Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold197
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: 1875808
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 64134 characters in sequence are not A, C, G, or T
File 4 of 6
Found at i:1021948 original size:31 final size:31
Alignment explanation
Indices: 1021819--1021954 Score: 107
Period size: 31 Copynumber: 4.4 Consensus size: 31
1021809 TTAATATAAC
* *
1021819 ATTTGGTACCTGAACTTGACACTTTTTTCCTA
1 ATTTGGTACTTAAACTTGACAC-TTTTTCCTA
* * *
1021851 ATTTGGTACCTAAACTTAACACTTTTTCTTA
1 ATTTGGTACTTAAACTTGACACTTTTTCCTA
* *** ***
1021882 AGTTGGTACTTAAACTTTTTGA-GGGTT-C-A
1 ATTTGGTACTTAAAC-TTGACACTTTTTCCTA
* *
1021911 ATTTGGTACTTGAACTTGACTCTTTTTCCTA
1 ATTTGGTACTTAAACTTGACACTTTTTCCTA
1021942 ATTTGGTACTTAA
1 ATTTGGTACTTAA
1021955 TCTTTTTTTT
Statistics
Matches: 78, Mismatches: 22, Indels: 9
0.72 0.20 0.08
Matches are distributed among these distances:
28 2 0.03
29 16 0.21
30 1 0.01
31 36 0.46
32 23 0.29
ACGTcount: A:0.24, C:0.17, G:0.14, T:0.45
Consensus pattern (31 bp):
ATTTGGTACTTAAACTTGACACTTTTTCCTA
Found at i:1024605 original size:14 final size:14
Alignment explanation
Indices: 1024573--1024606 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 14
1024563 AATAATAAAT
1024573 AAAATAATATGACTA
1 AAAATAATATGAC-A
1024588 AAAATAATATGAACA
1 AAAATAATATG-ACA
1024603 AAAA
1 AAAA
1024607 AACGAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 16 0.89
16 2 0.11
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.21
Consensus pattern (14 bp):
AAAATAATATGACA
Found at i:1024707 original size:2 final size:2
Alignment explanation
Indices: 1024700--1024729 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1024690 AATTCATAAA
*
1024700 AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1024730 GGACATGCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1025499 original size:14 final size:14
Alignment explanation
Indices: 1025467--1025500 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 14
1025457 AATAATAAAT
1025467 AAAATAATATGACTA
1 AAAATAATATGAC-A
1025482 AAAATAATATGAACA
1 AAAATAATATG-ACA
1025497 AAAA
1 AAAA
1025501 AACGAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 16 0.89
16 2 0.11
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.21
Consensus pattern (14 bp):
AAAATAATATGACA
Found at i:1025601 original size:2 final size:2
Alignment explanation
Indices: 1025594--1025623 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1025584 AATTCATAAA
*
1025594 AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1025624 GGACATGCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1028245 original size:88 final size:88
Alignment explanation
Indices: 1028103--1028380 Score: 418
Period size: 88 Copynumber: 3.2 Consensus size: 88
1028093 GATCTGAAAT
* * * * *
1028103 TCTTTAGCCAGCTCCA-CTACAACCGAGAGAGGTAAGG-TT-CGTCTTCGACCTGCTTCGCTGTC
1 TCTTTAACCAGCTCCATC-ACAACCGAGAGAGGCAAGGTTTGTGTCTTTGACCTGCTTCGCCGTC
* * *
1028165 AATGCAAGAAGGCAAGATCTGTTG
65 AATGCAGGAAGGCAAGATCTTTTA
* * * *
1028189 TCTTCAACCAGATCCATCATAACCGAGGGAGGCAAGGTTTGTGTCTTTGACCTGCTTCGCCGTCA
1 TCTTTAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTTGACCTGCTTCGCCGTCA
1028254 ATGCAGGAAGGCAAGATCTTTTA
66 ATGCAGGAAGGCAAGATCTTTTA
1028277 TCTTTAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTTGACCTGCTTCGCCGTCA
1 TCTTTAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTTGACCTGCTTCGCCGTCA
1028342 ATGCAGGAAGGCAAGATCTTTTA
66 ATGCAGGAAGGCAAGATCTTTTA
1028365 TCTTTAACCAGCTCCA
1 TCTTTAACCAGCTCCA
1028381 NNNNNNNNNN
Statistics
Matches: 173, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
86 29 0.17
87 3 0.02
88 141 0.82
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.27
Consensus pattern (88 bp):
TCTTTAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTTGACCTGCTTCGCCGTCA
ATGCAGGAAGGCAAGATCTTTTA
Found at i:1028266 original size:44 final size:44
Alignment explanation
Indices: 1028218--1028356 Score: 142
Period size: 44 Copynumber: 3.2 Consensus size: 44
1028208 TAACCGAGGG
1028218 AGGCAAGGTTTGTGTCTTTGACCTGCTTCGCCGTCAATGCAGGA
1 AGGCAAGGTTTGTGTCTTTGACCTGCTTCGCCGTCAATGCAGGA
* * * * * * * *
1028262 AGGCAAGATCTTTTATCTTTAACCAGC-T--CCATCACA-ACCGAGA
1 AGGCAAGGT-TTGTGTCTTTGACCTGCTTCGCCGTCA-ATGCAG-GA
1028305 GAGGCAAGGTTTGTGTCTTTGACCTGCTTCGCCGTCAATGCAGGA
1 -AGGCAAGGTTTGTGTCTTTGACCTGCTTCGCCGTCAATGCAGGA
1028350 AGGCAAG
1 AGGCAAG
1028357 ATCTTTTATC
Statistics
Matches: 71, Mismatches: 16, Indels: 16
0.69 0.16 0.16
Matches are distributed among these distances:
42 7 0.10
43 16 0.23
44 25 0.35
45 16 0.23
46 7 0.10
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.27
Consensus pattern (44 bp):
AGGCAAGGTTTGTGTCTTTGACCTGCTTCGCCGTCAATGCAGGA
Found at i:1031003 original size:42 final size:41
Alignment explanation
Indices: 1030955--1031064 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 41
1030945 TCTTTTCTTT
*
1030955 TCTTTTCTTTTCATATTTTTATTTTGACTTTGATTGATTTCTC
1 TCTTTTCTTTTCAT-TTTTTATTTTGACTTTAATT-ATTTCTC
** * *
1030998 T-TTTTCTTTTTGTTTTTTTATTTTGATTTTAATTTTTTCTC
1 TCTTTTC-TTTTCATTTTTTATTTTGACTTTAATTATTTCTC
*
1031039 TCTTTTCATTTTCCTTTTTT-TTTTGA
1 TCTTTTC-TTTTCATTTTTTATTTTGA
1031065 ATCGGATCGG
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
41 13 0.23
42 38 0.67
43 6 0.11
ACGTcount: A:0.11, C:0.12, G:0.05, T:0.72
Consensus pattern (41 bp):
TCTTTTCTTTTCATTTTTTATTTTGACTTTAATTATTTCTC
Found at i:1038919 original size:21 final size:20
Alignment explanation
Indices: 1038870--1038919 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
1038860 AATAATATTG
1038870 AGTTC-TTTTATAATTTTAA
1 AGTTCTTTTTATAATTTTAA
*
1038889 AATTCTTTTTTATAAATTTCT-A
1 AGTTC-TTTTTAT-AATTT-TAA
1038911 AGTTCTTTT
1 AGTTCTTTT
1038920 AATTATTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 4 0.16
21 10 0.40
22 10 0.40
23 1 0.04
ACGTcount: A:0.28, C:0.08, G:0.04, T:0.60
Consensus pattern (20 bp):
AGTTCTTTTTATAATTTTAA
Found at i:1043856 original size:22 final size:22
Alignment explanation
Indices: 1043827--1043871 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1043817 GAACATTAAG
1043827 TTTAACACATTAC-ATACCAAC
1 TTTAACACATTACAATACCAAC
*
1043848 TTTAGACACATTACAATTCCAAC
1 TTTA-ACACATTACAATACCAAC
1043871 T
1 T
1043872 AGAACATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.19
22 9 0.43
23 8 0.38
ACGTcount: A:0.40, C:0.27, G:0.02, T:0.31
Consensus pattern (22 bp):
TTTAACACATTACAATACCAAC
Found at i:1045895 original size:9 final size:9
Alignment explanation
Indices: 1045881--1045909 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
1045871 CTTCAACCCA
1045881 ACCCGATTC
1 ACCCGATTC
1045890 ACCCGATTC
1 ACCCGATTC
1045899 ACCCGATTC
1 ACCCGATTC
1045908 AC
1 AC
1045910 TAGGTACGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.24, C:0.45, G:0.10, T:0.21
Consensus pattern (9 bp):
ACCCGATTC
Found at i:1054651 original size:68 final size:71
Alignment explanation
Indices: 1054571--1054708 Score: 203
Period size: 72 Copynumber: 2.0 Consensus size: 71
1054561 TTTTAATAGT
*
1054571 TTAATATTAAATTTAATTTAATGCTTA-TATTA-AT-AGTATGT-TATTAATTTAATATTAAAGT
1 TTAATATTAAATTTAATTTAATGCTTACTATTAGATAAATAT-TATATTAATTTAATATTAAAGT
1054632 GATTATC
65 GATTATC
* *
1054639 TTAATATTAAATTTAATTTAATGTTTATCTTTTAGATAAATATTATATTAATTTAATATTAAAGT
1 TTAATATTAAATTTAATTTAATGCTTA-CTATTAGATAAATATTATATTAATTTAATATTAAAGT
1054704 GATTA
65 GATTA
1054709 AGTTTAATCA
Statistics
Matches: 62, Mismatches: 3, Indels: 6
0.87 0.04 0.08
Matches are distributed among these distances:
68 26 0.42
70 4 0.06
71 3 0.05
72 29 0.47
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.51
Consensus pattern (71 bp):
TTAATATTAAATTTAATTTAATGCTTACTATTAGATAAATATTATATTAATTTAATATTAAAGTG
ATTATC
Found at i:1057436 original size:28 final size:29
Alignment explanation
Indices: 1057404--1057487 Score: 100
Period size: 28 Copynumber: 3.0 Consensus size: 29
1057394 AAGCGATCCA
* *
1057404 TTCAGAGTTTGCCACATAGGCTATTCTT-
1 TTCAGAGTTCGCCACAAAGGCTATTCTTC
* *
1057432 TTCAGAATTCGCCACAAAGGTTATTCTTC
1 TTCAGAGTTCGCCACAAAGGCTATTCTTC
* *
1057461 TT-AGAGTTCACCACAAAGGCTTTTCTT
1 TTCAGAGTTCGCCACAAAGGCTATTCTT
1057488 AACTGTCATG
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
28 45 0.96
29 2 0.04
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (29 bp):
TTCAGAGTTCGCCACAAAGGCTATTCTTC
Found at i:1058666 original size:35 final size:35
Alignment explanation
Indices: 1058615--1058689 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
1058605 GACAAGAAGT
* *
1058615 TCCAACCTTTTACACATGCCAAACATACCAATTCA
1 TCCATCCTTTTACACATGCAAAACATACCAATTCA
1058650 TCCATCCTTTTACACATGCAAAACATACCAATTCA
1 TCCATCCTTTTACACATGCAAAACATACCAATTCA
1058685 TCCAT
1 TCCAT
1058690 ACCCTTCACA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.33, G:0.03, T:0.28
Consensus pattern (35 bp):
TCCATCCTTTTACACATGCAAAACATACCAATTCA
Found at i:1077108 original size:51 final size:50
Alignment explanation
Indices: 1077048--1077722 Score: 699
Period size: 51 Copynumber: 13.3 Consensus size: 50
1077038 AATGAACACG
* *
1077048 TGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT-ATGGTCACA
* * * * * * *
1077099 TGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACT
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAA-ATATGGTCACA
* *
