Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008645.1 Hibiscus syriacus cultivar Beakdansim tig00111621_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4138222
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 22
Found at i:1073604 original size:43 final size:43
Alignment explanation
Indices: 1073543--1073644 Score: 159
Period size: 43 Copynumber: 2.4 Consensus size: 43
1073533 ATCAAATTTG
*
1073543 TCATCAAGGAACCCCTACATATCACGACGGTCCCTCAAGCTTT
1 TCATCAAGAAACCCCTACATATCACGACGGTCCCTCAAGCTTT
* **
1073586 TCATCAAGAAACCCCTACATATCACGATGGTTTCTCAAGCTTT
1 TCATCAAGAAACCCCTACATATCACGACGGTCCCTCAAGCTTT
*
1073629 TCTTCAAGAAACCCCT
1 TCATCAAGAAACCCCT
1073645 GAAAATCAGG
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.29, C:0.32, G:0.12, T:0.26
Consensus pattern (43 bp):
TCATCAAGAAACCCCTACATATCACGACGGTCCCTCAAGCTTT
Found at i:1073758 original size:36 final size:36
Alignment explanation
Indices: 1073712--1073830 Score: 159
Period size: 36 Copynumber: 3.3 Consensus size: 36
1073702 GATAAAATCT
*
1073712 TTTGTTTCAAGTGAAATTGTCTCAAGGGAGACAAAA
1 TTTGTTTCAAGTGAAACTGTCTCAAGGGAGACAAAA
* * *
1073748 TTTGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGTGAAACTGTCTCAAGGGAGACAAAA
*
1073784 TTTGTTTTAA-TGGAAACTGTCTCAAGGGAGACAAAA
1 TTTGTTTCAAGT-GAAACTGTCTCAAGGGAGACAAAA
* *
1073820 TGTGTTCCAAG
1 TTTGTTTCAAG
1073831 GGAGACAAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
36 70 1.00
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (36 bp):
TTTGTTTCAAGTGAAACTGTCTCAAGGGAGACAAAA
Found at i:1073874 original size:36 final size:36
Alignment explanation
Indices: 1073827--1073944 Score: 155
Period size: 36 Copynumber: 3.3 Consensus size: 36
1073817 AAATGTGTTC
* * * *
1073827 CAAGGGAGACAAAATTTGATTCGAGAGAAACTATCT
1 CAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCT
* *
1073863 CAAGGGAGACAAAATTTTTTTCAAGGGAAACCGTCT
1 CAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCT
* * *
1073899 TAAAGGAGACAAAAATTGTTTCAAGGGAAACTGTCT
1 CAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCT
1073935 CAAGGGAGAC
1 CAAGGGAGAC
1073945 TGTCTCAAGG
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 69 1.00
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (36 bp):
CAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCT
Found at i:1073888 original size:57 final size:57
Alignment explanation
Indices: 1073769--1073890 Score: 156
Period size: 57 Copynumber: 2.1 Consensus size: 57
1073759 GGAAACCGTC
* * * *
1073769 TCAAGAGAGACAAAATTTGTTTTAATGGAAACTGTCTCAAGGGAGACAAAATGTGTT
1 TCAAGGGAGACAAAATTTGATTCAATGGAAACTATCTCAAGGGAGACAAAATGTGTT
* * * *
1073826 CCAAGGGAGACAAAATTTGATTCGA-GAGAAACTATCTCAAGGGAGACAAAATTTTTT
1 TCAAGGGAGACAAAATTTGATTCAATG-GAAACTATCTCAAGGGAGACAAAATGTGTT
1073883 TCAAGGGA
1 TCAAGGGA
1073891 AACCGTCTTA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
56 1 0.02
57 54 0.98
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.25
Consensus pattern (57 bp):
TCAAGGGAGACAAAATTTGATTCAATGGAAACTATCTCAAGGGAGACAAAATGTGTT
Found at i:1073893 original size:93 final size:91
Alignment explanation
Indices: 1073725--1074013 Score: 304
Period size: 93 Copynumber: 3.2 Consensus size: 91
1073715 GTTTCAAGTG
* * *
1073725 AAATTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAATTTGTT
1 AAATTGTTTCAAGGGAGACAAAATTTG-TTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT-TT
*
1073790 TT-AATGGAAACTGTCTCAAGGGAGACA
64 TTCAAGGGAAACTGTCTCAAGGGAGACA
* * * *
1073817 AAATGTGTTCCAAGGGAGACAAAATTTGATTCGAGAGAAACTATCTCAAGGGAGACAAAATTTTT
1 AAAT-TGTTTCAAGGGAGACAAAATTTG-TTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTTT
* * *
1073882 TTCAAGGGAAACCGTCTTAAAGGAGACAA
64 TTCAAGGGAAACTGTCTCAAGGGAGAC-A
* * *
1073911 AAATTGTTTCAA-GG-G---AAA-CTGTCTCAAGGGAGACTGTCTCAAGGGAGACAAAATTTGTT
1 AAATTGTTTCAAGGGAGACAAAATTTGT-TCAAGGGAAACTGTCTCAAGGGAGACAAAATTTTTT
* * * *
1073970 TCGAGAGAAATTATCTCAAGGGAGACA
65 TCAAGGGAAACTGTCTCAAGGGAGACA
1073997 AAATTTGTTTCAAGGGA
1 AAA-TTGTTTCAAGGGA
1074014 AATTGTCTCA
Statistics
Matches: 164, Mismatches: 26, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
86 5 0.03
87 61 0.37
88 5 0.03
91 1 0.01
92 10 0.06
93 77 0.47
94 5 0.03
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.25
Consensus pattern (91 bp):
AAATTGTTTCAAGGGAGACAAAATTTGTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTTTTT
CAAGGGAAACTGTCTCAAGGGAGACA
Found at i:1073957 original size:15 final size:15
Alignment explanation
Indices: 1073919--1073959 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
1073909 AAAAATTGTT
*
1073919 TCAAGGGAAACTGTC
1 TCAAGGGAGACTGTC
1073934 TCAAGGGAGACTGTC
1 TCAAGGGAGACTGTC
1073949 TCAAGGGAGAC
1 TCAAGGGAGAC
1073960 AAAATTTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.32, C:0.20, G:0.32, T:0.17
Consensus pattern (15 bp):
TCAAGGGAGACTGTC
Found at i:1073960 original size:51 final size:51
Alignment explanation
Indices: 1073883--1073995 Score: 145
Period size: 51 Copynumber: 2.2 Consensus size: 51
1073873 AAAATTTTTT
* * * *
1073883 TCAAGGGAAACCGTCTTAAAGGAGACAAAAATTGTTTCAAGGGAAACTGTC
1 TCAAGGGAGACCGTCTCAAAGGAGACAAAAATTGTTTCAAGAGAAACTATC
* * * * *
1073934 TCAAGGGAGACTGTCTCAAGGGAGACAAAATTTGTTTCGAGAGAAATTATC
1 TCAAGGGAGACCGTCTCAAAGGAGACAAAAATTGTTTCAAGAGAAACTATC
1073985 TCAAGGGAGAC
1 TCAAGGGAGAC
1073996 AAAATTTGTT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (51 bp):
TCAAGGGAGACCGTCTCAAAGGAGACAAAAATTGTTTCAAGAGAAACTATC
Found at i:1073994 original size:36 final size:36
Alignment explanation
Indices: 1073947--1074038 Score: 157
Period size: 36 Copynumber: 2.6 Consensus size: 36
1073937 AGGGAGACTG
*
1073947 TCTCAAGGGAGACAAAATTTGTTTCGAGAGAAATTA
1 TCTCAAGGGAGACAAAATTTGTTTCAAGAGAAATTA
* *
1073983 TCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATTG
1 TCTCAAGGGAGACAAAATTTGTTTCAAGAGAAATTA
1074019 TCTCAAGGGAGACAAAATTT
1 TCTCAAGGGAGACAAAATTT
1074039 TTCTGTTTCG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (36 bp):
TCTCAAGGGAGACAAAATTTGTTTCAAGAGAAATTA
Found at i:1073994 original size:87 final size:87
Alignment explanation
Indices: 1073860--1074031 Score: 254
Period size: 87 Copynumber: 2.0 Consensus size: 87
1073850 AGAGAAACTA
* * * *
1073860 TCTCAAGGGAGACAAAATTTTTTTCAAGGGAAACCGTCTTAAAGGAGACAAAAATTGTTTCAAGG
1 TCTCAAGGGAGACAAAATTTGTTTCAAGAGAAACCATCTCAAAGGAGACAAAAATTGTTTCAAGG
1073925 GAAACTGTCTCAAGGGAGACTG
66 GAAACTGTCTCAAGGGAGACTG
* ** * *
1073947 TCTCAAGGGAGACAAAATTTGTTTCGAGAGAAATTATCTCAAGGGAGACAAAATTTGTTTCAAGG
1 TCTCAAGGGAGACAAAATTTGTTTCAAGAGAAACCATCTCAAAGGAGACAAAAATTGTTTCAAGG
*
1074012 GAAATTGTCTCAAGGGAGAC
66 GAAACTGTCTCAAGGGAGAC
1074032 AAAATTTTTC
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 75 1.00
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (87 bp):
TCTCAAGGGAGACAAAATTTGTTTCAAGAGAAACCATCTCAAAGGAGACAAAAATTGTTTCAAGG
GAAACTGTCTCAAGGGAGACTG
Found at i:1074010 original size:21 final size:21
Alignment explanation
Indices: 1073949--1074013 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
1073939 GGAGACTGTC
1073949 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
* * *
1073970 TC----GAGA-GAAA-TTATC
1 TCAAGGGAGACAAAATTTGTT
1073985 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
1074006 TCAAGGGA
1 TCAAGGGA
1074014 AATTGTCTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
15 5 0.16
16 3 0.09
17 4 0.12
19 4 0.12
20 3 0.09
21 13 0.41
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.26
Consensus pattern (21 bp):
TCAAGGGAGACAAAATTTGTT
Found at i:1074403 original size:34 final size:34
Alignment explanation
Indices: 1074363--1074461 Score: 126
Period size: 34 Copynumber: 2.9 Consensus size: 34
1074353 TCTCAGAGAA
**
1074363 AAATTGTCTCAAGCGAGACGGAATTTGTTTTGAG
1 AAATTGTCTCAAGCGAGACAAAATTTGTTTTGAG
*
1074397 AAATTGTCTCAAGTGAGACAAAATTTGTTTTGAG
1 AAATTGTCTCAAGCGAGACAAAATTTGTTTTGAG
* * * * *
1074431 AAATTATCTCAAGTGACACAAATTTTTTTTT
1 AAATTGTCTCAAGCGAGACAAAATTTGTTTT
1074462 AAAGAAAAAC
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 58 1.00
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.37
Consensus pattern (34 bp):
AAATTGTCTCAAGCGAGACAAAATTTGTTTTGAG
Found at i:1074643 original size:32 final size:32
Alignment explanation
Indices: 1074558--1074724 Score: 210
Period size: 32 Copynumber: 5.2 Consensus size: 32
1074548 AGGATATTGA
** *
1074558 ATGCCCCAATATTCAATATTGAATCTCCAAAG
1 ATGCCCCAATATTTGATGTTGAATCTCCAAAG
* *
1074590 ATGCCCTAACATTTTGATGTTGAATCTCCAAAG
1 ATGCCCCAATA-TTTGATGTTGAATCTCCAAAG
1074623 ATGCCCCAATATTTGATGTTGAATCTCCAAAG
1 ATGCCCCAATATTTGATGTTGAATCTCCAAAG
* * *
1074655 ATACCCCAACATTTGATGTTGAATCTCCAAAT
1 ATGCCCCAATATTTGATGTTGAATCTCCAAAG
* * *
1074687 ATACTCCAATATGTGATGTTGAATCTTCC-AAG
1 ATGCCCCAATATTTGATGTTGAATC-TCCAAAG
1074719 ATGCCC
1 ATGCCC
1074725 TCTATTGCTT
Statistics
Matches: 117, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
32 87 0.74
33 30 0.26
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.31
Consensus pattern (32 bp):
ATGCCCCAATATTTGATGTTGAATCTCCAAAG
Found at i:1074666 original size:65 final size:64
Alignment explanation
Indices: 1074558--1074717 Score: 221
Period size: 65 Copynumber: 2.5 Consensus size: 64
1074548 AGGATATTGA
** * * *
1074558 ATGCCCCAATATTCAATATTGAATCTCCAAAGATGCCCTAACATTTTGATGTTGAATCTCCAAAG
1 ATGCCCCAATATTTGATGTTGAATCTCCAAAGATACCCCAACA-TTTGATGTTGAATCTCCAAAG
*
1074623 ATGCCCCAATATTTGATGTTGAATCTCCAAAGATACCCCAACATTTGATGTTGAATCTCCAAAT
1 ATGCCCCAATATTTGATGTTGAATCTCCAAAGATACCCCAACATTTGATGTTGAATCTCCAAAG
* * *
1074687 ATACTCCAATATGTGATGTTGAATCTTCCAA
1 ATGCCCCAATATTTGATGTTGAATC-TCCAA
1074718 GATGCCCTCT
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
64 42 0.49
65 43 0.51
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.32
Consensus pattern (64 bp):
ATGCCCCAATATTTGATGTTGAATCTCCAAAGATACCCCAACATTTGATGTTGAATCTCCAAAG
Found at i:1075757 original size:17 final size:16
Alignment explanation
Indices: 1075733--1075778 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
1075723 TTCTCGCCCC
*
1075733 TTTTTCTTTATTGTTT
1 TTTTTCTTTATTGCTT
1075749 TTCTTTCTTTCATTGCTT
1 TT-TTTCTTT-ATTGCTT
1075767 TTTTTCTTTATT
1 TTTTTCTTTATT
1075779 ATCCTTGCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 5 0.19
17 14 0.52
18 8 0.30
ACGTcount: A:0.07, C:0.13, G:0.04, T:0.76
Consensus pattern (16 bp):
TTTTTCTTTATTGCTT
Found at i:1075770 original size:21 final size:22
