Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002647.1 Hibiscus syriacus cultivar Beakdansim tig00005406_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: 7027529
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 26
Found at i:3799551 original size:14 final size:14
Alignment explanation
Indices: 3799526--3799563 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3799516 TCCAGCACTC
*
3799526 AAAAAGGAAAAA-A
1 AAAAAAGAAAAAGA
3799539 AATAAAAGAAAAAGA
1 AA-AAAAGAAAAAGA
3799554 AAAAAAGAAA
1 AAAAAAGAAA
3799564 GTTAAAGCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 2 0.09
14 17 0.77
15 3 0.14
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (14 bp):
AAAAAAGAAAAAGA
Found at i:3801006 original size:3 final size:3
Alignment explanation
Indices: 3801000--3801045 Score: 83
Period size: 3 Copynumber: 15.0 Consensus size: 3
3800990 AATTTTTTTC
3801000 TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
3801046 AATAAATATA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:3801054 original size:25 final size:25
Alignment explanation
Indices: 3801004--3801056 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
3800994 TTTTTCTTAT
* *
3801004 TATTATTATTATTATTATTATTATA
1 TATTATTATTATTATTAATATAATA
3801029 TATTATTATTATTATTAA-ATAAATA
1 TATTATTATTATTATTAATAT-AATA
3801054 TAT
1 TAT
3801057 ATATATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 2 0.08
25 23 0.92
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TATTATTATTATTATTAATATAATA
Found at i:3802477 original size:19 final size:21
Alignment explanation
Indices: 3802455--3802495 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
3802445 ATAGTTATAA
3802455 ATATATA-TAAT-AATTATTT
1 ATATATATTAATAAATTATTT
3802474 ATATATATTTAATAAATTATTT
1 ATATATA-TTAATAAATTATTT
3802496 TGATATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
21 4 0.21
22 8 0.42
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATATATATTAATAAATTATTT
Found at i:3802481 original size:21 final size:22
Alignment explanation
Indices: 3802455--3802495 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3802445 ATAGTTATAA
3802455 ATATATATAAT-AATTATTTAT
1 ATATATATAATAAATTATTTAT
*
3802476 ATATATTTAATAAATTATTT
1 ATATATATAATAAATTATTT
3802496 TGATATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATATATATAATAAATTATTTAT
Found at i:3805484 original size:11 final size:11
Alignment explanation
Indices: 3805470--3805500 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
3805460 CTCAAAAAGG
3805470 AAGAAAAAGAA
1 AAGAAAAAGAA
3805481 AAGAAAAAGAA
1 AAGAAAAAGAA
*
3805492 AAAAAAAAG
1 AAGAAAAAG
3805501 TTGAAGCACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAGAAAAAGAA
Found at i:3807699 original size:14 final size:14
Alignment explanation
Indices: 3807680--3807710 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3807670 ATATCATTTC
*
3807680 TTAGGATATTATTA
1 TTAGGATATTAATA
3807694 TTAGGATATTAATA
1 TTAGGATATTAATA
3807708 TTA
1 TTA
3807711 CATGTTTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (14 bp):
TTAGGATATTAATA
Found at i:3814704 original size:23 final size:23
Alignment explanation
Indices: 3814653--3814722 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
3814643 AATTTAATAA
*
3814653 CAAAAATGTTTGAATTTTAGTCA-
1 CAAAAATGTTTAAATTTTAGT-AG
* *
3814676 CTAAAATGTCTAAATTTTAGTAG
1 CAAAAATGTTTAAATTTTAGTAG
* *
3814699 CAAAAATATTTAAATTTTAATAG
1 CAAAAATGTTTAAATTTTAGTAG
3814722 C
1 C
3814723 TGTTTATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
22 1 0.03
23 38 0.97
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.39
Consensus pattern (23 bp):
CAAAAATGTTTAAATTTTAGTAG
Found at i:3817463 original size:17 final size:17
Alignment explanation
Indices: 3817441--3817481 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
3817431 AATGACTTGT
3817441 ATGTTCTCAATTTATCA
1 ATGTTCTCAATTTATCA
*
3817458 ATGTTCTCAATTTATCG
1 ATGTTCTCAATTTATCA
3817475 ATGTTCT
1 ATGTTCT
3817482 TGAAGTACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.24, C:0.17, G:0.10, T:0.49
Consensus pattern (17 bp):
ATGTTCTCAATTTATCA
Found at i:3823780 original size:17 final size:16
Alignment explanation
Indices: 3823758--3823814 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 16
3823748 CTTCCGGGTT
3823758 AGTAAAAAATAAAAAAA
1 AGTAAAAAA-AAAAAAA
3823775 AGTAAAAAAAAAACAAA
1 AGTAAAAAAAAAA-AAA
3823792 AG-AAAGAAAGAAAAAAA
1 AGTAAA-AAA-AAAAAAA
*
3823809 ATTAAA
1 AGTAAA
3823815 GAGGGAGGGA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
16 7 0.20
17 21 0.60
18 7 0.20
ACGTcount: A:0.81, C:0.02, G:0.09, T:0.09
Consensus pattern (16 bp):
AGTAAAAAAAAAAAAA
Found at i:3823815 original size:22 final size:21
Alignment explanation
Indices: 3823761--3823816 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
3823751 CCGGGTTAGT
* *
3823761 AAAAAATAAAAAAAAGTAAAA
1 AAAAAATAAAAGAAAGAAAAA
*
3823782 AAAAAACAAAAGAAAGAAAGAA
1 AAAAAATAAAAGAAAGAAA-AA
*
3823804 AAAAAATTAAAGA
1 AAAAAATAAAAGA
3823817 GGGAGGGAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.82, C:0.02, G:0.09, T:0.07
Consensus pattern (21 bp):
AAAAAATAAAAGAAAGAAAAA
Found at i:3824139 original size:17 final size:18
Alignment explanation
Indices: 3824113--3824148 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
3824103 TTTCTTGGAG
3824113 TGTTTGGTGAGGTT-TTT
1 TGTTTGGTGAGGTTATTT
*
3824130 TGTTTTGTGAGGTTATTT
1 TGTTTGGTGAGGTTATTT
3824148 T
1 T
3824149 TTATTACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.08, C:0.00, G:0.31, T:0.61
Consensus pattern (18 bp):
TGTTTGGTGAGGTTATTT
Found at i:3832995 original size:23 final size:24
Alignment explanation
Indices: 3832945--3832997 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
3832935 TTTCTTTTCT
* *
3832945 TTTCTTCTTTTTGAGTGATTGATT
1 TTTCTTCTTTTTGAGTGATTCATA
*
3832969 TTTCTTCTTTTTGAGTGTTTCA-A
1 TTTCTTCTTTTTGAGTGATTCATA
3832992 TTTCTT
1 TTTCTT
3832998 TTCTGATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.11, C:0.11, G:0.13, T:0.64
Consensus pattern (24 bp):
TTTCTTCTTTTTGAGTGATTCATA
Found at i:3838182 original size:18 final size:18
Alignment explanation
Indices: 3838140--3838183 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
3838130 ATATAAAGAT
*
3838140 CTAGTTT-AATTAATTAA
1 CTAGTTTAAATGAATTAA
* *
3838157 CCAATTTAAATGAATTAA
1 CTAGTTTAAATGAATTAA
3838175 CTAGTTTAA
1 CTAGTTTAA
3838184 TTAGTGAACT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (18 bp):
CTAGTTTAAATGAATTAA
Found at i:3844625 original size:32 final size:32
Alignment explanation
Indices: 3844588--3844676 Score: 90
Period size: 32 Copynumber: 2.8 Consensus size: 32
3844578 ACCATATATT
* *
3844588 AGTTAGTGTAGCAATTAGATAATGTACAGCAG
1 AGTTAGTGTAGCATTTAGATAATGTACAACAG
** * *
3844620 AGTTAGCATTGC-TTTCAAATAATGTACAACAG
1 AGTTAGTGTAGCATTT-AGATAATGTACAACAG
* *
3844652 TGTTAGTGTCGCATTTAGATAATGT
1 AGTTAGTGTAGCATTTAGATAATGT
3844677 GTAGCAGTTA
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
31 2 0.05
32 39 0.89
33 3 0.07
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (32 bp):
AGTTAGTGTAGCATTTAGATAATGTACAACAG
Found at i:3846184 original size:18 final size:20
Alignment explanation
Indices: 3846153--3846190 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
3846143 ATTATGAGAT
3846153 TTACATGCAAAATAT-GTGA
1 TTACATGCAAAATATCGTGA
3846172 TTACATG-AAAATATCGTGA
1 TTACATGCAAAATATCGTGA
3846191 ATCGTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (20 bp):
TTACATGCAAAATATCGTGA
Found at i:3854977 original size:134 final size:134
Alignment explanation
Indices: 3854799--3855618 Score: 913
Period size: 134 Copynumber: 6.1 Consensus size: 134
3854789 GCTGTCACTC
* * ** * *
3854799 AGGGAATATCAAATAT-GAGGATGTTGATCCATTCCACTATCACTCATGGAAGATTGAATCGAGG
1 AGGGAATATCAGATCTAGAGGA-GTTGATCCATTCTGCTGTCACTCAGGGAAGATTGAATCGAGG
* * * ** *
3854863 CAGACTTGTTCCACTATCACTCATGGAATATCAAATATTGGAAAAAAGGGATTTGTTCTGCTTCT
65 CAGACTTGTTCCACTGTCACTCAAGGAATATCAAATCTTGGAAAAAAGGGACATGTTCCGCTTCT
3854928 TCTGA
130 TCTGA
*
3854933 AGGGAATATCAGATCTAGAGGAGTTGATCCATTCTGCTGTCACTCAGGGAATATTTG-ATC-AGG
1 AGGGAATATCAGATCTAGAGGAGTTGATCCATTCTGCTGTCACTCAGGGAAGA-TTGAATCGA-G
* * *
3854996 GCATATTTGTTCCACTGTCACTCAAGGAATATGAAATCTTGGAAAAAAGGGACATGTTCCGCTTT