1077150 TGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT-ATGGTCACA
* * * * * * *
1077201 TGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACT
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAA-ATATGGTCACA
* *
1077252 TGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT-ATGGTCACA
* * * * * * *
1077303 TGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACT
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAA-ATATGGTCACA
* *
1077354 TGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT-ATGGTCACA
* * * * * * *
1077405 TGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACT
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAA-ATATGGTCACA
* *
1077456 TGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT-ATGGTCACA
* * * * * * *
1077507 TGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACT
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAA-ATATGGTCACA
* *
1077558 TGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT-ATGGTCACA
* * * *
1077609 TGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAAGCTTTGATCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAA--TATGGTCACA
* * * *
1077660 TGTGTAGTACTATGTGAAGGCTACTTCGTGAACCG-TAAA-ACTTGATCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATA--TGGTCACA
1077710 TGTGTAGTACTAT
1 TGTGTAGTACTAT
1077723 ATGTATCAGA
Statistics
Matches: 507, Mismatches: 102, Indels: 31
0.79 0.16 0.05
Matches are distributed among these distances:
50 28 0.06
51 473 0.93
52 6 0.01
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.31
Consensus pattern (50 bp):
TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATGGTCACA
Found at i:1077224 original size:102 final size:102
Alignment explanation
Indices: 1077048--1077689 Score: 1230
Period size: 102 Copynumber: 6.3 Consensus size: 102
1077038 AATGAACACG
1077048 TGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTAAG
1 TGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTAAG
1077113 TGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACT
66 TGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACT
1077150 TGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTAAG
1 TGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTAAG
1077215 TGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACT
66 TGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACT
1077252 TGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTAAG
1 TGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTAAG
1077317 TGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACT
66 TGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACT
1077354 TGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTAAG
1 TGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTAAG
1077419 TGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACT
66 TGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACT
1077456 TGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTAAG
1 TGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTAAG
1077521 TGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACT
66 TGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACT
1077558 TGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTAAG
1 TGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTAAG
* * * *
1077623 TGAAGGCTACTATGTGTACCGAAAAGCTTTGATCACA
66 TGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACT
* *
1077660 TGTGTAGTACTATGTGAAGGCTACTTCGTG
1 TGTGTAGTACTGTGTGAAGGCTACTACGTG
1077690 AACCGTAAAA
Statistics
Matches: 534, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 534 1.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (102 bp):
TGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTAAG
TGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACT
Found at i:1077802 original size:51 final size:50
Alignment explanation
Indices: 1077746--1077875 Score: 163
Period size: 51 Copynumber: 2.6 Consensus size: 50
1077736 ATAGGTCGCA
*
1077746 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCT-TCGATCACT
1 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAG-TAT-GATCACC
* * * * *
1077797 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGATAGTGATGTTCACC
1 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-ATGATCACC
*
1077848 TGTGTAGTACTATGTGCATGCTACTATG
1 TGTGTAGTACTATGTGCAGGCTACTATG
1077876 TGAACCGGCA
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
50 1 0.01
51 66 0.97
52 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (50 bp):
TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTATGATCACC
Found at i:1078050 original size:38 final size:37
Alignment explanation
Indices: 1078004--1078076 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 37
1077994 AGGTGTGGAA
*
1078004 TTGAATTGAATAT-TGACTTAGAAA-TGGAAAAGTGAATT
1 TTGAATTGAAT-TGTGA-TT-GAAAGTGAAAAAGTGAATT
1078042 TTGAATTGAATTGTGATTGAAAGTGAAAAAGTGAA
1 TTGAATTGAATTGTGATTGAAAGTGAAAAAGTGAA
1078077 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 14 0.44
38 14 0.44
ACGTcount: A:0.42, C:0.01, G:0.23, T:0.33
Consensus pattern (37 bp):
TTGAATTGAATTGTGATTGAAAGTGAAAAAGTGAATT
Found at i:1083618 original size:19 final size:19
Alignment explanation
Indices: 1083596--1083667 Score: 60
Period size: 19 Copynumber: 3.9 Consensus size: 19
1083586 ATATTGTTCA
1083596 TAATTTTATATTATTTTTT
1 TAATTTTATATTATTTTTT
* * **
1083615 TAATTCTCTATTATTTTAA
1 TAATTTTATATTATTTTTT
1083634 TAAGTTTTA-A-TATTTTTT
1 TAA-TTTTATATTATTTTTT
* *
1083652 CAATTTTCTATT-TTTT
1 TAATTTTATATTATTTT
1083668 ATAAACTTTG
Statistics
Matches: 40, Mismatches: 10, Indels: 7
0.70 0.18 0.12
Matches are distributed among these distances:
17 4 0.10
18 13 0.32
19 20 0.50
20 3 0.08
ACGTcount: A:0.26, C:0.06, G:0.01, T:0.67
Consensus pattern (19 bp):
TAATTTTATATTATTTTTT
Found at i:1087493 original size:27 final size:27
Alignment explanation
Indices: 1087455--1087522 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
1087445 GAGGGTATCT
1087455 CATAGGCGGCACCAAAGGTGCCTTTCC
1 CATAGGCGGCACCAAAGGTGCCTTTCC
*
1087482 CATAGGCGGCACCGAAGGTGCCTTTCC
1 CATAGGCGGCACCAAAGGTGCCTTTCC
*
1087509 CATTGGCGGCACCA
1 CATAGGCGGCACCA
1087523 CTTGTGTCAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.21, C:0.34, G:0.28, T:0.18
Consensus pattern (27 bp):
CATAGGCGGCACCAAAGGTGCCTTTCC
Found at i:1094250 original size:18 final size:18
Alignment explanation
Indices: 1094227--1094289 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
1094217 TTAAATTAAT
*
1094227 TCTTCTCTTTTTTTTTTC
1 TCTTCTCCTTTTTTTTTC
**
1094245 TCTTCTCC-TTTCATTT-
1 TCTTCTCCTTTTTTTTTC
*
1094261 TCTT-TCCTTCTTTTTTC
1 TCTTCTCCTTTTTTTTTC
1094278 TTCTTCTCCTTT
1 -TCTTCTCCTTT
1094290 CCTTTTCTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 7
0.71 0.15 0.15
Matches are distributed among these distances:
15 3 0.09
16 9 0.26
17 6 0.18
18 11 0.32
19 5 0.15
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.70
Consensus pattern (18 bp):
TCTTCTCCTTTTTTTTTC
Found at i:1094264 original size:34 final size:34
Alignment explanation
Indices: 1094226--1094357 Score: 149
Period size: 34 Copynumber: 3.7 Consensus size: 34
1094216 TTTAAATTAA
1094226 TTCTTCTCTTTTTTTTTTC-TCTTCTCCTTTCATT
1 TTCTT-TCTTTTTTTTTTCTTCTTCTCCTTTCATT
* * *
1094260 TTCTTTCCTTCTTTTTTCTTCTTCTCCTTTCCTT
1 TTCTTTCTTTTTTTTTTCTTCTTCTCCTTTCATT
* *
1094294 TTCTTTCCTTCTTTTTCTTTCTTTCCTCTCCTTTAATT
1 TTCTTT-CTT-TTTTT-TTTC-TTCTTCTCCTTTCATT
*
1094332 TTCTTTCTTTCTTTCTTTCTTCTTCT
1 TTCTTTCTTT-TTTTTTTCTTCTTCT
1094358 TTCCCTCTCC
Statistics
Matches: 82, Mismatches: 10, Indels: 11
0.80 0.10 0.11
Matches are distributed among these distances:
33 11 0.13
34 25 0.30
35 8 0.10
36 9 0.11
37 10 0.12
38 19 0.23
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (34 bp):
TTCTTTCTTTTTTTTTTCTTCTTCTCCTTTCATT
Found at i:1094272 original size:24 final size:24
Alignment explanation
Indices: 1094245--1094361 Score: 70
Period size: 24 Copynumber: 5.0 Consensus size: 24
1094235 TTTTTTTTTC
1094245 TCTTCTCCTTTCATTTTCTTTCCT
1 TCTTCTCCTTTCATTTTCTTTCCT
*
1094269 TCTT-T--TTTCTTCTTCTCCTTTCCT
1 TCTTCTCCTTTCAT-TT-T-CTTTCCT
* *
1094293 T-TTCTTTCC-TTCTTTTTCTTTCTT
1 TCTTC--TCCTTTCATTTTCTTTCCT
* * *
1094317 TCCTCTCCTTTAATTTTCTTTCTT
1 TCTTCTCCTTTCATTTTCTTTCCT
1094341 TCTT-T-CTTTC-TTCTTCTTTCC
1 TCTTCTCCTTTCATT-TTCTTTCC
1094362 CTCTCCTTCT
Statistics
Matches: 74, Mismatches: 8, Indels: 24
0.70 0.08 0.23
Matches are distributed among these distances:
21 7 0.09
22 13 0.18
23 8 0.11
24 35 0.47
25 3 0.04
26 3 0.04
27 5 0.07
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.67
Consensus pattern (24 bp):
TCTTCTCCTTTCATTTTCTTTCCT
Found at i:1094314 original size:4 final size:4
Alignment explanation
Indices: 1094259--1094360 Score: 54
Period size: 4 Copynumber: 25.0 Consensus size: 4
1094249 CTCCTTTCAT
* *
1094259 TTTC TTTC CTTC TTT- TTTC -TTC TTCTCC TTTCC TTTTC TTTC CTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TT-T-C TTT-C -TTTC TTTC TTTC
* *
1094305 -TT- TTTC TTTC TTTCC TCTCC TTTAAT TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTT-C T-TTC TTT--C TTTC TTTC TTTC TTTC TTTC
1094351 -TTC -TTC TTTC
1 TTTC TTTC TTTC
1094361 CCTCTCCTTC
Statistics
Matches: 79, Mismatches: 7, Indels: 24
0.72 0.06 0.22
Matches are distributed among these distances:
3 16 0.20
4 44 0.56
5 9 0.11
6 10 0.13
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTC
Found at i:1094443 original size:27 final size:27
Alignment explanation
Indices: 1094413--1094481 Score: 102
Period size: 27 Copynumber: 2.6 Consensus size: 27
1094403 TATATGGGCA
*
1094413 GTGCCGCCCATGGGAATGGCACCATCG
1 GTGCCGCCCATGGGAAAGGCACCATCG
* * *
1094440 GTGCCGCCTATGGGAAAGGCACCTTTG
1 GTGCCGCCCATGGGAAAGGCACCATCG
1094467 GTGCCGCCCATGGGA
1 GTGCCGCCCATGGGA
1094482 TACCCTCCTC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.17, C:0.30, G:0.35, T:0.17
Consensus pattern (27 bp):
GTGCCGCCCATGGGAAAGGCACCATCG
Found at i:1094657 original size:27 final size:27
Alignment explanation
Indices: 1094619--1094728 Score: 220
Period size: 27 Copynumber: 4.1 Consensus size: 27
1094609 TTTGTAAAAG
1094619 TCCCGAAATTAAATGAAGGCTACAGTT
1 TCCCGAAATTAAATGAAGGCTACAGTT
1094646 TCCCGAAATTAAATGAAGGCTACAGTT
1 TCCCGAAATTAAATGAAGGCTACAGTT
1094673 TCCCGAAATTAAATGAAGGCTACAGTT
1 TCCCGAAATTAAATGAAGGCTACAGTT
1094700 TCCCGAAATTAAATGAAGGCTACAGTT
1 TCCCGAAATTAAATGAAGGCTACAGTT
1094727 TC
1 TC
1094729 TTAGATCAAC
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 83 1.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.26
Consensus pattern (27 bp):
TCCCGAAATTAAATGAAGGCTACAGTT
Found at i:1094969 original size:19 final size:18
Alignment explanation
Indices: 1094932--1094969 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1094922 AATAATTTTT
1094932 AAAAATATAAAAAAATTC
1 AAAAATATAAAAAAATTC
1094950 AAAAA-ATAATAAAAAGTTC
1 AAAAATATAA-AAAAA-TTC
1094969 A
1 A
1094970 TACAAATTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 10 0.56
19 4 0.22
ACGTcount: A:0.71, C:0.05, G:0.03, T:0.21
Consensus pattern (18 bp):
AAAAATATAAAAAAATTC
Found at i:1095574 original size:13 final size:13
Alignment explanation
Indices: 1095556--1095605 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
1095546 GCAGGTGATA
1095556 TAATATAATAAAT
1 TAATATAATAAAT
1095569 TAATATAATAATAT
1 TAATATAATAA-AT
1095583 ATAA-A-AATATAAT
1 -TAATATAATA-AAT
*
1095596 TAAAATAATA
1 TAATATAATA
1095606 TTCATCATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
12 3 0.09
13 18 0.56
14 8 0.25
15 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAATATAATAAAT
Found at i:1095576 original size:18 final size:18
Alignment explanation
Indices: 1095555--1095595 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 18
1095545 TGCAGGTGAT
1095555 ATAATATAATAAATTAATATA
1 ATAATAT-ATAAA--AATATA
1095576 ATAATATATAAAAATATA
1 ATAATATATAAAAATATA
1095594 AT
1 AT
1095596 TAAAATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
20 5 0.25
21 7 0.35
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATAATATATAAAAATATA
Found at i:1095581 original size:21 final size:19
Alignment explanation
Indices: 1095555--1095605 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
1095545 TGCAGGTGAT
1095555 ATAATATAATAAATTAATATA
1 ATAATATAATAAA--AATATA
1095576 ATAATAT-ATAAAAATATA
1 ATAATATAATAAAAATATA
*
1095594 ATTAAAATAATA
1 A-TAATATAATA
1095606 TTCATCATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 7 0.26
19 5 0.19
20 8 0.30
21 7 0.26
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
ATAATATAATAAAAATATA
Found at i:1101789 original size:16 final size:16
Alignment explanation
Indices: 1101770--1101800 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1101760 GATTACGCCC
1101770 AAGAAAGAGCACACCT
1 AAGAAAGAGCACACCT
*
1101786 AAGAAAGAGTACACC
1 AAGAAAGAGCACACC
1101801 CTTGAGTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.23, G:0.19, T:0.06
Consensus pattern (16 bp):
AAGAAAGAGCACACCT
Found at i:1102566 original size:4 final size:4
Alignment explanation
Indices: 1102557--1102603 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
1102547 AGGAGTTATT
1102557 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT
1102604 GTATTGAAGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:1103295 original size:53 final size:53
Alignment explanation
Indices: 1103234--1103340 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
1103224 ACGTAGACAT
1103234 TATGGTCGAATCTGGAAGTGTTATGAAAAAAATTTATAAATCCGACTTCTTTC
1 TATGGTCGAATCTGGAAGTGTTATGAAAAAAATTTATAAATCCGACTTCTTTC
1103287 TATGGTCGAATCTGGAAGTGTTATGAAAAAAATTTATAAATCCGACTTCTTTC
1 TATGGTCGAATCTGGAAGTGTTATGAAAAAAATTTATAAATCCGACTTCTTTC
1103340 T
1 T
1103341 TTCTTTTTGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (53 bp):
TATGGTCGAATCTGGAAGTGTTATGAAAAAAATTTATAAATCCGACTTCTTTC
Found at i:1106512 original size:11 final size:13
Alignment explanation
Indices: 1106488--1106519 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1106478 TAGTTTATTA
1106488 ATATTTTAATATG
1 ATATTTTAATATG
1106501 AT-TTTTAA-ATG
1 ATATTTTAATATG
1106512 ATATTTTA
1 ATATTTTA
1106520 TTAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
ATATTTTAATATG
Found at i:1107996 original size:19 final size:21
Alignment explanation
Indices: 1107974--1108020 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
1107964 TGTTAATTTC
*
1107974 ATGAATTATATA-ATGTA-TG
1 ATGAAATATATATATGTATTG
*
1107993 ATGAAATATATATATTTATTG
1 ATGAAATATATATATGTATTG
1108014 ATGAAAT
1 ATGAAAT
1108021 GATAATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 11 0.46
20 4 0.17
21 9 0.38
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.43
Consensus pattern (21 bp):
ATGAAATATATATATGTATTG
Found at i:1108006 original size:21 final size:23
Alignment explanation
Indices: 1107980--1108028 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
1107970 TTTCATGAAT
1107980 TATATAATGTA-TGATGAAAT-A
1 TATATAATGTATTGATGAAATGA
*
1108001 TATAT-ATTTATTGATGAAATGA
1 TATATAATGTATTGATGAAATGA
1108023 TA-ATAA
1 TATATAA
1108029 AATAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 4 0.17
21 16 0.67
22 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (23 bp):
TATATAATGTATTGATGAAATGA
Found at i:1108333 original size:46 final size:46
Alignment explanation
Indices: 1108264--1108380 Score: 166
Period size: 46 Copynumber: 2.6 Consensus size: 46
1108254 TTTGAGTACT
* *
1108264 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCAATAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGAAGCAATAGCTACACTTA
* **
1108310 TTTGATCAAGTGACAAAGTGATAAGTGGAAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGAAGCAATAGCTACACTTA
*
1108356 TCTGATC-AGTGAC-AAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
1108381 ATGAGTGGTA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
44 11 0.17
45 6 0.09
46 47 0.73
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGAAGCAATAGCTACACTTA
Found at i:1108396 original size:51 final size:51
Alignment explanation
Indices: 1108316--1108435 Score: 170
Period size: 51 Copynumber: 2.3 Consensus size: 51
1108306 CTTATTTGAT
*
1108316 CAAGTGACAAAGTGATAAGTGGAAGCTTTAGCTACACTTAT-CTGATCAGTGA
1 CAAGTGAC-AAGTGATAAGTGGAAGCTTTAGCTACACTT-TCCTGATCAGGGA
* * * *
1108368 CAAGTGACAAGTGATGAGTGGTAGCTTTAGCTACCCTTTCCTGATTAGGGA
1 CAAGTGACAAGTGATAAGTGGAAGCTTTAGCTACACTTTCCTGATCAGGGA
1108419 CAAGTGACAAGTGATAA
1 CAAGTGACAAGTGATAA
1108436 ATGTGATCCA
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
50 1 0.02
51 52 0.85
52 8 0.13
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.27
Consensus pattern (51 bp):
CAAGTGACAAGTGATAAGTGGAAGCTTTAGCTACACTTTCCTGATCAGGGA
Found at i:1118034 original size:20 final size:20
Alignment explanation
Indices: 1118006--1118043 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1117996 CTCATTTAAT
* *
1118006 ATATTAAAAATGTTTTAAAA
1 ATATCAAAAATGCTTTAAAA
1118026 ATATCAAAAATGCTTTAA
1 ATATCAAAAATGCTTTAA
1118044 TACGAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (20 bp):
ATATCAAAAATGCTTTAAAA
Found at i:1119027 original size:18 final size:19
Alignment explanation
Indices: 1118994--1119029 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1118984 ATTGAGAGTA
*
1118994 TTAAAAATACATAATTTTT
1 TTAAAAATACAGAATTTTT
1119013 TTAAAAATA-AGAATTTT
1 TTAAAAATACAGAATTTT
1119030 AAAAATTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (19 bp):
TTAAAAATACAGAATTTTT
Found at i:1119158 original size:24 final size:25
Alignment explanation
Indices: 1119131--1119181 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
1119121 TATATATATA
1119131 TTTAATTTTTCTAT-ATTTTT-TAAT
1 TTTAATTTTT-TATAATTTTTATAAT
*
1119155 TTTAATTTTTTTTAATTTTTATAAT
1 TTTAATTTTTTATAATTTTTATAAT
1119180 TT
1 TT
1119182 GAATCCAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 2 0.08
24 16 0.67
25 6 0.25
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (25 bp):
TTTAATTTTTTATAATTTTTATAAT
Found at i:1120413 original size:56 final size:57
Alignment explanation
Indices: 1120317--1120428 Score: 163
Period size: 56 Copynumber: 2.0 Consensus size: 57
1120307 TGTTTGCTTG
*
1120317 CTGTCATAAATTGAATTAAAACTGTTGTTTGAGTGTTTCAAATTGAGCATTTTCATA
1 CTGTCATAAATTGAATTAAAACTGCTGTTTGAGTGTTTCAAATTGAGCATTTTCATA
* * * * *
1120374 CTGTCTTAAATTGAA-TCAAGCTGCTGTTTTAGTGTTTCAAATTGATCATTTTCAT
1 CTGTCATAAATTGAATTAAAACTGCTGTTTGAGTGTTTCAAATTGAGCATTTTCAT
1120429 GCTTTAGTGT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
56 35 0.71
57 14 0.29
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (57 bp):
CTGTCATAAATTGAATTAAAACTGCTGTTTGAGTGTTTCAAATTGAGCATTTTCATA
