Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 9 of 135
Found at i:4146493 original size:23 final size:23
Alignment explanation
Indices: 4146427--4146508 Score: 93
Period size: 23 Copynumber: 3.8 Consensus size: 23
4146417 GATCAATATA
*
4146427 GACACAT-AAGTACCTGA-A-AC
1 GACACATAAAGTGCCTGAGATAC
** *
4146447 GACACACGAGGTGCCT--GATAC
1 GACACATAAAGTGCCTGAGATAC
4146468 GACACATAAAGTGCCTGAGATAC
1 GACACATAAAGTGCCTGAGATAC
4146491 GACACATAAAGTGCCTGA
1 GACACATAAAGTGCCTGA
4146509 TCGACAAAGT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
20 7 0.14
21 21 0.41
23 23 0.45
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (23 bp):
GACACATAAAGTGCCTGAGATAC
Found at i:4146505 original size:44 final size:40
Alignment explanation
Indices: 4146427--4146514 Score: 104
Period size: 44 Copynumber: 2.1 Consensus size: 40
4146417 GATCAATATA
* *
4146427 GACACATAAGTACCTGAAACGACACACGAGGTGCCTGATAC
1 GACACATAAGTACCTGAAACGACACACAAAGTGCCTGAT-C
* *
4146468 GACACATAAAGTGCCTGAGATACGACACATAAAGTGCCTGATC
1 GACACAT-AAGTACCTGA-A-ACGACACACAAAGTGCCTGATC
4146511 GACA
1 GACA
4146515 AAGTCGATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
41 7 0.17
42 9 0.22
43 6 0.15
44 18 0.45
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.16
Consensus pattern (40 bp):
GACACATAAGTACCTGAAACGACACACAAAGTGCCTGATC
Found at i:4148894 original size:14 final size:15
Alignment explanation
Indices: 4148875--4148914 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
4148865 TTGATTGGCA
4148875 GTAAAAT-ATTTTTC
1 GTAAAATGATTTTTC
4148889 GTAAAATGATTTTT-
1 GTAAAATGATTTTTC
*
4148903 GGAAAATG-TTTT
1 GTAAAATGATTTT
4148915 ACTTTTCTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 4 0.17
14 14 0.58
15 6 0.25
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (15 bp):
GTAAAATGATTTTTC
Found at i:4151577 original size:5 final size:5
Alignment explanation
Indices: 4151569--4151614 Score: 65
Period size: 5 Copynumber: 9.2 Consensus size: 5
4151559 TATTTAATTT
* * *
4151569 ATATA ATATA ATACA ATACA ATACA ATATA ATATA ATATA ATATA A
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA A
4151615 AACATCTAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.33
Consensus pattern (5 bp):
ATATA
Found at i:4155967 original size:16 final size:17
Alignment explanation
Indices: 4155945--4155986 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
4155935 TAATCACTTA
4155945 AAAATTATAAAAACAAT
1 AAAATTATAAAAACAAT
*
4155962 -AAATTATAAAAATAAT
1 AAAATTATAAAAACAAT
4155978 AAAATTATA
1 AAAATTATA
4155987 TTTTTACTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATTATAAAAACAAT
Found at i:4157178 original size:20 final size:20
Alignment explanation
Indices: 4157153--4157194 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
4157143 GATAGTCCCT
*
4157153 ATACTTATTGATCTATATAG
1 ATACTTACTGATCTATATAG
4157173 ATACTTACTGATCTATATAG
1 ATACTTACTGATCTATATAG
4157193 AT
1 AT
4157195 TTATTATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.43
Consensus pattern (20 bp):
ATACTTACTGATCTATATAG
Found at i:4158703 original size:23 final size:23
Alignment explanation
Indices: 4158654--4158726 Score: 103
Period size: 23 Copynumber: 3.2 Consensus size: 23
4158644 AAATGTCATT
* *
4158654 TTGCACCGAAGTGCCAC-AACAC
1 TTGCACCGTAGTGCCACTATCAC
* *
4158676 TTGCACTGTAGTGCCGCTATCAC
1 TTGCACCGTAGTGCCACTATCAC
4158699 TTGCACCGTAGTGCCACTATCAC
1 TTGCACCGTAGTGCCACTATCAC
4158722 TTGCA
1 TTGCA
4158727 TGCATGGAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 14 0.32
23 30 0.68
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.25
Consensus pattern (23 bp):
TTGCACCGTAGTGCCACTATCAC
Found at i:4162279 original size:57 final size:60
Alignment explanation
Indices: 4162190--4162303 Score: 162
Period size: 57 Copynumber: 1.9 Consensus size: 60
4162180 AATAAGATTA
*
4162190 TTAATAAAAATAATAAATAATTTAATCATATTTTAACATAATTA-TTAT-TAAATATAAT
1 TTAATAAAAATAATAAATAATTTAATCATATTTCAACATAATTATTTATATAAATATAAT
* * * *
4162248 TTAAT-AAAATAATATATAATTTAATTATATTTCAATATATTTATTTATATAAATAT
1 TTAATAAAAATAATAAATAATTTAATCATATTTCAACATAATTATTTATATAAATAT
4162304 TCATTTTTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
57 33 0.67
58 9 0.18
59 7 0.14
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (60 bp):
TTAATAAAAATAATAAATAATTTAATCATATTTCAACATAATTATTTATATAAATATAAT
Found at i:4187697 original size:51 final size:51
Alignment explanation
Indices: 4187608--4187720 Score: 163
Period size: 51 Copynumber: 2.2 Consensus size: 51
4187598 ACCAGTAAAT
*
4187608 AGTAATCAGTAACAGTAACAGTATTCGACACACAAAGTGTCGAATCGGTAAC
1 AGTAA-CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCGGTAAC
* * **
4187660 GGTAACAGTGACAGTAACAGTATTCGACACATGAAGTGCCGAATCGGTAAC
1 AGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCGGTAAC
*
4187711 AATAACAGTA
1 AGTAACAGTA
4187721 GTCGGCACAT
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
51 49 0.92
52 4 0.08
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.20
Consensus pattern (51 bp):
AGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCGGTAAC
Found at i:4188687 original size:12 final size:12
Alignment explanation
Indices: 4188670--4188696 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4188660 CATTTGAATA
4188670 AATAATTATAAT
1 AATAATTATAAT
4188682 AATAATTATAAT
1 AATAATTATAAT
4188694 AAT
1 AAT
4188697 TATATACCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
AATAATTATAAT
Found at i:4192086 original size:21 final size:21
Alignment explanation
Indices: 4192028--4192086 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
4192018 GCTTCAGTTT
*
4192028 AACCCTTATAGGTTTCTGTTC
1 AACCCTTATGGGTTTCTGTTC
* * * * *
4192049 AGCTCTTACGAGCTTCTGTTC
1 AACCCTTATGGGTTTCTGTTC
4192070 AACCCTTATGGGTTTCT
1 AACCCTTATGGGTTTCT
4192087 ATTTAGCACT
Statistics
Matches: 27, Mismatches: 11, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.41
Consensus pattern (21 bp):
AACCCTTATGGGTTTCTGTTC
Found at i:4192107 original size:42 final size:42
Alignment explanation
Indices: 4191986--4192109 Score: 133
Period size: 42 Copynumber: 3.0 Consensus size: 42
4191976 GTTTTCGTTT
* * * * *
4191986 AACCCTAATAAGTTT-TACTTTAGCTCTTTTGTGCTTCAGTTT
1 AACCCTTATAGGTTTCTA-TTTAGCTCTTATGTGCTTCTGTTC
* * * *
4192028 AACCCTTATAGGTTTCTGTTCAGCTCTTACGAGCTTCTGTTC
1 AACCCTTATAGGTTTCTATTTAGCTCTTATGTGCTTCTGTTC
* *
4192070 AACCCTTATGGGTTTCTATTTAGCACTTATGTGCTTCTGT
1 AACCCTTATAGGTTTCTATTTAGCTCTTATGTGCTTCTGT
4192110 GCAGCCTTCG
Statistics
Matches: 66, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
42 65 0.98
43 1 0.02
ACGTcount: A:0.19, C:0.22, G:0.15, T:0.44
Consensus pattern (42 bp):
AACCCTTATAGGTTTCTATTTAGCTCTTATGTGCTTCTGTTC
Found at i:4195930 original size:13 final size:13
Alignment explanation
Indices: 4195914--4195967 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
4195904 TTTAAACCAA
4195914 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
* *
4195927 ACTTTTTTC-ACAGC
1 AC--TTTTCAAAAGT
*
4195941 ATTTTTCAAAAGT
1 ACTTTTCAAAAGT
4195954 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
4195967 A
1 A
4195968 ATAAAGAACT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
12 5 0.16
13 18 0.56
14 4 0.12
15 5 0.16
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.41
Consensus pattern (13 bp):
ACTTTTCAAAAGT
Found at i:4195933 original size:27 final size:27
Alignment explanation
Indices: 4195903--4195959 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
4195893 AACACTCAAA
4195903 TTTTAAACCA-AACTTTTCAAAAGTACT
1 TTTTAAA-CAGAACTTTTCAAAAGTACT
** * *
4195930 TTTTTCACAGCATTTTTCAAAAGTACT
1 TTTTAAACAGAACTTTTCAAAAGTACT
4195957 TTT
1 TTT
4195960 CAAAAGTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.33, C:0.18, G:0.05, T:0.44
Consensus pattern (27 bp):
TTTTAAACAGAACTTTTCAAAAGTACT
Found at i:4196143 original size:14 final size:15
Alignment explanation
Indices: 4196117--4196146 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4196107 TAAGGAGCCC
4196117 ATTTTTATAATTATT
1 ATTTTTATAATTATT
4196132 ATTTTTAT-ATTATT
1 ATTTTTATAATTATT
4196146 A
1 A
4196147 AAGTGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTTTATAATTATT
Found at i:4200247 original size:20 final size:21
Alignment explanation
Indices: 4200196--4200249 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
4200186 AATTTTTGAA