Alignment explanation
Indices: 1075746--1075789 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1075736 TTCTTTATTG
*
1075746 TTTTTCTTTCTT-TCATTGCTT
1 TTTTTCTTTATTATCATTGCTT
*
1075767 TTTTTCTTTATTATCCTTGCTT
1 TTTTTCTTTATTATCATTGCTT
1075789 T
1 T
1075790 AATTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.07, C:0.18, G:0.05, T:0.70
Consensus pattern (22 bp):
TTTTTCTTTATTATCATTGCTT
Found at i:1075786 original size:22 final size:21
Alignment explanation
Indices: 1075746--1075803 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 21
1075736 TTCTTTATTG
*
1075746 TTTTTCTTTCTTTCATTGCTT
1 TTTTTCTTTATTTCATTGCTT
*
1075767 TTTTTCTTTATTATCCTTGCTT
1 TTTTTCTTTATT-TCATTGCTT
*
1075789 TAATTTTTTTTATTT
1 T--TTTTCTTTATTT
1075804 TTCCCTCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 11 0.35
22 9 0.29
23 1 0.03
24 10 0.32
ACGTcount: A:0.10, C:0.14, G:0.03, T:0.72
Consensus pattern (21 bp):
TTTTTCTTTATTTCATTGCTT
Found at i:1080045 original size:17 final size:17
Alignment explanation
Indices: 1080008--1080046 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1079998 ATAGTGATCC
*
1080008 TACCCAAACATGATTTC
1 TACCCAAACATGATTTA
1080025 TACCCAAACATG-TTATA
1 TACCCAAACATGATT-TA
1080042 TACCC
1 TACCC
1080047 TCAATGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.36, C:0.31, G:0.05, T:0.28
Consensus pattern (17 bp):
TACCCAAACATGATTTA
Found at i:1083651 original size:3 final size:3
Alignment explanation
Indices: 1083643--1083711 Score: 95
Period size: 3 Copynumber: 23.0 Consensus size: 3
1083633 AAATTTGTAT
*
1083643 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TCA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
1083691 TAC T-A TAG TATA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA
1083712 ATATAATATA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
2 1 0.02
3 55 0.95
4 2 0.03
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1085177 original size:57 final size:57
Alignment explanation
Indices: 1085069--1085179 Score: 136
Period size: 57 Copynumber: 1.9 Consensus size: 57
1085059 TTTTGACTGA
* * * *
1085069 CATTCTGAATTAGTTCTCAAACTTTTGAACATTTCAGTTCCATCCCAAAACTATGAC
1 CATTCTAAATTAGTCCTCAAACTTTTGAACATTTCAATTCCAACCCAAAACTATGAC
* *
1085126 CATTCTAAATTAGTCC-CTAAACATTTTGAACATTTTAATTTCAACCC-AAACTAT
1 CATTCTAAATTAGTCCTC-AAAC-TTTTGAACATTTCAATTCCAACCCAAAACTAT
1085180 ATGTATATAC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
56 1 0.02
57 25 0.54
58 20 0.43
ACGTcount: A:0.34, C:0.23, G:0.06, T:0.36
Consensus pattern (57 bp):
CATTCTAAATTAGTCCTCAAACTTTTGAACATTTCAATTCCAACCCAAAACTATGAC
Found at i:1085387 original size:60 final size:60
Alignment explanation
Indices: 1085293--1085473 Score: 179
Period size: 60 Copynumber: 3.0 Consensus size: 60
1085283 TTACATATGT
* * ** * ** *
1085293 GGATGAAATTGGAAGATTCAAAAGTTTGGGGACTAACTTAAAATGAGTTTCTTA-ATTTG
1 GGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAGAGTCATAGATTTG
* * ** * *
1085352 GAGATGAAATTAGAATATTCAAGAGTTTAAAGACTAATTTGGAACGAGAGTCATAGTTTTG
1 G-GATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAGAGTCATAGATTTG
* *
1085413 GGATGAAATTAAAATATTCAAAAGTTTAAGGA-TCAATTTAAAATGAGAGTTATAG-TTTG
1 GGATGAAATTAGAATATTCAAAAGTTTAAGGACT-AATTTAAAATGAGAGTCATAGATTTG
1085472 GG
1 GG
1085474 GATATATGAT
Statistics
Matches: 98, Mismatches: 21, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
59 8 0.08
60 85 0.87
61 5 0.05
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.33
Consensus pattern (60 bp):
GGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAGAGTCATAGATTTG
Found at i:1087381 original size:16 final size:16
Alignment explanation
Indices: 1087349--1087388 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
1087339 TTTACTTCAA
1087349 AATGATT-AAATGCTG
1 AATGATTCAAATGCTG
*
1087364 AATGATTCAAATGTTG
1 AATGATTCAAATGCTG
1087380 AATGATTCA
1 AATGATTCA
1087389 GAGGCTCTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.35
Consensus pattern (16 bp):
AATGATTCAAATGCTG
Found at i:1087478 original size:27 final size:27
Alignment explanation
Indices: 1087440--1087532 Score: 168
Period size: 27 Copynumber: 3.4 Consensus size: 27
1087430 GATAATGGCT
1087440 CTGAATCATTCAGAATGTACTTCTGTG
1 CTGAATCATTCAGAATGTACTTCTGTG
*
1087467 CTGAATCATTCAGAATGTACTTCTATG
1 CTGAATCATTCAGAATGTACTTCTGTG
*
1087494 CTGAATCATTCAGATTGTACTTCTGTG
1 CTGAATCATTCAGAATGTACTTCTGTG
1087521 CTGAATCATTCA
1 CTGAATCATTCA
1087533 ACACTGTTTT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 63 1.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (27 bp):
CTGAATCATTCAGAATGTACTTCTGTG
Found at i:1089406 original size:20 final size:19
Alignment explanation
Indices: 1089367--1089418 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
1089357 TTTCTTTGAT
1089367 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
1089386 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
*
1089406 ATTTATAAAATAA
1 A-TTAAAAAATAA
1089419 GATATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:1089481 original size:120 final size:119
Alignment explanation
Indices: 1089275--1089504 Score: 284
Period size: 120 Copynumber: 1.9 Consensus size: 119
1089265 AAAAATATAT
* * * *
1089275 ATTAATTTATATATTTATAAATAAAATATTTATTTATTTAGAAATATAAGAAAATGACTTCTAGG
1 ATTAATATATATATTTATAAATAAAATATTTATTTATTTAAAAATATAAGAAAATGACATCCAGG
* * *
1089340 TGCCTTAAGACAGCTCTTTTCTTTGATATTAAAAAATAAATAAATAATTAAAACA
66 TACCTTAAGACAGCTCCTTTC-TTAATATTAAAAAATAAATAAATAATTAAAACA
* * *
1089395 ATTAATATATA-ATTTATAAAATAAGATATTTATTTATTTAAAAATATCATAAAATGAACATCCA
1 ATTAATATATATATTTAT-AAATAAAATATTTATTTATTTAAAAATATAAGAAAATG-ACATCCA
* ** * *
1089459 GTTATTTTAAGACTGC-CCTTTCTTAATATTGAAAAATAAATAAATA
64 GGTACCTTAAGACAGCTCCTTTCTTAATATTAAAAAATAAATAAATA
1089505 TATATTAAAA
Statistics
Matches: 93, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
119 28 0.30
120 49 0.53
121 16 0.17
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.39
Consensus pattern (119 bp):
ATTAATATATATATTTATAAATAAAATATTTATTTATTTAAAAATATAAGAAAATGACATCCAGG
TACCTTAAGACAGCTCCTTTCTTAATATTAAAAAATAAATAAATAATTAAAACA
Found at i:1089618 original size:3 final size:3
Alignment explanation
Indices: 1089603--1089704 Score: 81
Period size: 3 Copynumber: 35.0 Consensus size: 3
1089593 TATTTATATA
* *
1089603 AAT AAT AAG AAT AAT AAT AAA AAGT AAT AAT AAT AAT AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT
* * * *
1089648 AAT ATT GCA- AAT AAT AATT AAA AAT -AT AAT ATT AA- AAT -AT AA-
1 AAT AAT -AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT
1089690 AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT
1089705 CAAAAATAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
2 11 0.14
3 62 0.79
4 5 0.06
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1089631 original size:22 final size:22
Alignment explanation
Indices: 1089605--1089646 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1089595 TTTATATAAA
1089605 TAATAAGAATAATAATAAAAAG
1 TAATAAGAATAATAATAAAAAG
*
1089627 TAATAATAATAATAATAAAA
1 TAATAAGAATAATAATAAAA
1089647 TAATATTGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (22 bp):
TAATAAGAATAATAATAAAAAG
Found at i:1089691 original size:21 final size:22
Alignment explanation
Indices: 1089666--1089743 Score: 63
Period size: 21 Copynumber: 3.5 Consensus size: 22
1089656 AAATAATAAT
1089666 TAAAAATATAAT-ATTAAAATA
1 TAAAAATATAATAATTAAAATA
*
1089687 TAAAATAATAATAATAATCAAAA-A
1 T-AAA-AAT-ATAATAATTAAAATA
* *
1089711 T-AAAATTTGAATGATTAAAATA
1 TAAAAATAT-AATAATTAAAATA
*
1089733 TAAAATTATAA
1 TAAAAATATAA
1089744 AACTAGAGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 13
0.70 0.10 0.21
Matches are distributed among these distances:
20 1 0.02
21 13 0.30
22 9 0.20
23 8 0.18
24 7 0.16
25 6 0.14
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (22 bp):
TAAAAATATAATAATTAAAATA
Found at i:1089876 original size:2 final size:2
Alignment explanation
Indices: 1089869--1089937 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
1089859 ATTTACCTAA
1089869 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1089911 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
1089938 CTGATAAGGA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1090940 original size:3 final size:3
Alignment explanation
Indices: 1090934--1091013 Score: 92
Period size: 3 Copynumber: 26.0 Consensus size: 3
1090924 ATTATTTTTT
*
1090934 TAA TAA TAA TAA T-A TATA TATA TATA TAA TAA T-A TATA TAA TAA TTA
1 TAA TAA TAA TAA TAA TA-A TA-A TA-A TAA TAA TAA TA-A TAA TAA TAA
*
1090981 TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1091014 ATAAATAAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.06
3 51 0.74
4 14 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:1090968 original size:12 final size:13
Alignment explanation
Indices: 1090934--1091021 Score: 102
Period size: 12 Copynumber: 7.2 Consensus size: 13
1090924 ATTATTTTTT
1090934 TAATAATA-ATAA
1 TAATAATATATAA
1090946 T-ATATATATATATA
1 TAATA-ATATATA-A
1090960 TAATAATATAT-A
1 TAATAATATATAA
1090972 TAATAAT-TATAA
1 TAATAATATATAA
1090984 TAATAAT-TATAA
1 TAATAATATATAA
1090996 TAATAATA-ATAA
1 TAATAATATATAA
1091008 TAATAA-ATA-AA
1 TAATAATATATAA
1091019 TAA
1 TAA
1091022 AATGGGTAAA
Statistics
Matches: 69, Mismatches: 0, Indels: 15
0.82 0.00 0.18
Matches are distributed among these distances:
11 12 0.17
12 43 0.62
13 3 0.04
14 8 0.12
15 3 0.04
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TAATAATATATAA
Found at i:1091283 original size:17 final size:17
Alignment explanation
Indices: 1091261--1091319 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
1091251 TTGAACAAGC
1091261 TCTTCTCATTATGAACT
1 TCTTCTCATTATGAACT
*
1091278 TCTTCTTC-TTCA-GATAAGT
1 TCTTC-TCATT-ATG--AACT
*
1091297 TCTTCTCATTGTGAACT
1 TCTTCTCATTATGAACT
1091314 TCTTCT
1 TCTTCT
1091320 TCTTTCTTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
17 17 0.52
18 5 0.15
19 11 0.33
ACGTcount: A:0.19, C:0.24, G:0.08, T:0.49
Consensus pattern (17 bp):
TCTTCTCATTATGAACT
Found at i:1091338 original size:40 final size:38
Alignment explanation
Indices: 1091261--1091355 Score: 140
Period size: 40 Copynumber: 2.5 Consensus size: 38
1091251 TTGAACAAGC
1091261 TCTTCTCATTATGAA--CTTCTTCTTCTTCAGATAAGT
1 TCTTCTCATTATGAACTCTTCTTCTTCTTCAGATAAGT
* *
1091297 TCTTCTCATTGTGAACTTCTTCTTCTTTCTTCAGATGAGT
1 TCTTCTCATTATGAAC-TCTTCTTC-TTCTTCAGATAAGT