Found at i:1125187 original size:19 final size:18
Alignment explanation
Indices: 1125145--1125191 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
1125135 AAATCGTTTT
* *
1125145 CAAAGAAAAAAAAAGAAG
1 CAAAAAAAAAAAAAGAAC
1125163 CAAAAACAAAAAAAAGAACC
1 CAAAAA-AAAAAAAAGAA-C
1125183 CAAAAAAAA
1 CAAAAAAAA
1125192 GGAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 5 0.20
19 14 0.56
20 6 0.24
ACGTcount: A:0.79, C:0.13, G:0.09, T:0.00
Consensus pattern (18 bp):
CAAAAAAAAAAAAAGAAC
Found at i:1125246 original size:5 final size:5
Alignment explanation
Indices: 1125236--1125266 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
1125226 AGGAAAAGGA
*
1125236 ATAAT ATAAT ATGAT ATAAT ATAAT ATAAT A
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A
1125267 AAAAAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:1125690 original size:234 final size:235
Alignment explanation
Indices: 1125280--1125751 Score: 937
Period size: 234 Copynumber: 2.0 Consensus size: 235
1125270 AAATATAAAT
1125280 GGTTATATATTCTAACTTAAAAAAAACTACTATTTAACAAAAAAAAACAAAAAAAATATTTAACC
1 GGTTATATATTCTAACTTAAAAAAAACTACTATTTAACAAAAAAAAACAAAAAAAATATTTAACC
1125345 AAAACGCACACACAAGAACTCGAACCCAGAACCCAGAGGCACACTAACACTCACTCAACCACCAG
66 AAAACGCACACACAAGAACTCGAACCCAGAACCCAGAGGCACACTAACACTCACTCAACCACCAG
1125410 ATTAGCAGGACTATTCTAACACTTAAACGCACAACTAAGCACAATAGCGCAACCTTCTCACTGAC
131 ATTAGCAGGACTATTCTAACACTTAAACGCACAACTAAGCACAATAGCGCAACCTTCTCACTGAC
1125475 CCCAACCTCAAAAATCAAAACTTCTAACCCTAAAATTTGA
196 CCCAACCTCAAAAATCAAAACTTCTAACCCTAAAATTTGA
1125515 GGTTATATA-TCTAACTTAAAAAAAACTACTATTTAACAAAAAAAAACAAAAAAAATATTTAACC
1 GGTTATATATTCTAACTTAAAAAAAACTACTATTTAACAAAAAAAAACAAAAAAAATATTTAACC
1125579 AAAACGCACACACAAGAACTCGAACCCAGAACCCAGAGGCACACTAACACTCACTCAACCACCAG
66 AAAACGCACACACAAGAACTCGAACCCAGAACCCAGAGGCACACTAACACTCACTCAACCACCAG
1125644 ATTAGCAGGACTATTCTAACACTTAAACGCACAACTAAGCACAATAGCGCAACCTTCTCACTGAC
131 ATTAGCAGGACTATTCTAACACTTAAACGCACAACTAAGCACAATAGCGCAACCTTCTCACTGAC
1125709 CCCAACCTCAAAAATCAAAACTTCTAACCCTAAAATTTGA
196 CCCAACCTCAAAAATCAAAACTTCTAACCCTAAAATTTGA
1125749 GGT
1 GGT
1125752 GTTACAGTTA
Statistics
Matches: 237, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
234 228 0.96
235 9 0.04
ACGTcount: A:0.45, C:0.27, G:0.08, T:0.19
Consensus pattern (235 bp):
GGTTATATATTCTAACTTAAAAAAAACTACTATTTAACAAAAAAAAACAAAAAAAATATTTAACC
AAAACGCACACACAAGAACTCGAACCCAGAACCCAGAGGCACACTAACACTCACTCAACCACCAG
ATTAGCAGGACTATTCTAACACTTAAACGCACAACTAAGCACAATAGCGCAACCTTCTCACTGAC
CCCAACCTCAAAAATCAAAACTTCTAACCCTAAAATTTGA
Found at i:1135597 original size:22 final size:23
Alignment explanation
Indices: 1135559--1135604 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
1135549 TCCCTCACCA
*
1135559 TTTTTAGCTTTTAGGTT-TTTGT
1 TTTTTAGCTTGTAGGTTATTTGT
1135581 TTTTTAGCTTAGT-GGTTATTTGT
1 TTTTTAGCTT-GTAGGTTATTTGT
1135604 T
1 T
1135605 GTTGTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.11, C:0.04, G:0.20, T:0.65
Consensus pattern (23 bp):
TTTTTAGCTTGTAGGTTATTTGT
Found at i:1137846 original size:18 final size:18
Alignment explanation
Indices: 1137804--1137838 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1137794 TACTCGCAAT
*
1137804 TTTGGGCCAATTGATGGC
1 TTTGGGCCAAATGATGGC
1137822 TTTGGGCCAAATGATGG
1 TTTGGGCCAAATGATGG
1137839 TATTGGGCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.14, G:0.34, T:0.31
Consensus pattern (18 bp):
TTTGGGCCAAATGATGGC
Found at i:1146948 original size:24 final size:23
Alignment explanation
Indices: 1146921--1146974 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
1146911 ATTTGAGAAC
*
1146921 AAATAAAAAATAAAAATCATAAAT
1 AAATAAAAAATAAAAAT-ATAAAA
* * *
1146945 AAATAAGAAATAGAAATTTAAAA
1 AAATAAAAAATAAAAATATAAAA
1146968 AAATAAA
1 AAATAAA
1146975 GTGAAAGATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 10 0.40
24 15 0.60
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (23 bp):
AAATAAAAAATAAAAATATAAAA
Found at i:1147450 original size:8 final size:8
Alignment explanation
Indices: 1147439--1147465 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1147429 ATAAATAAAT
1147439 AAATAATA
1 AAATAATA
1147447 AAATAATA
1 AAATAATA
1147455 AAATAATA
1 AAATAATA
1147463 AAA
1 AAA
1147466 CCTAATCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
AAATAATA
Found at i:1147841 original size:17 final size:16
Alignment explanation
Indices: 1147820--1147860 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
1147810 TTCATCCTGT
*
1147820 ATTTCTTTTTTTTTCTC
1 ATTTCTTTTCTTTTC-C
*
1147837 TTTTCTTTTCTTTTCC
1 ATTTCTTTTCTTTTCC
1147853 ATTTCTTT
1 ATTTCTTT
1147861 ACATCATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.76
Consensus pattern (16 bp):
ATTTCTTTTCTTTTCC
Found at i:1149571 original size:2 final size:2
Alignment explanation
Indices: 1149564--1149590 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1149554 GGTTTGAAAG
1149564 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
1149591 ATTGGAATTC
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:1155355 original size:2 final size:2
Alignment explanation
Indices: 1155348--1155373 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1155338 AATACTTTCA
1155348 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
1155374 TTACTTTTAA
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:1161529 original size:4 final size:4
Alignment explanation
Indices: 1161520--1161571 Score: 95
Period size: 4 Copynumber: 13.0 Consensus size: 4
1161510 ACACTTCAAT
*
1161520 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA TATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1161568 CATA
1 CATA
1161572 TACTTCTTAG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
CATA
Found at i:1175723 original size:17 final size:16
Alignment explanation
Indices: 1175703--1175747 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 16
1175693 AAAAATAAAT
1175703 TTTTAAATAATTTTTT-A
1 TTTTAAAT--TTTTTTAA
1175720 TTTTAAATTTTTTTAA
1 TTTTAAATTTTTTTAA
1175736 TTTTAAAATTTT
1 TTTT-AAATTTT
1175748 AAGAATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.23
16 5 0.19
17 15 0.58
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTAAATTTTTTTAA
Found at i:1177543 original size:23 final size:21
Alignment explanation
Indices: 1177507--1177556 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
1177497 ATCATTGTTT
*
1177507 AATATTTTATATTATAAATAGTA
1 AATA-TTTATATTA-AAACAGTA
*
1177530 AATATTTATCATTAAAACATTA
1 AATATTTAT-ATTAAAACAGTA
1177552 AATAT
1 AATAT
1177557 ATATTTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (21 bp):
AATATTTATATTAAAACAGTA
Found at i:1190574 original size:25 final size:25
Alignment explanation
Indices: 1190545--1190603 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
1190535 AAGAGCCTAT
*
1190545 CAGGAAGCTTATCTGAGCTATATAA
1 CAGGAAGCTTATCCGAGCTATATAA
* *
1190570 CAGGAAGTTTATCCGGGCTATATAA
1 CAGGAAGCTTATCCGAGCTATATAA
1190595 CAGGAAGCT
1 CAGGAAGCT
1190604 CATAAGAGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (25 bp):
CAGGAAGCTTATCCGAGCTATATAA
Found at i:1190649 original size:26 final size:26
Alignment explanation
Indices: 1190615--1190675 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
1190605 ATAAGAGCCA
* *
1190615 TAATCAGGAAGTTCACAAAGAACTTT
1 TAATCAGGAAGCTCACAAAGAACCTT
* *
1190641 TAATTAGGAAGCTCACAAAGAGCCTT
1 TAATCAGGAAGCTCACAAAGAACCTT
1190667 TAATCAGGA
1 TAATCAGGA
1190676 GCTTCGGATA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (26 bp):
TAATCAGGAAGCTCACAAAGAACCTT
Found at i:1194477 original size:25 final size:26
Alignment explanation
Indices: 1194434--1194486 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
1194424 AAGTTGTAAA
1194434 CTAGAAAAATATCTCTAGA-AATTTT
1 CTAGAAAAATATCTCTAGAGAATTTT
* * *
1194459 CTAGAATAATCTCTTTAGAGAATTTT
1 CTAGAAAAATATCTCTAGAGAATTTT
1194485 CT
1 CT
1194487 CTCTACAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (26 bp):
CTAGAAAAATATCTCTAGAGAATTTT
Found at i:1194667 original size:60 final size:61
Alignment explanation
Indices: 1194595--1194712 Score: 148
Period size: 62 Copynumber: 1.9 Consensus size: 61
1194585 ATCACTTTAA
* * * ** * *
1194595 TATTAAATTAATATAATATTTATTT-AAGATAAGTATTAGATTAAATTTAATATTAAATCT
1 TATTAAAATAATAGAATATTTATTTCAAGAGAAACATTAAATTAAATTAAATATTAAATCT
*
1194655 TATTAAAATAATAGAATGTTTATTTGCAAGAGAAACATTAAATTAAATTAAATATTAA
1 TATTAAAATAATAGAATATTTATTT-CAAGAGAAACATTAAATTAAATTAAATATTAA
1194713 TATAATCATT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 22 0.46
62 26 0.54
ACGTcount: A:0.49, C:0.03, G:0.07, T:0.42
Consensus pattern (61 bp):
TATTAAAATAATAGAATATTTATTTCAAGAGAAACATTAAATTAAATTAAATATTAAATCT
Found at i:1197726 original size:178 final size:178
Alignment explanation
Indices: 1197427--1197778 Score: 618
Period size: 178 Copynumber: 2.0 Consensus size: 178
1197417 AATCATGGAG
*
1197427 TCAGTCCACAAGAAGTACCATGATTGAATACTCCTTATTGTATACTCTTTACGAAAGCAATTCAT
1 TCAGTCCACAAGAAGTACCATGATTGAAAACTCCTTATTGTATACTCTTTACGAAAGCAATTCAT
* *
1197492 CCAACTGCTTTGTCCAATGATCTCGTCATGTGTGTGTTACCCTCATATGATATCCTTGATTCTTT
66 CCAACTGCTTTGTCCAATAATCTCGTCATGTGTGTGTTACCCTCATATGATATCCTTGATTCCTT
*
1197557 TGAGTTTAAATCTGTTC-CTCCAAT-CAATCCTATTTTATCTCATTATCA
131 TGAG-TTAAATCCGTTCACT-CAATACAATCCTATTTTATCTCATTATCA
*
