATT
1 TTCGCATTGCGATT
1648009 CTCTCGTTGT
Statistics
Matches: 91, Mismatches: 17, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
14 11 0.12
16 12 0.13
17 13 0.14
19 39 0.43
20 16 0.18
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:1648008 original size:72 final size:66
Alignment explanation
Indices: 1647875--1648017 Score: 205
Period size: 72 Copynumber: 2.1 Consensus size: 66
1647865 ACTAAATTCG
*
1647875 CGTTGCGATTTTCATTTCACATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTACGATTCTC
1 CGTTGCGATTTTCATTTCACATTGCGATTCCCGCGTTGCGATTTTCATTTCGCATTACGATTCTC
1647940 T
66 T
* *
1647941 CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCGCGTTGCGATTTTCATTTCGCATTGCG
1 CGTTGCGATTTTCATTTCACATTGCGAT--TC----CCGCGTTGCGATTTTCATTTCGCATTACG
1648006 ATTCTCT
60 ATTCTCT
1648013 CGTTG
1 CGTTG
1648018 TGATAGTAAT
Statistics
Matches: 68, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
66 27 0.40
68 2 0.03
72 39 0.57
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (66 bp):
CGTTGCGATTTTCATTTCACATTGCGATTCCCGCGTTGCGATTTTCATTTCGCATTACGATTCTC
T
Found at i:1648030 original size:33 final size:33
Alignment explanation
Indices: 1647875--1648017 Score: 196
Period size: 33 Copynumber: 4.2 Consensus size: 33
1647865 ACTAAATTCG
* *
1647875 CGTTGCGATTTTCATTTCACATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
1647908 CGTTGCGATTTTCATTTCGCATTACGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
1647941 CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCGCATTGCGAT--TC---T-CT
1647980 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1648013 CGTTG
1 CGTTG
1648018 TGATAGTAAT
Statistics
Matches: 98, Mismatches: 6, Indels: 12
0.84 0.05 0.10
Matches are distributed among these distances:
33 63 0.64
34 1 0.01
35 2 0.02
37 2 0.02
38 1 0.01
39 29 0.30
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:1648030 original size:72 final size:73
Alignment explanation
Indices: 1647908--1648048 Score: 203
Period size: 72 Copynumber: 1.9 Consensus size: 73
1647898 GCGATTCCCT
** * * *
1647908 CGTTGCGATTTTCATTTCGCATTACGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATAGT
1 CGTTGCGATTTTCATTTCGCATTACGATTCTCTCGTTGCGATAGTAATTTCCGCATTGCAATAGA
1647972 CATTTCCG
66 CATTTCCG
* * *
1647980 CGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGTGATAGTAATTTCCGCGTTGCAATAGA
1 CGTTGCGATTTTCATTTCGCATTACGATTCTCTCGTTGCGATAGTAATTTCCGCATTGCAATAGA
1648045 CATT
66 CATT
1648049 AAGATGATTG
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
72 45 0.75
73 15 0.25
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (73 bp):
CGTTGCGATTTTCATTTCGCATTACGATTCTCTCGTTGCGATAGTAATTTCCGCATTGCAATAGA
CATTTCCG
Found at i:1650592 original size:24 final size:24
Alignment explanation
Indices: 1650565--1650610 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1650555 ATCATCAAAA
1650565 TCCGAGTATTGACCAAGATCAACG
1 TCCGAGTATTGACCAAGATCAACG
*
1650589 TCCGGGTATTGACCAAGATCAA
1 TCCGAGTATTGACCAAGATCAA