1091337 TCTTCTCATTATGAACTCT
1 TCTTCTCATTATGAACTCT
1091356 ACCTGGCAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
36 14 0.27
39 10 0.19
40 28 0.54
ACGTcount: A:0.19, C:0.23, G:0.09, T:0.48
Consensus pattern (38 bp):
TCTTCTCATTATGAACTCTTCTTCTTCTTCAGATAAGT
Found at i:1091458 original size:155 final size:154
Alignment explanation
Indices: 1091246--1091622 Score: 642
Period size: 155 Copynumber: 2.5 Consensus size: 154
1091236 GTAATCTAGC
1091246 AAAGGTTGAACAAGCTCTTCTCATTATGAA---CTTCTTCTTC--TTCAGATAAGTTCTTCTCAT
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTTTCAGATAAGTTCTTCTCAT
1091306 TGTGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGATGA
66 TGTGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGATGA
1091371 TCCATCAAATGATGAATTCAAACA
131 TCCATCAAATGATGAATTCAAACA
1091395 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTTTTCAGATAAGTTCTTCTCA
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTC-TTTTCAGATAAGTTCTTCTCA
*
1091460 TTGTGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGCTG
65 TTGTGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGATG
1091525 ATCCATCAAATGATGAATTCAAACA
130 ATCCATCAAATGATGAATTCAAACA
** *
1091550 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC--CTTCTTCAGATGAGTTCTTCTCA
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTT-TTCAGATAAGTTCTTCTCA
*
1091613 TTATGAACTT
65 TTGTGAACTT
1091623 TCTCTGGAAA
Statistics
Matches: 216, Mismatches: 5, Indels: 10
0.94 0.02 0.04
Matches are distributed among these distances:
149 30 0.14
152 12 0.06
153 28 0.13
155 146 0.68
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (154 bp):
AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTTTCAGATAAGTTCTTCTCAT
TGTGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGATGA
TCCATCAAATGATGAATTCAAACA
Found at i:1091496 original size:40 final size:42
Alignment explanation
Indices: 1091410--1091508 Score: 157
Period size: 40 Copynumber: 2.4 Consensus size: 42
1091400 TTGAACAAGC
*
1091410 TCTTCTCATTATGAACTTCTTCTTCTTCTTTTTCAGATAAGT
1 TCTTCTCATTATGAACTTCTTCTTCTTCTTCTTCAGATAAGT
* *
1091452 TCTTCTCATTGTGAACTTCTTCTTC-T-TTCTTCAGATGAGT
1 TCTTCTCATTATGAACTTCTTCTTCTTCTTCTTCAGATAAGT
1091492 TCTTCTCATTATGAACT
1 TCTTCTCATTATGAACT
1091509 CTACCTGGCA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
40 28 0.53
41 1 0.02
42 24 0.45
ACGTcount: A:0.18, C:0.22, G:0.09, T:0.51
Consensus pattern (42 bp):
TCTTCTCATTATGAACTTCTTCTTCTTCTTCTTCAGATAAGT
Found at i:1091595 original size:113 final size:112
Alignment explanation
Indices: 1091451--1092193 Score: 1045
Period size: 113 Copynumber: 6.5 Consensus size: 112
1091441 TTCAGATAAG
* * * *
1091451 TTCTTCTCATTGTGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCCTG
* * * * ** *
1091516 GCAATGCTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAA
65 GAAAAGTTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAA
*
1091564 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTC-CTG
* * *
1091629 GAAAAGCTGATTCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
65 GAAAAGTTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAA
* *
1091677 TTCTTCTTATTATGAATTTCTTCTTCCTTCTTCAGATAACGAGTTCTTCTCATTATGAACTCTAC
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTC
* * * * * * *
1091742 CTGGCAATGTTGATCTATCAAGTGATGAATTTAAACAAAAGGTTGAACAAA
62 CTGGAAAAGTTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAA
* * * * * *
1091793 CTCTTCTCATTATGAACTTCTTCTTCTTTTTTTTCAGATAAGTTCTTCTCATTATGAACTTTCTT
1 TTCTTCTCATTATGAATTTCTTCTTC--CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTC-C
* * * *
1091858 TTGAAATGATGATCCATCGAATGATGGATTTGAGCAAAAGGTTGAACAAA
63 TGGAAAAGTTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAA
* *
1091908 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTA
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTTCCTG
1091973 GAAAAGTTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAA
65 GAAAAGTTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAA
*
1092021 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTCT
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC--TTTCCT
1092086 GGAAAAGTTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAA
64 GGAAAAGTTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAA
1092135 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
1092194 CTTCTTTCTT
Statistics
Matches: 569, Mismatches: 51, Indels: 21
0.89 0.08 0.03
Matches are distributed among these distances:
112 4 0.01
113 265 0.47
114 117 0.21
115 85 0.15
116 87 0.15
117 2 0.00
118 9 0.02
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (112 bp):
TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCTGG
AAAAGTTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAA
Found at i:1091898 original size:344 final size:339
Alignment explanation
Indices: 1091452--1092193 Score: 1117
Period size: 344 Copynumber: 2.2 Consensus size: 339
1091442 TCAGATAAGT
*
1091452 TCTTCTCATTGTGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGG
1 TCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACT-TACCTGG
* *
1091517 CAATGCTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACT
65 AAATGATGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACT
* *
1091582 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATTCATCAA
130 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTAGAAAAGCTGATCCATCAA
* *
1091647 GTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTTATTATGAATTTCTTCTTCCTTCTTCAG
195 ATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAG
* * * *
1091712 ATAACGAGTTCTTCTCATTATGAAC-TCTACCTGGCAATGTTGATCTATCAAGTGATGAATTTAA
260 AT---GAGTTCTTCTCATTATGAACTTCTACCTGGAAAAGTTGATCCATCAAATGATGAATTTAA
1091776 ACAAAAGGTTGAACAAAC
322 ACAAAAGGTTGAACAAAC
* * * *
1091794 TCTTCTCATTATGAACTTCTTCTTCTTTTTTTTCAGATAAGTTCTTCTCATTATGAACTTTCTTT
1 TCTTCTCATTATGAACTTCTTCTTC--TTTCTTCAGATGAGTTCTTCTCATTATGAACTTAC-CT
* * * ** *
1091859 TGAAATGATGATCCATCGAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA
63 GGAAATGATGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAA
* * *
1091924 TTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTAGAAAAGTTGATCCATC
128 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTAGAAAAGCTGATCCATC
1091989 AAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTC
193 AAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTC
* ** * * *
1092054 AGATGAGTTCTTCTCATTATGAACTTTTTTCTGGAAAAGTTGATCCATCAAATGATGGATTTGAG
258 AGATGAGTTCTTCTCATTATGAACTTCTACCTGGAAAAGTTGATCCATCAAATGATGAATTTAAA
*
1092119 CAAAAGGTTGAACAAAT
323 CAAAAGGTTGAACAAAC
* *
1092136 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
1 TCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTT
1092194 CTTCTTTCTT
Statistics
Matches: 361, Mismatches: 35, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
340 30 0.08
341 20 0.06
342 94 0.26
343 2 0.01
344 215 0.60
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (339 bp):
TCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTACCTGGA
AATGATGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTAGAAAAGCTGATCCATCAAA
TGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGA
TGAGTTCTTCTCATTATGAACTTCTACCTGGAAAAGTTGATCCATCAAATGATGAATTTAAACAA
AAGGTTGAACAAAC
Found at i:1092190 original size:40 final size:40
Alignment explanation
Indices: 1092135--1092236 Score: 177
Period size: 40 Copynumber: 2.5 Consensus size: 40
1092125 GTTGAACAAA
1092135 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAG
* *
1092175 TTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAG
1092215 TTCTTCTCATTATGAACTTTCT
1 TTCTTCTCATTATGAA-TTTCT
1092237 CTGGAAAATT
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
40 54 0.93
41 4 0.07
ACGTcount: A:0.18, C:0.23, G:0.09, T:0.51
Consensus pattern (40 bp):
TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAG
Found at i:1092300 original size:153 final size:154
Alignment explanation
Indices: 1092021--1092351 Score: 592
Period size: 153 Copynumber: 2.2 Consensus size: 154
1092011 GTTGAACAAA
* *
1092021 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTCTCT
1092086 GGAAAAGTTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA
66 GGAAAAGTTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA
1092151 TTTCTTCTTCCTTCTTCAGATGAG
131 TTTCTTCTTCCTTCTTCAGATGAG
*
1092175 TTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTTCTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTCTCT
* * *
1092239 GGAAAATTTGATTCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA
66 GGAAAAGTTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA
1092304 TTTCTTCTTCCTTCTTCAGATGAG
131 TTTCTTCTTCCTTCTTCAGATGAG
*
1092328 TTCTTCTCATTATGAACTTTTTCT
1 TTCTTCTCATTATGAACTTCTTCT
1092352 GGAAAAGTTG
Statistics
Matches: 170, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
153 115 0.68
154 55 0.32
ACGTcount: A:0.24, C:0.18, G:0.13, T:0.44
Consensus pattern (154 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTCTCT
GGAAAAGTTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA
TTTCTTCTTCCTTCTTCAGATGAG
Found at i:1092373 original size:113 final size:113
Alignment explanation
Indices: 1092175--1092383 Score: 373
Period size: 113 Copynumber: 1.8 Consensus size: 113
1092165 TTCAGATGAG
*
1092175 TTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
1092240 GAAAATTTGATTCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
66 GAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
* *
1092288 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1092353 GAAAAGTTGATCCATCAAGTGATGGATTTGA
66 GAAAAGTTGATCCATCAAGTGATGGATTTGA
1092384 ATCTTTGCTA
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
113 91 1.00
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.43
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
Found at i:1092808 original size:22 final size:22
Alignment explanation
Indices: 1092783--1092837 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
1092773 GATAAAGCTT
*
1092783 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
1092805 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1092827 TCATCTTTGAA
1 TCATCTTTGAA
1092838 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1094334 original size:76 final size:76
Alignment explanation
Indices: 1094231--1094425 Score: 347
Period size: 76 Copynumber: 2.6 Consensus size: 76