4200196 AATATAAAAA-TAGAAAATTTT
1 AATA-AAAAATTAGAAAATTTT
* **
4200217 AAGAATCAATTAG-AAATTTT
1 AATAAAAAATTAGAAAATTTT
4200237 AATAAAAAATTAG
1 AATAAAAAATTAG
4200250 TTTGAGTAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
20 20 0.77
21 6 0.23
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.31
Consensus pattern (21 bp):
AATAAAAAATTAGAAAATTTT
Found at i:4201385 original size:6 final size:6
Alignment explanation
Indices: 4201376--4201402 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4201366 TTATATATAT
4201376 ATTGGA ATTGGA ATTGGA ATTGGA ATT
1 ATTGGA ATTGGA ATTGGA ATTGGA ATT
4201403 CTCAGTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.37
Consensus pattern (6 bp):
ATTGGA
Found at i:4221631 original size:30 final size:30
Alignment explanation
Indices: 4221595--4221651 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
4221585 CGTCTCCTCC
4221595 ACCTTTTTTCCTGATACCACAGCATCACCT
1 ACCTTTTTTCCTGATACCACAGCATCACCT
* *
4221625 ACCTTTTTTTCTGATACTACAGCATCA
1 ACCTTTTTTCCTGATACCACAGCATCA
4221652 TCTAAGAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.25, C:0.32, G:0.07, T:0.37
Consensus pattern (30 bp):
ACCTTTTTTCCTGATACCACAGCATCACCT
Found at i:4229184 original size:15 final size:15
Alignment explanation
Indices: 4229166--4229245 Score: 81
Period size: 15 Copynumber: 5.3 Consensus size: 15
4229156 GCTTGAGTTG
*
4229166 GATGATGAGGATGAA
1 GATGATGACGATGAA
* *
4229181 GATGA-AATTGATGAA
1 GATGATGA-CGATGAA
4229196 GATGATGACGATGAA
1 GATGATGACGATGAA
* * *
4229211 GATGAGGAGGATGAC
1 GATGATGACGATGAA
*
4229226 GATGATGACGATGAT
1 GATGATGACGATGAA
4229241 GATGA
1 GATGA
4229246 AGAAGAAGAA
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
14 1 0.02
15 51 0.96
16 1 0.02
ACGTcount: A:0.39, C:0.04, G:0.36, T:0.21
Consensus pattern (15 bp):
GATGATGACGATGAA
Found at i:4229200 original size:30 final size:29
Alignment explanation
Indices: 4229166--4229246 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 29
4229156 GCTTGAGTTG
* *
4229166 GATGATGAGGATGAAGATGAAATTGATGAA
1 GATGATGACGATGAAGATGAAA-GGATGAA
* *
4229196 GATGATGACGATGAAGATGAGGAGGATGAC
1 GATGATGACGATGAAGATGA-AAGGATGAA
*
4229226 GATGATGACGATGATGATGAA
1 GATGATGACGATGAAGATGAA
4229247 GAAGAAGAAG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
30 43 0.98
31 1 0.02
ACGTcount: A:0.40, C:0.04, G:0.36, T:0.21
Consensus pattern (29 bp):
GATGATGACGATGAAGATGAAAGGATGAA
Found at i:4233236 original size:27 final size:28
Alignment explanation
Indices: 4233179--4233245 Score: 100
Period size: 27 Copynumber: 2.4 Consensus size: 28
4233169 ATAAAAAATA
*
4233179 ACCAAAATATTATAACCTTTTTTTTTATTT
1 ACCAAAATATTATAA-C-ATTTTTTTATTT
4233209 ACCAAAATATTATAA-ATTTTTTTATTT
1 ACCAAAATATTATAACATTTTTTTATTT
4233236 ACCAAAATAT
1 ACCAAAATAT
4233246 ACCAAAAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
27 21 0.58
30 15 0.42
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (28 bp):
ACCAAAATATTATAACATTTTTTTATTT
Found at i:4233275 original size:17 final size:16
Alignment explanation
Indices: 4233255--4233286 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
4233245 TACCAAAAAT
4233255 AAAAAATAAAAACCTGC
1 AAAAAA-AAAAACCTGC
4233272 AAAAAAAAAAACCTG
1 AAAAAAAAAAACCTG
4233287 TGGCGGCACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.69, C:0.16, G:0.06, T:0.09
Consensus pattern (16 bp):
AAAAAAAAAAACCTGC
Found at i:4233559 original size:15 final size:15
Alignment explanation
Indices: 4233539--4233568 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4233529 AACTATTCTC
4233539 ATTTAATAAAATCTA
1 ATTTAATAAAATCTA
*
4233554 ATTTAATAAACTCTA
1 ATTTAATAAAATCTA
4233569 TTTTGGTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTTAATAAAATCTA
Found at i:4233602 original size:23 final size:23
Alignment explanation
Indices: 4233576--4233647 Score: 55
Period size: 23 Copynumber: 3.2 Consensus size: 23
4233566 CTATTTTGGT
4233576 AATTTGATAAGAATAGTTTATTA
1 AATTTGATAAGAATAGTTTATTA
*
4233599 AA-TT-A-AA-ATTGAG-TTATTAA
1 AATTTGATAAGAAT-AGTTTATT-A
*
4233619 GTAATTTGATGAGAATAGTTTATTA
1 --AATTTGATAAGAATAGTTTATTA
4233644 AATT
1 AATT
4233648 AAAATAGAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 18
0.64 0.05 0.31
Matches are distributed among these distances:
19 7 0.19
20 5 0.14
21 1 0.03
22 4 0.11
23 8 0.22
24 1 0.03
25 4 0.11
26 7 0.19
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (23 bp):
AATTTGATAAGAATAGTTTATTA
Found at i:4233669 original size:45 final size:45
Alignment explanation
Indices: 4233574--4233662 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
4233564 CTCTATTTTG
*
4233574 GTAATTTGATAAGAATAGTTTATTAAATTAAAATTGAGTTATTAA
1 GTAATTTGATAAGAATAGTTTATTAAATTAAAATAGAGTTATTAA
*
4233619 GTAATTTGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTA
1 GTAATTTGATAAGAATAGTTTATTAAATTAAAATAGAGTTATTA
4233663 CTTAATTAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.42
Consensus pattern (45 bp):
GTAATTTGATAAGAATAGTTTATTAAATTAAAATAGAGTTATTAA
Found at i:4234230 original size:15 final size:15
Alignment explanation
Indices: 4234210--4234239 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4234200 GTGCAGCCAC
*
4234210 AGGTTTTTTTTTTGT
1 AGGTTTTTGTTTTGT
4234225 AGGTTTTTGTTTTGT
1 AGGTTTTTGTTTTGT
4234240 TTTGGTATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.00, G:0.23, T:0.70
Consensus pattern (15 bp):
AGGTTTTTGTTTTGT
Found at i:4234404 original size:27 final size:27
Alignment explanation
Indices: 4234350--4234412 Score: 101
Period size: 27 Copynumber: 2.3 Consensus size: 27
4234340 TTTTTTTGGT
4234350 ATATTTTGGTAAATAAAAAAATTTTATA
1 ATATTTTGGTAAATAAAAAAA-TTTATA
4234378 ATATTTTGGTAAAATAAAAAAA-TTATA
1 ATATTTTGGT-AAATAAAAAAATTTATA
4234405 ATATTTTG
1 ATATTTTG
4234413 ATTATTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
27 13 0.38
28 10 0.29
29 11 0.32
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAATTTATA
Found at i:4238501 original size:13 final size:13
Alignment explanation
Indices: 4238483--4238508 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4238473 TGAAAAAGTC
4238483 TGGTGATCGTCCT
1 TGGTGATCGTCCT
4238496 TGGTGATCGTCCT
1 TGGTGATCGTCCT
4238509 CTTCTTCGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.23, G:0.31, T:0.38
Consensus pattern (13 bp):
TGGTGATCGTCCT
Found at i:4265717 original size:24 final size:23
Alignment explanation
Indices: 4265675--4265723 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
4265665 AATGTCTTAT
4265675 AAAAATATAGTAAAATATTT-TA
1 AAAAATATAGTAAAATATTTGTA
*
4265697 AAAAATACTCGTATAAATATTTGTA
1 AAAAATA-TAGTA-AAATATTTGTA
4265722 AA
1 AA
4265724 TGTTAAACAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 7 0.30
23 4 0.17
24 8 0.35
25 4 0.17
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (23 bp):
AAAAATATAGTAAAATATTTGTA
Found at i:4275516 original size:20 final size:20
Alignment explanation
Indices: 4275493--4275539 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
4275483 TCTAAACAAA
4275493 AATTATAAAAAAATCAAAAT
1 AATTATAAAAAAATCAAAAT
* * *
4275513 AATTTTTAAAAATTCAAAAT
1 AATTATAAAAAAATCAAAAT
*
4275533 ATTTATA
1 AATTATA
4275540 GAAATTTAAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (20 bp):
AATTATAAAAAAATCAAAAT
Found at i:4275536 original size:19 final size:20
Alignment explanation
Indices: 4275495--4275555 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
4275485 TAAACAAAAA
*
4275495 TTATAAAAAAATCAAAATAAT
1 TTAT-AAAAATTCAAAATAAT
*
4275516 TTTTAAAAATTCAAAAT-AT
1 TTATAAAAATTCAAAATAAT
* * *
4275535 TTATAGAAATTTAAAAAAAT
1 TTATAAAAATTCAAAATAAT
4275555 T
1 T
4275556 GTATTTAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 15 0.45
20 15 0.45
21 3 0.09
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (20 bp):
TTATAAAAATTCAAAATAAT
Found at i:4275554 original size:10 final size:10
Alignment explanation
Indices: 4275490--4275594 Score: 52
Period size: 10 Copynumber: 10.3 Consensus size: 10
4275480 CTCTCTAAAC
4275490 AAAAATTATAA
1 AAAAATT-TAA
*
4275501 AAAAA-TCAA
1 AAAAATTTAA
* **
4275510 AATAATTTTT
1 AAAAATTTAA
*
4275520 AAAAA-TTCA
1 AAAAATTTAA
* *
4275529 AAATATTTAT
1 AAAAATTTAA
*
4275539 AGAAATTTAA
1 AAAAATTTAA
*
4275549 AAAAATTGTATTT
1 AAAAATT-TA--A
* *
4275562 AAAAATATAT
1 AAAAATTTAA
4275572 AAAAATTTAA
1 AAAAATTTAA
*
4275582 AAAAATCTAA
1 AAAAATTTAA
4275592 AAA
1 AAA
4275595 CATACAAAGG