64 GCAGACTTGTTCCACTGTCACTCAAGGAATATCAAATCTTGGAAAAAAGGGACATGTTCCGC-TT
3855061 CTT-TGA
128 CTTCTGA
* * * ** * * *
3855067 AAGGAATATCATATCTTGAGGAGTTGATTTATT-TCGCTATCACTTAGGGAAGATTGAATCGAGA
1 AGGGAATATCAGATCTAGAGGAGTTGATCCATTCT-GCTGTCACTCAGGGAAGATTGAATCGAGG
*** * * * * *
3855131 CAGACTTGTTATGCTATCTCTCAGGGAATATCAAATCTTAGAAAAGAGGGACATGTTCCGCTTCT
65 CAGACTTGTTCCACTGTCACTCAAGGAATATCAAATCTTGGAAAAAAGGGACATGTTCCGCTTCT
3855196 TCT-A
130 TCTGA
* * * * *
3855200 ACGGGAATATCATATCTAGAGGAGTTGATCTATTCTGCTGTCACTTAGGGAAGATTGAATAGGGG
1 A-GGGAATATCAGATCTAGAGGAGTTGATCCATTCTGCTGTCACTCAGGGAAGATTGAATCGAGG
* * **
3855265 AAGACTTGTTCCGA-TGTCACTC-AGAGAATATCAAATCTTGGAAAAGAA-TGACATGTTCTTCT
65 CAGACTTGTTCC-ACTGTCACTCAAG-GAATATCAAATCTTGGAAAA-AAGGGACATGTTCCGCT
*
3855327 TCTTCTAA
127 TCTTCTGA
* * * *
3855335 AGGGAATATTAGATCTAGAGGAGTTGATCCCTTCCGCTGTCACTCAGGGAAGATTGAATCGGGGC
1 AGGGAATATCAGATCTAGAGGAGTTGATCCATTCTGCTGTCACTCAGGGAAGATTGAATCGAGGC
* * * ** *
3855400 AGACTTGTTTCA-TGTCACTCAAGGAATATCAAATCTTGGAAAAGAGGGACTTGTTTTGCATCTT
66 AGACTTGTTCCACTGTCACTCAAGGAATATCAAATCTTGGAAAAAAGGGACATGTTCCGCTTCTT
3855464 CTGA
131 CTGA
* * * * * *
3855468 AGGGAATATCATATCTGGAGGAGTTGATCAATTCTGCTGTCACTTAGGGAAGATTGAATCGGGGT
1 AGGGAATATCAGATCTAGAGGAGTTGATCCATTCTGCTGTCACTCAGGGAAGATTGAATCGAGGC
* * * * *
3855533 AGACTTGTTCTACTGTCACTTAGGGAATATCAAATCTTAGAAAAGAGGGACATGTTCCGCTTCTT
66 AGACTTGTTCCACTGTCACTCAAGGAATATCAAATCTTGGAAAAAAGGGACATGTTCCGCTTCTT
3855598 CTGA
131 CTGA
*
3855602 AGGGAACATCAGATCTA
1 AGGGAATATCAGATCTA
3855619 TAAATTAAAC
Statistics
Matches: 578, Mismatches: 91, Indels: 34
0.82 0.13 0.05
Matches are distributed among these distances:
132 1 0.00
133 125 0.22
134 434 0.75
135 18 0.03
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.30
Consensus pattern (134 bp):
AGGGAATATCAGATCTAGAGGAGTTGATCCATTCTGCTGTCACTCAGGGAAGATTGAATCGAGGC
AGACTTGTTCCACTGTCACTCAAGGAATATCAAATCTTGGAAAAAAGGGACATGTTCCGCTTCTT
CTGA
Found at i:3855525 original size:267 final size:267
Alignment explanation
Indices: 3854799--3855618 Score: 1012
Period size: 268 Copynumber: 3.1 Consensus size: 267
3854789 GCTGTCACTC
* * * *
3854799 AGGGAATATCAAATAT-GAGGATGTTGATCCATTCCACTATCACTCATGGAAGATTGAATCGAGG
1 AGGGAATATCAGATCTAGAGGA-GTTGATCCATTCCGCTATCACTCAGGGAAGATTGAATCGAGG
* * * * *
3854863 CAGACTTGTTCCACTATCACTCATGGAATATCAAATATTGGAAAAAAGGGATTTGTTCTGCTTCT
65 CAGACTTGTTTCA-TATCACTCAAGGAATATCAAATCTTGGAAAAGAGGGACTTGTTCTGCTTCT
* * * *
3854928 TCTGAAGGGAATATCAGATCTAGAGGAGTTGATCCATTCTGCTGTCACTCAGGGAATATTTG-AT
129 TCTGAAGGGAATATCATATCTAGAGGAGTTGATCAATTCTGCTGTCACTTAGGGAAGA-TTGAAT
* * * *
3854992 CA-GGGCATATTTGTTCCACTGTCACTCA-AGGAATATGAAATCTTGGAAAA-AAGGGACATGTT
193 -AGGGGAAGACTTGTTCCACTGTCACTCAGA-GAATATCAAATCTTGGAAAAGAA-GGACATGTT
3855054 CCGCTTTCTT-TGAA
255 CCGC-TTCTTCT-AA
* * ** * * *
3855068 A-GGAATATCATATCTTGAGGAGTTGATTTATTTCGCTATCACTTAGGGAAGATTGAATCGAGAC
1 AGGGAATATCAGATCTAGAGGAGTTGATCCATTCCGCTATCACTCAGGGAAGATTGAATCGAGGC
* * * * *
3855132 AGACTTGTTATGC-TATCTCTCAGGGAATATCAAATCTTAGAAAAGAGGGACATGTTCCGCTTCT
66 AGACTTGTT-T-CATATCACTCAAGGAATATCAAATCTTGGAAAAGAGGGACTTGTTCTGCTTCT
*
3855196 TCT-AACGGGAATATCATATCTAGAGGAGTTGATCTATTCTGCTGTCACTTAGGGAAGATTGAAT
129 TCTGAA-GGGAATATCATATCTAGAGGAGTTGATCAATTCTGCTGTCACTTAGGGAAGATTGAAT
* *
3855260 AGGGGAAGACTTGTTCCGA-TGTCACTCAGAGAATATCAAATCTTGGAAAAGAATGACATGTTCT
193 AGGGGAAGACTTGTTCC-ACTGTCACTCAGAGAATATCAAATCTTGGAAAAGAAGGACATGTTCC
*
3855324 TCTTCTTCTAA
257 GCTTCTTCTAA
* * * *
3855335 AGGGAATATTAGATCTAGAGGAGTTGATCCCTTCCGCTGTCACTCAGGGAAGATTGAATCGGGGC
1 AGGGAATATCAGATCTAGAGGAGTTGATCCATTCCGCTATCACTCAGGGAAGATTGAATCGAGGC
* * *
3855400 AGACTTGTTTCATGTCACTCAAGGAATATCAAATCTTGGAAAAGAGGGACTTGTTTTGCATCTTC
66 AGACTTGTTTCATATCACTCAAGGAATATCAAATCTTGGAAAAGAGGGACTTGTTCTGCTTCTTC
* *
3855465 TGAAGGGAATATCATATCTGGAGGAGTTGATCAATTCTGCTGTCACTTAGGGAAGATTGAATCGG
131 TGAAGGGAATATCATATCTAGAGGAGTTGATCAATTCTGCTGTCACTTAGGGAAGATTGAATAGG
* * * * * *
3855530 GGTAGACTTGTTCTACTGTCACTTAGGGAATATCAAATCTTAGAAAAGAGGGACATGTTCCGCTT
196 GGAAGACTTGTTCCACTGTCACTCAGAGAATATCAAATCTTGGAAAAGAAGGACATGTTCCGCTT
*
3855595 CTTCTGA
261 CTTCTAA
*
3855602 AGGGAACATCAGATCTA
1 AGGGAATATCAGATCTA
3855619 TAAATTAAAC
Statistics
Matches: 474, Mismatches: 63, Indels: 30
0.84 0.11 0.05
Matches are distributed among these distances:
266 2 0.00
267 194 0.41
268 267 0.56
269 10 0.02
270 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.30
Consensus pattern (267 bp):
AGGGAATATCAGATCTAGAGGAGTTGATCCATTCCGCTATCACTCAGGGAAGATTGAATCGAGGC
AGACTTGTTTCATATCACTCAAGGAATATCAAATCTTGGAAAAGAGGGACTTGTTCTGCTTCTTC
TGAAGGGAATATCATATCTAGAGGAGTTGATCAATTCTGCTGTCACTTAGGGAAGATTGAATAGG
GGAAGACTTGTTCCACTGTCACTCAGAGAATATCAAATCTTGGAAAAGAAGGACATGTTCCGCTT
CTTCTAA
Found at i:3858941 original size:19 final size:20
Alignment explanation
Indices: 3858919--3858959 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
3858909 TAGAAGTGTT
*
3858919 AAAATGATAAAGAATGT-AA
1 AAAATGACAAAGAATGTGAA
3858938 AAAATGACAAAGAATGTGAA
1 AAAATGACAAAGAATGTGAA
3858958 AA
1 AA
3858960 TGTATAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.63, C:0.02, G:0.17, T:0.17
Consensus pattern (20 bp):
AAAATGACAAAGAATGTGAA
Found at i:3860283 original size:12 final size:12
Alignment explanation
Indices: 3860266--3860296 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3860256 CTAGTGATCA
3860266 GGTCATTTTGAC
1 GGTCATTTTGAC
3860278 GGTCATTTTGAC
1 GGTCATTTTGAC
*
3860290 GATCATT
1 GGTCATT
3860297 GAAGTGTGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.16, G:0.23, T:0.42
Consensus pattern (12 bp):
GGTCATTTTGAC
Found at i:3862725 original size:16 final size:16
Alignment explanation
Indices: 3862704--3862741 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
3862694 TGGCTCCCTT
3862704 ATGAAGGTGAACGATA
1 ATGAAGGTGAACGATA
3862720 ATGAAGGTGAACGATA
1 ATGAAGGTGAACGATA
3862736 ATGAAG
1 ATGAAG
3862742 ATGATGGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.45, C:0.05, G:0.32, T:0.18
Consensus pattern (16 bp):
ATGAAGGTGAACGATA
Found at i:3862881 original size:59 final size:59
Alignment explanation
Indices: 3862782--3862898 Score: 155
Period size: 59 Copynumber: 2.0 Consensus size: 59
3862772 GATGGATAAG
*** * *
3862782 TGTCCTATCAAACCCTCCTAGTTGTAATGAAAAAGAAAACTCGATAATATGGCTCTAAA
1 TGTCCTATCAAACCCTCCTAGTCACAATGAAAAAGAAAACTCAATAATATAGCTCTAAA
* *
3862841 TGTCCTATCGAACCCTCCTAGTCACAAT-AAAAAGGCAAACTCAATAATATAGCTCTAA
1 TGTCCTATCAAACCCTCCTAGTCACAATGAAAAA-GAAAACTCAATAATATAGCTCTAA
3862899 CCAACCCTCC
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
58 5 0.10
59 45 0.90
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (59 bp):
TGTCCTATCAAACCCTCCTAGTCACAATGAAAAAGAAAACTCAATAATATAGCTCTAAA
Found at i:3867431 original size:13 final size:12
Alignment explanation
Indices: 3867418--3867457 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
3867408 AAAAAAAAAC
3867418 AAAAAAAGACAA
1 AAAAAAAGACAA
* *
3867430 CAAAAAAGGCAA
1 AAAAAAAGACAA
*
3867442 AAAAAAAAACAA
1 AAAAAAAGACAA
3867454 AAAA
1 AAAA
3867458 GCCAAAATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.82, C:0.10, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAGACAA
Found at i:3867435 original size:21 final size:21
Alignment explanation
Indices: 3867409--3867464 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
3867399 TTTTTTTTCA
* *
3867409 AAAAAAAACAAAAAAAGACAAC
1 AAAAAAGACAAAAAAA-AAAAC
*
3867431 AAAAAAGGCAAAAAAAAAAAC
1 AAAAAAGACAAAAAAAAAAAC
*
3867452 AAAAAAGCCAAAA
1 AAAAAAGACAAAA
3867465 TTTCAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 16 0.53
22 14 0.47
ACGTcount: A:0.80, C:0.12, G:0.07, T:0.00
Consensus pattern (21 bp):
AAAAAAGACAAAAAAAAAAAC
Found at i:3875330 original size:16 final size:17
Alignment explanation
Indices: 3875299--3875331 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3875289 CAATTGATAA
3875299 CATTTCTATCCTTTAAT
1 CATTTCTATCCTTTAAT
*
3875316 CATTTCT-TTCTTTAAT
1 CATTTCTATCCTTTAAT
3875332 TGGTGCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.58
Consensus pattern (17 bp):
CATTTCTATCCTTTAAT
Found at i:3883092 original size:12 final size:11
Alignment explanation
Indices: 3883056--3883106 Score: 70
Period size: 12 Copynumber: 4.6 Consensus size: 11
3883046 TGGACTAAAG
3883056 GTAGCT-GGAA
1 GTAGCTGGGAA