1094221 GCATCAGCAG
*
1094231 TCCTGATTCTGATTGAAAGGGGCTTTCAGCATGCCCTAACATTTTGCTGATATAAATATTCAGAA
1 TCCTGATTCTGATTGAAAGGGGTTTTCAGCATGCCCTAACATTTTGCTGATATAAATATTCAGAA
1094296 TACTTTAATAT
66 TACTTTAATAT
* *
1094307 TCCTGATTCTGATTGAATGGGGTTTTCAGCATGCCCTAACATTTTGCTGATATAAATATTCATAA
1 TCCTGATTCTGATTGAAAGGGGTTTTCAGCATGCCCTAACATTTTGCTGATATAAATATTCAGAA
1094372 TACTTTAATAT
66 TACTTTAATAT
1094383 TCCTGATTCTGATTGAAAGGGGTTTTCAGCATGCCAC-AACATT
1 TCCTGATTCTGATTGAAAGGGGTTTTCAGCATGCC-CTAACATT
1094426 CGCTTCTTGT
Statistics
Matches: 114, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
76 113 0.99
77 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.37
Consensus pattern (76 bp):
TCCTGATTCTGATTGAAAGGGGTTTTCAGCATGCCCTAACATTTTGCTGATATAAATATTCAGAA
TACTTTAATAT
Found at i:1097825 original size:12 final size:12
Alignment explanation
Indices: 1097804--1097893 Score: 148
Period size: 12 Copynumber: 7.6 Consensus size: 12
1097794 TTCTCCCCTT
1097804 TTTC-TTTTTTC
1 TTTCTTTTTTTC
1097815 -TTCTTTTTTTTC
1 TTTC-TTTTTTTC
1097827 TTTCTTTTTTTC
1 TTTCTTTTTTTC
1097839 TTTCTTTTTTTC
1 TTTCTTTTTTTC
1097851 TTTCTTTTTTTC
1 TTTCTTTTTTTC
1097863 TTTCTTTTTTTC
1 TTTCTTTTTTTC
1097875 TTTCTTTTTTTC
1 TTTCTTTTTTTC
*
1097887 CTTCTTT
1 TTTCTTT
1097894 GCTGGATTTT
Statistics
Matches: 75, Mismatches: 1, Indels: 5
0.93 0.01 0.06
Matches are distributed among these distances:
10 3 0.04
12 69 0.92
13 3 0.04
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTCTTTTTTTC
Found at i:1097904 original size:1 final size:1
Alignment explanation
Indices: 1097802--1097885 Score: 51
Period size: 1 Copynumber: 84.0 Consensus size: 1
1097792 ATTTCTCCCC
* * * * * * * * * * *
1097802 TTTTTCTTTTTTCTTCTTTTTTTTCTTTCTTTTTTTCTTTCTTTTTTTCTTTCTTTTTTTCTTTC
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
1097867 TTTTTTTCTTTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTT
1097886 CCTTCTTTGC
Statistics
Matches: 57, Mismatches: 26, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 57 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (1 bp):
T
Found at i:1097909 original size:26 final size:27
Alignment explanation
Indices: 1097875--1097926 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
1097865 TCTTTTTTTC
1097875 TTTCTTTTTTTCCTTCTTTGCTGGATT
1 TTTCTTTTTTTCCTTCTTTGCTGGATT
*
1097902 TTTC-TTTTTTCTTTCTTTGCTGGAT
1 TTTCTTTTTTTCCTTCTTTGCTGGAT
1097927 GAGTATCTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.04, C:0.17, G:0.12, T:0.67
Consensus pattern (27 bp):
TTTCTTTTTTTCCTTCTTTGCTGGATT
Found at i:1103628 original size:20 final size:19
Alignment explanation
Indices: 1103589--1103640 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
1103579 TTTCTTTGAT
1103589 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
1103608 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
*
1103628 ATTTATAAAATAA
1 A-TTAAAAAATAA
1103641 GATATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:1103703 original size:120 final size:119
Alignment explanation
Indices: 1103497--1103726 Score: 286
Period size: 120 Copynumber: 1.9 Consensus size: 119
1103487 AAAAATATAT
* * * *
1103497 ATTAATTTATATATTTATAAATAAAATATTTATTTATTTAGAAATATAAGAAAAAGACTTCTAGG
1 ATTAATATATATATTTATAAATAAAATATTTATTTATTTAAAAATATAAGAAAAAGACATCCAGG
* * *
1103562 TGCCTTAAGACATCTCTTTTCTTTGATATTAAAAAATAAATAAATAATTAAAACA
66 TACCTTAAGACATCTCATTTC-TTAATATTAAAAAATAAATAAATAATTAAAACA
* * *
1103617 ATTAATATATA-ATTTATAAAATAAGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCA
1 ATTAATATATATATTTAT-AAATAAAATATTTATTTATTTAAAAATATAAGAAAA-AGACATCCA
* **
1103681 GTTATTTTAAGAC-TGC-CATTTCTTAATATTAAAAAATAAATAAATA
64 GGTACCTTAAGACAT-CTCATTTCTTAATATTAAAAAATAAATAAATA
1103727 TATATTAAAA
Statistics
Matches: 94, Mismatches: 13, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
119 29 0.31
120 49 0.52
121 16 0.17
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.39
Consensus pattern (119 bp):
ATTAATATATATATTTATAAATAAAATATTTATTTATTTAAAAATATAAGAAAAAGACATCCAGG
TACCTTAAGACATCTCATTTCTTAATATTAAAAAATAAATAAATAATTAAAACA
Found at i:1103808 original size:2 final size:2
Alignment explanation
Indices: 1103801--1103830 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1103791 TATTATTTAT
*
1103801 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1103831 AATAATAAGA
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1103846 original size:3 final size:3
Alignment explanation
Indices: 1103831--1103929 Score: 66
Period size: 3 Copynumber: 34.0 Consensus size: 3
1103821 TATTTATATA
* *
1103831 AAT AAT AAG AAT AAT AAT AAA AAGT AAT AAT AAT AAT AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT
* * * *
1103876 ATT GCA- AAT AAT AATT AAA AAT -AT AAT ATT AA- AAT -AT AA- AAT
1 AAT -AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
1103918 AAA AAT AAT AAT
1 AAT AAT AAT AAT
1103930 CAAAAATAAA
Statistics
Matches: 73, Mismatches: 14, Indels: 18
0.70 0.13 0.17
Matches are distributed among these distances:
2 11 0.15
3 57 0.78
4 5 0.07
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1103875 original size:39 final size:39
Alignment explanation
Indices: 1103830--1103937 Score: 103
Period size: 39 Copynumber: 2.7 Consensus size: 39
1103820 ATATTTATAT
*
1103830 AAATAATAAGAATAATAATAAAAA-GTAATAATAATAATA
1 AAATAATAAGAATAATAATAAAAATATAATAATAA-AATA
* *
1103869 AAATAATATTGCAAATAATAATTAAAAATATAATATTAAAATA
1 AAATAATA-AG--AATAATAA-TAAAAATATAATAATAAAATA
* *
1103912 TAA-AATAAAAATAATAATCAAAAATA
1 AAATAATAAGAATAATAAT-AAAAATA
1103938 AAATTTGAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
38 1 0.02
39 23 0.40
40 1 0.02
42 12 0.21
43 12 0.21
44 8 0.14
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.28
Consensus pattern (39 bp):
AAATAATAAGAATAATAATAAAAATATAATAATAAAATA
Found at i:1103934 original size:13 final size:12
Alignment explanation
Indices: 1103831--1103938 Score: 74
Period size: 13 Copynumber: 8.2 Consensus size: 12
1103821 TATTTATATA
*
1103831 AATAATAAGAAT
1 AATAATAAAAAT
1103843 AATAATAAAAAGT
1 AATAATAAAAA-T
*
1103856 AATAATAATAATAA
1 AATAATAA-AA-AT
*
1103870 AATAATATTGCAAAT
1 AATAATA---AAAAT
1103885 AATAATTAAAAAT
1 AATAA-TAAAAAT
1103898 -ATAATATTAAAAT
1 AATAATA--AAAAT
*
1103911 ATAAAATAAAAAT
1 A-ATAATAAAAAT
1103924 AATAATCAAAAAT
1 AATAAT-AAAAAT
1103937 AA
1 AA
1103939 AATTTGAATG
Statistics
Matches: 77, Mismatches: 7, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
11 2 0.03
12 18 0.23
13 32 0.42
14 9 0.12
15 12 0.16
16 4 0.05
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.28
Consensus pattern (12 bp):
AATAATAAAAAT
Found at i:1103955 original size:39 final size:40
Alignment explanation
Indices: 1103881--1103968 Score: 101
Period size: 39 Copynumber: 2.2 Consensus size: 40
1103871 ATAATATTGC
* *
1103881 AAATAATAATTAAAAATATAATATTAAAATATAAAATA-A
1 AAATAATAATCAAAAATAAAATATTAAAATATAAAATATA
*
1103920 AAATAATAATCAAAAATAAAAT-TT-GAATGATTAAAATATA
1 AAATAATAATCAAAAATAAAATATTAAAAT-A-TAAAATATA
*
1103960 AAATTATAA
1 AAATAATAA
1103969 AACTAGAGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
37 3 0.07
38 3 0.07
39 27 0.64
40 9 0.21
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (40 bp):
AAATAATAATCAAAAATAAAATATTAAAATATAAAATATA
Found at i:1104100 original size:2 final size:2
Alignment explanation
Indices: 1104093--1104124 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1104083 GATATTTTTC
1104093 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1104125 CTGATAAGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1105137 original size:3 final size:3
Alignment explanation
Indices: 1105131--1105190 Score: 95
Period size: 3 Copynumber: 20.0 Consensus size: 3
1105121 ATTATTTTTT
*
1105131 TAA TAA TAA TAA TAA T-A TATA TAA TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
1105176 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
1105191 ATAAATAAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
2 2 0.04
3 48 0.91
4 3 0.06
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1105697 original size:21 final size:22
Alignment explanation
Indices: 1105655--1105704 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
1105645 AATTTATTAT
1105655 TATTATTAATAATATAATATAA
1 TATTATTAATAATATAATATAA
1105677 TATT-TTAATAATAT-ATAATAA
1 TATTATTAATAATATAAT-ATAA
*
1105698 AATTATT
1 TATTATT
1105705 TTTATTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 2 0.08
21 17 0.68
22 6 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TATTATTAATAATATAATATAA
Found at i:1106034 original size:24 final size:24
Alignment explanation
Indices: 1106005--1106050 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1105995 AATAATTCAA
*
1106005 TATTTTAAAATTAATAATATTAAT
1 TATTTTAAAATAAATAATATTAAT
**
1106029 TATTTTCTAATAAATAATATTA
1 TATTTTAAAATAAATAATATTA
1106051 CTTGTTATAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
TATTTTAAAATAAATAATATTAAT
Found at i:1106278 original size:6 final size:6
Alignment explanation
Indices: 1106267--1106338 Score: 126
Period size: 6 Copynumber: 12.0 Consensus size: 6
1106257 AAAGCCCCAT
* *
1106267 AGAGGA AGAGGA AGAGGA AGAGAA AGAGGA AGAGAA AGAGGA AGAGGA
1 AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA
1106315 AGAGGA AGAGGA AGAGGA AGAGGA
1 AGAGGA AGAGGA AGAGGA AGAGGA
1106339 GACAATTGCA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (6 bp):
AGAGGA
Found at i:1106837 original size:28 final size:28
Alignment explanation
Indices: 1106804--1106860 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
1106794 CCGCTTTTGC
* *
1106804 TTTTAAGCACTAACTTGACTACATAATA
1 TTTTAAGCACTAACTCGACGACATAATA
*
1106832 TTTTAAGCACTAGCTCGACGACATAATA
1 TTTTAAGCACTAACTCGACGACATAATA
1106860 T
1 T
1106861 AAACGCTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (28 bp):
TTTTAAGCACTAACTCGACGACATAATA
Found at i:1107412 original size:2 final size:2
Alignment explanation
Indices: 1107405--1107446 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
1107395 GTATCGATAT
*
1107405 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TA TC T- TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1107446 T
1 T
1107447 TCTTCTTCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.02, C:0.45, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1107450 original size:8 final size:9
Alignment explanation
Indices: 1107404--1107461 Score: 59