1197605 TCAGTCCACAAGAAGTACCATGATTGAAAACTCCTTATTGTATACTCTTTATGAAAGCAATTCAT
1 TCAGTCCACAAGAAGTACCATGATTGAAAACTCCTTATTGTATACTCTTTACGAAAGCAATTCAT
*
1197670 CCAACTGCTTTGTCCACTAATCTCGTCATGTGTGTGTTACCCTCATATGATATCCTTGATTCCTT
66 CCAACTGCTTTGTCCAATAATCTCGTCATGTGTGTGTTACCCTCATATGATATCCTTGATTCCTT
1197735 TGAGTTAAATCCGTTCACTCAATACAATCCTATTTTATCTCATT
131 TGAGTTAAATCCGTTCACTCAATACAATCCTATTTTATCTCATT
1197779 GTTACCATTG
Statistics
Matches: 166, Mismatches: 6, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
177 15 0.09
178 151 0.91
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (178 bp):
TCAGTCCACAAGAAGTACCATGATTGAAAACTCCTTATTGTATACTCTTTACGAAAGCAATTCAT
CCAACTGCTTTGTCCAATAATCTCGTCATGTGTGTGTTACCCTCATATGATATCCTTGATTCCTT
TGAGTTAAATCCGTTCACTCAATACAATCCTATTTTATCTCATTATCA
Found at i:1200140 original size:9 final size:9
Alignment explanation
Indices: 1200103--1200142 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
1200093 TTCAAATTGA
1200103 TTAATTCGG
1 TTAATTCGG
*
1200112 GTAATTCGG
1 TTAATTCGG
* *
1200121 GTAATTAGG
1 TTAATTCGG
1200130 TTAATTCGG
1 TTAATTCGG
1200139 TTAA
1 TTAA
1200143 CCGACCGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.28, C:0.07, G:0.25, T:0.40
Consensus pattern (9 bp):
TTAATTCGG
Found at i:1200196 original size:29 final size:29
Alignment explanation
Indices: 1200159--1200231 Score: 137
Period size: 29 Copynumber: 2.5 Consensus size: 29
1200149 GAATTAACCG
*
1200159 AAAAAATTTCGGTTCGGTAAATTTTTTTT
1 AAAAAATTTCGGTTCGGTAAATTTTTTTA
1200188 AAAAAATTTCGGTTCGGTAAATTTTTTTA
1 AAAAAATTTCGGTTCGGTAAATTTTTTTA
1200217 AAAAAATTTCGGTTC
1 AAAAAATTTCGGTTC
1200232 AGTTAACAGT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (29 bp):
AAAAAATTTCGGTTCGGTAAATTTTTTTA
Found at i:1218960 original size:14 final size:14
Alignment explanation
Indices: 1218941--1218973 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1218931 TTACCTCCGT
1218941 CCTCCACCGATCCA
1 CCTCCACCGATCCA
*
1218955 CCTCCACCGGTCCA
1 CCTCCACCGATCCA
1218969 CCTCC
1 CCTCC
1218974 GGCCCTCCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.61, G:0.09, T:0.15
Consensus pattern (14 bp):
CCTCCACCGATCCA
Found at i:1219262 original size:14 final size:14
Alignment explanation
Indices: 1219239--1219282 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
1219229 CTCCACCGAG
1219239 CACCGATCCACCTC
1 CACCGATCCACCTC
*
1219253 CACTGATCCACCTC
1 CACCGATCCACCTC
*
1219267 CACCGGTCCACCTC
1 CACCGATCCACCTC
1219281 CA
1 CA
1219283 GTCCTGCAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.20, C:0.55, G:0.09, T:0.16
Consensus pattern (14 bp):
CACCGATCCACCTC
Found at i:1219607 original size:44 final size:44
Alignment explanation
Indices: 1219554--1219659 Score: 176
Period size: 44 Copynumber: 2.4 Consensus size: 44
1219544 AAGAAGTAGA
*
1219554 GATATTGAGCATGTTTTGGGATGACTCGGTATTTTGAGTTTAGGT
1 GATA-TGAGCATGTTTTGGGATGACTCAGTATTTTGAGTTTAGGT
1219599 GATATGAGCATGTTTTGGGATGACTCAGTATTTTGAGTTTAGGT
1 GATATGAGCATGTTTTGGGATGACTCAGTATTTTGAGTTTAGGT
* *
1219643 GATTTGAGCATTTTTTG
1 GATATGAGCATGTTTTG
1219660 AAAGCCTACA
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
44 54 0.93
45 4 0.07
ACGTcount: A:0.21, C:0.07, G:0.29, T:0.43
Consensus pattern (44 bp):
GATATGAGCATGTTTTGGGATGACTCAGTATTTTGAGTTTAGGT
Found at i:1220923 original size:22 final size:22
Alignment explanation
Indices: 1220898--1220960 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
1220888 TGGTCATAAT
1220898 TAATTAAATAGTTAGTGAATTC
1 TAATTAAATAGTTAGTGAATTC
1220920 TAATCT-AAT-G---GTG-A-T-
1 TAAT-TAAATAGTTAGTGAATTC
1220935 TAATTAAATAGTTAGTGAATTC
1 TAATTAAATAGTTAGTGAATTC
1220957 TAAT
1 TAAT
1220961 CTAATGGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 18
0.64 0.00 0.36
Matches are distributed among these distances:
14 1 0.03
15 7 0.22
16 2 0.06
17 1 0.03
18 3 0.09
19 3 0.09
20 1 0.03
21 2 0.06
22 11 0.34
23 1 0.03
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.41
Consensus pattern (22 bp):
TAATTAAATAGTTAGTGAATTC
Found at i:1220937 original size:37 final size:37
Alignment explanation
Indices: 1220896--1220967 Score: 144
Period size: 37 Copynumber: 1.9 Consensus size: 37
1220886 GCTGGTCATA
1220896 ATTAATTAAATAGTTAGTGAATTCTAATCTAATGGTG
1 ATTAATTAAATAGTTAGTGAATTCTAATCTAATGGTG
1220933 ATTAATTAAATAGTTAGTGAATTCTAATCTAATGG
1 ATTAATTAAATAGTTAGTGAATTCTAATCTAATGG
1220968 AAAAAATAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.40
Consensus pattern (37 bp):
ATTAATTAAATAGTTAGTGAATTCTAATCTAATGGTG
Found at i:1221278 original size:14 final size:15
Alignment explanation
Indices: 1221256--1221332 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
1221246 CAATCAAACA
1221256 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
1221270 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
1221285 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
1221305 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
1221319 TCAAAAAAT-ATTTT
1 CCAGAAAATCATTTT
1221333 ACTGCCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.35
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:1221297 original size:20 final size:20
Alignment explanation
Indices: 1221272--1221311 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1221262 AATATTTTCC
*
1221272 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
1221292 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
1221312 TCATTTTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:1222106 original size:11 final size:11
Alignment explanation
Indices: 1222084--1222123 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
1222074 AACTAATCAT
1222084 CTCTCAAATTTC
1 CTCTC-AATTTC
1222096 CTCTCAATTTC
1 CTCTCAATTTC
1222107 CTCTCAATTTC
1 CTCTCAATTTC
1222118 CT-TCAA
1 CTCTCAA
1222124 AAATTCTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 4 0.14
11 19 0.68
12 5 0.18
ACGTcount: A:0.23, C:0.35, G:0.00, T:0.42
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:1222231 original size:12 final size:12
Alignment explanation
Indices: 1222192--1222235 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
1222182 CTTAACTCCC
*
1222192 TTTTTTTAAATA
1 TTTTTTAAAATA
* *
1222204 ATTTTAAAAATA
1 TTTTTTAAAATA
1222216 TTTTTTAAAAT-
1 TTTTTTAAAATA
1222227 TTTTTTAAA
1 TTTTTTAAA
1222236 CCGTAAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTTTTAAAATA
Found at i:1223125 original size:7 final size:7
Alignment explanation
Indices: 1223113--1223137 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1223103 AGTCGATTGA
1223113 TATTTAG
1 TATTTAG
1223120 TATTTAG
1 TATTTAG
1223127 TATTTAG
1 TATTTAG
1223134 TATT
1 TATT
1223138 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:1223815 original size:18 final size:18
Alignment explanation
Indices: 1223788--1223827 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1223778 CAGGTGCGTT
*
1223788 TCCTAGCCCTTATATGTA
1 TCCTAACCCTTATATGTA
*
1223806 TCCTAACCCTTATTTGTA
1 TCCTAACCCTTATATGTA
1223824 TCCT
1 TCCT
1223828 TTTCAGAGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.30, G:0.07, T:0.42
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:1227987 original size:21 final size:21
Alignment explanation
Indices: 1227961--1228003 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1227951 CTTTTACGAA
1227961 GTTCTGTCAAATCTATGTTCT
1 GTTCTGTCAAATCTATGTTCT
*
1227982 GTTCTGTCAAATTTATGTTCT
1 GTTCTGTCAAATCTATGTTCT
1228003 G
1 G
1228004 GTTAAAAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.49
Consensus pattern (21 bp):
GTTCTGTCAAATCTATGTTCT
Found at i:1228438 original size:124 final size:120
Alignment explanation
Indices: 1228211--1228577 Score: 460
Period size: 124 Copynumber: 3.0 Consensus size: 120
1228201 CCCAAACATG
*
1228211 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTCACAAATTCTTCTCAAATAGCATCCTA
1 CTACTGTAGCAAAAG-GCGTCCACGA-GGC-CGATTTT-ACAAATTCTTCTCAAATAGCATCCTG
* *
1228276 ATCGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTCCATGAC
62 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTCCATGAC
* *
1228335 CTACAGTAGCAAAAGTGCGTCCACGAAGGCTCGATTTTACAAATTCTTCTCAAAATAGCATCTTG
1 CTACTGTAGCAAAAG-GCGTCCACG-AGGC-CGATTTTACAAATTCTTCTC-AAATAGCATCCTG
* *
1228400 CTAGAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAAAATATTTCTTCCATGAC
62 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTC-AAAAAAATTATTTCTTCCATGAC
* * *
1228460 CTACTGTAGCAAAA-GCG----CG-TGCAG-TTTCACAAATTCTTCTCAAATAGCATCCTGCTAG
1 CTACTGTAGCAAAAGGCGTCCACGAGGCCGATTTTACAAATTCTTCTCAAATAGCATCCTGCTAG
* ** *
1228518 AAGCGATTTTATACTATTTGATCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
66 AAGCGATTTTATACTATTTGCTCAGAAACGTCAA--AAAAATTATTTCTTCCATGAC
1228575 CTA
1 CTA
1228578 AAAACCCTAA
Statistics
Matches: 218, Mismatches: 20, Indels: 19
0.85 0.08 0.07
Matches are distributed among these distances:
113 2 0.01
114 46 0.21
115 36 0.17
116 1 0.00
117 2 0.01
119 2 0.01
123 16 0.07
124 77 0.35
125 36 0.17
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (120 bp):
CTACTGTAGCAAAAGGCGTCCACGAGGCCGATTTTACAAATTCTTCTCAAATAGCATCCTGCTAG
AAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTCCATGAC
Found at i:1235545 original size:18 final size:18
Alignment explanation
Indices: 1235524--1235563 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1235514 TCTTATGCAC