3883066 GTAGCT-GGAA
1 GTAGCTGGGAA
3883076 GTAGCTGGGAGA
1 GTAGCTGGGA-A
3883088 GTAGCTGGGAGA
1 GTAGCTGGGA-A
3883100 GTAGCTG
1 GTAGCTG
3883107 AGGGGGATGA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
10 16 0.41
11 3 0.08
12 20 0.51
ACGTcount: A:0.25, C:0.10, G:0.45, T:0.20
Consensus pattern (11 bp):
GTAGCTGGGAA
Found at i:3884397 original size:17 final size:16
Alignment explanation
Indices: 3884370--3884412 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
3884360 GGTTCAAAAC
3884370 AAAAG-AGAAAAGAACA
1 AAAAGAAGAAAAG-ACA
*
3884386 AAAAGAAGAAAAGCCA
1 AAAAGAAGAAAAGACA
3884402 AAAAGAA-AAAA
1 AAAAGAAGAAAA
3884413 ATTCTAGCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 4 0.16
16 14 0.56
17 7 0.28
ACGTcount: A:0.77, C:0.07, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAGAAGAAAAGACA
Found at i:3886355 original size:2 final size:2
Alignment explanation
Indices: 3886348--3886382 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3886338 AGGTAGCAAA
3886348 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3886383 AGTTGGTGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3889199 original size:1 final size:1
Alignment explanation
Indices: 3889150--3889190 Score: 64
Period size: 1 Copynumber: 41.0 Consensus size: 1
3889140 TATTTTTTTT
* *
3889150 AAAAAAAAAAAAAAAAAAACAAAAAAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3889191 GCCAAAAAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.95, C:0.05, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3889199 original size:13 final size:12
Alignment explanation
Indices: 3889150--3889190 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
3889140 TATTTTTTTT
3889150 AAAAAAAA-AAA
1 AAAAAAAACAAA
3889161 AAAAAAAACAAA
1 AAAAAAAACAAA
3889173 AAAAAAAACAAA
1 AAAAAAAACAAA
3889185 AAAAAA
1 AAAAAA
3889191 GCCAAAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 8 0.28
12 21 0.72
ACGTcount: A:0.95, C:0.05, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAACAAA
Found at i:3897938 original size:161 final size:161
Alignment explanation
Indices: 3897649--3897949 Score: 476
Period size: 161 Copynumber: 1.9 Consensus size: 161
3897639 TTTGAAGTAA
* * * *
3897649 GTAAAATGTTGGCAGCATTGAATGAACATCTCTATTAATAAAAAATTAAAAGAGATGTTGAAAGA
1 GTAAAACGTTGGCAACATTGAATGAACATCTCTATTAACAAAAAATTAAAACAGATGTTGAAAGA
* * * * *
3897714 GTGTATGAAATATGCCTCATTTGTAAACAGGCAAAATCAAAAGTTATGCCCATGGTCTATACATG
66 GTGTATGAAAGATGCCTCATTTGCAAACAGGCAAAATAAAAAGTTAAGCCCATGGTATATACATG
*
3897779 TCTCTTCCAATTCCAAATGATCTTTAAGTTT
131 CCTCTTCCAATTCCAAATGATCTTTAAGTTT
* *
3897810 GTAAAACGTTGGCAACATTGAATGAACATCTCTATTGACCAAAAATTAAAACAGATGTTGAAAGA
1 GTAAAACGTTGGCAACATTGAATGAACATCTCTATTAACAAAAAATTAAAACAGATGTTGAAAGA
* *
3897875 GTGTATGAAAGATGCCTCTTTTGCAAACAGGCAAAATAAAAAGTTAAGCTCATGGTATATACATG
66 GTGTATGAAAGATGCCTCATTTGCAAACAGGCAAAATAAAAAGTTAAGCCCATGGTATATACATG
3897940 CCTCTTCCAA
131 CCTCTTCCAA
3897950 GGACAAAAAA
Statistics
Matches: 126, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
161 126 1.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (161 bp):
GTAAAACGTTGGCAACATTGAATGAACATCTCTATTAACAAAAAATTAAAACAGATGTTGAAAGA
GTGTATGAAAGATGCCTCATTTGCAAACAGGCAAAATAAAAAGTTAAGCCCATGGTATATACATG
CCTCTTCCAATTCCAAATGATCTTTAAGTTT
Found at i:3898478 original size:31 final size:31
Alignment explanation
Indices: 3898440--3898507 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
3898430 AGATAGAAAG
3898440 AACAAGGCAGAGTTCATAAAAAAGCTTCATC
1 AACAAGGCAGAGTTCATAAAAAAGCTTCATC
* *
3898471 AACAAGGCAGATTTCATCAAAAAGCTTCATC
1 AACAAGGCAGAGTTCATAAAAAAGCTTCATC
3898502 AACAAG
1 AACAAG
3898508 TTAGAGATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.46, C:0.21, G:0.15, T:0.19
Consensus pattern (31 bp):
AACAAGGCAGAGTTCATAAAAAAGCTTCATC
Found at i:3908649 original size:23 final size:25
Alignment explanation
Indices: 3908623--3908676 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 25
3908613 AAATCCAGCA
3908623 AAGAAAAAT-AAAGCACTC-AAAAG
1 AAGAAAAATGAAAGCACTCAAAAAG
*
3908646 AAG-AAATTGAAAGCACTCAAAAAG
1 AAGAAAAATGAAAGCACTCAAAAAG
3908670 AAGAAAA
1 AAGAAAA
3908677 GCAAAGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 4 0.15
23 12 0.44
24 8 0.30
25 3 0.11
ACGTcount: A:0.65, C:0.11, G:0.15, T:0.09
Consensus pattern (25 bp):
AAGAAAAATGAAAGCACTCAAAAAG
Found at i:3908682 original size:24 final size:22
Alignment explanation
Indices: 3908627--3908682 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 22
3908617 CCAGCAAAGA
*
3908627 AAAATAAAGCACTCAAAAGAAG
1 AAAAGAAAGCACTCAAAAGAAG
*
3908649 AAATTGAAAGCACTCAAAAAGAAG
1 AAA-AGAAAGCACTC-AAAAGAAG
3908673 AAAAGCAAAG
1 AAAAG-AAAG
3908683 AAAACAAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 3 0.11
23 10 0.36
24 15 0.54
ACGTcount: A:0.62, C:0.12, G:0.16, T:0.09
Consensus pattern (22 bp):
AAAAGAAAGCACTCAAAAGAAG
Found at i:3915311 original size:27 final size:27
Alignment explanation
Indices: 3915259--3915311 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
3915249 CAAAAAAAAG
*
3915259 AAAAAATTCAGAAAAGGAAGGAAAGAA
1 AAAAAATTCAGAAAAGGAAAGAAAGAA
*
3915286 AAAAAATTCA-AAAAGAGAAAGCAAGA
1 AAAAAATTCAGAAAAG-GAAAGAAAGA
3915312 CAAGGAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.68, C:0.06, G:0.19, T:0.08
Consensus pattern (27 bp):
AAAAAATTCAGAAAAGGAAAGAAAGAA
Found at i:3919435 original size:22 final size:21
Alignment explanation
Indices: 3919398--3919438 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
3919388 CCATCTCTAT
3919398 TTCATCATCAACACCATCATC
1 TTCATCATCAACACCATCATC
*
3919419 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
3919439 ATTCTGCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.34, C:0.37, G:0.02, T:0.27
Consensus pattern (21 bp):
TTCATCATCAACACCATCATC
Found at i:3920256 original size:327 final size:327
Alignment explanation
Indices: 3919662--3920320 Score: 1318
Period size: 327 Copynumber: 2.0 Consensus size: 327
3919652 TACTTGTGGC
3919662 ATCAACCCTTTCCCCTTGATAATTCAGGTTCCAAGTTCTTATAACTAGTGGGTCAAAGTCCTTTA
1 ATCAACCCTTTCCCCTTGATAATTCAGGTTCCAAGTTCTTATAACTAGTGGGTCAAAGTCCTTTA
3919727 TACCACCCTTTAAAGAAGAAATATAAAGTATTGGTATTTGCTCTCTATAGCATTGGTTCTTCTTT
66 TACCACCCTTTAAAGAAGAAATATAAAGTATTGGTATTTGCTCTCTATAGCATTGGTTCTTCTTT
3919792 GAGTATTCTTTAAGATACTACCCTCACAACCATCCAATTGTTTCATTAACCAAACCCATAACAAT
131 GAGTATTCTTTAAGATACTACCCTCACAACCATCCAATTGTTTCATTAACCAAACCCATAACAAT
3919857 AGCAATTATCTTCCGCTTCCATCTCTCATTTATTAAACAACCTACTTATTCACCTATACGTTTAC
196 AGCAATTATCTTCCGCTTCCATCTCTCATTTATTAAACAACCTACTTATTCACCTATACGTTTAC
3919922 CACCCTTAACCATCTCATTTGAGTCATTCACTTATACAGGTTGTTTAGCTTCCTCCCTAGATCCA
261 CACCCTTAACCATCTCATTTGAGTCATTCACTTATACAGGTTGTTTAGCTTCCTCCCTAGATCCA
3919987 CA
326 CA
3919989 ATCAACCCTTTCCCCTTGATAATTCAGGTTCCAAGTTCTTATAACTAGTGGGTCAAAGTCCTTTA
1 ATCAACCCTTTCCCCTTGATAATTCAGGTTCCAAGTTCTTATAACTAGTGGGTCAAAGTCCTTTA
3920054 TACCACCCTTTAAAGAAGAAATATAAAGTATTGGTATTTGCTCTCTATAGCATTGGTTCTTCTTT
66 TACCACCCTTTAAAGAAGAAATATAAAGTATTGGTATTTGCTCTCTATAGCATTGGTTCTTCTTT
3920119 GAGTATTCTTTAAGATACTACCCTCACAACCATCCAATTGTTTCATTAACCAAACCCATAACAAT
131 GAGTATTCTTTAAGATACTACCCTCACAACCATCCAATTGTTTCATTAACCAAACCCATAACAAT
3920184 AGCAATTATCTTCCGCTTCCATCTCTCATTTATTAAACAACCTACTTATTCACCTATACGTTTAC
196 AGCAATTATCTTCCGCTTCCATCTCTCATTTATTAAACAACCTACTTATTCACCTATACGTTTAC
3920249 CACCCTTAACCATCTCATTTGAGTCATTCACTTATACAGGTTGTTTAGCTTCCTCCCTAGATCCA
261 CACCCTTAACCATCTCATTTGAGTCATTCACTTATACAGGTTGTTTAGCTTCCTCCCTAGATCCA
3920314 CA
326 CA
3920316 ATCAA
1 ATCAA
3920321 TCGATAAGGT
Statistics
Matches: 332, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
327 332 1.00
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.35
Consensus pattern (327 bp):
ATCAACCCTTTCCCCTTGATAATTCAGGTTCCAAGTTCTTATAACTAGTGGGTCAAAGTCCTTTA
TACCACCCTTTAAAGAAGAAATATAAAGTATTGGTATTTGCTCTCTATAGCATTGGTTCTTCTTT
GAGTATTCTTTAAGATACTACCCTCACAACCATCCAATTGTTTCATTAACCAAACCCATAACAAT
AGCAATTATCTTCCGCTTCCATCTCTCATTTATTAAACAACCTACTTATTCACCTATACGTTTAC
CACCCTTAACCATCTCATTTGAGTCATTCACTTATACAGGTTGTTTAGCTTCCTCCCTAGATCCA
CA
Found at i:3920806 original size:26 final size:26
Alignment explanation
Indices: 3920766--3920825 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
3920756 CCCTAGAACC
3920766 CCATGTGCGTGCCATATGACAAGCAA