Period size: 10 Copynumber: 6.4 Consensus size: 9
1107394 GGTATCGATA
1107404 TTCTCTCTC
1 TTCTCTCTC
1107413 -TCTCTCTC
1 TTCTCTCTC
1107421 TCTCTCTCTC
1 T-TCTCTCTC
*
1107431 TCTCTCTATC
1 T-TCTCTCTC
1107441 TTCTCT-TC
1 TTCTCTCTC
1107449 TTCT-TCTTC
1 TTCTCTC-TC
1107458 TTCT
1 TTCT
1107462 TATTATTATT
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
7 1 0.02
8 14 0.32
9 11 0.25
10 18 0.41
ACGTcount: A:0.02, C:0.41, G:0.00, T:0.57
Consensus pattern (9 bp):
TTCTCTCTC
Found at i:1110514 original size:18 final size:18
Alignment explanation
Indices: 1110493--1110537 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
1110483 GGAGGAGGAG
1110493 GAGGAGGAGTGGAACGAT
1 GAGGAGGAGTGGAACGAT
1110511 GAGGAGGAGTGGAACGAT
1 GAGGAGGAGTGGAACGAT
1110529 GAGGAGGAG
1 GAGGAGGAG
1110538 AAGAGCGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.33, C:0.04, G:0.53, T:0.09
Consensus pattern (18 bp):
GAGGAGGAGTGGAACGAT
Found at i:1110519 original size:3 final size:3
Alignment explanation
Indices: 1110477--1110501 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1110467 CTATTGATTT
1110477 GGA GGA GGA GGA GGA GGA GGA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA G
1110502 TGGAACGATG
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:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:1118579 original size:21 final size:21
Alignment explanation
Indices: 1118553--1118603 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
1118543 AACGCGATCT
* *
1118553 CCATTATGATAGTATTGTTTA
1 CCATTACGATAGTAATGTTTA
1118574 CCATTACGATAGTAATGTTTA
1 CCATTACGATAGTAATGTTTA
1118595 CCATTACGA
1 CCATTACGA
1118604 AAGATGAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (21 bp):
CCATTACGATAGTAATGTTTA
Found at i:1119137 original size:21 final size:21
Alignment explanation
Indices: 1119111--1119243 Score: 142
Period size: 21 Copynumber: 6.4 Consensus size: 21
1119101 TATCGTAAAT
* *
1119111 TCGCAATGGTGAACACTTCTA
1 TCGCAATGGTGAACAATGCTA
* *
1119132 TCGCAACGGTGAACAGTGCTA
1 TCGCAATGGTGAACAATGCTA
*
1119153 TCGCAACGGTGAACAATGCTA
1 TCGCAATGGTGAACAATGCTA
**
1119174 TCGCAATGGTGAACAATATTA
1 TCGCAATGGTGAACAATGCTA
* *
1119195 TCGCAAT-GTGAACAGTACTA
1 TCGCAATGGTGAACAATGCTA
* * *
1119215 TCGAAATGGTGAACAGTGCTG
1 TCGCAATGGTGAACAATGCTA
*
1119236 TCACAATG
1 TCGCAATG
1119244 CGATTTTTGA
Statistics
Matches: 97, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
20 17 0.18
21 80 0.82
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.24
Consensus pattern (21 bp):
TCGCAATGGTGAACAATGCTA
Found at i:1119229 original size:62 final size:63
Alignment explanation
Indices: 1119111--1119243 Score: 171
Period size: 62 Copynumber: 2.1 Consensus size: 63
1119101 TATCGTAAAT
* * *
1119111 TCGCAATGGTGAACACTTCTATCGCAACGGTGAACAGTGCTATCGCAACGGTGAACAATGCTA
1 TCGCAATGGTGAACAATTCTATCGCAACGGTGAACAGTACTATCGAAACGGTGAACAATGCTA
* * * *
1119174 TCGCAATGGTGAACAATAT-TATCGCAA-TGTGAACAGTACTATCGAAATGGTGAACAGTGCTG
1 TCGCAATGGTGAACAAT-TCTATCGCAACGGTGAACAGTACTATCGAAACGGTGAACAATGCTA
*
1119236 TCACAATG
1 TCGCAATG
1119244 CGATTTTTGA
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
62 36 0.59
63 24 0.39
64 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.24
Consensus pattern (63 bp):
TCGCAATGGTGAACAATTCTATCGCAACGGTGAACAGTACTATCGAAACGGTGAACAATGCTA
Found at i:1125752 original size:13 final size:13
Alignment explanation
Indices: 1125731--1125797 Score: 77
Period size: 13 Copynumber: 5.4 Consensus size: 13
1125721 ACCCGACCCA
1125731 ACCCGACCCGTTT
1 ACCCGACCCGTTT
*
1125744 ACCCAACCCGTTT
1 ACCCGACCCGTTT
1125757 ACCCGACCCG---
1 ACCCGACCCGTTT
* *
1125767 ACCCGACCTGTTG
1 ACCCGACCCGTTT
*
1125780 ACCCGACCCGTTC
1 ACCCGACCCGTTT
1125793 ACCCG
1 ACCCG
1125798 TTGACAGACG
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
10 9 0.20
13 37 0.80
ACGTcount: A:0.18, C:0.49, G:0.16, T:0.16
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:1125770 original size:23 final size:23
Alignment explanation
Indices: 1125744--1125789 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1125734 CGACCCGTTT
*
1125744 ACCCAACCCGTTTACCCGACCCG
1 ACCCAACCCGTTGACCCGACCCG
* *
1125767 ACCCGACCTGTTGACCCGACCCG
1 ACCCAACCCGTTGACCCGACCCG
1125790 TTCACCCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.50, G:0.17, T:0.13
Consensus pattern (23 bp):
ACCCAACCCGTTGACCCGACCCG
Found at i:1125771 original size:36 final size:36
Alignment explanation
Indices: 1125721--1125797 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
1125711 ACCGGTCATA
* *
1125721 ACCCGACCCAACCCGACCCGTTTACCCAACCCGTTT
1 ACCCGACCCAACCCGACCCGTTGACCCAACCCGTTC
* * *
1125757 ACCCGACCCGACCCGACCTGTTGACCCGACCCGTTC
1 ACCCGACCCAACCCGACCCGTTGACCCAACCCGTTC
1125793 ACCCG
1 ACCCG
1125798 TTGACAGACG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.19, C:0.51, G:0.16, T:0.14
Consensus pattern (36 bp):
ACCCGACCCAACCCGACCCGTTGACCCAACCCGTTC
Found at i:1128305 original size:24 final size:24
Alignment explanation
Indices: 1128278--1128341 Score: 101
Period size: 24 Copynumber: 2.7 Consensus size: 24
1128268 TTCTATTATA
*
1128278 ATACCTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
* *
1128302 ATACTTGACCTGGATTTTGATCTG
1 ATACTTGACCTGGATTCTGATCGG
1128326 ATACTTGACCTGGATT
1 ATACTTGACCTGGATT
1128342 ATTTTATGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATCGG
Found at i:1130517 original size:13 final size:13
Alignment explanation
Indices: 1130492--1130547 Score: 76
Period size: 13 Copynumber: 4.3 Consensus size: 13
1130482 AACTCGACCC
1130492 GACCCGACCTGTT
1 GACCCGACCTGTT
* *
1130505 GACCTGACATGTT
1 GACCCGACCTGTT
*
1130518 GACCCGACCCGTT
1 GACCCGACCTGTT
*
1130531 GACCCGACCCGTT
1 GACCCGACCTGTT
1130544 GACC
1 GACC
1130548 GTTGACTGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.18, C:0.39, G:0.23, T:0.20
Consensus pattern (13 bp):
GACCCGACCTGTT
Found at i:1133077 original size:24 final size:24
Alignment explanation
Indices: 1133050--1133137 Score: 131
Period size: 24 Copynumber: 3.7 Consensus size: 24
1133040 TTCTATTATA
* *
1133050 ATACCTGACCTAGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
1133074 ATACTTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
* * *
1133098 ATACTTGACCTGAATTTTGATCTG
1 ATACTTGACCTGGATTCTGATCGG
1133122 ATACTTGACCTGGATT
1 ATACTTGACCTGGATT
1133138 ATTTTATGAT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.35
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATCGG
Found at i:1137121 original size:8 final size:8
Alignment explanation
Indices: 1137110--1137135 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1137100 TATTGTATTA
1137110 TAATAAAT
1 TAATAAAT
1137118 TAATAAAT
1 TAATAAAT
1137126 TAATAAAT
1 TAATAAAT
1137134 TA
1 TA
1137136 TTATTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
TAATAAAT
Found at i:1137160 original size:15 final size:15
Alignment explanation
Indices: 1137129--1137172 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
1137119 AATAAATTAA
*
1137129 TAAATTATTATTTTAT
1 TAAATT-TTATTATAT
1137145 TAAATTTTATTATAT
1 TAAATTTTATTATAT
*
1137160 TAACCTTTTATTA
1 TAA-ATTTTATTA
1137173 ATTTTTGCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (15 bp):
TAAATTTTATTATAT
Found at i:1144847 original size:2 final size:2
Alignment explanation
Indices: 1144840--1144864 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1144830 TGTACATGTA
1144840 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 A
1144865 CTTAATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1146147 original size:21 final size:21
Alignment explanation
Indices: 1146123--1146163 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1146113 TAACTAGGAC
1146123 TGTAAAATCATGTAATCGGAT
1 TGTAAAATCATGTAATCGGAT
1146144 TGTAAAATCATGTAATCGGA
1 TGTAAAATCATGTAATCGGA
1146164 CAGGTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.32
Consensus pattern (21 bp):
TGTAAAATCATGTAATCGGAT
Found at i:1146335 original size:65 final size:65
Alignment explanation
Indices: 1146264--1146402 Score: 242
Period size: 65 Copynumber: 2.1 Consensus size: 65
1146254 ACATGTCAAA
* *
1146264 TCAGTTCGGGTCATTTTCAGGTTGATTTGATACCAGATCCAGATCGGGTTCAGGTCGGGTCATTT
1 TCAGTTCGGGTCATTTTCAGGTTGATTTGACACCAGATCCAGATCGGGTTCAAGTCGGGTCATTT
* *
1146329 TTAGTTCGGGTCATTTTCAGGTTGATTTGACACCAGATCCAGATTGGGTTCAAGTCGGGTCATTT
1 TCAGTTCGGGTCATTTTCAGGTTGATTTGACACCAGATCCAGATCGGGTTCAAGTCGGGTCATTT
1146394 TCAGTTCGG
1 TCAGTTCGG
1146403 ATCGATGTAA
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 69 1.00
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.36
Consensus pattern (65 bp):
TCAGTTCGGGTCATTTTCAGGTTGATTTGACACCAGATCCAGATCGGGTTCAAGTCGGGTCATTT
Found at i:1147117 original size:20 final size:19
Alignment explanation
Indices: 1147066--1147250 Score: 106
Period size: 20 Copynumber: 9.3 Consensus size: 19
1147056 TGAAAAAAAT
1147066 TATAATATATATATATATA
1 TATAATATATATATATATA
* * *
1147085 TAAAGACAAATATATAATATA
1 TATA-ATATATATAT-ATATA
* * * *
1147106 TATAGTTTATATGTAGTTTA
1 TATAATATATATATA-TATA
* *
1147126 T-TAATAAACTATGTA-ATA
1 TATAATATA-TATATATATA
1147144 TAT-ATATATATATATATA
1 TATAATATATATATATATA
1147162 TATATATATATATATATATAA
1 TATA-ATATATATATATAT-A
* * *
1147183 TATAATATAAGATTTATGTA
1 TATAATAT-ATATATATATA
* *
1147203 TATAGTTTATATATATAGTA
1 TATAATATATATATATA-TA
*
1147223 TATTAAGTACATATATATTACTA
1 TA-TAA-TATATATATA-TA-TA
1147246 TATAA
1 TATAA
1147251 ATAGTTACAT
Statistics
Matches: 124, Mismatches: 28, Indels: 25
0.70 0.16 0.14
Matches are distributed among these distances:
17 5 0.04
18 13 0.10
19 15 0.12
20 52 0.42
21 22 0.18
22 11 0.09
23 6 0.05
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (19 bp):
TATAATATATATATATATA
Found at i:1147240 original size:2 final size:2
Alignment explanation
Indices: 1147066--1147225 Score: 102
Period size: 2 Copynumber: 81.5 Consensus size: 2
1147056 TGAAAAAAAT
* * * *
1147066 TA TA -A TA TA TA TA TA TA TA TA AA GA CA AA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
1147106 TA TA GTT TA TA TG TA GTT TA T- TA -A TA AA CTA TG TA -A TA TA
1 TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA
1147146 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
1147187 -A TA TA -A GA TT TA TG TA TA TA GTT TA TA TA TA TA GTA TA T
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA T
1147226 TAAGTACATA
Statistics
Matches: 123, Mismatches: 22, Indels: 26