1235524 CAAAACTATCTTTAAAAT
1 CAAAACTATCTTTAAAAT
*
1235542 CAAAACTATCTTTAAGAT
1 CAAAACTATCTTTAAAAT
1235560 CAAA
1 CAAA
1235564 GATATGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.50, C:0.17, G:0.03, T:0.30
Consensus pattern (18 bp):
CAAAACTATCTTTAAAAT
Found at i:1237555 original size:21 final size:21
Alignment explanation
Indices: 1237481--1237576 Score: 111
Period size: 21 Copynumber: 4.6 Consensus size: 21
1237471 ATGTTTTACT
*
1237481 TTCTGTTTAGCTCTTATGAGC
1 TTCTGTTCAGCTCTTATGAGC
* * * *
1237502 TTGTGTTCAACTCCTATGAGT
1 TTCTGTTCAGCTCTTATGAGC
* * **
1237523 TTCTATTTAGCTCTTACAAGC
1 TTCTGTTCAGCTCTTATGAGC
1237544 TTCTGTTCAGCTCTTATGAGC
1 TTCTGTTCAGCTCTTATGAGC
1237565 TTCTGTTCAGCT
1 TTCTGTTCAGCT
1237577 TTCGACTTCT
Statistics
Matches: 58, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.45
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTATGAGC
Found at i:1237587 original size:18 final size:21
Alignment explanation
Indices: 1237481--1237589 Score: 98
Period size: 21 Copynumber: 5.3 Consensus size: 21
1237471 ATGTTTTACT
* *
1237481 TTCTGTTTAGCTCTTATGAGC
1 TTCTGTTCAGCTCTTACGAGC
* * * * *
1237502 TTGTGTTCAACTCCTATGAGT
1 TTCTGTTCAGCTCTTACGAGC
* * *
1237523 TTCTATTTAGCTCTTACAAGC
1 TTCTGTTCAGCTCTTACGAGC
*
1237544 TTCTGTTCAGCTCTTATGAGC
1 TTCTGTTCAGCTCTTACGAGC
1237565 TTCTGTTCAGCT-TT-CGA-C
1 TTCTGTTCAGCTCTTACGAGC
1237583 TTCTGTT
1 TTCTGTT
1237590 GGCGTATTCG
Statistics
Matches: 70, Mismatches: 18, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
18 8 0.11
19 2 0.03
20 2 0.03
21 58 0.83
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTACGAGC
Found at i:1237789 original size:21 final size:20
Alignment explanation
Indices: 1237762--1237810 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
1237752 AATAGAAGTT
*
1237762 ATGAATGACAGGAAATTGTC
1 ATGAATGACAGGAAATTGAC
*
1237782 AGTGAATGACAGGGAATTGAC
1 A-TGAATGACAGGAAATTGAC
1237803 ATGAATGA
1 ATGAATGA
1237811 TTTCATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.41, C:0.08, G:0.29, T:0.22
Consensus pattern (20 bp):
ATGAATGACAGGAAATTGAC
Found at i:1238421 original size:55 final size:55
Alignment explanation
Indices: 1238360--1238469 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
1238350 TGTTGAGGTT
*
1238360 AGGTTGGTGTCAACTTGGGTGAGAAATGTGGCTTAGAAAATGGCCTAGTTTCGTC
1 AGGTTGGTGTCAACTTGGGTGAGAAATGTGGCTTAGAAAATGCCCTAGTTTCGTC
1238415 AGGTTGGTGTCAACTTGGGTGAGAAATGTGGCTTAGAAAATGCCCTAGTTTCGTC
1 AGGTTGGTGTCAACTTGGGTGAGAAATGTGGCTTAGAAAATGCCCTAGTTTCGTC
1238470 CACATGGGTA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.24, C:0.14, G:0.32, T:0.31
Consensus pattern (55 bp):
AGGTTGGTGTCAACTTGGGTGAGAAATGTGGCTTAGAAAATGCCCTAGTTTCGTC
Found at i:1242532 original size:13 final size:14
Alignment explanation
Indices: 1242511--1242547 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
1242501 TCCAAGTCAG
1242511 ATAAAATAATTAAA
1 ATAAAATAATTAAA
*
1242525 AT-AAATAACTAAA
1 ATAAAATAATTAAA
1242538 ATAAAATAAT
1 ATAAAATAAT
1242548 AAATCAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (14 bp):
ATAAAATAATTAAA
Found at i:1247148 original size:20 final size:20
Alignment explanation
Indices: 1247125--1247165 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1247115 TATATCTTAC
1247125 TTCAATAATTAATATTAACT
1 TTCAATAATTAATATTAACT
1247145 TTCAATAATTAATATTAACT
1 TTCAATAATTAATATTAACT
1247165 T
1 T
1247166 ACACTTAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (20 bp):
TTCAATAATTAATATTAACT
Found at i:1249161 original size:44 final size:43
Alignment explanation
Indices: 1249079--1249198 Score: 131
Period size: 44 Copynumber: 2.8 Consensus size: 43
1249069 AGAATTGTGT
* *
1249079 TATGTG-TTATCGTGTAAGACCACGTCTGGGACGTTGGCATCGAC
1 TATGTGATTA-CGTGTAAGACCACGTCTAGGACGTTGGCATC-AA
1249123 T-TGTGACTTACGTGTAAGACC-CTGTCTAGGACAG-TGGCATCAA
1 TATGTGA-TTACGTGTAAGACCAC-GTCTAGGAC-GTTGGCATCAA
* *
1249166 TATGTGATTACATGTAAGACCACGTCTGGGACG
1 TATGTGATTACGTGTAAGACCACGTCTAGGACG
1249199 ATAGCGTTGT
Statistics
Matches: 66, Mismatches: 4, Indels: 14
0.79 0.05 0.17
Matches are distributed among these distances:
42 1 0.02
43 28 0.42
44 33 0.50
45 4 0.06
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (43 bp):
TATGTGATTACGTGTAAGACCACGTCTAGGACGTTGGCATCAA
Found at i:1253658 original size:15 final size:15
Alignment explanation
Indices: 1253638--1253668 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1253628 AAAGTTGTAG
*
1253638 AGAAATTTTTTTTAA
1 AGAAATTGTTTTTAA
1253653 AGAAATTGTTTTTAA
1 AGAAATTGTTTTTAA
1253668 A
1 A
1253669 AAAAAATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (15 bp):
AGAAATTGTTTTTAA
Found at i:1262180 original size:3 final size:3
Alignment explanation
Indices: 1262161--1262224 Score: 110
Period size: 3 Copynumber: 21.3 Consensus size: 3
1262151 GGTAAGCAAA
* *
1262161 AAT AAT AAA AAT GAT 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 AAT AAT AAT
1262209 AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT A
1262225 TTTTTAGGTG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1262436 original size:15 final size:15
Alignment explanation
Indices: 1262416--1262445 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1262406 GTAATGTACT
1262416 TGCTTATTTGTATAA
1 TGCTTATTTGTATAA
1262431 TGCTTATTTGTATAA
1 TGCTTATTTGTATAA
1262446 AGAAAAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (15 bp):
TGCTTATTTGTATAA
Found at i:1266075 original size:21 final size:21
Alignment explanation
Indices: 1266034--1266102 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
1266024 ATTTGAGTTG
1266034 AATTATATAAAATCATAAAAA
1 AATTATATAAAATCATAAAAA
* *
1266055 AATTGTATGAAAATTATAAAAA
1 AATTATAT-AAAATCATAAAAA
*
1266077 TAATT-T-TACAAATTATAAAAA
1 -AATTATATA-AAATCATAAAAA
1266098 TAATT
1 -AATT
1266103 TTTGACATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
20 1 0.02
21 25 0.58
22 13 0.30
23 4 0.09
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (21 bp):
AATTATATAAAATCATAAAAA
Found at i:1266115 original size:21 final size:21
Alignment explanation
Indices: 1266065--1266104 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1266055 AATTGTATGA
1266065 AAATTATAAAAATAATTTTAC
1 AAATTATAAAAATAATTTTAC
1266086 AAATTATAAAAATAATTTT
1 AAATTATAAAAATAATTTT
1266105 TGACATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATTATAAAAATAATTTTAC
Found at i:1266232 original size:39 final size:38
Alignment explanation
Indices: 1266183--1266324 Score: 133
Period size: 39 Copynumber: 3.7 Consensus size: 38
1266173 ACCTAGTCAC
* * *
1266183 ATGTGTTTTCAATAGGAATTATAGTATTTGGTTATAAAA
1 ATGTTTTTTCAATAGGAATTTTAGTATTTAGTTA-AAAA
* *
1266222 ATGTTTTTTCAATAGGAATTTTAGTA-ATAGTTGAAAGA
1 ATGTTTTTTCAATAGGAATTTTAGTATTTAGTT-AAAAA
* * * *
1266260 TTTTGTTTTTCAATAGAAATTTTAGTATTTTGTTACAAAA
1 ATGT-TTTTTCAATAGGAATTTTAGTATTTAGTTA-AAAA
* * *
1266300 TTGATTTTCCAATAGGAATTTTAGT
1 ATGTTTTTTCAATAGGAATTTTAGT
1266325 TATGGAATTT
Statistics
Matches: 84, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
38 9 0.11
39 66 0.79
40 9 0.11
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.46
Consensus pattern (38 bp):
ATGTTTTTTCAATAGGAATTTTAGTATTTAGTTAAAAA
Found at i:1266417 original size:40 final size:39
Alignment explanation
Indices: 1266337--1266453 Score: 189
Period size: 39 Copynumber: 3.0 Consensus size: 39
1266327 TGGAATTTAT
1266337 TTTCCAATAGAAAATTTAGTGATAGTTGAGAGATTTTGG
1 TTTCCAATAGAAAATTTAGTGATAGTTGAGAGATTTTGG
*
1266376 TTTCCAATAGAAAATTTAGTGATGATTTGAGAGATTTTGG
1 TTTCCAATAGAAAATTTAGTGAT-AGTTGAGAGATTTTGG
** *
1266416 TTTCCAATAGGGAATTTAGTAATAGTTGAGAGATTTTG
1 TTTCCAATAGAAAATTTAGTGATAGTTGAGAGATTTTG
1266454 ATAGTTGCTA
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
39 37 0.51
40 35 0.49
ACGTcount: A:0.32, C:0.05, G:0.23, T:0.39
Consensus pattern (39 bp):
TTTCCAATAGAAAATTTAGTGATAGTTGAGAGATTTTGG
Found at i:1278979 original size:21 final size:20
Alignment explanation
Indices: 1278941--1278980 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1278931 AATTTTAAAA
*
1278941 TATTTTTAAAATACTTTTTT
1 TATTTTTAAAATAATTTTTT
1278961 TATTTTTAAAATAAATTTTT
1 TATTTTTAAAAT-AATTTTT
1278981 GGTGTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTTAAAATAATTTTTT
Found at i:1282516 original size:21 final size:19
Alignment explanation
Indices: 1282492--1282559 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 19
1282482 TTCAACTGTA
1282492 TTAATATCTAATTATAAATAT
1 TTAATAT-TAATT-TAAATAT
1282513 TTAATGATTATATTTAAATAT
1 TTAAT-ATTA-ATTTAAATAT
* *
1282534 TTAAAATATAATTTATATAT
1 TTAATAT-TAATTTAAATAT
1282554 TCTAAT
1 T-TAAT
1282560 TAAATTTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 12 0.30
21 23 0.57
22 5 0.12
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (19 bp):
TTAATATTAATTTAAATAT
Found at i:1285266 original size:19 final size:19
Alignment explanation
Indices: 1285244--1285364 Score: 65
Period size: 20 Copynumber: 6.3 Consensus size: 19
1285234 ATAATAAAAA
1285244 ATAAAAATCAATAAAATTT
1 ATAAAAATCAATAAAATTT
* * *
1285263 ATAAAAATGATTAAATTTT
1 ATAAAAATCAATAAAATTT
*
1285282 AATAAAAAT-ATATAAAA-GT
1 -ATAAAAATCA-ATAAAATTT
* *
1285301 ATAAAAATCGTAAAAAAATAT
1 ATAAAAATC--AATAAAATTT
* *
1285322 A-AAAAAT--GTAAATTTTT
1 ATAAAAATCAATAAA-ATTT
1285339 ATAAAAATC-ATAAAATAATT
1 ATAAAAATCAATAAAAT--TT
1285359 ATAAAA