1 CCATGTGCGTGCCATATGACAAGCAA
* *
3920792 CCATGTGTGTTCCATATGACAAGCAA
1 CCATGTGCGTGCCATATGACAAGCAA
3920818 CCATGTGC
1 CCATGTGC
3920826 CTTGCATGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (26 bp):
CCATGTGCGTGCCATATGACAAGCAA
Found at i:3921000 original size:31 final size:31
Alignment explanation
Indices: 3920962--3921023 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
3920952 TATTCTTTCT
3920962 TTATACCATAGTTATAATAATAGTTTACATA
1 TTATACCATAGTTATAATAATAGTTTACATA
3920993 TTATACCATAGTTATAATAATAGTTTACATA
1 TTATACCATAGTTATAATAATAGTTTACATA
3921024 CATTATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (31 bp):
TTATACCATAGTTATAATAATAGTTTACATA
Found at i:3922074 original size:422 final size:422
Alignment explanation
Indices: 3921270--3922102 Score: 1326
Period size: 422 Copynumber: 2.0 Consensus size: 422
3921260 TGGAGACTAC
* *
3921270 TGAGCTAGCTAGAGACCTTATTTCAGCTGGAGAGTTATACTACCATCACCACCACACAGAGCACT
1 TGAGCTAGCTAGAGACCTTATTTCAGCTGGAGAGTTACACCACCATCACCACCACACAGAGCACT
3921335 TCAAATATGATATAGATCAATTTTTGTTGATTCGTACCTTTTCGCGAAGAGTTGAAATTCCAAGA
66 TCAAATATGATATAGATCAATTTTTGTTGATTCGTACCTTTTCGCGAAGAGTTGAAATTCCAAGA
* * *
3921400 GGTGCCTTTTCACAAGGAGTTGTCCTAAGATTCACCTACATGTCCTTCATCTAAGGCCAGCTGAT
131 GGTGCCTTTTCACAAGGAGTTATCCTAAGACTCACCTACATGTCCTTCATCTAAGGCCAGCTCAT
*
3921465 CTTAAGCTCAAACACATGGAAAGTAGCTCAAATGATGAAAGGTTACCTTCTACAAATATGACCTT
196 CTTAAGCTCAAACACATGGAAAGTAGCTCAAATGATGAAAGGTTACCTTCTACAAATATGACATT
**
3921530 TCATAACAACTTCCTGTCCAATTGATGACATGTCATTCAGACACATGTTGGATGCCAAGTCACAC
261 TCATAACAACTTCCTACCCAATTGATGACATGTCATTCAGACACATGTTGGATGCCAAGTCACAC
* * *
3921595 CTAACTTTCTGCTTATATACACGCCATGAAGGAGCCAAATCATAAGCATCATATGCCTCCAATGT
326 CTAACTTGCTGCTTATATACACGCCATGAAGGAGCCAAACCATAAGCATCATATGCCTCCAATAT
3921660 GAGTGCCTAATGACCAGCCCATTCTGGACTTT
391 GAGTGCCTAATGACCAGCCCATTCTGGACTTT
* *
3921692 TGAGCTAGCTAGAGA-CTTCATTTCAGCTGGAGAGTTACACCATCATCACCACCACACAGAGCAT
1 TGAGCTAGCTAGAGACCTT-ATTTCAGCTGGAGAGTTACACCACCATCACCACCACACAGAGCAC
* * * * * * ***
3921756 TTCAATTATGGTCTAGGTTAATTTTTGTTGATTTGTACCTTTTCGCGAAGAGTTTCCATTCCAAG
65 TTCAAATATGATATAGATCAATTTTTGTTGATTCGTACCTTTTCGCGAAGAGTTGAAATTCCAAG
* *
3921821 AGGTGCCTTTTCACAAGGAGTTATCCTAAGACTCACCTATATGTCCTTCATCTAAGGCTAGCTCA
130 AGGTGCCTTTTCACAAGGAGTTATCCTAAGACTCACCTACATGTCCTTCATCTAAGGCCAGCTCA
* *
3921886 TCTTCAGCTCAAACATATGGAAAGTAGCTCAAATGATGAAAGGTTACCTTCTACAAATATGACAT
195 TCTTAAGCTCAAACACATGGAAAGTAGCTCAAATGATGAAAGGTTACCTTCTACAAATATGACAT
* * *
3921951 TTCATAACAAGTTCCTACCCAATTGATGACATGTCATTTAGACACATGTTGGATGCCAAGTCACG
260 TTCATAACAACTTCCTACCCAATTGATGACATGTCATTCAGACACATGTTGGATGCCAAGTCACA
* * * * * * *
3922016 TCTAACTTGCTGCTTATCTACACGCCATGCAGGAGCCACACCATATGCATCGTATGCCTCCCATA
325 CCTAACTTGCTGCTTATATACACGCCATGAAGGAGCCAAACCATAAGCATCATATGCCTCCAATA
3922081 TGAGTGCCTAATGACCAGCCCA
390 TGAGTGCCTAATGACCAGCCCA
3922103 CACATGTGCC
Statistics
Matches: 374, Mismatches: 36, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
421 3 0.01
422 371 0.99
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (422 bp):
TGAGCTAGCTAGAGACCTTATTTCAGCTGGAGAGTTACACCACCATCACCACCACACAGAGCACT
TCAAATATGATATAGATCAATTTTTGTTGATTCGTACCTTTTCGCGAAGAGTTGAAATTCCAAGA
GGTGCCTTTTCACAAGGAGTTATCCTAAGACTCACCTACATGTCCTTCATCTAAGGCCAGCTCAT
CTTAAGCTCAAACACATGGAAAGTAGCTCAAATGATGAAAGGTTACCTTCTACAAATATGACATT
TCATAACAACTTCCTACCCAATTGATGACATGTCATTCAGACACATGTTGGATGCCAAGTCACAC
CTAACTTGCTGCTTATATACACGCCATGAAGGAGCCAAACCATAAGCATCATATGCCTCCAATAT
GAGTGCCTAATGACCAGCCCATTCTGGACTTT
Found at i:3923479 original size:25 final size:25
Alignment explanation
Indices: 3923451--3923504 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
3923441 AAGCATTCAA
3923451 GGCTGATTTAATCATCCAAACCAAG
1 GGCTGATTTAATCATCCAAACCAAG
*
3923476 GGCTGATTTAATCATTCAAACCAAG
1 GGCTGATTTAATCATCCAAACCAAG
3923501 GGCT
1 GGCT
3923505 ATTCATATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (25 bp):
GGCTGATTTAATCATCCAAACCAAG
Found at i:3926232 original size:406 final size:406
Alignment explanation
Indices: 3925480--3926237 Score: 1074
Period size: 406 Copynumber: 1.9 Consensus size: 406
3925470 ACTTGAGCTG
** * *
3925480 GACTTTTAAGCTAGCTTGAGACCTTATTTCAGCTGGAGAGTTATACCACCATCACCACCACACAG
1 GACTTTTAAGCTAGCTAAAGACCTCATTTCAGCTGGAGAGTTACACCACCATCACCACCACACAG
* * * * * * ** *
3925545 AGCACTTTAAATGTGGTTTAGGTTAATTTTTTTTTATTCGAACCTTTTTGCGAAGAGTTGTCATT
66 AGCACTTCAAATATAGTCTAGGTCAATTTTTGTAGATTCGAACCTTTTTACGAAGAGTTGTCATT
* * * *
3925610 CCAAGAGGTTCCTTTTCAAAAGGAGTTATCCTAAGACTCACCTACATGTCCTTCATCTAAGGCCA
131 CCAAGAGGTGCCTTTTCAAAAGGAGCTATCCTAAGACTCACATACATGTCATTCATCTAAGGCCA
* * *
3925675 GCTCATCTTCAGCTCAAACACATGGAAAGTATATCAAATGATGAAAGGTTACCTTCTACAAATAT
196 GCTCATCTTCAGCTCAAACACATGGAAAATAGATCAAATGATGAAAGGTGACCTTCTACAAATAT
* * *
3925740 GACCTTTCATAAGAAGTTCCTGCCCAATTGATGACATGTCATTCAGACACATGTTGGATGTCAAG
261 GACATTTCATAACAAGTTCCTGCCCAATTGATGACATGTCATTCAGACACATGTTGGATGCCAAG
*
3925805 TCACGCCTAACTTGCTGCTTATCTACACACCATAAGCATCATATGCCTCCAATGCGAGTGCCTCA
326 TCACGCCTAACTTGATGCTTATCTACACACCATAAGCATCATATGCCTCCAATGCGAGTGCCTCA
3925870 TGACCAGACCACGCTA
391 TGACCAGACCACGCTA
* * *
3925886 GACTTTTGAGCTAGCTAAAGACCTCATTTCAG-TCGGAGAGTTACACTATCATCACCACCACACA
1 GACTTTTAAGCTAGCTAAAGACCTCATTTCAGCT-GGAGAGTTACACCACCATCACCACCACACA
* *
3925950 TAGCACTTCAAATATAGTCTAGGTCAATTTTTGTAGATTCGTA-CTTTTTCACGAAGAGTTG-CA
65 GAGCACTTCAAATATAGTCTAGGTCAATTTTTGTAGATTCGAACCTTTTT-ACGAAGAGTTGTC-
* * * * *
3926013 ATTCCGAA-AGGTGCCTTTTCACAAGTAGCTATCCTAATACTCACATATATGTCATTCATCTATG
128 ATTCC-AAGAGGTGCCTTTTCAAAAGGAGCTATCCTAAGACTCACATACATGTCATTCATCTAAG
* * *
3926077 GCCAGCTCATCTTCAGCTCAAACACATGGAAAATAGCTCAAATGATTAAAGGTGGCCTTCTACAA
192 GCCAGCTCATCTTCAGCTCAAACACATGGAAAATAGATCAAATGATGAAAGGTGACCTTCTACAA
* * * *
3926142 ATGTGACATTTCATAACAAGTTGCTGGCCAATTGATGACATGTCATTTAGACACATGTTGGATGC
257 ATATGACATTTCATAACAAGTTCCTGCCCAATTGATGACATGTCATTCAGACACATGTTGGATGC
*
3926207 CAAGTCATGCCTAACTTGATGCTTATCTACA
322 CAAGTCACGCCTAACTTGATGCTTATCTACA
3926238 GGCCATGTAG
Statistics
Matches: 306, Mismatches: 42, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
405 8 0.03
406 296 0.97
407 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (406 bp):
GACTTTTAAGCTAGCTAAAGACCTCATTTCAGCTGGAGAGTTACACCACCATCACCACCACACAG
AGCACTTCAAATATAGTCTAGGTCAATTTTTGTAGATTCGAACCTTTTTACGAAGAGTTGTCATT
CCAAGAGGTGCCTTTTCAAAAGGAGCTATCCTAAGACTCACATACATGTCATTCATCTAAGGCCA
GCTCATCTTCAGCTCAAACACATGGAAAATAGATCAAATGATGAAAGGTGACCTTCTACAAATAT
GACATTTCATAACAAGTTCCTGCCCAATTGATGACATGTCATTCAGACACATGTTGGATGCCAAG
TCACGCCTAACTTGATGCTTATCTACACACCATAAGCATCATATGCCTCCAATGCGAGTGCCTCA
TGACCAGACCACGCTA
Found at i:3929525 original size:15 final size:16
Alignment explanation
Indices: 3929493--3929534 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
3929483 GATTTCTTTA
3929493 TTATCTTATTTCATCTT
1 TTAT-TTATTTCATCTT
3929510 TTATTTATTT-ATCTT
1 TTATTTATTTCATCTT
*
3929525 TTGTTTATTT
1 TTATTTATTT
3929535 TATTCTTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 14 0.58
16 6 0.25
17 4 0.17
ACGTcount: A:0.17, C:0.10, G:0.02, T:0.71
Consensus pattern (16 bp):
TTATTTATTTCATCTT
Found at i:3929903 original size:9 final size:9
Alignment explanation
Indices: 3929889--3929913 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3929879 TTTTTTTTTC
3929889 AAAAAAACA
1 AAAAAAACA
3929898 AAAAAAACA
1 AAAAAAACA
3929907 AAAAAAA
1 AAAAAAA
3929914 AGGCAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAACA
Found at i:3929922 original size:13 final size:15
Alignment explanation
Indices: 3929906--3929943 Score: 53
Period size: 13 Copynumber: 2.6 Consensus size: 15
3929896 CAAAAAAAAC
3929906 AAAAAAAAA-GG-CA
1 AAAAAAAAAGGGCCA
3929919 AAAAAAAAAGGGCCA
1 AAAAAAAAAGGGCCA
3929934 AAAAACAAAA
1 AAAAA-AAAA
3929944 CAAAAAAGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.41
14 2 0.09
15 7 0.32
16 4 0.18
ACGTcount: A:0.76, C:0.11, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAGGGCCA
Found at i:3929923 original size:14 final size:15
Alignment explanation
Indices: 3929906--3929943 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
3929896 CAAAAAAAAC
3929906 AAAAAAAAAGG-CAA
1 AAAAAAAAAGGCCAA
*
3929920 AAAAAAAAGGGCCAA
1 AAAAAAAAAGGCCAA
3929935 AAAACAAAA
1 AAAA-AAAA
3929944 CAAAAAAGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.48