Statistics
Matches: 69, Mismatches: 20, Indels: 11
0.69 0.20 0.11
Matches are distributed among these distances:
9 12 0.17
10 42 0.61
11 7 0.10
12 2 0.03
13 6 0.09
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (10 bp):
AAAAATTTAA
Found at i:4275581 original size:18 final size:18
Alignment explanation
Indices: 4275558--4275594 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4275548 AAAAAATTGT
*
4275558 ATTTAAAAATATATAAAA
1 ATTTAAAAAAATATAAAA
*
4275576 ATTTAAAAAAATCTAAAA
1 ATTTAAAAAAATATAAAA
4275594 A
1 A
4275595 CATACAAAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
ATTTAAAAAAATATAAAA
Found at i:4300484 original size:27 final size:28
Alignment explanation
Indices: 4300452--4300509 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 28
4300442 AACGCAGGAT
4300452 TGAGT-ATGATCGTTCCGTAGAAAAGAA
1 TGAGTAATGATCGTTCCGTAGAAAAGAA
* * *
4300479 TGAGTAGATTATGGTTCCGTGGAAAAGAA
1 TGAGTA-ATGATCGTTCCGTAGAAAAGAA
4300508 TG
1 TG
4300510 TTTAAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 5 0.19
29 21 0.81
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.28
Consensus pattern (28 bp):
TGAGTAATGATCGTTCCGTAGAAAAGAA
Found at i:4311793 original size:30 final size:30
Alignment explanation
Indices: 4311753--4311815 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
4311743 GAGATTCTTT
4311753 TATTCGATTTATTTCATTAAACGCCACCTC
1 TATTCGATTTATTTCATTAAACGCCACCTC
* *
4311783 TATTCTATTTATTTCATTAAATGCCACCTC
1 TATTCGATTTATTTCATTAAACGCCACCTC
4311813 TAT
1 TAT
4311816 CATGCAGGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.27, C:0.24, G:0.05, T:0.44
Consensus pattern (30 bp):
TATTCGATTTATTTCATTAAACGCCACCTC
Found at i:4318453 original size:17 final size:18
Alignment explanation
Indices: 4318424--4318458 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
4318414 ATATAGTTAC
4318424 AAAAGAGTAATTATGATT
1 AAAAGAGTAATTATGATT
4318442 AAAAGA-TAATTATGATT
1 AAAAGAGTAATTATGATT
4318459 GATTTATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.34
Consensus pattern (18 bp):
AAAAGAGTAATTATGATT
Found at i:4326199 original size:27 final size:27
Alignment explanation
Indices: 4326139--4326199 Score: 63
Period size: 27 Copynumber: 2.2 Consensus size: 27
4326129 AATTCAAAAG
*
4326139 TTATATAAATATTAATATAAAAAATTCA
1 TTAT-TAAATATTAATAGAAAAAATTCA
*
4326167 TAATTAAAT-TTAAATAGAAAAAATT-A
1 TTATTAAATATT-AATAGAAAAAATTCA
4326193 TTTATTA
1 -TTATTA
4326200 CACTACAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 3 0.11
27 22 0.79
28 3 0.11
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (27 bp):
TTATTAAATATTAATAGAAAAAATTCA
Found at i:4333183 original size:23 final size:23
Alignment explanation
Indices: 4333157--4333200 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
4333147 TAAATATTGT
4333157 TTTATTAATATTTTACTTAGATA
1 TTTATTAATATTTTACTTAGATA
* *
4333180 TTTATTATTATTTTATTTAGA
1 TTTATTAATATTTTACTTAGA
4333201 AAATGGTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (23 bp):
TTTATTAATATTTTACTTAGATA
Found at i:4334288 original size:2 final size:2
Alignment explanation
Indices: 4334283--4334309 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4334273 AAATATATGA
4334283 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
4334310 GTAGATGAAT
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:4335770 original size:129 final size:130
Alignment explanation
Indices: 4335571--4335829 Score: 511
Period size: 129 Copynumber: 2.0 Consensus size: 130
4335561 TATTTAGAAG
4335571 TGATAAATCCGAAAATTATACGTGAATAATAGTTTAATATGTAATTGTATATATAAACTTTTGAT
1 TGATAAATCCGAAAATTATACGTGAATAATAGTTTAATATGTAATTGTATATATAAACTTTTGAT
4335636 TCGATTAAATTCTTGTAAATTATATATTACATACATGAATAATTATATTTATTC-ATATAAAAAT
66 TCGATTAAATTCTTGTAAATTATATATTACATACATGAATAATTATATTTATTCAATATAAAAAT
4335700 TGATAAATCCGAAAATTATACGTGAATAATAGTTTAATATGTAATTGTATATATAAACTTTTGAT
1 TGATAAATCCGAAAATTATACGTGAATAATAGTTTAATATGTAATTGTATATATAAACTTTTGAT
4335765 TCGATTAAATTCTTGTAAATTATATATTACATACATGAATAATTATATTTATTCAATATAAAAAT
66 TCGATTAAATTCTTGTAAATTATATATTACATACATGAATAATTATATTTATTCAATATAAAAAT
4335830 AAATTGATGT
Statistics
Matches: 129, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
129 119 0.92
130 10 0.08
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (130 bp):
TGATAAATCCGAAAATTATACGTGAATAATAGTTTAATATGTAATTGTATATATAAACTTTTGAT
TCGATTAAATTCTTGTAAATTATATATTACATACATGAATAATTATATTTATTCAATATAAAAAT
Found at i:4347397 original size:87 final size:87
Alignment explanation
Indices: 4347301--4347469 Score: 275
Period size: 87 Copynumber: 1.9 Consensus size: 87
4347291 AAGGAGCTGA
* * *
4347301 AAAGGAGAAGATAAAAATTTTAGCTTTTTCTCTCCCAAAAGCATTTTTGGTGCTTAATTACTTTT
1 AAAGGAGAAGATAAAAATTTTAACTTTTCCTCTCCCAAAAGCACTTTTGGTGCTTAATTACTTTT
* *
4347366 TCACCTCTCCAATAACATAGTG
66 TCACCCCTCCAACAACATAGTG
* *
4347388 AAAGGAGAAGCTAAAATTTTTAACTTTTCCTCTCCCAAAAGCACTTTTGGTGCTTAATTACTTTT
1 AAAGGAGAAGATAAAAATTTTAACTTTTCCTCTCCCAAAAGCACTTTTGGTGCTTAATTACTTTT
4347453 TCACCCCTCCAACAACA
66 TCACCCCTCCAACAACA
4347470 AAGTACTTTC
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 75 1.00
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (87 bp):
AAAGGAGAAGATAAAAATTTTAACTTTTCCTCTCCCAAAAGCACTTTTGGTGCTTAATTACTTTT
TCACCCCTCCAACAACATAGTG
Found at i:4349629 original size:18 final size:18
Alignment explanation
Indices: 4349606--4349642 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
4349596 TGTACGAGAC
4349606 TAAAAAAATCAATTGAAG
1 TAAAAAAATCAATTGAAG
4349624 TAAAAAAATCAATTGAAG
1 TAAAAAAATCAATTGAAG
4349642 T
1 T
4349643 GACAATTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.59, C:0.05, G:0.11, T:0.24
Consensus pattern (18 bp):
TAAAAAAATCAATTGAAG
Found at i:4351490 original size:38 final size:38
Alignment explanation
Indices: 4351435--4351512 Score: 122
Period size: 38 Copynumber: 2.1 Consensus size: 38
4351425 ATAGATATGC
*
4351435 AATTGAAGAAGACAATAAATTGTGCATATTACAATAAA
1 AATTGAAGAAGACAATAAATTGTACATATTACAATAAA
*
4351473 AATTGATA-AAGATAATAAATTGTACATATTACAATAAA
1 AATTGA-AGAAGACAATAAATTGTACATATTACAATAAA
4351511 AA
1 AA
4351513 AAGTAAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 36 0.97
39 1 0.03
ACGTcount: A:0.55, C:0.06, G:0.10, T:0.28
Consensus pattern (38 bp):
AATTGAAGAAGACAATAAATTGTACATATTACAATAAA
Found at i:4351508 original size:19 final size:19
Alignment explanation
Indices: 4351446--4351510 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 19
4351436 ATTGAAGAAG
*
4351446 ACAATAAATTGTGCATATT
1 ACAATAAATTGTACATATT
*
4351465 ACAATAAAAATTGATA-A-A-G
1 ACAAT--AAATTG-TACATATT
*
4351484 ATAATAAATTGTACATATT
1 ACAATAAATTGTACATATT
4351503 ACAATAAA
1 ACAATAAA
4351511 AAAAGTAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 12
0.67 0.10 0.23
Matches are distributed among these distances:
16 2 0.06
17 7 0.20
18 1 0.03
19 16 0.46
20 1 0.03
21 7 0.20
22 1 0.03
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (19 bp):
ACAATAAATTGTACATATT
Found at i:4351532 original size:39 final size:38
Alignment explanation
Indices: 4351448--4351533 Score: 102
Period size: 38 Copynumber: 2.2 Consensus size: 38
4351438 TGAAGAAGAC
* ** * *
4351448 AATAAATTGTGCATATTACAATAAAAATTGATAAAGAT
1 AATAAATTGTACATATTACAATAAAAAAAGAAAAAAAT
4351486 AATAAATTGTACATATTACAATAAAAAAAGTAAAAAAAT
1 AATAAATTGTACATATTACAATAAAAAAAG-AAAAAAAT
4351525 -ATCAAATTG
1 AAT-AAATTG
4351534 AAACTTTAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
38 29 0.71
39 12 0.29
ACGTcount: A:0.57, C:0.06, G:0.08, T:0.29
Consensus pattern (38 bp):
AATAAATTGTACATATTACAATAAAAAAAGAAAAAAAT
Found at i:4351836 original size:11 final size:11
Alignment explanation
Indices: 4351820--4351868 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
4351810 AATAAATACA
4351820 AAAAATATTTT
1 AAAAATATTTT
***
4351831 AAAAATAAAAAT
1 AAAAAT-ATTTT
4351843 AAAAATATTTT
1 AAAAATATTTT
*
4351854 AAAAGTATTTT
1 AAAAATATTTT
4351865 AAAA
1 AAAA
4351869 TTAAAAAATA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
11 22 0.73
12 8 0.27
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:4352110 original size:23 final size:23
Alignment explanation
Indices: 4352074--4352119 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
4352064 ACCCTCGCTA
*
4352074 AAAAGATAAAAAAATTTATACCC
1 AAAAGATAAAAAAAGTTATACCC
*
4352097 AAAAGA-AAAGAAAAGTTCTACCC
1 AAAAGATAAA-AAAAGTTATACCC