1650611 ATTTCGAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.22
Consensus pattern (24 bp):
TCCGAGTATTGACCAAGATCAACG
Found at i:1651486 original size:20 final size:20
Alignment explanation
Indices: 1651473--1651601 Score: 172
Period size: 20 Copynumber: 6.5 Consensus size: 20
1651463 CAGAATCTCG
1651473 TTGCGATTTACAGATTCGCA
1 TTGCGATTTACAGATTCGCA
1651493 TTGCGATTTACAGATTCGCA
1 TTGCGATTTACAGATTCGCA
1651513 TTGCGATTTAC-GTATTCGCA
1 TTGCGATTTACAG-ATTCGCA
*
1651533 TTGCGATTTAC-GTATTCACA
1 TTGCGATTTACAG-ATTCGCA
* *
1651553 TTGCGATTTACGGATACGCA
1 TTGCGATTTACAGATTCGCA
* * *
1651573 TTGCGATTTACATATTCTCG
1 TTGCGATTTACAGATTCGCA
1651593 TTGCGATTT
1 TTGCGATTT
1651602 CCGCGTTGCG
Statistics
Matches: 99, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
19 1 0.01
20 97 0.98
21 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.39
Consensus pattern (20 bp):
TTGCGATTTACAGATTCGCA
Found at i:1651499 original size:40 final size:40
Alignment explanation
Indices: 1651452--1651584 Score: 128
Period size: 40 Copynumber: 3.3 Consensus size: 40
1651442 GAAATTCAGT
* *
1651452 ATTGCGATAGT-CAGAATCTCGTTGCGATTTACAG-ATTCGC
1 ATTGCGAT-GTACAGAATCGCATTGCGATTTAC-GTATTCGC
* *
1651492 ATTGCGATTTACAGATTCGCATTGCGATTTACGTATTCGC
1 ATTGCGATGTACAGAATCGCATTGCGATTTACGTATTCGC
* * * * *
1651532 ATTGCGATTTAC-GTATTCACATTGCGATTTACGGATACGC
1 ATTGCGATGTACAG-AATCGCATTGCGATTTACGTATTCGC
*
1651572 ATTGCGATTTACA
1 ATTGCGATGTACA
1651585 TATTCTCGTT
Statistics
Matches: 82, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
39 3 0.04
40 79 0.96
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (40 bp):
ATTGCGATGTACAGAATCGCATTGCGATTTACGTATTCGC
Found at i:1651631 original size:20 final size:20
Alignment explanation
Indices: 1651605--1651771 Score: 139
Period size: 21 Copynumber: 8.4 Consensus size: 20
1651595 GCGATTTCCG
1651605 CGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGTATTCT
* *
1651625 TGTTGCGATTTTACGTATTGT
1 CGTTGCGA-TTTACGTATTCT
*
1651646 CGTTGCGATTT-C-----CG
1 CGTTGCGATTTACGTATTCT
1651660 CGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGTATTCT
* *
1651680 TGTTGCGATTTTACGTATTGT
1 CGTTGCGA-TTTACGTATTCT
* * *
1651701 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCT
* * *
1651721 CGTTGCGATTTTACGGATACG
1 CGTTGCGA-TTTACGTATTCT
* *
1651742 CGTTGCGATTTTACGGATCCT
1 CGTTGCGA-TTTACGTATTCT
1651763 CGTTGCGAT
1 CGTTGCGAT
1651772 AGTCAGAATC
Statistics
Matches: 123, Mismatches: 15, Indels: 18
0.79 0.10 0.12
Matches are distributed among these distances:
14 11 0.09
15 1 0.01
19 1 0.01
20 35 0.28
21 75 0.61
ACGTcount: A:0.15, C:0.19, G:0.25, T:0.41
Consensus pattern (20 bp):
CGTTGCGATTTACGTATTCT
Found at i:1651660 original size:55 final size:55
Alignment explanation
Indices: 1651573--1651711 Score: 253
Period size: 55 Copynumber: 2.5 Consensus size: 55
1651563 CGGATACGCA
* *
1651573 TTGCGA-TTTACATATTCTCGTTGCGATTTCCGCGTTGCGATTTACGTATTCTTG
1 TTGCGATTTTACGTATTGTCGTTGCGATTTCCGCGTTGCGATTTACGTATTCTTG