15 7 0.33
16 4 0.19
ACGTcount: A:0.76, C:0.11, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAGGCCAA
Found at i:3934232 original size:15 final size:16
Alignment explanation
Indices: 3934200--3934241 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
3934190 GATTTCTTTA
3934200 TTATCTTATTTCATCTT
1 TTAT-TTATTTCATCTT
3934217 TTATTTATTT-ATCTT
1 TTATTTATTTCATCTT
*
3934232 TTGTTTATTT
1 TTATTTATTT
3934242 TATTCTTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 14 0.58
16 6 0.25
17 4 0.17
ACGTcount: A:0.17, C:0.10, G:0.02, T:0.71
Consensus pattern (16 bp):
TTATTTATTTCATCTT
Found at i:3939104 original size:19 final size:19
Alignment explanation
Indices: 3939077--3939114 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3939067 AGTGCTTCAA
3939077 CTTTATTTCTTTTTCTTTT
1 CTTTATTTCTTTTTCTTTT
*
3939096 CTTTGTTTCTTTTTCTTTT
1 CTTTATTTCTTTTTCTTTT
3939115 TGAGTGCTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.79
Consensus pattern (19 bp):
CTTTATTTCTTTTTCTTTT
Found at i:3942961 original size:24 final size:24
Alignment explanation
Indices: 3942934--3942979 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3942924 TAGTGACCTC
**
3942934 TTTTTT-TTTTTTGCCTTTCTCTG
1 TTTTTTCTTTTTTTACTTTCTCTG
3942957 TTTTTTCTTTTTTTACTTTCTCT
1 TTTTTTCTTTTTTTACTTTCTCT
3942980 ACCTTCTCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.76
Consensus pattern (24 bp):
TTTTTTCTTTTTTTACTTTCTCTG
Found at i:3944996 original size:50 final size:50
Alignment explanation
Indices: 3944919--3945047 Score: 179
Period size: 50 Copynumber: 2.6 Consensus size: 50
3944909 TGTCCTATCG
*
3944919 AGCCCTCCTAGTCGCAA-CAAAATGGCAAACACAATAATATAGCTCTAACC
1 AGCCCTCCTAGTCGCAATGAAAA-GGCAAACACAATAATATAGCTCTAACC
*
3944969 AGCCCTCCTAGTCGCAATGAAAAGGCAAACACAATAATATGGCTCTAACC
1 AGCCCTCCTAGTCGCAATGAAAAGGCAAACACAATAATATAGCTCTAACC
* * * **
3945019 AACCCTCATATTCATAATGAAAAGGCAAA
1 AGCCCTCCTAGTCGCAATGAAAAGGCAAA
3945048 TTGGAGTGTG
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
50 67 0.94
51 4 0.06
ACGTcount: A:0.41, C:0.27, G:0.13, T:0.19
Consensus pattern (50 bp):
AGCCCTCCTAGTCGCAATGAAAAGGCAAACACAATAATATAGCTCTAACC
Found at i:3953442 original size:17 final size:17
Alignment explanation
Indices: 3953420--3953454 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3953410 CGAGTCCTTT
3953420 TAAGTTCCATAACAGCA
1 TAAGTTCCATAACAGCA
3953437 TAAGTTCCATAACAGCA
1 TAAGTTCCATAACAGCA
3953454 T
1 T
3953455 GTCCAGCTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (17 bp):
TAAGTTCCATAACAGCA
Found at i:3954341 original size:24 final size:22
Alignment explanation
Indices: 3954314--3954368 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 22
3954304 TTCAATTGGC
*
3954314 ACATTCTTTCAAATTTCAAGAGG
1 ACATTCTTTCAAATGTCAA-AGG
* *
3954337 TACATCCTTTGAAATGTCAAAGG
1 -ACATTCTTTCAAATGTCAAAGG
3954360 ACATGTCTT
1 ACAT-TCTT
3954369 ATTGATCACC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 4 0.15
23 6 0.23
24 16 0.62
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.35
Consensus pattern (22 bp):
ACATTCTTTCAAATGTCAAAGG
Found at i:3965679 original size:89 final size:89
Alignment explanation
Indices: 3965549--3965720 Score: 247
Period size: 89 Copynumber: 1.9 Consensus size: 89
3965539 ACACACCCTT
* * * *
3965549 TTATAGCCAAGTTACCCTAATTATATTAGGGTTTTATTATTTCAAATTAATTCAATATAGATTTA
1 TTATAGCCAAGTTACCATAATCATAATAGGGTTTTATTATTTCAAATTAATTAAATATAGATTTA
* *
3965614 ATTAATTGGAATTTAATAATCCTC
66 ATTAATTGAAATTAAATAATCCTC
* * *
3965638 TTATATCCAAGTTACCATAATCATAAT-GGGATTTTATTATTTCAAATTAATTAAATCTATATTT
1 TTATAGCCAAGTTACCATAATCATAATAGGG-TTTTATTATTTCAAATTAATTAAATATAGATTT
3965702 AATTAATTGAAATTAAATA
65 AATTAATTGAAATTAAATA
3965721 TTGGGGATTA
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
88 3 0.04
89 70 0.96
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.44
Consensus pattern (89 bp):
TTATAGCCAAGTTACCATAATCATAATAGGGTTTTATTATTTCAAATTAATTAAATATAGATTTA
ATTAATTGAAATTAAATAATCCTC
Found at i:3966928 original size:21 final size:21
Alignment explanation
Indices: 3966889--3966928 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3966879 AAGCATGATT
*
3966889 ATGATAGAATAGAATATATAA
1 ATGATAGAATAGAAGATATAA
* *
3966910 ATGATATAATATAAGATAT
1 ATGATAGAATAGAAGATAT
3966929 GGTAAGGAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (21 bp):
ATGATAGAATAGAAGATATAA
Found at i:3971384 original size:15 final size:16
Alignment explanation
Indices: 3971364--3971401 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
3971354 GATTAGAATA
3971364 AAATAAACAAAAGAT-
1 AAATAAACAAAAGATG
**
3971379 AAATAAACGGAAGATG
1 AAATAAACAAAAGATG
3971395 AAATAAA
1 AAATAAA
3971402 ATAATAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.68, C:0.05, G:0.13, T:0.13
Consensus pattern (16 bp):
AAATAAACAAAAGATG
Found at i:3975572 original size:23 final size:22
Alignment explanation
Indices: 3975546--3975597 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
3975536 AAATTTTGGC
3975546 TTTTTTTGTT-CTATTGTTTTTGT
1 TTTTTTTGTTGC-ATT-TTTTTGT
* *
3975569 TTTTTTTTTTGCCTTTTTTTGT
1 TTTTTTTGTTGCATTTTTTTGT
3975591 TTTTTTT
1 TTTTTTT
3975598 TTAAATAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 14 0.54
23 11 0.42
24 1 0.04
ACGTcount: A:0.02, C:0.06, G:0.10, T:0.83
Consensus pattern (22 bp):
TTTTTTTGTTGCATTTTTTTGT
Found at i:3977671 original size:24 final size:21
Alignment explanation
Indices: 3977636--3977678 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
3977626 GGCTCATTCT
*
3977636 TTTGAATTTCAAGAGGTACATTA
1 TTTGAATGTCAA-AGG-ACATTA
3977659 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
3977679 ATCTTGGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATTA
Found at i:3983203 original size:13 final size:13
Alignment explanation
Indices: 3983185--3983214 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3983175 ATACTATCCG
3983185 TTCATCACCATCT
1 TTCATCACCATCT
*
3983198 TTCATCACCATTT
1 TTCATCACCATCT
3983211 TTCA
1 TTCA
3983215 CGCCTATAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.33, G:0.00, T:0.43
Consensus pattern (13 bp):
TTCATCACCATCT
Found at i:3983669 original size:12 final size:11
Alignment explanation
Indices: 3983640--3983689 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
3983630 CTGTTGCAAC
*
3983640 AAAAGCAAA-A
1 AAAAGAAAAGA
3983650 AAAA-AAAAGA
1 AAAAGAAAAGA
*
3983660 AAGAAGAAAAACA
1 AA-AAG-AAAAGA
3983673 AAAAGAAAAGA
1 AAAAGAAAAGA
3983684 AAAAGA
1 AAAAGA
3983690 CTCCTACATC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
9 3 0.09
10 7 0.21
11 13 0.39
12 3 0.09
13 7 0.21
ACGTcount: A:0.82, C:0.04, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:3983676 original size:26 final size:26
Alignment explanation
Indices: 3983640--3983689 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
3983630 CTGTTGCAAC
*
3983640 AAAAGCAAAAA-AAAAAAAGAAAGAAG
1 AAAAACAAAAAGAAAAAAA-AAAGAAG
*
3983666 AAAAACAAAAAGAAAAGAAAAAGA
1 AAAAACAAAAAGAAAAAAAAAAGA
3983690 CTCCTACATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.82, C:0.04, G:0.14, T:0.00
Consensus pattern (26 bp):
AAAAACAAAAAGAAAAAAAAAAGAAG
Found at i:3983688 original size:6 final size:6
Alignment explanation
Indices: 3983647--3983689 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
3983637 AACAAAAGCA
* *
3983647 AAAAAA AAAAAG AAAGAAG AAAAAC AAAAAG -AAAAG AAAAAG A
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG A
3983690 CTCCTACATC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
5 5 0.16
6 21 0.66
7 6 0.19
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:3983938 original size:25 final size:24
Alignment explanation
Indices: 3983910--3983964 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
3983900 TTACTATTTC
*
3983910 ATTTCTTATT-CTTTCATCTTTTCTT
1 ATTTCTTATTACTTT-ATCCTTT-TT
3983935 ATTT-TTATTACTTTATCCTTTTT
1 ATTTCTTATTACTTTATCCTTTTT
3983958 -TTTCTTA
1 ATTTCTTA
3983965 ACCTTTTCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 3 0.11
23 5 0.19
24 11 0.41
25 8 0.30
ACGTcount: A:0.15, C:0.16, G:0.00, T:0.69
Consensus pattern (24 bp):
ATTTCTTATTACTTTATCCTTTTT
Found at i:3999431 original size:59 final size:59
Alignment explanation
Indices: 3999301--3999419 Score: 177