0.72 0.13 0.15
Matches are distributed among these distances:
1 8 0.07
2 109 0.89
3 6 0.05
ACGTcount: A:0.47, C:0.01, G:0.06, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1147334 original size:9 final size:9
Alignment explanation
Indices: 1147320--1147352 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1147310 GTGCAAACAA
*
1147320 TATATAAAC
1 TATATAAAG
1147329 TATATAAAG
1 TATATAAAG
1147338 TAT-TAAAG
1 TATATAAAG
1147346 TATATAA
1 TATATAA
1147353 TTTATATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (9 bp):
TATATAAAG
Found at i:1147360 original size:19 final size:19
Alignment explanation
Indices: 1147338--1147391 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 19
1147328 CTATATAAAG
1147338 TATTAAAGTATATAA-TTTA
1 TATTAAA-TATATAACTTTA
1147357 TATTAATATAATATAACTTTA
1 TATTAA-AT-ATATAACTTTA
1147378 TATATAAACTATAT
1 TAT-TAAA-TATAT
1147392 TTATATTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
19 7 0.23
20 7 0.23
21 12 0.40
22 4 0.13
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (19 bp):
TATTAAATATATAACTTTA
Found at i:1147382 original size:32 final size:31
Alignment explanation
Indices: 1147346--1147410 Score: 76
Period size: 32 Copynumber: 2.1 Consensus size: 31
1147336 AGTATTAAAG
** *
1147346 TATATAATTTATATTAATATAATATAACTTTA
1 TATATAAACTATATTAATATAATA-AACTATA
* *
1147378 TATATAAACTATATTTATATTATAAACTATA
1 TATATAAACTATATTAATATAATAAACTATA
1147409 TA
1 TA
1147411 CTTATTATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 8 0.29
32 20 0.71
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (31 bp):
TATATAAACTATATTAATATAATAAACTATA
Found at i:1147396 original size:13 final size:13
Alignment explanation
Indices: 1147393--1147495 Score: 55
Period size: 15 Copynumber: 7.3 Consensus size: 13
1147383 AAACTATATT
1147393 TATA-TTATAAAC
1 TATATTTATAAAC
1147405 TATATACTTATTATAAGC
1 TATAT--TTA-TA-AA-C
* *
1147423 TATATATATAAAT
1 TATATTTATAAAC
*
1147436 TATGTTTATATGAAC
1 TATATTTATA--AAC
* *
1147451 TATATATATAAAA
1 TATATTTATAAAC
* *
1147464 TATGTATATAAAC
1 TATATTTATAAAC
1147477 TATATATGTATAAAC
1 TATAT-T-TATAAAC
1147492 TATA
1 TATA
1147496 AAAAGTATAT
Statistics
Matches: 69, Mismatches: 12, Indels: 17
0.70 0.12 0.17
Matches are distributed among these distances:
12 4 0.06
13 25 0.36
14 2 0.03
15 26 0.38
16 4 0.06
17 2 0.03
18 6 0.09
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.43
Consensus pattern (13 bp):
TATATTTATAAAC
Found at i:1147403 original size:18 final size:18
Alignment explanation
Indices: 1147352--1147432 Score: 69
Period size: 18 Copynumber: 4.4 Consensus size: 18
1147342 AAAGTATATA
1147352 ATTTATATTAATATAA-TAT
1 ATTTATATT-ATA-AACTAT
1147371 AACTTTATA-TATAAACTAT
1 -A-TTTATATTATAAACTAT
1147390 ATTTATATTATAAACTAT
1 ATTTATATTATAAACTAT
* *
1147408 ATACT-TATTATAAGCTAT
1 AT-TTATATTATAAACTAT
*
1147426 ATATATA
1 ATTTATA
1147433 AATTATGTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
17 7 0.13
18 31 0.58
19 7 0.13
20 2 0.04
21 6 0.11
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.47
Consensus pattern (18 bp):
ATTTATATTATAAACTAT
Found at i:1147429 original size:38 final size:38
Alignment explanation
Indices: 1147322--1147438 Score: 93
Period size: 38 Copynumber: 3.1 Consensus size: 38
1147312 GCAAACAATA
**
1147322 TATAAACTATATAAAGTATTA-AAG-TATATAATTTATAT
1 TATAAACTATAT-ACTTATTATAAGCTATAT-ATTTATAT
*
1147360 TAATATAA-TATA-ACTTTATATATAAAC--TATATTTATAT
1 T-ATA-AACTATATAC-TTAT-TATAAGCTATATATTTATAT
* *
1147398 TATAAACTATATACTTATTATAAGCTATATATATAAAT
1 TATAAACTATATACTTATTATAAGCTATATATTTATAT
1147436 TAT
1 TAT
1147439 GTTTATATGA
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
36 8 0.13
37 12 0.19
38 27 0.43
39 12 0.19
40 4 0.06
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (38 bp):
TATAAACTATATACTTATTATAAGCTATATATTTATAT
Found at i:1147462 original size:28 final size:26
Alignment explanation
Indices: 1147416--1147483 Score: 91
Period size: 28 Copynumber: 2.5 Consensus size: 26
1147406 ATATACTTAT
* *
1147416 TATAAGCTATATATATAAATTATGTTTA
1 TATAAACTATATATATAAAATATG--TA
*
1147444 TATGAACTATATATATAAAATATGTA
1 TATAAACTATATATATAAAATATGTA
1147470 TATAAACTATATAT
1 TATAAACTATATAT
1147484 GTATAAACTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
26 15 0.42
28 21 0.58
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (26 bp):
TATAAACTATATATATAAAATATGTA
Found at i:1147488 original size:28 final size:28
Alignment explanation
Indices: 1147393--1147490 Score: 85
Period size: 28 Copynumber: 3.4 Consensus size: 28
1147383 AAACTATATT
* *
1147393 TATATTATAAACTATATACTTATTATAAGCTA
1 TATATTATAAA--ATAT-GTTA-TATAAACTA
* *
1147425 TATA-TATAAATTATGTTTATATGAACTA
1 TATATTATAAAATATG-TTATATAAACTA
1147453 TATA-TATAAAATATG-TATATAAACTA
1 TATATTATAAAATATGTTATATAAACTA
1147479 TATATGTATAAA
1 TATAT-TATAAA
1147491 CTATAAAAAG
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
26 14 0.25
28 27 0.47
29 6 0.11
31 6 0.11
32 4 0.07
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (28 bp):
TATATTATAAAATATGTTATATAAACTA
Found at i:1147644 original size:99 final size:99
Alignment explanation
Indices: 1147466--1147644 Score: 313
Period size: 99 Copynumber: 1.8 Consensus size: 99
1147456 ATATAAAATA
1147466 TGTATATAAACTATATATGTATAAACTATAAAAAGTATATAGTTTATAAACTATAATTTATATTA
1 TGTATATAAACTATATATGTATAAACTATAAAAAGTATATAGTTTATAAACTATAATTTATATTA
* *
1147531 ATATAGTGTGTATATATATATATATATATATGTG
66 ATATAGTATATATATATATATATATATATATGTG
* * *
1147565 TGTATATAAATTATATATGTATAAACTATATAAAGTATATAGTTTATAAATTATAATTTATATTA
1 TGTATATAAACTATATATGTATAAACTATAAAAAGTATATAGTTTATAAACTATAATTTATATTA
1147630 ATATAGTATATATAT
66 ATATAGTATATATAT
1147645 GTATGTATGT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
99 75 1.00
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (99 bp):
TGTATATAAACTATATATGTATAAACTATAAAAAGTATATAGTTTATAAACTATAATTTATATTA
ATATAGTATATATATATATATATATATATATGTG
Found at i:1148075 original size:16 final size:16
Alignment explanation
Indices: 1148054--1148089 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1148044 ATAATTCATA
1148054 TATAGTTTATATAAAC
1 TATAGTTTATATAAAC
*
1148070 TATAGTTTATATAAAT
1 TATAGTTTATATAAAC
1148086 TATA
1 TATA
1148090 TATGTAACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (16 bp):
TATAGTTTATATAAAC
Found at i:1148197 original size:35 final size:36
Alignment explanation
Indices: 1148127--1148200 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 36
1148117 ACAATAGTTA
* *
1148127 ATATATGTAACATATAGTATATGTATACATGTAAACT
1 ATATATGTAACATATAGTACATGTATA-ATATAAACT
* *
1148164 ATATATGTAACTTATAGTACATGTAT-GTATAAACT
1 ATATATGTAACATATAGTACATGTATAATATAAACT
1148199 AT
1 AT
1148201 GTATAGTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 9 0.27
37 24 0.73
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (36 bp):
ATATATGTAACATATAGTACATGTATAATATAAACT
Found at i:1148209 original size:20 final size:20
Alignment explanation
Indices: 1148186--1148225 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1148176 TATAGTACAT
* *
1148186 GTATGTATAAACTATGTATA
1 GTATATATAAACTATATATA
1148206 GTATATATAAACTATATATA
1 GTATATATAAACTATATATA
1148226 TAACCTATAG
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:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (20 bp):
GTATATATAAACTATATATA
Found at i:1148225 original size:13 final size:13
Alignment explanation
Indices: 1148207--1148240 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1148197 CTATGTATAG
1148207 TATATATAAACTA
1 TATATATAAACTA
*
1148220 TATATATAACCTA
1 TATATATAAACTA
1148233 TAGTATAT
1 TA-TATAT
1148241 GTATATATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:1148262 original size:17 final size:17
Alignment explanation
Indices: 1148236--1148274 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1148226 TAACCTATAG
*
1148236 TATATGTATATATACAA
1 TATATGTATATATAAAA
* *
1148253 TATATTTATATGTAAAA
1 TATATGTATATATAAAA
1148270 TATAT
1 TATAT
1148275 ATGTAACCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (17 bp):
TATATGTATATATAAAA
Found at i:1148309 original size:59 final size:60
Alignment explanation
Indices: 1148238--1148409 Score: 240
Period size: 59 Copynumber: 2.8 Consensus size: 60
1148228 ACCTATAGTA
*
1148238 TATGTATATATACAATATATTTATATGTAAAATATATATGTAACCTATAT-TATATATAT
1 TATGTATATATACAATATATTTATATGTAAACTATATATGTAACCTATATCTATATATAT
*
1148297 TATGTATATATACAATTTATTTATATGTAAACTATATATGTAACCTAT-TCTATATATAT
1 TATGTATATATACAATATATTTATATGTAAACTATATATGTAACCTATATCTATATATAT
* * *
1148356 TATGTATAGATACAATCTATATATAGTTTATATAAACTATATATGTAACCTATA
1 TATGTATATATACAA--TATAT-T--TATATGTAAACTATATATGTAACCTATA
1148410 GTTTATAAAC
Statistics
Matches: 100, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
58 1 0.01
59 69 0.69
61 4 0.04
62 1 0.01
64 25 0.25
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.45
Consensus pattern (60 bp):
TATGTATATATACAATATATTTATATGTAAACTATATATGTAACCTATATCTATATATAT
Found at i:1148458 original size:50 final size:51
Alignment explanation
Indices: 1148403--1148508 Score: 124
Period size: 57 Copynumber: 2.0 Consensus size: 51
1148393 TATATATGTA
* *
1148403 ACCTATAG-TTTATAAACAATAGTTTATATTAGTGTATTATATAGTTTATT
1 ACCTATAGATTTATAAACAATAGTTTATATTAATGTACTATATAGTTTATT
*
1148453 ACCTATAGTATATAATTTATAAACTATAGTTTATATTAATGTACTATATAGTTTAT
1 ACCTATAG------ATTTATAAACAATAGTTTATATTAATGTACTATATAGTTTAT
1148509 ATTAATGTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
50 8 0.17
57 38 0.83
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.47
Consensus pattern (51 bp):
ACCTATAGATTTATAAACAATAGTTTATATTAATGTACTATATAGTTTATT
Found at i:1148466 original size:21 final size:21
Alignment explanation
Indices: 1148440--1148487 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1148430 ATTAGTGTAT
* * *
1148440 TATATAGTTTATTACCTATAG
1 TATATAATTTATAAACTATAG
1148461 TATATAATTTATAAACTATAG
1 TATATAATTTATAAACTATAG
*
1148482 TTTATA
1 TATATA
1148488 TTAATGTACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (21 bp):
TATATAATTTATAAACTATAG
Found at i:1148548 original size:15 final size:15
Alignment explanation
Indices: 1148498--1148548 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
1148488 TTAATGTACT
*
1148498 ATATAGTTTATATTA
1 ATATAATTTATATTA
* *
1148513 ATGTTAA-TTATCTTA
1 AT-ATAATTTATATTA
1148528 ACTATAATTTATATTA
1 A-TATAATTTATATTA
1148544 ATATA
1 ATATA