1651627 TTGCGATTTTACGTATTGTCGTTGCGATTTCCGCGTTGCGATTTACGTATTCTTG
1 TTGCGATTTTACGTATTGTCGTTGCGATTTCCGCGTTGCGATTTACGTATTCTTG
1651682 TTGCGATTTTACGTATTGTCGTTGCGATTT
1 TTGCGATTTTACGTATTGTCGTTGCGATTT
1651712 ACGGATACGC
Statistics
Matches: 82, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
54 6 0.07
55 76 0.93
ACGTcount: A:0.14, C:0.18, G:0.22, T:0.46
Consensus pattern (55 bp):
TTGCGATTTTACGTATTGTCGTTGCGATTTCCGCGTTGCGATTTACGTATTCTTG
Found at i:1651785 original size:41 final size:42
Alignment explanation
Indices: 1651701--1651793 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 42
1651691 TACGTATTGT
* * *
1651701 CGTTGCGA-TTTACGGATACGCGTTGCGATTTTACGGATACG
1 CGTTGCGATTTTACGGATACGCGTTGCGATGTCACGAATACG
* *
1651742 CGTTGCGATTTTACGGATCCTCGTTGCGATAGTCA-GAAT-CG
1 CGTTGCGATTTTACGGATACGCGTTGCGAT-GTCACGAATACG
1651783 CGTTGCGATTT
1 CGTTGCGATTT
1651794 ATATGTTCGC
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
41 21 0.47
42 22 0.49
43 2 0.04
ACGTcount: A:0.18, C:0.20, G:0.28, T:0.33
Consensus pattern (42 bp):
CGTTGCGATTTTACGGATACGCGTTGCGATGTCACGAATACG
Found at i:1651803 original size:20 final size:20
Alignment explanation
Indices: 1651780--1651832 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
1651770 ATAGTCAGAA
*
1651780 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
1651800 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
1651820 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1651833 CTGGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:1651893 original size:42 final size:43
Alignment explanation
Indices: 1651800--1651898 Score: 98
Period size: 42 Copynumber: 2.4 Consensus size: 43
1651790 ATTTATATGT
* *
1651800 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTGCAAAA
** * *
1651841 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTCTTCATAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTGCAAAA
*
1651883 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1651899 GGGACTGATT
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
41 8 0.17
42 35 0.76
43 3 0.07
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTGCAAAA
Found at i:1656124 original size:50 final size:51
Alignment explanation
Indices: 1656054--1656159 Score: 142
Period size: 50 Copynumber: 2.1 Consensus size: 51
1656044 GTGTTAAGTA
* * * *
1656054 TTGAACAATGGGGTACTAAAATGAAACAAAAACTAAATATTAGGTATGGTT
1 TTGAACAATCGGGTACTAAAATAAAACAAAAACTAAACATTAGGTATGATT
* * *
1656105 TTGAACAA-CGGGTATTAAAATAAAATAAAAATTAAACATTAGGTATGATT
1 TTGAACAATCGGGTACTAAAATAAAACAAAAACTAAACATTAGGTATGATT
1656155 TTGAA
1 TTGAA
1656160 AAAAAAATAA
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
50 40 0.83
51 8 0.17
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.29
Consensus pattern (51 bp):
TTGAACAATCGGGTACTAAAATAAAACAAAAACTAAACATTAGGTATGATT
Found at i:1657271 original size:55 final size:54
Alignment explanation
Indices: 1657188--1657296 Score: 209