Period size: 59 Copynumber: 2.0 Consensus size: 59
3999291 GGAGAGTTGG
* ** * * *
3999301 TTAGAGCCATATTATCGAGTTTTCCTTTTCATTGTGACTAGGAGGGTTCTATATGACAC
1 TTAGAGCCATATTATCGAGTTTGCCTTTTCATTACGACTAGGAGGGTTCGATAGGACAA
3999360 TTAGAGCCATATTATCGAGTTTGCCTTTTCATTACGACTAGGAGGGTTCGATAGGA-AA
1 TTAGAGCCATATTATCGAGTTTGCCTTTTCATTACGACTAGGAGGGTTCGATAGGACAA
3999418 TT
1 TT
3999420 TATCCATATA
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
58 3 0.06
59 51 0.94
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (59 bp):
TTAGAGCCATATTATCGAGTTTGCCTTTTCATTACGACTAGGAGGGTTCGATAGGACAA
Found at i:4003336 original size:15 final size:15
Alignment explanation
Indices: 4003316--4003345 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4003306 ATGAATAATT
4003316 AAGAAAGGAAATGGA
1 AAGAAAGGAAATGGA
*
4003331 AAGAAATGAAATGGA
1 AAGAAAGGAAATGGA
4003346 TAAAATAGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.30, T:0.10
Consensus pattern (15 bp):
AAGAAAGGAAATGGA
Found at i:4004903 original size:6 final size:6
Alignment explanation
Indices: 4004880--4004923 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
4004870 GTTGTAGGAG
* *
4004880 TCTTTT TCTTTC TCTTTT TGTTTT TCTTCTT TCTTTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCTTTT T
4004924 GTTGCTTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
6 27 0.82
7 6 0.18
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:4004913 original size:25 final size:24
Alignment explanation
Indices: 4004880--4004926 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
4004870 GTTGTAGGAG
4004880 TCTTTTTCTTTCTCTTTTTGTTTT
1 TCTTTTTCTTTCTCTTTTTGTTTT
*
4004904 TCTTCTTTCTTTTTCTTTTTGTT
1 TCTT-TTTCTTTCTCTTTTTGTT
4004927 GCTTTTGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.79
Consensus pattern (24 bp):
TCTTTTTCTTTCTCTTTTTGTTTT
Found at i:4004914 original size:19 final size:18
Alignment explanation
Indices: 4004880--4004923 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
4004870 GTTGTAGGAG
4004880 TCTTTTTCTTTCTCTTTT
1 TCTTTTTCTTTCTCTTTT
* *
4004898 TGTTTTTCTTCTTTCTTTT
1 TCTTTTTCTT-TCTCTTTT
4004917 TCTTTTT
1 TCTTTTT
4004924 GTTGCTTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (18 bp):
TCTTTTTCTTTCTCTTTT
Found at i:4006471 original size:16 final size:17
Alignment explanation
Indices: 4006433--4006481 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
4006423 AAGATAGTGA
4006433 AATAAGAAAAAATGAAAG
1 AATAAG-AAAAATGAAAG
*
4006451 AATAA-AGAAATGAAATG
1 AATAAGAAAAATGAAA-G
4006468 -ATAAGAAAAATGAA
1 AATAAGAAAAATGAA
4006482 GATAACTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 13 0.48
17 9 0.33
18 5 0.19
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.14
Consensus pattern (17 bp):
AATAAGAAAAATGAAAG
Found at i:4006628 original size:5 final size:5
Alignment explanation
Indices: 4006610--4006652 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
4006600 TGCAACTTGC
*
4006610 TTCTT TTCCTT TTCTT TTCGTT TTCTT CT-TT TTCTT TTCTT TT
1 TTCTT TT-CTT TTCTT TTC-TT TTCTT TTCTT TTCTT TTCTT TT
4006653 GCACTCCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
4 3 0.09
5 20 0.61
6 10 0.30
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (5 bp):
TTCTT
Found at i:4008242 original size:16 final size:16
Alignment explanation
Indices: 4008216--4008257 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
4008206 GTGAAAAAAG
*
4008216 AAAAGATGAAA-GAATA
1 AAAAAATGAAATG-ATA
*
4008232 AAGAAATGAAATGATA
1 AAAAAATGAAATGATA
4008248 AAAAAATGAA
1 AAAAAATGAA
4008258 GATAACTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 21 0.95
17 1 0.05
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (16 bp):
AAAAAATGAAATGATA
Found at i:4008505 original size:7 final size:7
Alignment explanation
Indices: 4008441--4008502 Score: 76
Period size: 7 Copynumber: 9.1 Consensus size: 7
4008431 GTTGTAGGAG
4008441 TCTTT-T
1 TCTTTCT
4008447 TCTTTC-
1 TCTTTCT
*
4008453 TCTTTTT
1 TCTTTCT
*
4008460 GTTTTTCT
1 -TCTTTCT
4008468 TCTTTCT
1 TCTTTCT
4008475 TCTTTCT
1 TCTTTCT
4008482 TCTTTCT
1 TCTTTCT
4008489 TCTTTCT
1 TCTTTCT
4008496 T-TTTCT
1 TCTTTCT
4008502 T
1 T
4008503 TTTGTTTCTT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
6 16 0.33
7 28 0.57
8 5 0.10
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.76
Consensus pattern (7 bp):
TCTTTCT
Found at i:4008510 original size:10 final size:9
Alignment explanation
Indices: 4008441--4008514 Score: 51
Period size: 10 Copynumber: 7.7 Consensus size: 9
4008431 GTTGTAGGAG
4008441 TCTTTTTCTT
1 TCTTTTT-TT
*
4008451 TC-TCTTTT
1 TCTTTTTTT
* *
4008459 TGTTTTTCT
1 TCTTTTTTT
4008468 TCTTTCTTCTT
1 TCTTT-TT-TT
*
4008479 TCTTCTTTCT
1 TCTT-TTTTT
4008489 TCTTTCTTTT
1 TCTTT-TTTT
4008499 TCTTTTTGTT
1 TCTTTTT-TT
4008509 TCTTTT
1 TCTTTT
4008515 GTTGTAACAC
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
8 3 0.06
9 14 0.28
10 25 0.50
11 7 0.14
12 1 0.02
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (9 bp):
TCTTTTTTT
Found at i:4011475 original size:36 final size:35
Alignment explanation
Indices: 4011415--4011482 Score: 109
Period size: 36 Copynumber: 1.9 Consensus size: 35
4011405 GGTGGTTATT
*
4011415 TAGGCGTGAAATGGTGATATAAGATGGTAATGATA
1 TAGGCGTGAAATGGTGATAGAAGATGGTAATGATA
*
4011450 TAGGCGTGAAAATGGTGATGGAAGATGGTAATG
1 TAGGCGTG-AAATGGTGATAGAAGATGGTAATG
4011483 TTTAGGTAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 8 0.27
36 22 0.73
ACGTcount: A:0.35, C:0.03, G:0.35, T:0.26
Consensus pattern (35 bp):
TAGGCGTGAAATGGTGATAGAAGATGGTAATGATA
Found at i:4029467 original size:24 final size:21
Alignment explanation
Indices: 4029433--4029475 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
4029423 TCCACAAGAT
*
4029433 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
4029455 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
4029476 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:4030262 original size:25 final size:25
Alignment explanation
Indices: 4030228--4030287 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
4030218 CACCATGGAT
4030228 GCTCTTCATTGCTGTTTCTAAGGGA
1 GCTCTTCATTGCTGTTTCTAAGGGA
* *
4030253 GCTCTTCATTGTTGTTTCTATGGGA
1 GCTCTTCATTGCTGTTTCTAAGGGA
*
4030278 GTTCTTCATT
1 GCTCTTCATT
4030288 ACCCTATCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.13, C:0.18, G:0.22, T:0.47
Consensus pattern (25 bp):
GCTCTTCATTGCTGTTTCTAAGGGA
Found at i:4039143 original size:19 final size:20
Alignment explanation
Indices: 4039119--4039163 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
4039109 TTGTTTGCAA
4039119 TTTTTTGA-AATTTTGGCTT
1 TTTTTTGATAATTTTGGCTT
* **
4039138 TTTTTTTATTTTTTTGGCTT
1 TTTTTTGATAATTTTGGCTT
4039158 TTTTTT
1 TTTTTT
4039164 TTCCTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.09, C:0.04, G:0.11, T:0.76
Consensus pattern (20 bp):
TTTTTTGATAATTTTGGCTT
Found at i:4039144 original size:20 final size:20
Alignment explanation
Indices: 4039127--4039164 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4039117 AATTTTTTGA
4039127 AATTTTGGCTTTTTTTTTAT
1 AATTTTGGCTTTTTTTTTAT
**
4039147 TTTTTTGGCTTTTTTTTT
1 AATTTTGGCTTTTTTTTT
4039165 TCCTTTTTTT
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:0.08, C:0.05, G:0.11, T:0.76
Consensus pattern (20 bp):
AATTTTGGCTTTTTTTTTAT
Found at i:4039162 original size:13 final size:13
Alignment explanation
Indices: 4039146--4039178 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
4039136 TTTTTTTTTA
*
4039146 TTTTTTTGGCTTT
1 TTTTTTTGCCTTT
4039159 TTTTTTT-CCTTT
1 TTTTTTTGCCTTT
4039171 TTTTTTTG
1 TTTTTTTG
4039179 ATAAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (13 bp):
TTTTTTTGCCTTT
Found at i:4042154 original size:10 final size:10
Alignment explanation
Indices: 4042141--4042183 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
4042131 TTTTTTAAAA
4042141 TTTTGGTTTT
1 TTTTGGTTTT
*
4042151 TTTTGTTTTT
1 TTTTGGTTTT
***
4042161 TTTTTCATTT
1 TTTTGGTTTT
4042171 TTTTGGTTTT
1 TTTTGGTTTT
4042181 TTT
1 TTT
4042184 AGTTTTTTAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.02, C:0.02, G:0.12, T:0.84
Consensus pattern (10 bp):
TTTTGGTTTT
Found at i:4042190 original size:10 final size:9
Alignment explanation
Indices: 4042141--4042200 Score: 50
Period size: 9 Copynumber: 6.3 Consensus size: 9