4352120 TATGGAGAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.59, C:0.15, G:0.09, T:0.17
Consensus pattern (23 bp):
AAAAGATAAAAAAAGTTATACCC
Found at i:4353121 original size:70 final size:72
Alignment explanation
Indices: 4353039--4353175 Score: 233
Period size: 72 Copynumber: 1.9 Consensus size: 72
4353029 ACGTATGCCG
*
4353039 ATCATTGAATCTCAAAAGTGTGT-AAATTACTTTC-TTTACTGTTTCATTAAGTGATTTTAAACG
1 ATCATTGAATCTCAAAAGTGTGTAAAATTACTTTCTTTTACTGTTTCATGAAGTGATTTTAAACG
4353102 CCTTTTT
66 CCTTTTT
* *
4353109 ATCATTGAATCTCAAAAGTGTGTAAAATTACTTTCTTTTACTGTTTCATGAATTGATTTTAATCG
1 ATCATTGAATCTCAAAAGTGTGTAAAATTACTTTCTTTTACTGTTTCATGAAGTGATTTTAAACG
4353174 CC
66 CC
4353176 CTTTATGGAT
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
70 23 0.37
71 11 0.18
72 28 0.45
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.45
Consensus pattern (72 bp):
ATCATTGAATCTCAAAAGTGTGTAAAATTACTTTCTTTTACTGTTTCATGAAGTGATTTTAAACG
CCTTTTT
Found at i:4359762 original size:338 final size:338
Alignment explanation
Indices: 4359139--4359821 Score: 1357
Period size: 338 Copynumber: 2.0 Consensus size: 338
4359129 GGAAGGAACT
*
4359139 GACCTCGATATTTCATGATATTAAGAAAGGAAGATATGACGGTGGAGATTGGTTTCAGTTCCACC
1 GACCTCTATATTTCATGATATTAAGAAAGGAAGATATGACGGTGGAGATTGGTTTCAGTTCCACC
4359204 GTGGCCTTGCCCCTCCTCTCAGCATTCACTATTGACCTTAACGCATCGTTCAGTATCCTCCTTCC
66 GTGGCCTTGCCCCTCCTCTCAGCATTCACTATTGACCTTAACGCATCGTTCAGTATCCTCCTTCC
4359269 CATCTCTCTCTCGAACCAGTTCCAGAGCCGAACGGTTAAACCCTCAAAGTTACAGCCAAAACCTC
131 CATCTCTCTCTCGAACCAGTTCCAGAGCCGAACGGTTAAACCCTCAAAGTTACAGCCAAAACCTC
4359334 GATTGCACTAACGAAAATGTTGTCGTTCAATCGCTTATATTATATGGCATCTCACTGTTGGATTA
196 GATTGCACTAACGAAAATGTTGTCGTTCAATCGCTTATATTATATGGCATCTCACTGTTGGATTA
4359399 GTAAATAAAAAAATTAAGAAAATAAAAATAGCTAAAAGCTAAACTTCATAAATGGGGCGTTCCGA
261 GTAAATAAAAAAATTAAGAAAATAAAAATAGCTAAAAGCTAAACTTCATAAATGGGGCGTTCCGA
4359464 GAATCGAACTCGG
326 GAATCGAACTCGG
4359477 GACCTCTATATTTCATGATATTAAGAAAGGAAGATATGACGGTGGAGATTGGTTTCAGTTCCACC
1 GACCTCTATATTTCATGATATTAAGAAAGGAAGATATGACGGTGGAGATTGGTTTCAGTTCCACC
4359542 GTGGCCTTGCCCCTCCTCTCAGCATTCACTATTGACCTTAACGCATCGTTCAGTATCCTCCTTCC
66 GTGGCCTTGCCCCTCCTCTCAGCATTCACTATTGACCTTAACGCATCGTTCAGTATCCTCCTTCC
4359607 CATCTCTCTCTCGAACCAGTTCCAGAGCCGAACGGTTAAACCCTCAAAGTTACAGCCAAAACCTC
131 CATCTCTCTCTCGAACCAGTTCCAGAGCCGAACGGTTAAACCCTCAAAGTTACAGCCAAAACCTC
4359672 GATTGCACTAACGAAAATGTTGTCGTTCAATCGCTTATATTATATGGCATCTCACTGTTGGATTA
196 GATTGCACTAACGAAAATGTTGTCGTTCAATCGCTTATATTATATGGCATCTCACTGTTGGATTA
4359737 GTAAATAAAAAAATTAAGAAAATAAAAATAGCTAAAAGCTAAACTTCATAAATGGGGCGTTCCGA
261 GTAAATAAAAAAATTAAGAAAATAAAAATAGCTAAAAGCTAAACTTCATAAATGGGGCGTTCCGA
4359802 GAATCGAACTCGG
326 GAATCGAACTCGG
4359815 GACCTCT
1 GACCTCT
4359822 CGCACCCAAA
Statistics
Matches: 344, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
338 344 1.00
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.28
Consensus pattern (338 bp):
GACCTCTATATTTCATGATATTAAGAAAGGAAGATATGACGGTGGAGATTGGTTTCAGTTCCACC
GTGGCCTTGCCCCTCCTCTCAGCATTCACTATTGACCTTAACGCATCGTTCAGTATCCTCCTTCC
CATCTCTCTCTCGAACCAGTTCCAGAGCCGAACGGTTAAACCCTCAAAGTTACAGCCAAAACCTC
GATTGCACTAACGAAAATGTTGTCGTTCAATCGCTTATATTATATGGCATCTCACTGTTGGATTA
GTAAATAAAAAAATTAAGAAAATAAAAATAGCTAAAAGCTAAACTTCATAAATGGGGCGTTCCGA
GAATCGAACTCGG
Found at i:4368706 original size:13 final size:13
Alignment explanation
Indices: 4368688--4368712 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4368678 ACTTCGTGGG
4368688 TTTAAAATAATAT
1 TTTAAAATAATAT
4368701 TTTAAAATAATA
1 TTTAAAATAATA
4368713 ATATTTATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTAAAATAATAT
Found at i:4368731 original size:19 final size:18
Alignment explanation
Indices: 4368692--4368735 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
4368682 CGTGGGTTTA
4368692 AAATAATA-TTTTAAAAT
1 AAATAATATTTTTAAAAT
4368709 -AATAATATTTATTAAAAT
1 AAATAATATTT-TTAAAAT
4368727 AAAT-ATATT
1 AAATAATATT
4368736 CTGAAAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 7 0.29
17 2 0.08
18 12 0.50
19 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATAATATTTTTAAAAT
Found at i:4377242 original size:42 final size:42
Alignment explanation
Indices: 4377178--4377272 Score: 172
Period size: 42 Copynumber: 2.2 Consensus size: 42
4377168 ACAATTTTTG
*
4377178 ATGTATTATGACCACCTCATGATGTCTCAAAGATTGTTCCACC
1 ATGT-TTATGACCACCTCATGATGTCTCAAAGATTATTCCACC
4377221 ATGTTTATGACCACCTCATGATGTCTCAAAGATTATTCCACC
1 ATGTTTATGACCACCTCATGATGTCTCAAAGATTATTCCACC
4377263 ATGTTTATGA
1 ATGTTTATGA
4377273 ATATCAGTAA
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 47 0.92
43 4 0.08
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (42 bp):
ATGTTTATGACCACCTCATGATGTCTCAAAGATTATTCCACC
Found at i:4383567 original size:52 final size:52
Alignment explanation
Indices: 4383481--4383634 Score: 254
Period size: 52 Copynumber: 3.0 Consensus size: 52
4383471 ATGAATAATC
* * *
4383481 GTCTTTCACTTTGTAAAAGTAGATCCCCTTTTATCTGCTCGTTTGGCTTTAT
1 GTCTTTCACTTTGTAAAAGCAGATTCCCTTTTATCTGCTCGTTTAGCTTTAT
* *
4383533 GTCTTTCACTTTGTAAAAGCAGATTCCCTCTTATCTGCTCATTTAGCTTTAT
1 GTCTTTCACTTTGTAAAAGCAGATTCCCTTTTATCTGCTCGTTTAGCTTTAT
*
4383585 GTCTTTCATTTTGTAAAAGCAGATTCCCTTTTATCTGCTCGTTTAGCTTT
1 GTCTTTCACTTTGTAAAAGCAGATTCCCTTTTATCTGCTCGTTTAGCTTT
4383635 TATCCCCTAT
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 94 1.00
ACGTcount: A:0.19, C:0.21, G:0.14, T:0.46
Consensus pattern (52 bp):
GTCTTTCACTTTGTAAAAGCAGATTCCCTTTTATCTGCTCGTTTAGCTTTAT
Found at i:4410804 original size:16 final size:16
Alignment explanation
Indices: 4410783--4410814 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4410773 TCCAAAAATG
4410783 AAAGAGATACTAAAAC
1 AAAGAGATACTAAAAC
*
4410799 AAAGAGATATTAAAAC
1 AAAGAGATACTAAAAC
4410815 CCTGTCATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.62, C:0.09, G:0.12, T:0.16
Consensus pattern (16 bp):
AAAGAGATACTAAAAC
Found at i:4413687 original size:18 final size:18
Alignment explanation
Indices: 4413664--4413711 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
4413654 AAAATATGAG
*
4413664 AAATGATGTTCACATTTT
1 AAATGATGTTCACATTTC
4413682 AAATGATGTTCACATTTC
1 AAATGATGTTCACATTTC
4413700 AAATGATGTTCA
1 AAATGATGTTCA
4413712 AATTGATGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (18 bp):
AAATGATGTTCACATTTC
Found at i:4414222 original size:72 final size:72
Alignment explanation
Indices: 4414146--4414379 Score: 384
Period size: 72 Copynumber: 3.3 Consensus size: 72
4414136 TAAACTAGTT
*
4414146 TTTTATCAATAGTTATTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATGTGT
1 TTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATGTGT
4414211 AATCTAG
66 AATCTAG
*
4414218 TTTTATCAATGGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATGTGT
1 TTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATGTGT
4414283 AATCTAG
66 AATCTAG
* *
4414290 TTTTATCAATGGTTGTTTATGTTTGGTTTTTGGATATTGAATTTA-GTTCTACTTATTTATACT-
1 TTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT-GTG
* *
4414353 AAAT-TAA
65 TAATCTAG
4414360 TTTTATCAATAGTTGTTTAT
1 TTTTATCAATAGTTGTTTAT
4414380 ATATGATTTT
Statistics
Matches: 155, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
70 21 0.14
71 18 0.12
72 116 0.75
ACGTcount: A:0.24, C:0.06, G:0.15, T:0.56
Consensus pattern (72 bp):
TTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATGTGT
AATCTAG
Found at i:4432194 original size:23 final size:22
Alignment explanation
Indices: 4432168--4432210 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
4432158 ATATTTAAAT
4432168 TTTAAAATA-TTATTTTGTTTTAC
1 TTTAAAA-AGTTATTTT-TTTTAC
4432191 TTTAAAAAGTTATTTTTTTT
1 TTTAAAAAGTTATTTTTTTT
4432211 GATAAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (22 bp):
TTTAAAAAGTTATTTTTTTTAC
Found at i:4439716 original size:24 final size:23
Alignment explanation
Indices: 4439679--4439726 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
4439669 GTAAAGTTTT
4439679 ATTATGCAAAAAATATAACAATAA
1 ATTATGCAAAAAATATAA-AATAA
* * *
4439703 ATTATTCAATAAATTTAAAATAA
1 ATTATGCAAAAAATATAAAATAA
4439726 A
1 A
4439727 CAATATAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.31
Consensus pattern (23 bp):
ATTATGCAAAAAATATAAAATAA
Found at i:4445701 original size:2 final size:2
Alignment explanation
Indices: 4445694--4445726 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4445684 TTGTGTTGAA