1148549 GTATATAGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (15 bp):
ATATAATTTATATTA
Found at i:1148572 original size:35 final size:35
Alignment explanation
Indices: 1148527--1148658 Score: 141
Period size: 35 Copynumber: 3.9 Consensus size: 35
1148517 TAATTATCTT
1148527 AACTATAATTTATATTAATATAGTATATAGTTATA
1 AACTATAATTTATATTAATATAGTATATAGTTATA
* * *
1148562 AACTATAATTTGTATTAATGTAGTAGATAGTTTATA
1 AACTATAATTTATATTAATATAGTATATAG-TTATA
* * *
1148598 AACTATAGTTTACATTAATAT--TA-ACA--TATTA
1 AACTATAATTTATATTAATATAGTATATAGTTA-TA
*
1148629 AA-TATAGTTTATATTAATATAGTATATAGT
1 AACTATAATTTATATTAATATAGTATATAGT
1148659 ATTAATATTA
Statistics
Matches: 80, Mismatches: 10, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
30 19 0.24
31 4 0.05
32 2 0.03
33 4 0.05
34 2 0.03
35 27 0.34
36 22 0.28
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (35 bp):
AACTATAATTTATATTAATATAGTATATAGTTATA
Found at i:1148647 original size:15 final size:17
Alignment explanation
Indices: 1148623--1148666 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
1148613 TAATATTAAC
1148623 ATATTAAATATAGT-T-T
1 ATATT-AATATAGTATAT
1148639 ATATTAATATAGTATAT
1 ATATTAATATAGTATAT
1148656 AGTATTAATAT
1 A-TATTAATAT
1148667 TAATTATAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.32
16 6 0.24
17 2 0.08
18 9 0.36
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (17 bp):
ATATTAATATAGTATAT
Found at i:1148666 original size:24 final size:24
Alignment explanation
Indices: 1148611--1148681 Score: 74
Period size: 24 Copynumber: 2.9 Consensus size: 24
1148601 TATAGTTTAC
* *
1148611 ATTAATATTAACATATTAAATATAGT
1 ATTAATATTAATATAGT--ATATAGT
1148637 -TT-ATATTAATATAGTATATAGT
1 ATTAATATTAATATAGTATATAGT
*
1148659 ATTAATATTAATTATAGTCTATA
1 ATTAATATTAA-TATAGTATATA
1148682 AACCATATAC
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
22 7 0.18
23 2 0.05
24 18 0.46
25 12 0.31
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (24 bp):
ATTAATATTAATATAGTATATAGT
Found at i:1148769 original size:6 final size:6
Alignment explanation
Indices: 1148758--1148880 Score: 52
Period size: 6 Copynumber: 21.2 Consensus size: 6
1148748 AAATATAGTT
* * * * *
1148758 TATTAA TATTAA TTTTATA GACTATA TTTTA- TATTAA TATTAA T-TAAA
1 TATTAA TATTAA TATTA-A TATTA-A TATTAA TATTAA TATTAA TATTAA
*
1148806 TACTATAA -ACTA- TATT-A TATTAA TA-TAA GTA--AA TATTAA TATT-A
1 TA-T-TAA TATTAA TATTAA TATTAA TATTAA -TATTAA TATTAA TATTAA
1148850 TAATTAA TATATAA T-TT-A TATTAA TATTAA T
1 T-ATTAA TAT-TAA TATTAA TATTAA TATTAA T
1148881 TATAAATAGT
Statistics
Matches: 89, Mismatches: 12, Indels: 32
0.67 0.09 0.24
Matches are distributed among these distances:
4 4 0.04
5 26 0.29
6 42 0.47
7 15 0.17
8 2 0.02
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (6 bp):
TATTAA
Found at i:1148783 original size:29 final size:31
Alignment explanation
Indices: 1148742--1148802 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
1148732 TACTATATAA
1148742 TTTATAAAATATA-GTT-TATTAATATTAAT
1 TTTATAAAATATATGTTATATTAATATTAAT
* * *
1148771 TTTATAGACTATATTTTATATTAATATTAAT
1 TTTATAAAATATATGTTATATTAATATTAAT
1148802 T
1 T
1148803 AAATACTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 11 0.41
30 2 0.07
31 14 0.52
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (31 bp):
TTTATAAAATATATGTTATATTAATATTAAT
Found at i:1148843 original size:50 final size:52
Alignment explanation
Indices: 1148788--1148885 Score: 132
Period size: 50 Copynumber: 1.9 Consensus size: 52
1148778 ACTATATTTT
1148788 ATATTAATA-T-TAATTAAATACTATAAACTATATT-ATATTAA-TATAAGTAA
1 ATATTAATATTATAATT-AATA-TATAAACTATATTAATATTAATTATAAGTAA
**
1148838 ATATTAATATTATAATTAATATATAATTTATATTAATATTAATTATAA
1 ATATTAATATTATAATTAATATATAAACTATATTAATATTAATTATAA
1148886 ATAGTTTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
50 20 0.48
51 12 0.29
52 10 0.24
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (52 bp):
ATATTAATATTATAATTAATATATAAACTATATTAATATTAATTATAAGTAA
Found at i:1148857 original size:12 final size:12
Alignment explanation
Indices: 1148840--1148872 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1148830 ATAAGTAAAT
1148840 ATTAATATTATA
1 ATTAATATTATA
1148852 ATTAATA-TATA
1 ATTAATATTATA
*
1148863 ATTTATATTA
1 ATTAATATTA
1148873 ATATTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
ATTAATATTATA
Found at i:1148902 original size:50 final size:50
Alignment explanation
Indices: 1148789--1148910 Score: 117
Period size: 50 Copynumber: 2.4 Consensus size: 50
1148779 CTATATTTTA
1148789 TATTAATATTAATTAAATACTATAAACTATATTATATTAATATAAGTAAATAT
1 TATTAATA-TAATT-AATA-TATAAACTATATTATATTAATATAAGTAAATAT
* * **
1148842 TAATATTATAATTAATATATAATTTATATTAATATTAAT-T-A-TAAATAGTT
1 TATTAATATAATTAATATATAAACTATATT-ATATTAATATAAGTAAATA--T
1148892 TATTAATATAAATT-ATATA
1 TATTAATAT-AATTAATATA
1148911 GGGATGAAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
48 6 0.10
49 1 0.02
50 25 0.42
51 16 0.27
52 5 0.08
53 6 0.10
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (50 bp):
TATTAATATAATTAATATATAAACTATATTATATTAATATAAGTAAATAT
Found at i:1149701 original size:23 final size:24
Alignment explanation
Indices: 1149675--1149731 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
1149665 TATAAACCCT
1149675 AACCCAAACCTG-ATCTGAACACA
1 AACCCAAACCTGAATCTGAACACA
* *
1149698 AACCCAAAACTGAATCTGAACCCA
1 AACCCAAACCTGAATCTGAACACA
*
1149722 AATCCAAACC
1 AACCCAAACC
1149732 CAAACCTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 11 0.38
24 18 0.62
ACGTcount: A:0.46, C:0.35, G:0.07, T:0.12
Consensus pattern (24 bp):
AACCCAAACCTGAATCTGAACACA
Found at i:1153558 original size:16 final size:16
Alignment explanation
Indices: 1153539--1153593 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
1153529 TAAAAACATG
1153539 TCAGGTTCATCACAGA
1 TCAGGTTCATCACAGA
* **
1153555 TCAGGTTAAAAACAGA
1 TCAGGTTCATCACAGA
1153571 TCAGGTTCATCACATG-
1 TCAGGTTCATCACA-GA
1153587 TCAGGTT
1 TCAGGTT
1153594 GAAAACATGT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
16 31 0.97
17 1 0.03
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (16 bp):
TCAGGTTCATCACAGA
Found at i:1153568 original size:32 final size:32
Alignment explanation
Indices: 1153522--1153603 Score: 114
Period size: 32 Copynumber: 2.6 Consensus size: 32
1153512 TCATTTACAA
*
1153522 GTCATGTTAAAAACATGTCAGGTTCATCACA-
1 GTCAGGTTAAAAACATGTCAGGTTCATCACAT
1153553 GATCAGGTTAAAAACA-GATCAGGTTCATCACAT
1 G-TCAGGTTAAAAACATG-TCAGGTTCATCACAT
*
1153586 GTCAGGTTGAAAACATGT
1 GTCAGGTTAAAAACATGT
1153604 TGGGTAATAC
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
31 2 0.04
32 41 0.91
33 2 0.04
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (32 bp):
GTCAGGTTAAAAACATGTCAGGTTCATCACAT
Found at i:1153601 original size:16 final size:16
Alignment explanation
Indices: 1153531--1153603 Score: 60
Period size: 16 Copynumber: 4.6 Consensus size: 16
1153521 AGTCATGTTA
1153531 AAAACATGTCAGGTTC
1 AAAACATGTCAGGTTC
** *
1153547 ATCACA-GATCAGGTTA
1 AAAACATG-TCAGGTTC
1153563 AAAACA-GATCAGGTTC
1 AAAACATG-TCAGGTTC
** *
1153579 ATCACATGTCAGGTTG
1 AAAACATGTCAGGTTC
1153595 AAAACATGT
1 AAAACATGT
1153604 TGGGTAATAC
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
15 1 0.02
16 42 0.95
17 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (16 bp):
AAAACATGTCAGGTTC
Found at i:1158940 original size:76 final size:76
Alignment explanation
Indices: 1158144--1158913 Score: 1396
Period size: 76 Copynumber: 10.1 Consensus size: 76
1158134 CATTAAAGGG
* *
1158144 CTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCAT
1 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
*
1158209 GCACTACAGGA
66 GCACTGCAGGA
1158220 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
1 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
*
1158285 GCACTGCAAGA
66 GCACTGCAGGA
1158296 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
1 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
1158361 GCACTGCAGGA
66 GCACTGCAGGA
1158372 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
1 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
*
1158437 GCACTGAAGGA
66 GCACTGCAGGA
* * *
1158448 TTTACAGATGACCCTAATGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
1 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
*
1158513 GCACTGAAGGA
66 GCACTGCAGGA
*
1158524 CTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
1 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
1158589 GCACTGCAGGA
66 GCACTGCAGGA
*
1158600 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCTGAAGGCTTTTTGGAAACATCAT
1 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
1158665 GCACTGCAGGA
66 GCACTGCAGGA
1158676 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
1 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
*
1158741 GCACTGCGGGA
66 GCACTGCAGGA
* *
1158752 CTTACAGAAGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
1 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
*
1158817 GCACTTCAGGA
66 GCACTGCAGGA
*
1158828 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGTTTTTTGGAAACATCAT
1 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
1158893 GCACTGCAGGA
66 GCACTGCAGGA
1158904 CTTACAGATG
1 CTTACAGATG
1158914 TGGGAAATAG
Statistics
Matches: 670, Mismatches: 24, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 670 1.00
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (76 bp):
CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
GCACTGCAGGA
Found at i:1159620 original size:22 final size:21
Alignment explanation
Indices: 1159592--1159645 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 21
1159582 CATAAAGCTT
1159592 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAA-CTA
*
1159614 TCATCTTTAAAAAGAGAACTA
1 TCATCTTTGAAAAGAGAACTA
1159635 TCATCTTTGAA
1 TCATCTTTGAA
1159646 GTGTGTAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 13 0.43
22 17 0.57
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (21 bp):
TCATCTTTGAAAAGAGAACTA
Found at i:1162344 original size:114 final size:114
Alignment explanation
Indices: 1162144--1162363 Score: 377
Period size: 114 Copynumber: 1.9 Consensus size: 114
1162134 GATCATGCAG
* * * *
1162144 TTCATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTATCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
1162209 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCATTATTTCTACTATGAGCAAA
* *
1162258 TTCATCTTTCAAATCTAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1162323 ACACTTCCAGAAGATGCTATTGGGTCTCATTATTTCTACTA
66 ACACTTCCAGAAGATGCTATTGGGTCTCATTATTTCTACTA
1162364 CGATAACGTG
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 99 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCATTATTTCTACTATGAGCAAA
Found at i:1171081 original size:3 final size:3
Alignment explanation
Indices: 1171073--1171130 Score: 75
Period size: 3 Copynumber: 19.7 Consensus size: 3
1171063 ATTTATTTAT
* *
1171073 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA TTA TTA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1171120 A-A ACTA ATA AT
1 ATA A-TA ATA AT
1171131 TTTAATTTTA
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
2 4 0.08
3 44 0.88
4 2 0.04
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:1171283 original size:42 final size:42
Alignment explanation
Indices: 1171230--1171475 Score: 204
Period size: 42 Copynumber: 5.5 Consensus size: 42
1171220 TCAATGTTAC
* * * *
1171230 TTTTACCTTTATAATTAAGATCTCTAATTTTTAAATCTCACT
1 TTTTACATTTATAATTGAGACCCCTAATTTTTAAATCTCACT
* * *
1171272 TTTCACATTTATAATCGAGATTCGAGACCCCTAATTTTTTTAATCTCATT
1 TTTTACA-TT-T-AT--A-ATT-GAGACCCCTAA-TTTTTAAATCTCACT
* *
1171322 TTTTACATTTATTATTGAGGCCCCTAATTTTTAAATCTCACT
1 TTTTACATTTATAATTGAGACCCCTAATTTTTAAATCTCACT
* * *
1171364 TTTTACATTTATAATCGAGATTCGAGGCCCCTAATTTTTTCAATCCCACT
1 TTTTACA-TT-T-AT--A-ATT-GAGACCCCTAA-TTTTTAAATCTCACT
* * *
1171414 TTTTACCTTTATAATTGAGGCCTCTAATTTTTAAATCTCACT
1 TTTTACATTTATAATTGAGACCCCTAATTTTTAAATCTCACT
*
1171456 TTTTACATTTATAATCGAGA
1 TTTTACATTTATAATTGAGA
1171476 TTCGAGGAAC
Statistics
Matches: 166, Mismatches: 22, Indels: 32
0.75 0.10 0.15
Matches are distributed among these distances:
42 55 0.33
43 24 0.14
44 8 0.05
45 5 0.03
47 5 0.03
48 8 0.05
49 23 0.14
50 38 0.23
ACGTcount: A:0.28, C:0.19, G:0.07, T:0.46
Consensus pattern (42 bp):
TTTTACATTTATAATTGAGACCCCTAATTTTTAAATCTCACT
Found at i:1171311 original size:92 final size:92
Alignment explanation
Indices: 1171212--1171564 Score: 469
Period size: 92 Copynumber: 3.8 Consensus size: 92
1171202 TTGAGGCTCT
*** * ** *
1171212 TAATTTTTTCAATGTTAC-TTTTACCTTTATAATTAAGATCTCTAATTTTTAAATCTCACTTTTC
1 TAATTTTTTCAATCCCACTTTTTACCTTTATAATTGAGGCCTCTAATTTTTAAATCTCACTTTTT
1171276 ACATTTATAATCGAGATTCGAGACCCC
66 ACATTTATAATCGAGATTCGAGACCCC
* * * * * *
1171303 TAATTTTTTTAATCTCATTTTTTACATTTATTATTGAGGCCCCTAATTTTTAAATCTCACTTTTT
1 TAATTTTTTCAATCCCACTTTTTACCTTTATAATTGAGGCCTCTAATTTTTAAATCTCACTTTTT
*
1171368 ACATTTATAATCGAGATTCGAGGCCCC
66 ACATTTATAATCGAGATTCGAGACCCC
1171395 TAATTTTTTCAATCCCACTTTTTACCTTTATAATTGAGGCCTCTAATTTTTAAATCTCACTTTTT
1 TAATTTTTTCAATCCCACTTTTTACCTTTATAATTGAGGCCTCTAATTTTTAAATCTCACTTTTT
*
1171460 ACATTTATAATCGAGATTCGAGGA-ACC
66 ACATTTATAATCGAGATTCGA-GACCCC
* * * *
1171487 TAATTTTTTCAATCCCACTTTTTACCGTTACAATTGAGGTCTCTAATTTTTTTTAATCTCACTTT
1 TAATTTTTTCAATCCCACTTTTTACCTTTATAATTGAGGCCTCTAA--TTTTTAAATCTCACTTT
*
1171552 CTACCA-TTATAAT
64 TTA-CATTTATAAT
1171565 TTGAATCTCT
Statistics
Matches: 232, Mismatches: 25, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
91 14 0.06
92 190 0.82
93 1 0.00
94 25 0.11
95 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.07, T:0.46
Consensus pattern (92 bp):
TAATTTTTTCAATCCCACTTTTTACCTTTATAATTGAGGCCTCTAATTTTTAAATCTCACTTTTT
ACATTTATAATCGAGATTCGAGACCCC
Found at i:1171317 original size:50 final size:49
Alignment explanation
Indices: 1171253--1171511 Score: 285
Period size: 50 Copynumber: 5.5 Consensus size: 49
1171243 ATTAAGATCT
* *
1171253 CTAATTTTTAAATCTCACTTTTCACATTTATAATCGAGATTCGAGACCC
1 CTAATTTTTAAATCTCACTTTTTACATTTATAATCGAGATTCGAGGCCC
* *
1171302 CTAATTTTTTTAATCTCATTTTTTACATTTAT--T----ATT-GAGGCCC
1 CTAA-TTTTTAAATCTCACTTTTTACATTTATAATCGAGATTCGAGGCCC
1171345 CTAATTTTTAAATCTCACTTTTTACATTTATAATCGAGATTCGAGGCCC
1 CTAATTTTTAAATCTCACTTTTTACATTTATAATCGAGATTCGAGGCCC
* * * *
1171394 CTAATTTTTTCAATCCCACTTTTTAC-CTT-T-AT--A-ATT-GAGGCCT
1 CTAA-TTTTTAAATCTCACTTTTTACATTTATAATCGAGATTCGAGGCCC
**
1171437 CTAATTTTTAAATCTCACTTTTTACATTTATAATCGAGATTCGAGGAAC
1 CTAATTTTTAAATCTCACTTTTTACATTTATAATCGAGATTCGAGGCCC
* *
1171486 CTAATTTTTTCAATCCCACTTTTTAC
1 CTAA-TTTTTAAATCTCACTTTTTAC
1171512 CGTTACAATT
Statistics
Matches: 175, Mismatches: 18, Indels: 33
0.77 0.08 0.15
Matches are distributed among these distances:
42 44 0.25
43 22 0.13
44 8 0.05
45 3 0.02
47 3 0.02
48 8 0.05
49 25 0.14
50 62 0.35
ACGTcount: A:0.27, C:0.20, G:0.08, T:0.44
Consensus pattern (49 bp):
CTAATTTTTAAATCTCACTTTTTACATTTATAATCGAGATTCGAGGCCC
Found at i:1171580 original size:45 final size:44
Alignment explanation
Indices: 1171486--1171583 Score: 110
Period size: 44 Copynumber: 2.2 Consensus size: 44
1171476 TTCGAGGAAC
* * *
1171486 CTAA-TTTTTTCAATCCCACTTTTTACCGTTACAATTGAGGTCT
1 CTAATTTTTTTCAATCCCACTTTCTACCATTACAATTGAGATCT
* * *
1171529 CTAATTTTTTTTAATCTCACTTTCTACCATTATAATTTGA-ATCT
1 CTAATTTTTTTCAATCCCACTTTCTACCATTACAA-TTGAGATCT
1171573 CTTAATTTTTT
1 C-TAATTTTTT
1171584 AAAGCTATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
43 4 0.09
44 29 0.63
45 13 0.28
ACGTcount: A:0.24, C:0.19, G:0.05, T:0.51
Consensus pattern (44 bp):
CTAATTTTTTTCAATCCCACTTTCTACCATTACAATTGAGATCT
Found at i:1171636 original size:40 final size:39
Alignment explanation
Indices: 1171592--1171667 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 39
1171582 TTAAAGCTAT
* *
1171592 TTTTTACCTTTATAATTAATTCCCCTATTTTTAATCACAC
1 TTTTTACCTTTATAATTAATGCCCCTA-ATTTAATCACAC
**
1171632 TTTTTATTTTTATAATTAATGCCCCTAATTTAATCA
1 TTTTTACCTTTATAATTAATGCCCCTAATTTAATCA
1171668 TTTTTCCAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
39 8 0.25
40 24 0.75
ACGTcount: A:0.29, C:0.18, G:0.01, T:0.51
Consensus pattern (39 bp):
TTTTTACCTTTATAATTAATGCCCCTAATTTAATCACAC
Found at i:1181837 original size:19 final size:20
Alignment explanation
Indices: 1181813--1181860 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1181803 AAAAATACAC
1181813 TAAATATTAG-AACATC-ATT
1 TAAATATTAGTAACA-CGATT
1181832 TAAATATGT-GTAACACGATT
1 TAAATAT-TAGTAACACGATT
1181852 TAAATATTA
1 TAAATATTA
1181861 AATTAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (20 bp):
TAAATATTAGTAACACGATT
Found at i:1183009 original size:28 final size:28
Alignment explanation
Indices: 1182955--1183009 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
1182945 AATATATATA
*
1182955 AAAACAAAGAAATAAAAAAGAATACATG
1 AAAACAAAGAAATAAAAAAGAAAACATG
1182983 AAAACAAAGAAATAAAAACA-AAAACAT
1 AAAACAAAGAAATAAAAA-AGAAAACAT
1183010 ACACTAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.75, C:0.09, G:0.07, T:0.09
Consensus pattern (28 bp):
AAAACAAAGAAATAAAAAAGAAAACATG
Found at i:1183098 original size:13 final size:13
Alignment explanation
Indices: 1183067--1183091 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1183057 CAATAAAGAG
1183067 AAAATAAATAAAT
1 AAAATAAATAAAT
1183080 AAAATAAATAAA
1 AAAATAAATAAA
1183092 AAGAATATAC
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:1185093 original size:83 final size:84
Alignment explanation
Indices: 1184963--1185999 Score: 1101
Period size: 84 Copynumber: 12.4 Consensus size: 84
1184953 TTTTATTTGG
* * * * * *
1184963 CTTTGAGTTGAGCGTAGTCGAACTCGAAGG-CCTTTGTTGACATATAACCTTTCTAGCCTTGAGT
1 CTTTGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGT
* *
1185027 TATGCTGTAAATGATATGC
66 TATGCTGCAAATGATGTGC
* * ** * *
1185046 CTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTGGTTGATAGATAACCCTTCTTGCCTTGAGC
1 CTTTGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGT
* * *
1185110 TATGTTACAAATAATGTGC
66 TATGCTGCAAATGATGTGC
* * * ***
1185129 CTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTATTGGCAGATAATAATTCTCA-CCTTGAG
1 CTTTGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCT-AGCCTTGAG
* **
1185193 CTATGCTGCAAATGATGCAC
65 TTATGCTGCAAATGATGTGC
* * * **
1185213 CTTTGAGCTGGGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTTCCTTGA-T
1 CTTTGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGT
* *
1185277 CTATGTTGCAAATGATGTGT
66 -TATGCTGCAAATGATGTGC
* * * * *
1185297 CTTTGAGCTGAGTGTAATCGAACTCGAAGATATTTTGTTGGCAGATAACCCTTATTGCCTTGAGT
1 CTTTGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGT
* *
1185362 TATGCTACGAATTTGATGTGC
66 TATGCTGC-AA-ATGATGTGC
* * * * * *
1185383 CTTTGAGCTGAGTGTAATCGAACTTGAAGGTC-TTGGTTAGTAGATAACCCTTATAGCCTTGAGT
1 CTTTGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGT
* **
1185447 TATGCTGTAAACAATGTGC
66 TATGCTGCAAATGATGTGC
* * * * *
1185466 CTTTGAGCTGAGTGTAATCCAACTCGAAGGTC---T-TTGGCAGATAACCCTTCTTGCCTTAAGC
1 CTTTGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGT
1185527 TATGCTGCAAATGATGTGC
66 TATGCTGCAAATGATGTGC
* * * * * *
1185546 C-TTGAGCTGAGCGTAGTCAAACTCGGAA-GTCTTTTGTTGGAAAATAGCCCTTCTTGCCTTGAG
1 CTTTGAGCTGAGTGTAGTCGAACTC-GAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAG
* * *
1185609 CTATGTTGCAAATGATGTGT
65 TTATGCTGCAAATGATGTGC
* * * * *
1185629 CTTGGAGCTGAGCGTAGTTGAACTCGAAGGTCTTTTGTTGGTAGATAAACCTTCTAGCCTTGAGT
1 CTTTGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGT
* *
1185694 TATACTGTAAATGATGTGC
66 TATGCTGCAAATGATGTGC
* * * * * ** * *
1185713 CTTAGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTGGCAAATAACCCATCTTTCTTTGAGC
1 CTTTGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGT
** *
1185778 TATATTGCAAATGATGTGA
66 TATGCTGCAAATGATGTGC
* * * * *
1185797 CTTGGAACTAAGCGTAGTCTAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGT
1 CTTTGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGT
*
1185862 TATGCTG-TAATGATGTGC
66 TATGCTGCAAATGATGTGC
*
1185880 CTTGGAGCTGAGCT-TAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAG
1 CTTTGAGCTGAG-TGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAG
*
1185944 TTATGCTGCAAATGATGTGT
65 TTATGCTGCAAATGATGTGC
* *
1185964 CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTT
1 CTTTGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTT
1186000 AACATATCAA
Statistics
Matches: 804, Mismatches: 132, Indels: 35
0.83 0.14 0.04
Matches are distributed among these distances:
79 23 0.03
80 42 0.05
82 1 0.00
83 255 0.32
84 410 0.51
85 37 0.05
86 36 0.04
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (84 bp):
CTTTGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGT
TATGCTGCAAATGATGTGC
Done.