Period size: 55 Copynumber: 2.0 Consensus size: 54
1657178 CCCACGAAAG
1657188 TAAACGAGGGAAAAAAAGAGTTAATTAATATTAAACTCTTTTAATGTAAAGTAC
1 TAAACGAGGGAAAAAAAGAGTTAATTAATATTAAACTCTTTTAATGTAAAGTAC
1657242 TAAACGAGGGAAAAAAAGGAGTTAATTAATATTAAACTCTTTTAATGTAAAGTAC
1 TAAACGAGGGAAAAAAA-GAGTTAATTAATATTAAACTCTTTTAATGTAAAGTAC
1657297 AAAAACAACG
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 17 0.31
55 37 0.69
ACGTcount: A:0.48, C:0.07, G:0.16, T:0.29
Consensus pattern (54 bp):
TAAACGAGGGAAAAAAAGAGTTAATTAATATTAAACTCTTTTAATGTAAAGTAC
Found at i:1662341 original size:25 final size:25
Alignment explanation
Indices: 1662307--1662357 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
1662297 CCCTCTGATC
*
1662307 CCTCATGCATGCGTTGCATCCATAG
1 CCTCATGCATGCGTTCCATCCATAG
1662332 CCTCATGCATGCGTTCCATCCATAG
1 CCTCATGCATGCGTTCCATCCATAG
1662357 C
1 C
1662358 TGGGAGATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.35, G:0.18, T:0.27
Consensus pattern (25 bp):
CCTCATGCATGCGTTCCATCCATAG
Found at i:1662799 original size:21 final size:21
Alignment explanation
Indices: 1662774--1662817 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1662764 AATTTAGTTA
1662774 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
1662795 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
1662816 AT
1 AT
1662818 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:1662827 original size:28 final size:30
Alignment explanation
Indices: 1662794--1662856 Score: 112
Period size: 28 Copynumber: 2.2 Consensus size: 30
1662784 TAGTATAAAT
1662794 TATTAGTTTGTTAGTTTAAG-T-TATATTA
1 TATTAGTTTGTTAGTTTAAGTTATATATTA
1662822 TATTAGTTTGTTAGTTTAAGTTATATATTA
1 TATTAGTTTGTTAGTTTAAGTTATATATTA
1662852 TATTA
1 TATTA
1662857 TATAAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 20 0.61
29 1 0.03
30 12 0.36
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (30 bp):
TATTAGTTTGTTAGTTTAAGTTATATATTA
Found at i:1663397 original size:23 final size:24
Alignment explanation
Indices: 1663353--1663397 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
1663343 TATTGTGTTT
**
1663353 AAAAATATTTAGTGTTGTTTTAAA
1 AAAAATATTTAGTGTTAATTTAAA
*
1663377 AAAAATATTTTGT-TTAATTTA
1 AAAAATATTTAGTGTTAATTTA
1663398 TATTATATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 6 0.33
24 12 0.67
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (24 bp):
AAAAATATTTAGTGTTAATTTAAA
Found at i:1666726 original size:13 final size:14
Alignment explanation
Indices: 1666701--1666733 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1666691 TATTAATATT
*
1666701 TAATGATTTAGTAG
1 TAATGATTTAGTAA
1666715 TAATGA-TTAGTAA
1 TAATGATTTAGTAA
1666728 TAATGA
1 TAATGA
1666734 AATTATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.39
Consensus pattern (14 bp):
TAATGATTTAGTAA
Found at i:1666743 original size:49 final size:48
Alignment explanation
Indices: 1666556--1666876 Score: 416
Period size: 49 Copynumber: 6.6 Consensus size: 48
1666546 TTTGATTTAG
* * * *