*
4445694 AC AC AC AC AC AC AC AC AC AC AC AC AC TC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
4445727 AAAGATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.48, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:4447003 original size:5 final size:5
Alignment explanation
Indices: 4446993--4447018 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
4446983 TGAATGCTAA
4446993 AGGTC AGGTC AGGTC AGGTC AGGTC A
1 AGGTC AGGTC AGGTC AGGTC AGGTC A
4447019 ACTAATCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.38, T:0.19
Consensus pattern (5 bp):
AGGTC
Found at i:4450136 original size:13 final size:13
Alignment explanation
Indices: 4450118--4450142 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4450108 AAACCTTATC
4450118 CCTTTTATTTTTA
1 CCTTTTATTTTTA
4450131 CCTTTTATTTTT
1 CCTTTTATTTTT
4450143 TTTCTTCCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (13 bp):
CCTTTTATTTTTA
Found at i:4452131 original size:81 final size:81
Alignment explanation
Indices: 4451994--4452160 Score: 289
Period size: 81 Copynumber: 2.1 Consensus size: 81
4451984 CTGTTCCTAA
* *
4451994 TTTCTCGGTTGGTTATTTAGAAACTCAAGTTACTAAGAGAAAAAATTGTATGAAACTATGATTTT
1 TTTCTCGGTTGGTTATTTAGAAACTCAAGTTACTAAGAGAAAAAATTGTATAAAACTATGATTTC
*
4452059 ACGTCACTCTTATCTT
66 AAGTCACTCTTATCTT
*
4452075 TTTCTCGGTTGGTTATTTAGAAACTCAAGTTACTAAGAGAAAAAATTGTATAAAACTGTGATTTC
1 TTTCTCGGTTGGTTATTTAGAAACTCAAGTTACTAAGAGAAAAAATTGTATAAAACTATGATTTC
*
4452140 AAGTCATTCTTATCTT
66 AAGTCACTCTTATCTT
4452156 TTTCT
1 TTTCT
4452161 AATAGTAGAA
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (81 bp):
TTTCTCGGTTGGTTATTTAGAAACTCAAGTTACTAAGAGAAAAAATTGTATAAAACTATGATTTC
AAGTCACTCTTATCTT
Found at i:4456770 original size:116 final size:117
Alignment explanation
Indices: 4456566--4456798 Score: 459
Period size: 116 Copynumber: 2.0 Consensus size: 117
4456556 GGTGGCTAGG
4456566 AATACATTTCCAGCCTATTTTTTAATCTTTTTTATATCTTTATAGTATATTTCTCAATCCTTGAA
1 AATACATTTCCAGCCTATTTTTTAATCTTTTTTATATCTTTATAGTATATTTCTCAATCCTTGAA
4456631 TCTGTTTTGAAAATTTAAATATTATCAAATAATTTTTTAG-ATTTATTTAAT
66 TCTGTTTTGAAAATTTAAATATTATCAAATAATTTTTTAGAATTTATTTAAT
4456682 AATACATTTCCAGCCTATTTTTTAATCTTTTTTATATCTTTATAGTATATTTCTCAATCCTTGAA
1 AATACATTTCCAGCCTATTTTTTAATCTTTTTTATATCTTTATAGTATATTTCTCAATCCTTGAA
4456747 TCTGTTTTGAAAATTTAAATATTATCAAATAATTTTTTAGAATTTATTTAAT
66 TCTGTTTTGAAAATTTAAATATTATCAAATAATTTTTTAGAATTTATTTAAT
4456799 TATATTTTAT
Statistics
Matches: 116, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
116 105 0.91
117 11 0.09
ACGTcount: A:0.32, C:0.11, G:0.05, T:0.52
Consensus pattern (117 bp):
AATACATTTCCAGCCTATTTTTTAATCTTTTTTATATCTTTATAGTATATTTCTCAATCCTTGAA
TCTGTTTTGAAAATTTAAATATTATCAAATAATTTTTTAGAATTTATTTAAT
Found at i:4459721 original size:29 final size:29
Alignment explanation
Indices: 4459679--4459745 Score: 116
Period size: 29 Copynumber: 2.3 Consensus size: 29
4459669 CTCACATGCA
4459679 TTCTTACATTTTGTTTAATACAAATAGAT
1 TTCTTACATTTTGTTTAATACAAATAGAT
* *
4459708 TTCTTACATTTTGTTTAATGCAAATGGAT
1 TTCTTACATTTTGTTTAATACAAATAGAT
4459737 TTCTTACAT
1 TTCTTACAT
4459746 GTTCCAAGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.49
Consensus pattern (29 bp):
TTCTTACATTTTGTTTAATACAAATAGAT
Found at i:4470124 original size:15 final size:16
Alignment explanation
Indices: 4470089--4470134 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
4470079 AGATTTGAGA
4470089 TTATTTTATATAATAT
1 TTATTTTATATAATAT
* *
4470105 TTATTTT-TATTATTT
1 TTATTTTATATAATAT
*
4470120 TTA-TTTAAATAATAT
1 TTATTTTATATAATAT
4470135 CTGTAAAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
14 3 0.12
15 14 0.58
16 7 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTTTATATAATAT
Found at i:4480422 original size:15 final size:16
Alignment explanation
Indices: 4480387--4480432 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
4480377 AGATTTGAGA
4480387 TTATTTTATATAATAT
1 TTATTTTATATAATAT
* *
4480403 TTATTTT-TATTATTT
1 TTATTTTATATAATAT
*
4480418 TTA-TTTAAATAATAT
1 TTATTTTATATAATAT
4480433 CTGTAAAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
14 3 0.12
15 14 0.58
16 7 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTTTATATAATAT
Found at i:4485026 original size:51 final size:51
Alignment explanation
Indices: 4484936--4485062 Score: 150
Period size: 51 Copynumber: 2.5 Consensus size: 51
4484926 TGATGGGTCG
** *
4484936 CATGTGTAGTACTATATGCAGGCTACTATGCGTACCGGATAGT-TTCGATCA
1 CATGTGTAGTACTATATGCAGGCTACTACACGTACCGGATAGTAAT-GATCA
* * * *
4484987 CGA-GTGTAGTACTATATGCAGGCTACTACATGTATCGGATGGTAATGGTCA
1 C-ATGTGTAGTACTATATGCAGGCTACTACACGTACCGGATAGTAATGATCA
*
4485038 CATGTGTAGTACTATGTGCAGGCTA
1 CATGTGTAGTACTATATGCAGGCTA
4485063 TTATGTGAAC
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
50 1 0.02
51 62 0.95
52 2 0.03
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (51 bp):
CATGTGTAGTACTATATGCAGGCTACTACACGTACCGGATAGTAATGATCA
Found at i:4485241 original size:38 final size:37
Alignment explanation
Indices: 4485198--4485270 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 37
4485188 AGATATGGAA
4485198 TTGAATTGAATAT-CGACTTAGAAA-TGAAAAAGTGAATT
1 TTGAATTGAAT-TGCGA-TT-GAAAGTGAAAAAGTGAATT
*
4485236 TTGAATTGAATTGTGATTGAAAGTGAAAAAGTGAA
1 TTGAATTGAATTGCGATTGAAAGTGAAAAAGTGAA
4485271 ATTATGAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
36 4 0.12
37 15 0.47
38 13 0.41
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.32
Consensus pattern (37 bp):
TTGAATTGAATTGCGATTGAAAGTGAAAAAGTGAATT
Found at i:4490984 original size:2 final size:2
Alignment explanation
Indices: 4490977--4491002 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4490967 ATTTTTGCAA
4490977 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
4491003 GTTCATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4491125 original size:2 final size:2
Alignment explanation
Indices: 4491118--4491143 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4491108 ATTTTTGCAA
4491118 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
4491144 GTTCATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4491131 original size:141 final size:142
Alignment explanation
Indices: 4490939--4491221 Score: 559
Period size: 141 Copynumber: 2.0 Consensus size: 142
4490929 TGAATTCGGC
4490939 ATAAACAAAGTTTATTTAATTTACTCATATTTTTGCAAATATATATATATATATATATATATATG
1 ATAAACAAAGTTTATTTAATTTACTCATATTTTTGCAAATATATATATATATATATATATATATG
4491004 TTCATTTATAGCACTGGTATAATAAATCATTTCGAACTGTTGAATTTTATATAATTTATAATATT
66 TTCATTTATAGCACTGGTATAATAAATCATTTCGAACTGTTGAATTTTATATAATTTATAATATT
4491069 -ATAATATAGTT
131 AATAATATAGTT
4491080 ATAAACAAAGTTTATTTAATTTACTCATATTTTTGCAAATATATATATATATATATATATATATG
1 ATAAACAAAGTTTATTTAATTTACTCATATTTTTGCAAATATATATATATATATATATATATATG
4491145 TTCATTTATAGCACTGGTATAATAAATCATTTCGAACTGTTGAATTTTATATAATTTATAATATT
66 TTCATTTATAGCACTGGTATAATAAATCATTTCGAACTGTTGAATTTTATATAATTTATAATATT
4491210 AATAATATAGTT
131 AATAATATAGTT
4491222 TTGTGTATTT
Statistics
Matches: 141, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
141 130 0.92
142 11 0.08
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (142 bp):
ATAAACAAAGTTTATTTAATTTACTCATATTTTTGCAAATATATATATATATATATATATATATG
TTCATTTATAGCACTGGTATAATAAATCATTTCGAACTGTTGAATTTTATATAATTTATAATATT
AATAATATAGTT
Found at i:4495808 original size:7 final size:7
Alignment explanation
Indices: 4495796--4495824 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
4495786 TACATAGAGA
4495796 TTGACAT
1 TTGACAT
4495803 TTGACAT
1 TTGACAT
4495810 TTGACAT
1 TTGACAT
4495817 TTGACAT
1 TTGACAT
4495824 T
1 T
4495825 ACTTACTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.45
Consensus pattern (7 bp):
TTGACAT
Found at i:4497296 original size:68 final size:68
Alignment explanation
Indices: 4497187--4497323 Score: 274
Period size: 68 Copynumber: 2.0 Consensus size: 68
4497177 AGCCACAACA
4497187 AGCAAAGCCAAATCCAAAAGGAATACTATTCAGGAAAGAAAGTCGATGACATAAAAGCAAAACAG
1 AGCAAAGCCAAATCCAAAAGGAATACTATTCAGGAAAGAAAGTCGATGACATAAAAGCAAAACAG
4497252 AGG
66 AGG
4497255 AGCAAAGCCAAATCCAAAAGGAATACTATTCAGGAAAGAAAGTCGATGACATAAAAGCAAAACAG
1 AGCAAAGCCAAATCCAAAAGGAATACTATTCAGGAAAGAAAGTCGATGACATAAAAGCAAAACAG
4497320 AGG
66 AGG
4497323 A
1 A
4497324 ATGTGTGAAC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.52, C:0.16, G:0.20, T:0.12