1 ATAAAA
1285365 TATATAGAAA
Statistics
Matches: 77, Mismatches: 14, Indels: 21
0.69 0.12 0.19
Matches are distributed among these distances:
16 3 0.04
17 3 0.04
18 15 0.19
19 22 0.29
20 31 0.40
21 3 0.04
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.31
Consensus pattern (19 bp):
ATAAAAATCAATAAAATTT
Found at i:1285278 original size:18 final size:18
Alignment explanation
Indices: 1285244--1285403 Score: 58
Period size: 19 Copynumber: 8.3 Consensus size: 18
1285234 ATAATAAAAA
1285244 ATAAAAATCA-ATAAAATTT
1 ATAAAAAT-ATAT-AAATTT
1285263 ATAAAAATGAT-TAAATTTT
1 ATAAAAAT-ATATAAA-TTT
**
1285282 AATAAAAATATATAAAAGT
1 -ATAAAAATATATAAATTT
* * **
1285301 ATAAAAATCGTAAAAAAAT
1 ATAAAAAT-ATATAAATTT
*
1285320 ATAAAAA-ATGTAAATTTTT
1 ATAAAAATATATAAA--TTT
1285339 ATAAAAATCATA-AAATAATT
1 ATAAAAAT-ATATAAAT--TT
* *
1285359 ATAAAATATATAGAAATAT
1 ATAAAA-ATATATAAATTT
* *
1285378 AGAAAAAAATTATAAAATTTT
1 ATAAAAATA-TAT-AAA-TTT
1285399 ATAAA
1 ATAAA
1285404 GTGGTAAGAA
Statistics
Matches: 107, Mismatches: 18, Indels: 30
0.69 0.12 0.19
Matches are distributed among these distances:
17 4 0.04
18 14 0.13
19 46 0.43
20 29 0.27
21 14 0.13
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (18 bp):
ATAAAAATATATAAATTT
Found at i:1285286 original size:20 final size:20
Alignment explanation
Indices: 1285243--1285290 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1285233 AATAATAAAA
1285243 AATAAAAATCAATAAAATTT
1 AATAAAAATCAATAAAATTT
* * *
1285263 -ATAAAAATGATTAAATTTT
1 AATAAAAATCAATAAAATTT
1285282 AATAAAAAT
1 AATAAAAAT
1285291 ATATAAAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
AATAAAAATCAATAAAATTT
Found at i:1285303 original size:10 final size:10
Alignment explanation
Indices: 1285283--1285394 Score: 51
Period size: 10 Copynumber: 11.6 Consensus size: 10
1285273 TTAAATTTTA
1285283 ATAAAAATAT
1 ATAAAAATAT
*
1285293 AT-AAAA-GT
1 ATAAAAATAT
*
1285301 ATAAAAATCGT
1 ATAAAAAT-AT
1285312 A-AAAAA-AT
1 ATAAAAATAT
1285320 ATAAAAA-AT
1 ATAAAAATAT
* ** *
1285329 GTAAATTTTT
1 ATAAAAATAT
1285339 ATAAAAATCAT
1 ATAAAAAT-AT
1285350 A-AAATAAT-T
1 ATAAA-AATAT
1285359 AT-AAAATAT
1 ATAAAAATAT
*
1285368 ATAGAAATAT
1 ATAAAAATAT
* *
1285378 AGAAAAAAATT
1 ATAAAAATA-T
1285389 ATAAAA
1 ATAAAA
1285395 TTTTATAAAG
Statistics
Matches: 76, Mismatches: 15, Indels: 21
0.68 0.13 0.19
Matches are distributed among these distances:
8 8 0.11
9 26 0.34
10 28 0.37
11 14 0.18
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (10 bp):
ATAAAAATAT
Found at i:1285436 original size:20 final size:21
Alignment explanation
Indices: 1285407--1285461 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 21
1285397 TTATAAAGTG
*
1285407 GTAAGAAAATTATAAAAAAT-
1 GTAAAAAAATTATAAAAAATC
* *
1285427 GTAAAGAAA-TAT-AAAATTC
1 GTAAAAAAATTATAAAAAATC
1285446 GTAAAAAAATTATAAA
1 GTAAAAAAATTATAAA
1285462 CATTATCGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 10 0.36
21 2 0.07
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.25
Consensus pattern (21 bp):
GTAAAAAAATTATAAAAAATC
Found at i:1286375 original size:19 final size:18
Alignment explanation
Indices: 1286351--1286391 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
1286341 TTATAATTAT
1286351 TTTTATGATTTTTATAAAA
1 TTTTATGATTTTT-TAAAA
*
1286370 TTTTATGATTTTTTATAA
1 TTTTATGATTTTTTAAAA
1286388 TTTT
1 TTTT
1286392 TTTAAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (18 bp):
TTTTATGATTTTTTAAAA
Found at i:1286877 original size:20 final size:19
Alignment explanation
Indices: 1286852--1286899 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
1286842 NNNNNNTTAA
*
1286852 TAAAATTTTAAATTATTTAT
1 TAAAATTTTAAATAATTT-T
1286872 TAAAA-TTT-AATAATTTT
1 TAAAATTTTAAATAATTTT
1286889 TATAAATTTTA
1 TA-AAATTTTA
1286900 TTTTTTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 3 0.12
18 10 0.42
19 6 0.25
20 5 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TAAAATTTTAAATAATTTT
Found at i:1286894 original size:19 final size:19
Alignment explanation
Indices: 1286851--1286899 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
1286841 NNNNNNNTTA
*
1286851 ATAAAATTTTAAATTATTT
1 ATAAAATTTAAAATTATTT
1286870 ATTAAAATTTAATAATT-TTT
1 A-TAAAATTTAA-AATTATTT
*
1286890 ATAAATTTTA
1 ATAAAATTTA
1286900 TTTTTTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 9 0.35
20 13 0.50
21 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATAAAATTTAAAATTATTT
Found at i:1288642 original size:18 final size:19
Alignment explanation
Indices: 1288621--1288661 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
1288611 ACAGGTTTCT
*
1288621 TTTGAATGATTATTATT-G
1 TTTGAATGATTATAATTAG
*
1288639 TTTGAATTATTATAATTAG
1 TTTGAATGATTATAATTAG
1288658 TTTG
1 TTTG
1288662 GTAAGATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (19 bp):
TTTGAATGATTATAATTAG
Found at i:1299210 original size:38 final size:38
Alignment explanation
Indices: 1299154--1299240 Score: 147
Period size: 38 Copynumber: 2.3 Consensus size: 38
1299144 ACATTATTTA
*
1299154 GGCTTTGTGCCTAGCAGGCTTTGTGCCGGTCATATTCG
1 GGCTCTGTGCCTAGCAGGCTTTGTGCCGGTCATATTCG
* *
1299192 GGCTCTGTGCCTAGCAGGCTTTGTGCTGGTGATATTCG
1 GGCTCTGTGCCTAGCAGGCTTTGTGCCGGTCATATTCG
1299230 GGCTCTGTGCC
1 GGCTCTGTGCC
1299241 AGTGATATTC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.09, C:0.24, G:0.33, T:0.33
Consensus pattern (38 bp):
GGCTCTGTGCCTAGCAGGCTTTGTGCCGGTCATATTCG
Found at i:1299330 original size:41 final size:41
Alignment explanation
Indices: 1299252--1299331 Score: 97
Period size: 41 Copynumber: 2.0 Consensus size: 41
1299242 GTGATATTCG
* *
1299252 GGTTATGTGTCTAGCAGGCTTAGTGCTGATGTATTATATCA
1 GGTTATGTGCCTAGCAGGCTTAGTGCCGATGTATTATATCA
* * * * *
1299293 GGTTTTGTGCCTAGTAGGCTTTGTGCCGGTGTGTTATAT
1 GGTTATGTGCCTAGCAGGCTTAGTGCCGATGTATTATAT
1299332 TAGGCTTCGA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.16, C:0.12, G:0.30, T:0.41
Consensus pattern (41 bp):
GGTTATGTGCCTAGCAGGCTTAGTGCCGATGTATTATATCA
Found at i:1302774 original size:16 final size:16
Alignment explanation
Indices: 1302755--1302786 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1302745 ATTTAATCCC
*
1302755 CATTTGTTATTATTAT
1 CATTTATTATTATTAT
1302771 CATTTATTATTATTAT
1 CATTTATTATTATTAT
1302787 ATATATATAC
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:0.28, C:0.06, G:0.03, T:0.62
Consensus pattern (16 bp):
CATTTATTATTATTAT
Found at i:1306377 original size:38 final size:38
Alignment explanation
Indices: 1306326--1306401 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
1306316 AAGAATCGAA
1306326 GAACTAGAAACAACACTGCAAAATTGTGAGATCCAGAT
1 GAACTAGAAACAACACTGCAAAATTGTGAGATCCAGAT
1306364 GAACTAGAAACAACACTGCAAAATTGTGAGATCCAGAT
1 GAACTAGAAACAACACTGCAAAATTGTGAGATCCAGAT
1306402 CAAGTACTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.18
Consensus pattern (38 bp):
GAACTAGAAACAACACTGCAAAATTGTGAGATCCAGAT
Found at i:1317163 original size:44 final size:44
Alignment explanation
Indices: 1317072--1317540 Score: 436
Period size: 44 Copynumber: 10.7 Consensus size: 44
1317062 GCAGGCTAAA
* * *
1317072 AAGA-AGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCG
* * * *
1317115 AAGATAGCAGATCCTGTCTTCCTATATTTGTAGGAAAT-GAATCT
1 AAGATAGCAGATCTTGTCTTCCTATATTGGTAGGAAGTAG-ATCG
* * *
1317159 AAGAT-GCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCG
* * * * *
1317203 AAGAAAGCAGATCTCGTCTTCATGTATTGG-CGTGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCG
* *
1317247 AATG-TAGCAGATCCTGTCTTCCTATATTGGTAGGAAGTGGATCG
1 AA-GATAGCAGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCG
* *
1317291 AAGAT-GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCG
* * * * *
1317335 AAGAAAGCAGATCTTGTCTTCATGTATTGGCT-TGAAATAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGG-TAGGAAGTAGATCG
*
1317379 AAGATTA-CAGATCTTGTCTTCCTATATTGGTAGGAAGTGGATCG
1 AAGA-TAGCAGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCG
* * *
1317423 AAGAT-GTAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCG
* * * * * * *
1317467 AAGAAAGTAGATCTTGTCTTCATGTATTGGCATGAAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCG
* * * *
1317511 AAAATAACAGATCCTGTCTTCTTATATTGG
1 AAGATAGCAGATCTTGTCTTCCTATATTGG
1317541 CAGTGAGGCA
Statistics
Matches: 346, Mismatches: 63, Indels: 33
0.78 0.14 0.07
Matches are distributed among these distances:
43 77 0.22
44 202 0.58
45 66 0.19
46 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (44 bp):
AAGATAGCAGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCG
Found at i:1317312 original size:132 final size:132
Alignment explanation
Indices: 1317075--1317540 Score: 747
Period size: 132 Copynumber: 3.5 Consensus size: 132
1317065 GGCTAAAAAG
1317075 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTAT
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTAT
* * * * * *
1317140 ATTTGTAGGAAATGAATCTAAGATGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAA
66 ATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAA
1317205 GA
131 GA
*
1317207 AAGCAGATCTCGTCTTCATGTATTGGCGTGAAGTAGATCGAATG-TAGCAGATCCTGTCTTCCTA
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAA-GATAGCAGATCCTGTCTTCCTA
1317271 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA
65 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA
1317336 AGA
130 AGA