4042131 TTTTTTAAAA
*
4042141 TTTTGGTTT
1 TTTTTGTTT
4042150 TTTTTGTTT
1 TTTTTGTTT
*
4042159 TTTTTTTCATT
1 TTTTTGT--TT
4042170 TTTTTGGTTT
1 TTTTT-GTTT
*
4042180 TTTTAGTTT
1 TTTTTGTTT
4042189 TTTATT-TTT
1 TTT-TTGTTT
4042198 TTT
1 TTT
4042201 AAAACAACAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
9 27 0.64
10 7 0.17
11 7 0.17
12 1 0.02
ACGTcount: A:0.05, C:0.02, G:0.10, T:0.83
Consensus pattern (9 bp):
TTTTTGTTT
Found at i:4042201 original size:17 final size:17
Alignment explanation
Indices: 4042158--4042201 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
4042148 TTTTTTTGTT
* *
4042158 TTTTTTTTCATTTTTTTG
1 TTTTTTTT-AGTTTTTTA
*
4042176 GTTTTTTTAGTTTTTTA
1 TTTTTTTTAGTTTTTTA
4042193 TTTTTTTTA
1 TTTTTTTTA
4042202 AAACAACAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.09, C:0.02, G:0.07, T:0.82
Consensus pattern (17 bp):
TTTTTTTTAGTTTTTTA
Found at i:4046761 original size:15 final size:17
Alignment explanation
Indices: 4046740--4046779 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
4046730 TGTCCTATGA
4046740 CTCATCTTCAT-GTCAG
1 CTCATCTTCATGGTCAG
4046756 -TCATC-T-ATGGTCAG
1 CTCATCTTCATGGTCAG
4046770 CTCATCTTCA
1 CTCATCTTCA
4046780 GCTTATACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 7
0.74 0.00 0.26
Matches are distributed among these distances:
13 2 0.10
14 6 0.30
15 10 0.50
16 1 0.05
17 1 0.05
ACGTcount: A:0.20, C:0.30, G:0.12, T:0.38
Consensus pattern (17 bp):
CTCATCTTCATGGTCAG
Found at i:4049027 original size:24 final size:24
Alignment explanation
Indices: 4049000--4049046 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
4048990 ATCAGAAAAG
* *
4049000 AAATTGAAGCACTCCAAAAGAAGT
1 AAATTCAAGCACTCAAAAAGAAGT
*
4049024 AAATTCCAGCACTCAAAAAGAAG
1 AAATTCAAGCACTCAAAAAGAAG
4049047 AAAAGTAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.51, C:0.19, G:0.15, T:0.15
Consensus pattern (24 bp):
AAATTCAAGCACTCAAAAAGAAGT
Found at i:4051268 original size:15 final size:16
Alignment explanation
Indices: 4051241--4051278 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
4051231 TTTGATAATT
*
4051241 AAAGAAA-TGAAATGG
1 AAAGAAATTGAAATAG
4051256 AAA-AAATTGAAATAG
1 AAAGAAATTGAAATAG
4051271 AAAGAAAT
1 AAAGAAAT
4051279 GTTATCAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 3 0.15
15 13 0.65
16 4 0.20
ACGTcount: A:0.66, C:0.00, G:0.18, T:0.16
Consensus pattern (16 bp):
AAAGAAATTGAAATAG
Found at i:4055509 original size:11 final size:11
Alignment explanation
Indices: 4055493--4055546 Score: 58
Period size: 11 Copynumber: 4.7 Consensus size: 11
4055483 TGTAGGAGTT
4055493 TTTTTTTTCTC
1 TTTTTTTTCTC
4055504 TTTTTTTT-T-
1 TTTTTTTTCTC
4055513 TGTTTTTTTCTTC
1 T-TTTTTTTC-TC
4055526 TTTCTTCTTTCTC
1 TTT-TT-TTTCTC
4055539 TTTTTTTT
1 TTTTTTTT
4055547 GTTACTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
9 1 0.03
10 8 0.22
11 11 0.30
12 5 0.14
13 8 0.22
14 4 0.11
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (11 bp):
TTTTTTTTCTC
Found at i:4057140 original size:21 final size:23
Alignment explanation
Indices: 4057092--4057138 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
4057082 CAAAGAAAGC
4057092 ATATATATATAATAATCTAAATA
1 ATATATATATAATAATCTAAATA
* *
4057115 ATATAATATATAATCATATAAATA
1 ATAT-ATATATAATAATCTAAATA
4057139 TATGGTTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (23 bp):
ATATATATATAATAATCTAAATA
Found at i:4062811 original size:15 final size:15
Alignment explanation
Indices: 4062791--4062836 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 15
4062781 TTTGATATCA
4062791 TTTCTTTCCATTTCC
1 TTTCTTTCCATTTCC
4062806 TTTCTTAT-CATTTCC
1 TTTCTT-TCCATTTCC
4062821 TTTCTTCTTCCATTTC
1 TTTC-T-TTCCATTTC
4062837 TTATTTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 17 0.63
16 3 0.11
17 7 0.26
ACGTcount: A:0.09, C:0.30, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTCTTTCCATTTCC
Found at i:4083670 original size:11 final size:11
Alignment explanation
Indices: 4083656--4083719 Score: 56
Period size: 11 Copynumber: 5.6 Consensus size: 11
4083646 AAATTTTGGA
4083656 TTTTTTGGCTTTT
1 TTTTTTGGC--TT
**
4083669 TTTTTTGTTTT
1 TTTTTTGGCTT
4083680 TTTTTTGGCTT
1 TTTTTTGGCTT
**
4083691 TTTTTTTCCTT
1 TTTTTTGGCTT
**
4083702 TTTTTTGTTTT
1 TTTTTTGGCTT
4083713 TTTTTTG
1 TTTTTTG
4083720 TTGTTTTTGA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
11 35 0.83
13 7 0.17
ACGTcount: A:0.00, C:0.06, G:0.11, T:0.83
Consensus pattern (11 bp):
TTTTTTGGCTT
Found at i:4083674 original size:13 final size:13
Alignment explanation
Indices: 4083656--4083697 Score: 70
Period size: 13 Copynumber: 3.4 Consensus size: 13
4083646 AAATTTTGGA
4083656 TTTTTTGGCTTTT
1 TTTTTTGGCTTTT
4083669 TTTTTT-G-TTTT
1 TTTTTTGGCTTTT
4083680 TTTTTTGGCTTTT
1 TTTTTTGGCTTTT
4083693 TTTTT
1 TTTTT
4083698 CCTTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 10 0.37
12 2 0.07
13 15 0.56
ACGTcount: A:0.00, C:0.05, G:0.12, T:0.83
Consensus pattern (13 bp):
TTTTTTGGCTTTT
Found at i:4083683 original size:24 final size:24
Alignment explanation
Indices: 4083656--4083727 Score: 89
Period size: 22 Copynumber: 3.2 Consensus size: 24
4083646 AAATTTTGGA
4083656 TTTTTTGGCTTTTTTTTTTGTTTT
1 TTTTTTGGCTTTTTTTTTTGTTTT
**
4083680 TTTTTTGGC-TTTTTTTTT-CCTT
1 TTTTTTGGCTTTTTTTTTTGTTTT
*
4083702 TTTTTT-G-TTTTTTTTTTGTTGT
1 TTTTTTGGCTTTTTTTTTTGTTTT
4083724 TTTT
1 TTTT
4083728 GAAAAAAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
21 10 0.24
22 13 0.32
23 9 0.22
24 9 0.22
ACGTcount: A:0.00, C:0.06, G:0.11, T:0.83
Consensus pattern (24 bp):
TTTTTTGGCTTTTTTTTTTGTTTT
Found at i:4083693 original size:33 final size:32
Alignment explanation
Indices: 4083649--4083719 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 32
4083639 TTTTTTGAAA
4083649 TTTTGGATTTTTTGGCTT-TTTTTTTTGTTTTTT
1 TTTTGGATTTTTT--CTTCTTTTTTTTGTTTTTT
* *
4083682 TTTTGGCTTTTTTTTTCCTTTTTTTTGTTTTTT
1 TTTTGGATTTTTTCTT-CTTTTTTTTGTTTTTT
4083715 TTTTG
1 TTTTG
4083720 TTGTTTTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 2 0.06
33 32 0.94
ACGTcount: A:0.01, C:0.06, G:0.13, T:0.80
Consensus pattern (32 bp):
TTTTGGATTTTTTCTTCTTTTTTTTGTTTTTT
Found at i:4083720 original size:11 final size:11
Alignment explanation
Indices: 4083665--4083727 Score: 74
Period size: 11 Copynumber: 5.6 Consensus size: 11
4083655 ATTTTTTGGC
4083665 TTTTTTTTTTG
1 TTTTTTTTTTG
4083676 TTTTTTTTTTGG
1 TTTTTTTTTT-G
*
4083688 CTTTTTTTTT-
1 TTTTTTTTTTG
**
4083698 CCTTTTTTTTG
1 TTTTTTTTTTG
4083709 TTTTTTTTTTG
1 TTTTTTTTTTG
4083720 TTGTTTTT
1 TT-TTTTT
4083728 GAAAAAAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
10 9 0.20
11 21 0.47
12 15 0.33
ACGTcount: A:0.00, C:0.05, G:0.10, T:0.86
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:4099254 original size:5 final size:5
Alignment explanation
Indices: 4099244--4099269 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
4099234 TATTATTATT
4099244 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
4099270 TTCTAAGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:4104226 original size:46 final size:46
Alignment explanation
Indices: 4104173--4104276 Score: 199
Period size: 46 Copynumber: 2.3 Consensus size: 46
4104163 GACACACCAT
4104173 CATTTGGCCAAGGTAAGAAAATGGCACCAAGATGAACAAGCATGCC
1 CATTTGGCCAAGGTAAGAAAATGGCACCAAGATGAACAAGCATGCC
4104219 CATTTGGCCAAGGTAAGAAAATGGCACCAAGATGAACAAGCATGCC
1 CATTTGGCCAAGGTAAGAAAATGGCACCAAGATGAACAAGCATGCC
*
4104265 CATTCGGCCAAG
1 CATTTGGCCAAG
4104277 AGAGATGTCT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 57 1.00
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (46 bp):
CATTTGGCCAAGGTAAGAAAATGGCACCAAGATGAACAAGCATGCC
Found at i:4106425 original size:24 final size:24
Alignment explanation
Indices: 4106398--4106443 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
4106388 AAACAAAGTG
*
4106398 AAGCACT-TAAAAGAAAGAAAAATC
1 AAGCACTCAAAAAG-AAGAAAAATC
4106422 AAGCACTCAAAAAGAAGAAAAA
1 AAGCACTCAAAAAGAAGAAAAA
4106444 CAAAGAAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.65, C:0.13, G:0.13, T:0.09
Consensus pattern (24 bp):
AAGCACTCAAAAAGAAGAAAAATC
Found at i:4107093 original size:12 final size:12
Alignment explanation
Indices: 4107076--4107105 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