Consensus pattern (68 bp):
AGCAAAGCCAAATCCAAAAGGAATACTATTCAGGAAAGAAAGTCGATGACATAAAAGCAAAACAG
AGG
Found at i:4501435 original size:17 final size:17
Alignment explanation
Indices: 4501408--4501453 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
4501398 CCGATATAAT
* * *
4501408 AAATATATTTATTTTTT
1 AAATATTTTTAATTTTA
*
4501425 AAATTTTTTTAATTTTA
1 AAATATTTTTAATTTTA
4501442 AAATATTTTTAA
1 AAATATTTTTAA
4501454 AATACTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:4501872 original size:7 final size:7
Alignment explanation
Indices: 4501860--4501892 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
4501850 TATTGTTATT
4501860 ATCTACA
1 ATCTACA
4501867 ATCTACA
1 ATCTACA
4501874 ATCTACA
1 ATCTACA
4501881 ATCTACA
1 ATCTACA
4501888 ATCTA
1 ATCTA
4501893 TATTTATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.30
Consensus pattern (7 bp):
ATCTACA
Found at i:4515472 original size:21 final size:21
Alignment explanation
Indices: 4515448--4515500 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
4515438 CATTGTTTCT
*
4515448 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
* *
4515469 AATCTCACCGTTACAGTAACT
1 AATCTCACCGCTACAGTAACC
4515490 AATCTCACCGC
1 AATCTCACCGC
4515501 CACTATTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.30, C:0.36, G:0.09, T:0.25
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:4520436 original size:45 final size:46
Alignment explanation
Indices: 4520370--4520463 Score: 147
Period size: 45 Copynumber: 2.1 Consensus size: 46
4520360 CATTTATTCA
* *
4520370 TTTTACTCTTTTAATCTTTAGACCAGAATTCACTAAGTTATGCAAT
1 TTTTAATCTTTTAATCTTTAGAACAGAATTCACTAAGTTATGCAAT
4520416 TTTTAATC-TTTAAT-TATTAGAACAGAATTCACTAAGTTATGCAAT
1 TTTTAATCTTTTAATCT-TTAGAACAGAATTCACTAAGTTATGCAAT
4520461 TTT
1 TTT
4520464 ATGTTATTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
44 1 0.02
45 37 0.82
46 7 0.16
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.45
Consensus pattern (46 bp):
TTTTAATCTTTTAATCTTTAGAACAGAATTCACTAAGTTATGCAAT
Found at i:4524175 original size:22 final size:21
Alignment explanation
Indices: 4524134--4524178 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
4524124 TATATGATAT
4524134 ATATTTTTATTGAAATAAAAA
1 ATATTTTTATTGAAATAAAAA
* *
4524155 ATATTTTCTGTTG-AAGAAAAA
1 ATATTTT-TATTGAAATAAAAA
4524176 ATA
1 ATA
4524179 GAATTACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (21 bp):
ATATTTTTATTGAAATAAAAA
Found at i:4527433 original size:3 final size:3
Alignment explanation
Indices: 4527425--4527449 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4527415 GATTCTATAA
4527425 AGT AGT AGT AGT AGT AGT AGT AGT A
1 AGT AGT AGT AGT AGT AGT AGT AGT A
4527450 CATTTTTTCC
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:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
AGT
Found at i:4529910 original size:26 final size:26
Alignment explanation
Indices: 4529881--4529931 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
4529871 AATTAATATA
*
4529881 TATTAGAAA-AGTAATAATTTAATTTT
1 TATTA-AAAGAGTAATAATTAAATTTT
*
4529907 TATTAAAAGATTAATAATTAAATTT
1 TATTAAAAGAGTAATAATTAAATTT
4529932 AATTATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (26 bp):
TATTAAAAGAGTAATAATTAAATTTT
Found at i:4531060 original size:26 final size:26
Alignment explanation
Indices: 4531031--4531081 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
4531021 AATTAATATA
*
4531031 TATTAGAAA-AGTAATAATTTAATTTT
1 TATTA-AAAGAGTAATAATTAAATTTT
*
4531057 TATTAAAAGATTAATAATTAAATTT
1 TATTAAAAGAGTAATAATTAAATTT
4531082 AATTATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (26 bp):
TATTAAAAGAGTAATAATTAAATTTT
Found at i:4547094 original size:9 final size:9
Alignment explanation
Indices: 4547080--4547109 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
4547070 TAATAAATCA
4547080 TAATTAACT
1 TAATTAACT
4547089 TAATTAACCT
1 TAATTAA-CT
4547099 TAATTAACT
1 TAATTAACT
4547108 TA
1 TA
4547110 GGCTAATGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.43
Consensus pattern (9 bp):
TAATTAACT
Found at i:4551156 original size:3 final size:3
Alignment explanation
Indices: 4551150--4551176 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4551140 GTCGTCGCCG
4551150 TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT
4551177 GATCTTTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:4554150 original size:3 final size:3
Alignment explanation
Indices: 4554142--4554201 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
4554132 ACCTGACTGC
4554142 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4554190 ATT ATT ATT ATT
1 ATT ATT ATT ATT
4554202 TGGATCACTG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:4568253 original size:2 final size:2
Alignment explanation
Indices: 4568230--4568266 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
4568220 CACCAAGCAA
*
4568230 AT AT A- AT AT A- AT AT AA AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4568267 AGTAAGATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:4571360 original size:20 final size:20
Alignment explanation
Indices: 4571335--4571374 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
4571325 ATAAGATAGT
4571335 GTATTTTCCTTTTAGTTTTA
1 GTATTTTCCTTTTAGTTTTA
4571355 GTATTTTCCTTTTAGTTTTA
1 GTATTTTCCTTTTAGTTTTA
4571375 CACAAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.10, G:0.10, T:0.65
Consensus pattern (20 bp):
GTATTTTCCTTTTAGTTTTA
Found at i:4571737 original size:13 final size:13
Alignment explanation
Indices: 4571719--4571745 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4571709 GCCATGAAAG
4571719 AAGCTTGAACCAT
1 AAGCTTGAACCAT
4571732 AAGCTTGAACCAT
1 AAGCTTGAACCAT
4571745 A
1 A
4571746 GTCTACTTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (13 bp):
AAGCTTGAACCAT
Found at i:4575189 original size:185 final size:186
Alignment explanation
Indices: 4574877--4575247 Score: 735
Period size: 185 Copynumber: 2.0 Consensus size: 186
4574867 CTTTTTTCTT
4574877 GGTAAATATTTATCTATTAATAAATGTAATAATGTAAAAGAAATTTGCCTCCTTCGTCCTACTTA
1 GGTAAATATTTATCTATTAATAAATGTAATAATGTAAAAGAAATTTGCCTCCTTCGTCCTACTTA
4574942 ATTTTCTTTATTACTTATTTATATATAAGATAAATTTGAAATAATTTTATTTTCACATTTAATTA
66 ATTTTCTTTATTACTTATTTATATATAAGATAAATTTGAAATAATTTTATTTTCACATTTAATTA
4575007 CAAATTTAAAAATAATTTAAAACTATCAATTAAATTTTATTTTT-AATATTTGTTA
131 CAAATTTAAAAATAATTTAAAACTATCAATTAAATTTTATTTTTAAATATTTGTTA
4575062 GGTAAATATTTATCTATTAATAAATGTAATAATGTAAAAGAAATTTGCCTCCTTCGTCCTACTTA
1 GGTAAATATTTATCTATTAATAAATGTAATAATGTAAAAGAAATTTGCCTCCTTCGTCCTACTTA
4575127 ATTTTCTTTATTACTTATTTATATATAAGATAAATTTGAAATAATTTTATTTTCACATTTAATTA
66 ATTTTCTTTATTACTTATTTATATATAAGATAAATTTGAAATAATTTTATTTTCACATTTAATTA
4575192 CAAATTTAAAAATAATTTAAAACTATCAATTAAATTTTATTTTTAAATATTTGTTA
131 CAAATTTAAAAATAATTTAAAACTATCAATTAAATTTTATTTTTAAATATTTGTTA
4575248 AGATTGAAAT
Statistics
Matches: 185, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
185 174 0.94
186 11 0.06
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.46
Consensus pattern (186 bp):
GGTAAATATTTATCTATTAATAAATGTAATAATGTAAAAGAAATTTGCCTCCTTCGTCCTACTTA
ATTTTCTTTATTACTTATTTATATATAAGATAAATTTGAAATAATTTTATTTTCACATTTAATTA
CAAATTTAAAAATAATTTAAAACTATCAATTAAATTTTATTTTTAAATATTTGTTA
Found at i:4596421 original size:31 final size:30
Alignment explanation
Indices: 4596350--4596423 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
4596340 TCTCTAACCT
* * *
4596350 GTACTTAAACTTGATATTTTTTCTTAATTT
1 GTACTTAAATTTAATATTTTTTCTTAATTA
4596380 GATACTTAAATTTAATATATTTTT-TTAAATTA
1 G-TACTTAAATTTAATAT-TTTTTCTT-AATTA
4596412 GTACTTAAATTT
1 GTACTTAAATTT
4596424 TTTGGGTCTA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
30 1 0.03
31 27 0.71
32 10 0.26
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (30 bp):
GTACTTAAATTTAATATTTTTTCTTAATTA
Found at i:4596960 original size:61 final size:60
Alignment explanation
Indices: 4596877--4597049 Score: 208
Period size: 61 Copynumber: 2.9 Consensus size: 60
4596867 AATGAACCTA
* * * *
4596877 AAAAAAAGG-TTAGGTACTAAATTAGGAAAAAATGCCAAGTTGACGTACAAAATTGGGCC
1 AAAAAAAGGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAAGTACAAAATTGGGCC
* * *
4596936 AAAAAAATGGTTTAGGTGCCAAATTA-GAAAAAAGTGTCAAGTTCAAGTACCAAATTGGGCT
1 AAAAAAA-GGTTTAGGTACCAAATTAGGAAAAAA-TGTCAAGTTCAAGTACAAAATTGGGCC