1666556 TAATGATTTGCTAATCATGATT--TAATAATGAATTTA-TATTTAAAATT
1 TAATGATTTG-TAGTAATGATTAGTAATAATGAAATTATTA-TTAATATT
* * *
1666603 ATAATAATTATTTTGTAATGATTAGTAATAATGAAATTATTATTAATATT
1 -TAATGATT-TGTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
*
1666653 TAATGATTTGATAGTAAT-ATTAGTAATAATAAAATTATTATTAATATT
1 TAATGATTTG-TAGTAATGATTAGTAATAATGAAATTATTATTAATATT
1666701 TAATGATTTAGTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
1 TAATGATTT-GTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
*
1666750 TAATGATTTGGTAGTAATGATTAGTAATAATTAAATTATTATTAATATT
1 TAATGATTT-GTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
* *
1666799 TAATGATTTGGTAGTAATGATTAGTAATAATTAAATTATTGTTAATATT
1 TAATGATTT-GTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
*
1666848 TAATGATTTGATAGTAATGCTTTAGTAAT
1 TAATGATTTG-TAGTAATG-ATTAGTAAT
1666877 TATTAGTAAT
Statistics
Matches: 248, Mismatches: 16, Indels: 16
0.89 0.06 0.06
Matches are distributed among these distances:
48 62 0.25
49 156 0.63
50 28 0.11
51 2 0.01
ACGTcount: A:0.41, C:0.01, G:0.11, T:0.46
Consensus pattern (48 bp):
TAATGATTTGTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
Found at i:1667111 original size:19 final size:19
Alignment explanation
Indices: 1667087--1667178 Score: 65
Period size: 19 Copynumber: 5.2 Consensus size: 19
1667077 CATAAAAATG
1667087 ATTTAATAATGATTTTAAT
1 ATTTAATAATGATTTTAAT
*
1667106 A-TT--TAATGA-TTTGAT
1 ATTTAATAATGATTTTAAT
* *
1667121 GATTTAGTAATGATTTTGAT
1 -ATTTAATAATGATTTTAAT
*
1667141 ATTTAAT--T-A-TTTATT
1 ATTTAATAATGATTTTAAT
*
1667156 GATTTAGTAATGATTTTAAT
1 -ATTTAATAATGATTTTAAT
1667176 ATT
1 ATT
1667179 ATGATTTAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
15 9 0.16
16 14 0.25
17 3 0.05
18 3 0.05
19 17 0.30
20 11 0.19
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (19 bp):
ATTTAATAATGATTTTAAT
Found at i:1667123 original size:35 final size:34
Alignment explanation
Indices: 1667084--1667186 Score: 147
Period size: 35 Copynumber: 3.0 Consensus size: 34
1667074 AACCATAAAA
*
1667084 ATGATTTAATAATGATTTTAATATTTAATGATTT
1 ATGATTTAGTAATGATTTTAATATTTAATGATTT
* *
1667118 GATGATTTAGTAATGATTTTGATATTTAATTATTT
1 -ATGATTTAGTAATGATTTTAATATTTAATGATTT
1667153 ATTGATTTAGTAATGATTTTAATA-TT-ATGATTT
1 A-TGATTTAGTAATGATTTTAATATTTAATGATTT
1667186 A
1 A
1667187 ATAATGATTT
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
33 7 0.11
34 3 0.05
35 52 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (34 bp):
ATGATTTAGTAATGATTTTAATATTTAATGATTT
Found at i:1667135 original size:11 final size:11
Alignment explanation
Indices: 1667119--1667202 Score: 51
Period size: 11 Copynumber: 7.2 Consensus size: 11
1667109 TAATGATTTG
1667119 ATGATTTAGTA
1 ATGATTTAGTA
*
1667130 ATGATTTTGATA
1 ATGATTTAG-TA
* * * * *
1667142 TTTAATTATTT
1 ATGATTTAGTA
1667153 ATTGATTTAGTA
1 AT-GATTTAGTA
*
1667165 ATGATTTTAATA
1 ATGA-TTTAGTA
*
1667177 TTATGATTTAATA
1 --ATGATTTAGTA
1667190 ATGATTTAGTA
1 ATGATTTAGTA
1667201 AT