* * *
1317339 AAGCAGATCTTGTCTTCATGTATTGGCTTGAAATAGATCGAAGATTA-CAGATCTTGTCTTCCTA
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGA-TAGCAGATCCTGTCTTCCTA
*
1317403 TATTGGTAGGAAGTGGATCGAAGATGTAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA
65 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA
1317468 AGA
130 AGA
* * * * * *
1317471 AAGTAGATCTTGTCTTCATGTATTGGCATGAAGTGGATCGAAAATAACAGATCCTGTCTTCTTAT
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTAT
1317536 ATTGG
66 ATTGG
1317541 CAGTGAGGCA
Statistics
Matches: 311, Mismatches: 19, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
131 3 0.01
132 305 0.98
133 3 0.01
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (132 bp):
AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTAT
ATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAA
GA
Found at i:1317669 original size:43 final size:44
Alignment explanation
Indices: 1317565--1317680 Score: 135
Period size: 43 Copynumber: 2.7 Consensus size: 44
1317555 GAAGTGGGCG
* * * **
1317565 AATCTTATTTCCCTAAAGTTGCAGTGGAGAATATTAAGGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAACCAAT
* *
1317609 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TAAAACCGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAACCAAT
* * *
1317652 AATTTTATCTCCTTGAAGTTACAGTGGAG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAG
1317681 TGGACCCAAG
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
43 33 0.53
44 29 0.47
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAACCAAT
Found at i:1318990 original size:16 final size:16
Alignment explanation
Indices: 1318971--1319002 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1318961 ATTTAATCCC
*
1318971 CATTTGTTATTATTAT
1 CATTTATTATTATTAT
1318987 CATTTATTATTATTAT
1 CATTTATTATTATTAT
1319003 ATATATATAC
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:0.28, C:0.06, G:0.03, T:0.62
Consensus pattern (16 bp):
CATTTATTATTATTAT
Found at i:1319039 original size:28 final size:30
Alignment explanation
Indices: 1318990--1319045 Score: 82
Period size: 28 Copynumber: 1.9 Consensus size: 30
1318980 TTATTATCAT
1318990 TTATTATTATTATATATATATACATACACA
1 TTATTATTATTATATATATATACATACACA
1319020 TTATT-TT-TTATA-ATAGTATACATACA
1 TTATTATTATTATATATA-TATACATACA
1319046 TTTTAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 3 0.12
28 15 0.60
29 2 0.08
30 5 0.20
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (30 bp):
TTATTATTATTATATATATATACATACACA
Found at i:1329102 original size:25 final size:25
Alignment explanation
Indices: 1329074--1329144 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
1329064 CCAGTAAGTT
* *
1329074 TCCTGAAACTATTTTTGATAGTATA
1 TCCTGAAACTATTATAGATAGTATA
*
1329099 TCCTGAAACTATTATAGGTAGTATA
1 TCCTGAAACTATTATAGATAGTATA
* * *
1329124 TACTGAGACTACTATAGATAG
1 TCCTGAAACTATTATAGATAG
1329145 ACTGTACTGA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (25 bp):
TCCTGAAACTATTATAGATAGTATA
Found at i:1335830 original size:60 final size:61
Alignment explanation
Indices: 1335734--1335857 Score: 241
Period size: 60 Copynumber: 2.0 Consensus size: 61
1335724 ATATATATTA
1335734 TCACATAACCAATTAAAATAAAACATGCATCTTTAATCAAATTTCATATAATAACCATGTT
1 TCACATAACCAATTAAAATAAAACATGCATCTTTAATCAAATTTCATATAATAACCATGTT
1335795 TCACATAACCAATT-AAATAAAACATGCATCTTTAATCAAATTTCATATAATAACCATGTT
1 TCACATAACCAATTAAAATAAAACATGCATCTTTAATCAAATTTCATATAATAACCATGTT
1335855 TCA
1 TCA
1335858 ACAATTCATC
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
60 49 0.78
61 14 0.22
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.33
Consensus pattern (61 bp):
TCACATAACCAATTAAAATAAAACATGCATCTTTAATCAAATTTCATATAATAACCATGTT
Found at i:1335836 original size:28 final size:29
Alignment explanation
Indices: 1335744--1335836 Score: 73
Period size: 30 Copynumber: 3.1 Consensus size: 29
1335734 TCACATAACC
1335744 AATTAAAATAAAACATGCATCTTTAATCA
1 AATTAAAATAAAACATGCATCTTTAATCA
* * ** ** *
1335773 AATTTCATATAATAACCATGTTTCACATAA-CC
1 AA-TTAAAATAA-AA-CATGCATC-TTTAATCA
1335805 AATT-AAATAAAACATGCATCTTTAATCA
1 AATTAAAATAAAACATGCATCTTTAATCA
1335833 AATT
1 AATT
1335837 TCATATAATA
Statistics
Matches: 46, Mismatches: 13, Indels: 11
0.66 0.19 0.16
Matches are distributed among these distances:
27 3 0.07
28 11 0.24
29 4 0.09
30 12 0.26
31 4 0.09
32 9 0.20
33 3 0.07
ACGTcount: A:0.47, C:0.16, G:0.03, T:0.33
Consensus pattern (29 bp):
AATTAAAATAAAACATGCATCTTTAATCA
Found at i:1341784 original size:2 final size:2
Alignment explanation
Indices: 1341777--1341805 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1341767 AGGGAAGTAA
1341777 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1341806 AAGGGGCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1344750 original size:25 final size:25
Alignment explanation
Indices: 1344696--1344751 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
1344686 TTAATTAATG
*
1344696 TTTTTAATTAATAACTATTTTCAAA
1 TTTTTAATTAAAAACTATTTTCAAA
*
1344721 TTTTTAATTAACAAAC-ATGTTTTAAA
1 TTTTTAATTAA-AAACTAT-TTTCAAA
1344747 TTTTT
1 TTTTT
1344752 TTATTTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 13 0.48
26 14 0.52
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.54
Consensus pattern (25 bp):
TTTTTAATTAAAAACTATTTTCAAA
Found at i:1346689 original size:30 final size:30
Alignment explanation
Indices: 1346653--1346713 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
1346643 AGAAGAGGTC
1346653 TGTTTTTAGGATGAACAAATGATTATTGTG
1 TGTTTTTAGGATGAACAAATGATTATTGTG
*
1346683 TGTTTTTAGGATGAACAAGTGATTATTGTG
1 TGTTTTTAGGATGAACAAATGATTATTGTG
1346713 T
1 T
1346714 TCAAATTAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.28, C:0.03, G:0.25, T:0.44
Consensus pattern (30 bp):
TGTTTTTAGGATGAACAAATGATTATTGTG
Found at i:1349858 original size:51 final size:51
Alignment explanation
Indices: 1349798--1349908 Score: 177
Period size: 51 Copynumber: 2.2 Consensus size: 51
1349788 TCAAGAGATA
* *
1349798 AAGTGATAAGTGGTAGCTTTAGCTACACTTATCCGATCAGTGACAAGTAAC
1 AAGTGATAAGTAGTAGCTTTAGCTACACTTATCCGATCAATGACAAGTAAC
* **
1349849 AAGTGATAAGTAGTAGCTTTAGCTACACTTATCTGATCAATGACAAGTGGC
1 AAGTGATAAGTAGTAGCTTTAGCTACACTTATCCGATCAATGACAAGTAAC
1349900 AAGTGATAA
1 AAGTGATAA
1349909 ATGTGATCTG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (51 bp):
AAGTGATAAGTAGTAGCTTTAGCTACACTTATCCGATCAATGACAAGTAAC
Found at i:1352514 original size:68 final size:68
Alignment explanation
Indices: 1352436--1352663 Score: 258
Period size: 68 Copynumber: 3.5 Consensus size: 68
1352426 TTTTAATAGT
* *
1352436 TTAATATTAAATTTAATTTAATATTTATCTTAATAGTATGTTATTAATTTAATATTGAAGTGATT
1 TTAATATTAAATTAAATTAAATATTTATCTTAATAGTATGTTATTAATTTAATATTGAAGTGATT
1352501 ATC
66 ATC
* * * * * *
1352504 TTAATATTAAATTAAATTAAATGTTTATC-T--T-GTA-GATA-AACATTCTATTTTTTAA-T-A
1 TTAATATTAAATTAAATTAAATATTTATCTTAATAGTATGTTATTA-ATT-TAATATTGAAGTGA
**
1352561 AGAT-
64 TTATC
* *
1352565 TTAATATTAAATTTAATTTAATATTTATCTTAATAGTATGTTATTAATTTAATATTGAAGTGATT
1 TTAATATTAAATTAAATTAAATATTTATCTTAATAGTATGTTATTAATTTAATATTGAAGTGATT
1352630 ATC
66 ATC
*
1352633 TTAATATTAAATTAAATTAAATGTTTATCTT
1 TTAATATTAAATTAAATTAAATATTTATCTT
1352664 GTAGATAAAC
Statistics
Matches: 126, Mismatches: 23, Indels: 22
0.74 0.13 0.13
Matches are distributed among these distances:
61 26 0.21
62 5 0.04
63 7 0.06
64 11 0.09
65 11 0.09
66 7 0.06
67 5 0.04
68 54 0.43
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (68 bp):
TTAATATTAAATTAAATTAAATATTTATCTTAATAGTATGTTATTAATTTAATATTGAAGTGATT
ATC
Found at i:1352665 original size:129 final size:129
Alignment explanation
Indices: 1352421--1352760 Score: 596
Period size: 129 Copynumber: 2.6 Consensus size: 129
1352411 CCAAATATAA
1352421 TATTATTTTAAT-AG-TTTAATATTAAATTTAATTTAATATTTATCTTAATAGTATGTTATTAAT
1 TATT-TTTTAATAAGATTTAATATTAAATTTAATTTAATATTTATCTTAATAGTATGTTATTAAT
1352484 TTAATATTGAAGTGATTATCTTAATATTAAATTAAATTAAATGTTTATCTTGTAGATAAACATTC
65 TTAATATTGAAGTGATTATCTTAATATTAAATTAAATTAAATGTTTATCTTGTAGATAAACATTC
1352549 TATTTTTTAATAAGATTTAATATTAAATTTAATTTAATATTTATCTTAATAGTATGTTATTAATT
1 TATTTTTTAATAAGATTTAATATTAAATTTAATTTAATATTTATCTTAATAGTATGTTATTAATT
1352614 TAATATTGAAGTGATTATCTTAATATTAAATTAAATTAAATGTTTATCTTGTAGATAAACATTC
66 TAATATTGAAGTGATTATCTTAATATTAAATTAAATTAAATGTTTATCTTGTAGATAAACATTC
* * *
1352678 TATTTTTTAATAAGATTTAATATTAAATTTAATCTAATATTTATCTTTATAAATAT-TATATTAA
1 TATTTTTTAATAAGATTTAATATTAAATTTAATTTAATATTTATCTTAAT-AGTATGT-TATTAA
*
1352742 TTTAATATTAAAGTGATTA
64 TTTAATATTGAAGTGATTA
1352761 AGTTTACTGT
Statistics
Matches: 204, Mismatches: 4, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
127 7 0.03
128 6 0.03
129 163 0.80
130 28 0.14
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (129 bp):
TATTTTTTAATAAGATTTAATATTAAATTTAATTTAATATTTATCTTAATAGTATGTTATTAATT
TAATATTGAAGTGATTATCTTAATATTAAATTAAATTAAATGTTTATCTTGTAGATAAACATTC
Found at i:1357207 original size:12 final size:12
Alignment explanation
Indices: 1357190--1357222 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1357180 TAAATTAGTT
1357190 AGCAGTTAGCAG
1 AGCAGTTAGCAG
1357202 AGCAGTTAGCAG
1 AGCAGTTAGCAG
*
1357214 AGTAGTTAG
1 AGCAGTTAG
1357223 TATTAGTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.33, C:0.12, G:0.33, T:0.21
Consensus pattern (12 bp):
AGCAGTTAGCAG
Done.