* * * *
4596997 AAAAAAA-GTTTAGATACCAAATTAGGAAAAAGTGTCAAGTTCAGGTAGAAAAT
1 AAAAAAAGGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAAGTACAAAAT
4597050 GTTATATTAA
Statistics
Matches: 97, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
59 40 0.41
60 15 0.15
61 42 0.43
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.23
Consensus pattern (60 bp):
AAAAAAAGGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAAGTACAAAATTGGGCC
Found at i:4597017 original size:59 final size:59
Alignment explanation
Indices: 4596877--4597049 Score: 204
Period size: 59 Copynumber: 2.9 Consensus size: 59
4596867 AATGAACCTA
* * * * *
4596877 AAAAAAAGGTTAGGTACTAAATTAGGAAAAAA-TGCCAAGTTGACGTACAAAATTGGGCC
1 AAAAAAAGTTTAGGTACCAAATTA-GAAAAAAGTGTCAAGTTCAAGTACAAAATTGGGCC
* * *
4596936 AAAAAAATGGTTTAGGTGCCAAATTAGAAAAAAGTGTCAAGTTCAAGTACCAAATTGGGCT
1 AAAAAAA--GTTTAGGTACCAAATTAGAAAAAAGTGTCAAGTTCAAGTACAAAATTGGGCC
* * * *
4596997 AAAAAAAGTTTAGATACCAAATTAGGAAAAAGTGTCAAGTTCAGGTAGAAAAT
1 AAAAAAAGTTTAGGTACCAAATTAGAAAAAAGTGTCAAGTTCAAGTACAAAAT
4597050 GTTATATTAA
Statistics
Matches: 97, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
59 47 0.48
60 7 0.07
61 43 0.44
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.23
Consensus pattern (59 bp):
AAAAAAAGTTTAGGTACCAAATTAGAAAAAAGTGTCAAGTTCAAGTACAAAATTGGGCC
Found at i:4597873 original size:68 final size:68
Alignment explanation
Indices: 4597800--4597929 Score: 181
Period size: 68 Copynumber: 1.9 Consensus size: 68
4597790 CTAACCTAAC
* *
4597800 GTTTAAGAAACGTAACTTCAAACCCTTAAATAATTATATTTAG-CGATTCAACCTTAATTCAACT
1 GTTTAAGAAACATAACTTCAAAACCTTAAATAATTAT-TTTAGCCGATTCAACCTTAATTCAACT
4597864 TAAT
65 TAAT
* * * * *
4597868 GTTTAAGAAATATGACTTTAAAACTTTAAATAATTATTTTTGCCGATTCAACCTTAATTCAA
1 GTTTAAGAAACATAACTTCAAAACCTTAAATAATTATTTTAGCCGATTCAACCTTAATTCAA
4597930 TACAACAATT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
67 4 0.07
68 50 0.93
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.38
Consensus pattern (68 bp):
GTTTAAGAAACATAACTTCAAAACCTTAAATAATTATTTTAGCCGATTCAACCTTAATTCAACTT
AAT
Found at i:4606166 original size:15 final size:15
Alignment explanation
Indices: 4606143--4606172 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4606133 GTGATAAATT
*
4606143 TTAATAAAAAATAAA
1 TTAACAAAAAATAAA
4606158 TTAACAAAAAATAAA
1 TTAACAAAAAATAAA
4606173 AGCCTACAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (15 bp):
TTAACAAAAAATAAA
Found at i:4614159 original size:1 final size:1
Alignment explanation
Indices: 4614153--4614179 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
4614143 GGACAAAGGC
4614153 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
4614180 CGGGAACATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4618505 original size:3 final size:3
Alignment explanation
Indices: 4618497--4618535 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
4618487 CTATTTTCCN
4618497 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4618536 TTCCTTCCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4619039 original size:25 final size:26
Alignment explanation
Indices: 4619011--4619064 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
4619001 GGCTAACAAG
4619011 TAAG-TTTTTTTTTAATTTCAAAATA
1 TAAGTTTTTTTTTTAATTTCAAAATA
4619036 TAAGTTTTTTTTTTAATTTCAAAATA
1 TAAGTTTTTTTTTTAATTTCAAAATA
4619062 TAA
1 TAA
4619065 CATTAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 4 0.14
26 24 0.86
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (26 bp):
TAAGTTTTTTTTTTAATTTCAAAATA
Found at i:4622799 original size:20 final size:20
Alignment explanation
Indices: 4622774--4622813 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
4622764 TTTCTTTGGA
4622774 GTATTTCGTCGATCATGTTG
1 GTATTTCGTCGATCATGTTG
4622794 GTATTTCGTCGATCATGTTG
1 GTATTTCGTCGATCATGTTG
4622814 TGTGCTTAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.25, T:0.45
Consensus pattern (20 bp):
GTATTTCGTCGATCATGTTG
Found at i:4635785 original size:7 final size:7
Alignment explanation
Indices: 4635771--4635801 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
4635761 TTTTTTCAGG
4635771 TTTC-AT
1 TTTCAAT
4635777 TTTCAAT
1 TTTCAAT
4635784 TTTCAAT
1 TTTCAAT
4635791 TTTCAAT
1 TTTCAAT
4635798 TTTC
1 TTTC
4635802 TCCAAATCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 20 0.83
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (7 bp):
TTTCAAT
Found at i:4647338 original size:24 final size:23
Alignment explanation
Indices: 4647306--4647352 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 23
4647296 GGAATTATCT
4647306 ACACTCACATGTACTGACATCGTC
1 ACACTCACATGTACTGACA-CGTC
4647330 ACACTCACATGTACTGACACGTC
1 ACACTCACATGTACTGACACGTC
4647353 TGGTGGTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (23 bp):
ACACTCACATGTACTGACACGTC
Found at i:4651155 original size:3 final size:3
Alignment explanation
Indices: 4651147--4651183 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
4651137 GTAATTACAT
4651147 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
4651184 AGCAAAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:4664310 original size:7 final size:7
Alignment explanation
Indices: 4664300--4664329 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
4664290 GTAAAAAAAT
4664300 AAAAACA
1 AAAAACA
4664307 AAAAACA
1 AAAAACA
4664314 AAAAAC-
1 AAAAACA
4664320 AAAAACA
1 AAAAACA
4664327 AAA
1 AAA
4664330 GAAAGGGCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAACA
Found at i:4664311 original size:14 final size:14
Alignment explanation
Indices: 4664300--4664329 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
4664290 GTAAAAAAAT
4664300 AAAAACAAAAAACA
1 AAAAACAAAAAACA
4664314 AAAAAC-AAAAACA
1 AAAAACAAAAAACA
4664327 AAA
1 AAA
4664330 GAAAGGGCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAACAAAAAACA
Found at i:4665680 original size:97 final size:98
Alignment explanation
Indices: 4665571--4665765 Score: 383
Period size: 97 Copynumber: 2.0 Consensus size: 98
4665561 TAATTTGAAC
4665571 AATTTTAGACTCACTATATTATTATTAAACTTTTTTTAAATATATATAGACATACAATTCTTTAC
1 AATTTTAGACTCACTATATTATTATTAAACTTTTTTTAAATATATATAGACATACAATTCTTTAC
4665636 ATTATAATATTATATATTAGTA-TACTATGAGA
66 ATTATAATATTATATATTAGTATTACTATGAGA
4665668 AATTTTAGACTCACTATATTATTATTAAACTTTTTTTAAATATATATAGACATACAATTCTTTAC
1 AATTTTAGACTCACTATATTATTATTAAACTTTTTTTAAATATATATAGACATACAATTCTTTAC
4665733 ATTATAATATTATATATTAGTATTACTATGAGA
66 ATTATAATATTATATATTAGTATTACTATGAGA
4665766 TTAATTTTCT
Statistics
Matches: 97, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
97 87 0.90
98 10 0.10
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.46
Consensus pattern (98 bp):
AATTTTAGACTCACTATATTATTATTAAACTTTTTTTAAATATATATAGACATACAATTCTTTAC
ATTATAATATTATATATTAGTATTACTATGAGA
Found at i:4668251 original size:106 final size:106
Alignment explanation
Indices: 4668066--4668259 Score: 327
Period size: 106 Copynumber: 1.8 Consensus size: 106
4668056 TAGAAAAGAA
* * *
4668066 AATAAATAAAATAAAAATAAAGATTTTATTGAAAGGATATATGAAAAGAACAAAAGCCTAAACTT
1 AATAAATAAAATAAAAATAAAGATTTTATTAAAAAGAAATATGAAAAGAACAAAAGCCTAAACTT
*
4668131 TTGGGGATAGAGTGTTTACAGAAGAAGAAAAATGGGATCCC
66 TTGGGGAGAGAGTGTTTACAGAAGAAGAAAAATGGGATCCC
*
4668172 AATAAATAAAATAAAAATAAAGATTTTATTAAAAAGAAATATGAGAAGAACAAAAGCCTAAACTT
1 AATAAATAAAATAAAAATAAAGATTTTATTAAAAAGAAATATGAAAAGAACAAAAGCCTAAACTT
4668237 TT-GGGAGGAGAGTGTTTACAGAA
66 TTGGGGA-GAGAGTGTTTACAGAA
4668260 AAACATAAGA
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
105 4 0.05
106 78 0.95
ACGTcount: A:0.52, C:0.07, G:0.18, T:0.24
Consensus pattern (106 bp):
AATAAATAAAATAAAAATAAAGATTTTATTAAAAAGAAATATGAAAAGAACAAAAGCCTAAACTT
TTGGGGAGAGAGTGTTTACAGAAGAAGAAAAATGGGATCCC
Found at i:4694624 original size:36 final size:36
Alignment explanation
Indices: 4694584--4694676 Score: 105
Period size: 36 Copynumber: 2.6 Consensus size: 36
4694574 TGGAATCAGA
* *
4694584 CGGAGGCGGAGGAGGAGATGGAGTCCCGGAATTCCT
1 CGGAGGCGGAGGAGGAGATGGAGTACCGGAACTCCT
* * * *
4694620 CGGAGGCGGTGGTGGAGATGCAGTACCGGGACTCCT
1 CGGAGGCGGAGGAGGAGATGGAGTACCGGAACTCCT
* * *
4694656 CGGTGGCGGCGGCGGAGATGG
1 CGGAGGCGGAGGAGGAGATGG
4694677 TGTTGATGAG
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.17, C:0.20, G:0.48, T:0.14
Consensus pattern (36 bp):
CGGAGGCGGAGGAGGAGATGGAGTACCGGAACTCCT