1 AT
1667203 AATCATTATA
Statistics
Matches: 54, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
11 24 0.44
12 19 0.35
13 7 0.13
14 4 0.07
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (11 bp):
ATGATTTAGTA
Found at i:1667222 original size:26 final size:25
Alignment explanation
Indices: 1667155--1667479 Score: 189
Period size: 26 Copynumber: 12.6 Consensus size: 25
1667145 AATTATTTAT
* * *
1667155 TGATTTAGTAATGATTTTAAT-ATTA
1 TGATTTAATAAT-AATTTAATAATAA
* *
1667180 TGATTTAATAATGATTTAGTAATAA
1 TGATTTAATAATAATTTAATAATAA
*
1667205 TCATTATAATAATAATTTAATAATGACTAA
1 TGATT-TAATAATAATTTAAT-A--A-TAA
* * *
1667235 T-ATTTAATGAT-TTGATTATTTAATAA
1 TGATTTAATAATAAT--TTA-ATAATAA
*
1667261 TGATTTGATAATAATCATT-ATAATAA
1 TGATTTAATAATAAT--TTAATAATAA
*
1667287 TGATTTAGTAATAATCATT-ATAATAA
1 TGATTTAATAATAAT--TTAATAATAA
1667313 TGATTTAATAATAATGATTTAATAATAA
1 TGATTTAATAAT-A--ATTTAATAATAA
* *
1667341 TCATTATAATAATGATTTAATAATAA
1 TGATT-TAATAATAATTTAATAATAA
* * *
1667367 TCATTATAATAATGATTTAATAGTAA
1 TGATT-TAATAATAATTTAATAATAA
* * *
1667393 TGATTTAATAATGA-TTAGTAATGA
1 TGATTTAATAATAATTTAATAATAA
* * *
1667417 T-TTTATAATAATGATTTTATAATAA
1 TGATT-TAATAATAATTTAATAATAA
* *
1667442 TGATTTAATAATTA-TTACTAATAA
1 TGATTTAATAATAATTTAATAATAA
* *
1667466 TTATTGAATAATAA
1 TGATTTAATAATAA
1667480 CAAATGAGTG
Statistics
Matches: 244, Mismatches: 37, Indels: 39
0.76 0.12 0.12
Matches are distributed among these distances:
23 2 0.01
24 41 0.17
25 43 0.18
26 101 0.41
27 14 0.06
28 21 0.09
29 17 0.07
30 5 0.02
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (25 bp):
TGATTTAATAATAATTTAATAATAA
Found at i:1667223 original size:70 final size:71
Alignment explanation
Indices: 1667084--1667451 Score: 226
Period size: 70 Copynumber: 5.3 Consensus size: 71
1667074 AACCATAAAA
* * * *
1667084 ATGATTTAATAATGATTTTAATATTTAATGA-TT--TGATGATTTAGTAATGAT-TTTGATATTT
1 ATGATTTAATAATGATTTTAATATTTAATGATTTAATAATGATTTAGTAATAATCATT-ATA-AT
*
1667145 AATTATTT
64 AATGATTT
*
1667153 ATTGATTTAGTAATGATTTTAATA-TT-ATGATTTAATAATGATTTAGTAATAATCATTATAATA
1 A-TGATTTAATAATGATTTTAATATTTAATGATTTAATAATGATTTAGTAATAATCATTATAATA
*
1667216 ATAATTT
65 ATGATTT
* * * * *
1667223 AAT-AATGACTAAT-A-TTTAATGATTTGATTATTTAATAATGATTT-GATAATAATCATTATAA
1 -ATGATTTAATAATGATTTTAAT-ATTTAATGATTTAATAATGATTTAG-TAATAATCATTATAA
1667284 TAATGATTT
63 TAATGATTT
* * * * * * * *
1667293 A-G---TAATAATCATTATAATAATGATTTA-ATAATAATGATTTAATAATAATCATTATAATAA
1 ATGATTTAATAATGATTTTAATATTTAATGATTTAATAATGATTTAGTAATAATCATTATAATAA
1667353 TGATTTAATAAT
66 TGA--T--T--T
* * * *
1667365 AATCATTATAATAATGA-TTTAATA-GTAATGATTTAATAATGA-TTAGTAATGAT-TTTATAAT
1 -ATGATT-TAATAATGATTTTAATATTTAATGATTTAATAATGATTTAGTAATAATCATTATAAT
1667426 AATGATTT
64 AATGATTT
1667434 -T-A--TAATAATGA-TTTAATA
1 ATGATTTAATAATGATTTTAATA
1667452 ATTATTACTA
Statistics
Matches: 241, Mismatches: 31, Indels: 60
0.73 0.09 0.18
Matches are distributed among these distances:
63 16 0.07
66 39 0.16
67 13 0.05
68 12 0.05