Found at i:4696917 original size:21 final size:21
Alignment explanation
Indices: 4696886--4696927 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
4696876 AAAACTAAAT
4696886 TTTTATATAATCACATTCGGTG
1 TTTTATATAATCA-ATTCGGTG
*
4696908 TTTTA-ATAATCAATTTGGTG
1 TTTTATATAATCAATTCGGTG
4696928 GTTCAACTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 7 0.37
22 5 0.26
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.48
Consensus pattern (21 bp):
TTTTATATAATCAATTCGGTG
Found at i:4713625 original size:42 final size:42
Alignment explanation
Indices: 4713578--4713670 Score: 152
Period size: 42 Copynumber: 2.2 Consensus size: 42
4713568 AAGTTCAAAT
*
4713578 CATAGAGC-GGACATTGTTGAAAGGCTAACAATTAATCATGAA
1 CATAGA-CTGGACATTGTTGAAAGGCTAAAAATTAATCATGAA
4713620 CATAGACTGGACATTGTTGAAAGGCTAAAAATTAATCATGAA
1 CATAGACTGGACATTGTTGAAAGGCTAAAAATTAATCATGAA
*
4713662 CATAAACTG
1 CATAGACTG
4713671 CAAAAAAAAC
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
41 1 0.02
42 47 0.98
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (42 bp):
CATAGACTGGACATTGTTGAAAGGCTAAAAATTAATCATGAA
Found at i:4728810 original size:7 final size:7
Alignment explanation
Indices: 4728796--4728826 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
4728786 TGATATATCA
4728796 TAAT-TT
1 TAATATT
4728802 TAATATT
1 TAATATT
4728809 TAATATT
1 TAATATT
4728816 TAATATT
1 TAATATT
4728823 TAAT
1 TAAT
4728827 TTTTTGATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 20 0.83
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TAATATT
Found at i:4729022 original size:21 final size:21
Alignment explanation
Indices: 4728997--4729037 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
4728987 ACTTAAATTT
*
4728997 TAAAATTTTAAAAATTAAAAG
1 TAAAATTTTAAAAATAAAAAG
4729018 TAAAATTTTAAAAATAAAAA
1 TAAAATTTTAAAAATAAAAA
4729038 TATAAAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
TAAAATTTTAAAAATAAAAAG
Found at i:4733361 original size:46 final size:46
Alignment explanation
Indices: 4733308--4733468 Score: 295
Period size: 46 Copynumber: 3.5 Consensus size: 46
4733298 ACATTGCTAT
* *
4733308 AACTCAGTATGGTTTTCTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCAC
*
4733354 AACTCAGTATGGTTTTCTTTACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCAC
4733400 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCAC
4733446 AACTCAGTATGGTTTTCTTTACC
1 AACTCAGTATGGTTTTCTTTACC
4733469 NNNNNNNNNN
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 111 1.00
ACGTcount: A:0.27, C:0.26, G:0.10, T:0.37
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCAC
Found at i:4743829 original size:2 final size:2
Alignment explanation
Indices: 4743824--4743850 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4743814 TTTATTATTT
4743824 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4743851 TTAAGAGAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4744187 original size:21 final size:22
Alignment explanation
Indices: 4744161--4744201 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
4744151 TTCGATTATA
4744161 TTTAAAAAAAT-AAAATAAAAT
1 TTTAAAAAAATCAAAATAAAAT
**
4744182 TTTAAATTAATCAAAATAAA
1 TTTAAAAAAATCAAAATAAA
4744202 TTATTTGAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (22 bp):
TTTAAAAAAATCAAAATAAAAT
Found at i:4744482 original size:16 final size:16
Alignment explanation
Indices: 4744441--4744484 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
4744431 TTAATTCAAA
4744441 TAATTTTACTC-AATT
1 TAATTTTACTCGAATT
**
4744456 TAATTCGACTCGAATT
1 TAATTTTACTCGAATT
*
4744472 TCATTTTACTCGA
1 TAATTTTACTCGA
4744485 CTCTATTAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.30, C:0.18, G:0.07, T:0.45
Consensus pattern (16 bp):
TAATTTTACTCGAATT
Found at i:4747107 original size:44 final size:44
Alignment explanation
Indices: 4747044--4747220 Score: 345
Period size: 44 Copynumber: 4.0 Consensus size: 44
4747034 TGCCAGTTAG
*
4747044 AATATTAAAGTTATCTAGGAGACTAGGATTCTGTTTTACAGAGA
1 AATATTAAAGTCATCTAGGAGACTAGGATTCTGTTTTACAGAGA
4747088 AATATTAAAGTCATCTAGGAGACTAGGATTCTGTTTTACAGAGA
1 AATATTAAAGTCATCTAGGAGACTAGGATTCTGTTTTACAGAGA
4747132 AATATTAAAGTCATCTAGGAGACTAGGATTCTGTTTTACAGAGA
1 AATATTAAAGTCATCTAGGAGACTAGGATTCTGTTTTACAGAGA
4747176 AATATTAAAGTCATCTAGGAGACTAGGATTCTGTTTTACAGAGA
1 AATATTAAAGTCATCTAGGAGACTAGGATTCTGTTTTACAGAGA
4747220 A
1 A
4747221 CCAAGATATG
Statistics
Matches: 132, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
44 132 1.00
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (44 bp):
AATATTAAAGTCATCTAGGAGACTAGGATTCTGTTTTACAGAGA
Found at i:4754336 original size:39 final size:40
Alignment explanation
Indices: 4754308--4754393 Score: 136
Period size: 40 Copynumber: 2.1 Consensus size: 40
4754298 TAATTTTTTT
4754308 TAATTTTAAAATACTTTTTTTTAATTTTTTAATTTTAAAA
1 TAATTTTAAAATACTTTTTTTTAATTTTTTAATTTTAAAA
*
4754348 TATTTTTAAAATACTTTTTTTTAATTTTTTAAAATTTTTAAAA
1 TAATTTTAAAATACTTTTTTTTAATTTTTT--AA-TTTTAAAA
4754391 TAA
1 TAA
4754394 AAATGGGCCG
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
40 29 0.71
42 2 0.05
43 10 0.24
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.59
Consensus pattern (40 bp):
TAATTTTAAAATACTTTTTTTTAATTTTTTAATTTTAAAA
Found at i:4754338 original size:29 final size:29
Alignment explanation
Indices: 4754293--4754354 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 29
4754283 TTTTACATAC
4754293 TTTTTTAATTTTTTTTAATTTTAAAATACTT
1 TTTTTTAA-TTTTTTTAATTTTAAAATA-TT
4754324 TTTTTTAA-TTTTTTAATTTTAAAATATT
1 TTTTTTAATTTTTTTAATTTTAAAATATT
4754352 TTT
1 TTT
4754355 AAAATACTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
28 5 0.16
29 18 0.58
31 8 0.26
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (29 bp):
TTTTTTAATTTTTTTAATTTTAAAATATT
Found at i:4754368 original size:32 final size:32
Alignment explanation
Indices: 4754332--4754392 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
4754322 TTTTTTTTAA
4754332 TTTTTTAA-TTTTAAAATATTTTTAAAATACTT
1 TTTTTTAATTTTTAAAA-ATTTTTAAAATACTT
*
4754364 TTTTTTAATTTTTTAAAATTTTTAAAATA
1 TTTTTTAATTTTTAAAAATTTTTAAAATA
4754393 AAAATGGGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
32 20 0.74
33 7 0.26
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (32 bp):
TTTTTTAATTTTTAAAAATTTTTAAAATACTT
Found at i:4758518 original size:21 final size:20
Alignment explanation
Indices: 4758494--4758546 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
4758484 GATTAAATAG
4758494 ATTTTATTTTATTATAAAAAT
1 ATTTTATTTTATTA-AAAAAT
* *
4758515 ATTTTGTTTTTATTAAAATAT
1 ATTTT-ATTTTATTAAAAAAT
4758536 ATTTTTATTTT
1 A-TTTTATTTT
4758547 TAGAGTTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
ATTTTATTTTATTAAAAAAT
Found at i:4758541 original size:22 final size:22
Alignment explanation
Indices: 4758494--4758548 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
4758484 GATTAAATAG
4758494 ATTTTA-TTTTATTATAAAAAT
1 ATTTTATTTTTATTATAAAAAT
* *
4758515 ATTTTGTTTTTATTA-AAATAT
1 ATTTTATTTTTATTATAAAAAT
4758536 ATTTTTATTTTTA
1 A-TTTTATTTTTA
4758549 GAGTTATACC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.38
22 18 0.62
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
ATTTTATTTTTATTATAAAAAT
Found at i:4763243 original size:125 final size:126
Alignment explanation
Indices: 4763094--4763346 Score: 499
Period size: 125 Copynumber: 2.0 Consensus size: 126
4763084 ACAATTTTTG
4763094 GAGTGATATGTGCTTTTGAACGTCAAAGCAAAAGCTATTTTTTTTAGCATAAGCATTTTTAGGAA
1 GAGTGATATGTGCTTTTGAACGTCAAAGCAAAAGCTATTTTTTTTAGCATAAGCATTTTTAGGAA
4763159 CAAAAGACAATTTTAACTCTTATAAAATATTCTATATTGGGTATGTAATT-CTTTCCTATT
66 CAAAAGACAATTTTAACTCTTATAAAATATTCTATATTGGGTATGTAATTACTTTCCTATT
4763219 GAGTGATATGTGCTTTTGAACGTCAAAGCAAAAGCTATTTTTTTTAGCATAAGCATTTTTAGGAA
1 GAGTGATATGTGCTTTTGAACGTCAAAGCAAAAGCTATTTTTTTTAGCATAAGCATTTTTAGGAA
4763284 CAAAAGACAATTTTAACTCTTATAAAATATTCTATATTGGGTATGTAATTACTTTCCTATT
66 CAAAAGACAATTTTAACTCTTATAAAATATTCTATATTGGGTATGTAATTACTTTCCTATT
4763345 GA
1 GA
4763347 AATTTATTTT
Statistics
Matches: 127, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
125 115 0.91
126 12 0.09
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.40
Consensus pattern (126 bp):
GAGTGATATGTGCTTTTGAACGTCAAAGCAAAAGCTATTTTTTTTAGCATAAGCATTTTTAGGAA
CAAAAGACAATTTTAACTCTTATAAAATATTCTATATTGGGTATGTAATTACTTTCCTATT
Done.