69 17 0.07
70 71 0.29
71 21 0.09
72 3 0.01
73 2 0.01
75 12 0.05
76 12 0.05
77 15 0.06
78 8 0.03
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.47
Consensus pattern (71 bp):
ATGATTTAATAATGATTTTAATATTTAATGATTTAATAATGATTTAGTAATAATCATTATAATAA
TGATTT
Found at i:1667340 original size:66 final size:66
Alignment explanation
Indices: 1667185--1667453 Score: 309
Period size: 66 Copynumber: 4.1 Consensus size: 66
1667175 TATTATGATT
* * * * *
1667185 TAATAATGATTTAGTAATAATCATTATAATAATAATTTAATAATGA-C-TAATATTTAATGATTT
1 TAATAATGATTTAATAATAATCATTATAATAATGATTTAATAATAATCATTATA-ATAATGATTT
1667248 GATTA
65 -A--A
* *
1667253 TTTAATAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAATAATGATT
1 --TAATAATGATTTAATAATAATCATTATAATAATGATTTAATAATAATCATTATAATAATGATT
1667318 TAA
64 TAA
1667321 TAATAATGATTTAATAATAATCATTATAATAATGATTTAATAATAATCATTATAATAATGATTTA
1 TAATAATGATTTAATAATAATCATTATAATAATGATTTAATAATAATCATTATAATAATGATTTA
1667386 A
66 A
* * * * *
1667387 TAGTAATGA-TT--TAATAATGA-T-TAGTAATGATTTTATAATAATGATTTTATAATAATGATT
1 TAATAATGATTTAATAATAATCATTATAATAATGATTTAATAATAATCA--TTATAATAATGATT
1667447 TAA
64 TAA
1667450 TAAT
1 TAAT
1667454 TATTACTAAT
Statistics
Matches: 180, Mismatches: 15, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
61 20 0.11
62 1 0.01
63 28 0.16
65 2 0.01
66 72 0.40
68 1 0.01
70 42 0.23
71 10 0.06
72 4 0.02
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.44
Consensus pattern (66 bp):
TAATAATGATTTAATAATAATCATTATAATAATGATTTAATAATAATCATTATAATAATGATTTA
A
Found at i:1667479 original size:14 final size:12
Alignment explanation
Indices: 1667163--1667466 Score: 214
Period size: 14 Copynumber: 24.3 Consensus size: 12
1667153 ATTGATTTAG
*
1667163 TAATGATTTTAA
1 TAATGATTATAA
1667175 TATTATGATT-TAA
1 TA--ATGATTATAA
1667188 TAATGATTTAGTAA
1 TAATGA-TTA-TAA
*
1667202 TAATCATTATAA
1 TAATGATTATAA
*
1667214 TAATAATT-TAA
1 TAATGATTATAA
* *
1667225 TAATGACTAATATT
1 TAATGA-TTATA-A
*
1667239 TAATGATT-TGA
1 TAATGATTATAA
1667250 T--T-ATT-TAA
1 TAATGATTATAA
1667258 TAATGATTTGATAA
1 TAATGA-TT-ATAA
*
1667272 TAATCATTATAA
1 TAATGATTATAA
1667284 TAATGATTTAGTAA
1 TAATGA-TTA-TAA
*
1667298 TAATCATTATAA
1 TAATGATTATAA
1667310 TAATGATTTAATAA
1 TAATGA-TT-ATAA
1667324 TAATGATTTAATAA
1 TAATGA-TT-ATAA
*
1667338 TAATCATTATAA
1 TAATGATTATAA
1667350 TAATGATTTAATAA
1 TAATGA-TT-ATAA
*
1667364 TAATCATTATAA
1 TAATGATTATAA
*
1667376 TAATGATTTAATAG
1 TAATGA-TT-ATAA
1667390 TAATGATT-TAA
1 TAATGATTATAA
1667401 TAATGATTAGTAA
1 TAATGATTA-TAA
* *
1667414 TGAT-TTTATAA
1 TAATGATTATAA
1667425 TAATGATTTTATAA
1 TAATGA--TTATAA
1667439 TAATGATT-TAA
1 TAATGATTATAA
*
1667450 TAATTATTACTAA
1 TAATGATTA-TAA
1667463 TAAT
1 TAAT
1667467 TATTGAATAA
Statistics
Matches: 239, Mismatches: 24, Indels: 57
0.75 0.08 0.18
Matches are distributed among these distances:
8 6 0.03
9 1 0.00
10 1 0.00
11 40 0.17
12 58 0.24
13 44 0.18
14 89 0.37
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (12 bp):
TAATGATTATAA
Done.