4107066 CCCTAGAATG
4107076 GAAGAAAAAATC
1 GAAGAAAAAATC
4107088 GAAGAAAAAATC
1 GAAGAAAAAATC
4107100 GAAGAA
1 GAAGAA
4107106 GATGAGGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.67, C:0.07, G:0.20, T:0.07
Consensus pattern (12 bp):
GAAGAAAAAATC
Found at i:4121195 original size:19 final size:20
Alignment explanation
Indices: 4121159--4121201 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
4121149 TGAAACCCTT
*
4121159 TGAAAAAACATGATTTTTAA
1 TGAAAAAACATGAATTTTAA
*
4121179 TGAAAATACAT-AATTTTAA
1 TGAAAAAACATGAATTTTAA
4121198 TGAA
1 TGAA
4121202 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAAAACATGAATTTTAA
Found at i:4129508 original size:25 final size:26
Alignment explanation
Indices: 4129462--4129521 Score: 79
Period size: 25 Copynumber: 2.3 Consensus size: 26
4129452 AAAAAGAATG
* *
4129462 AAAAAGAGAAAAGAAGAGAAAAATT-
1 AAAAAGAAAAAAAAAGAGAAAAATTC
4129487 AGAAAAGAAAAAAAAAGA-AAAAATTC
1 A-AAAAGAAAAAAAAAGAGAAAAATTC
4129513 AAAAAGAAA
1 AAAAAGAAA
4129522 GCAAGCCAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 16 0.52
26 15 0.48
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.07
Consensus pattern (26 bp):
AAAAAGAAAAAAAAAGAGAAAAATTC
Found at i:4132448 original size:14 final size:11
Alignment explanation
Indices: 4132410--4132439 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
4132400 TCATCTAAGG
4132410 CCAGCTCACCA
1 CCAGCTCACCA
4132421 CCAGCTCACCA
1 CCAGCTCACCA
4132432 CCAGCTCA
1 CCAGCTCA
4132440 TTCACACCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.27, C:0.53, G:0.10, T:0.10
Consensus pattern (11 bp):
CCAGCTCACCA
Found at i:4142195 original size:709 final size:711
Alignment explanation
Indices: 4140837--4142253 Score: 2577
Period size: 709 Copynumber: 2.0 Consensus size: 711
4140827 ATCCTTGCAC
4140837 CTCCTCACAAATGTTCTGATTCATTTTAATATTCTTTTCTCGTCCATGCATGTCTTCATTAATTC
1 CTCCTCACAAATGTTCTGATTCATTTTAATATTCTTTTCTCGTCCATGCATGTCTTCATTAATTC
*
4140902 CTCCCATGCATAAGTCCTTTGAAGGAGATGAATGGTTGCAAATCCCGTATTAATTTCCAGCCTGC
66 CTCCCATGCATAAGTCCTTTGAAGGAGATGAATGGTAGCAAATCCCGTATTAATTTCCAGCCTGC
* * *
4140967 ACTGTCTTCATTAATCTAGGCATATCTAAAGCTCCCGATATCGGATTAATGTGATTAAAAATGCG
131 ACTGTCTTCAGTAATCTAGGCATATCTAAAGCTCCCGATATCAGATTAATGTGATTAAAAATGAG
* *
4141032 TTAGAAAGCTACGAGATAGGGGATTAAATGTTAAGAAGACTTCATCACCCAAATATTCTTGGAAC
196 TTAGAAAGCTACGAGATAGGGGATTAAATGTTAAGAAGACTTCATCACCCAAAGATGCTTGGAAC
*
4141097 ATGTTCAAATATGTAGATCAATCTGACTGACGTGAACTGTCCAACCAACTCTTCAATTGCCTTTA
261 ATGTTAAAATATGTAGATCAATCTGACTGACGTGAACTGTCCAACCAACTCTTCAATTGCCTTTA
4141162 GTCTTCTTAGCATCCAATGAACCTAGACAAAGTATGTAAACAAATAATTAGATAGGAATTGAGCT
326 GTCTTCTTAGCATCCAATGAACCTAGACAAAGTATGTAAACAAATAATTAGATAGGAATTGAGCT
* *
4141227 ATGATAATTATGAATGCATGCTTCCACCTATGTTAATAATGCAAATGATCTAACTATGAATGCAT
391 ATGATAATTATGAATGCATGCTTCCACCTATGTTAATAATGAAAATGAGCTAACTATGAATGCAT
4141292 ATGCATTGAATGAGTTATATAAAGATGCGAATTAATAAGTCATGCATGAATATCATATATTATAC
456 ATGCATTGAATGAGTTATATAAAGATGCGAATTAATAAGTCATGCATGAATATCATATATTATAC
4141357 ATATAAATGACAGCATATAATATTCAAGAAAAAATTAAGAATAAGATAAACATATTCACGTGACA
521 ATATAAATGACAGCATATAATATTCAAGAAAAAATTAAGAATAAGATAAACATATTCACGTGACA
4141422 TGTAATGCATAAATGAGTAAATAAATAATAAAATAAGGCAAGACTCCCTGAGAATCATCTTGGAA
586 TGTAATGCATAAATGAGTAAATAAATAATAAAATAAGGCAAGACTCCCTGAGAATCATCTTGGAA
*
4141487 GAACTTCAAAGTTGTGAGCATG-TTTGTTTGATCTTGGTGGTCGGTAGGATCACATCACAG
651 GAACTTCAAAGTTGTGAGCATGTTTTGTTTGAACTTGGTGGTCGGTAGGATCACATCACAG
* * *
4141547 CTCCTCACAAATGTTTTTATTCATTTTAATATTCTTTTCTCTTCCATGCATGTCTTCATTAATTC
1 CTCCTCACAAATGTTCTGATTCATTTTAATATTCTTTTCTCGTCCATGCATGTCTTCATTAATTC
*
4141612 CTCCCATGGATAAGTCCTTTGAAGGAGATGAATGGTAGCAAATCCCGTATTAATTTCCAGCCTGC
66 CTCCCATGCATAAGTCCTTTGAAGGAGATGAATGGTAGCAAATCCCGTATTAATTTCCAGCCTGC
* * *
4141677 ACTGTCTTCAGTAATCTAGGCATATCTCAAGCTCCCGGTATCAGATTAATGTGATTCAAAATGAG
131 ACTGTCTTCAGTAATCTAGGCATATCTAAAGCTCCCGATATCAGATTAATGTGATTAAAAATGAG
*
4141742 TTTGAAAGCTACGAGATAGGGGATTAAATGTTAAG-AGACTTCATCACCCAAAGATGCTTGGAAC
196 TTAGAAAGCTACGAGATAGGGGATTAAATGTTAAGAAGACTTCATCACCCAAAGATGCTTGGAAC
* * *
4141806 ATGTTAAAATATTTAGATCAATCTGACTGATGTGAACTGTCCAACCAACTCTTTAATTGCCTTTA
261 ATGTTAAAATATGTAGATCAATCTGACTGACGTGAACTGTCCAACCAACTCTTCAATTGCCTTTA
*
4141871 GTCTTCTTAGCTTCCAATGAACCTAGACAAAGTATGTAAACAAATAATTAGATAGGAATTGAGCT
326 GTCTTCTTAGCATCCAATGAACCTAGACAAAGTATGTAAACAAATAATTAGATAGGAATTGAGCT
4141936 ATGATAATTATGAATGCATGCTTCCACCTATGTTAATAATGAAAATGAGCTAACTATGAATGCAT
391 ATGATAATTATGAATGCATGCTTCCACCTATGTTAATAATGAAAATGAGCTAACTATGAATGCAT
*
4142001 ATGCATTGAATGAGTTATATAAAGATGTGAATTAATAAGTCATGCATGAATATCATATATTATAC
456 ATGCATTGAATGAGTTATATAAAGATGCGAATTAATAAGTCATGCATGAATATCATATATTATAC
* * *
4142066 ATATAAATGACAGCATATAATATTCAAGCAAAAATTAAGAATAAGATAAACATATTCACTTGATA
521 ATATAAATGACAGCATATAATATTCAAGAAAAAATTAAGAATAAGATAAACATATTCACGTGACA
*
4142131 TGTAATGCATAAATGAGTAAATAAATAATAAAATAAGGCAAGACTCCCTTAGAATCATCTTGGAA
586 TGTAATGCATAAATGAGTAAATAAATAATAAAATAAGGCAAGACTCCCTGAGAATCATCTTGGAA
4142196 GAACTTCAAAGTTGTGAGCATGTTTTGTTTGAACTTGGTGGTCGGTAGGATCACATCA
651 GAACTTCAAAGTTGTGAGCATGTTTTGTTTGAACTTGGTGGTCGGTAGGATCACATCA
4142254 TTGTAAGTCC
Statistics
Matches: 679, Mismatches: 27, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
709 427 0.63
710 252 0.37
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (711 bp):
CTCCTCACAAATGTTCTGATTCATTTTAATATTCTTTTCTCGTCCATGCATGTCTTCATTAATTC
CTCCCATGCATAAGTCCTTTGAAGGAGATGAATGGTAGCAAATCCCGTATTAATTTCCAGCCTGC
ACTGTCTTCAGTAATCTAGGCATATCTAAAGCTCCCGATATCAGATTAATGTGATTAAAAATGAG
TTAGAAAGCTACGAGATAGGGGATTAAATGTTAAGAAGACTTCATCACCCAAAGATGCTTGGAAC
ATGTTAAAATATGTAGATCAATCTGACTGACGTGAACTGTCCAACCAACTCTTCAATTGCCTTTA
GTCTTCTTAGCATCCAATGAACCTAGACAAAGTATGTAAACAAATAATTAGATAGGAATTGAGCT
ATGATAATTATGAATGCATGCTTCCACCTATGTTAATAATGAAAATGAGCTAACTATGAATGCAT
ATGCATTGAATGAGTTATATAAAGATGCGAATTAATAAGTCATGCATGAATATCATATATTATAC
ATATAAATGACAGCATATAATATTCAAGAAAAAATTAAGAATAAGATAAACATATTCACGTGACA
TGTAATGCATAAATGAGTAAATAAATAATAAAATAAGGCAAGACTCCCTGAGAATCATCTTGGAA
GAACTTCAAAGTTGTGAGCATGTTTTGTTTGAACTTGGTGGTCGGTAGGATCACATCACAG
Found at i:4145961 original size:13 final size:13
Alignment explanation
Indices: 4145943--4145973 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4145933 TGTTATAGGC
4145943 ATGAAAAATGGTG
1 ATGAAAAATGGTG
*
4145956 ATGAAAGATGGTG
1 ATGAAAAATGGTG
4145969 ATGAA
1 ATGAA
4145974 CAGATAGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.32, T:0.23
Consensus pattern (13 bp):
ATGAAAAATGGTG
Found at i:4146355 original size:19 final size:20
Alignment explanation
Indices: 4146317--4146359 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
4146307 GAAACTCCTT
*
4146317 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
4146337 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
4146356 TGAA
1 TGAA
4146360 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:4147102 original size:20 final size:21
Alignment explanation
Indices: 4147064--4147102 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
4147054 GATCATCTAG
* *
4147064 AAGCTAAGATAACATGTATAT
1 AAGCTAAGATAAAAGGTATAT
4147085 AAGCT-AGATAAAAGGTAT
1 AAGCTAAGATAAAAGGTAT
4147103 TGGACGTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.49, C:0.08, G:0.18, T:0.26
Consensus pattern (21 bp):
AAGCTAAGATAAAAGGTATAT
Found at i:4147376 original size:20 final size:19
Alignment explanation
Indices: 4147340--4147378 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
4147330 AATAAAGATG
**
4147340 TGAAAACATATGTTATGCA
1 TGAAAACATATAATATGCA
4147359 TGAAAATCATATAATATGCA
1 TGAAAA-CATATAATATGCA
4147379 AGTGAATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (19 bp):
TGAAAACATATAATATGCA
Found at i:4158511 original size:1 final size:1
Alignment explanation
Indices: 4158507--4158556 Score: 55
Period size: 1 Copynumber: 50.0 Consensus size: 1
4158497 ATAAAAAGTT
* * * * *
4158507 AAAAAAATAAAAAGAAAAAAAAAAAGAAAAAAAGAAAAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4158557 TTAAAGAGGG
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.90, C:0.00, G:0.08, T:0.02
Consensus pattern (1 bp):
A
Found at i:4158515 original size:16 final size:14
Alignment explanation
Indices: 4158485--4158555 Score: 67
Period size: 16 Copynumber: 5.0 Consensus size: 14
4158475 TCCAGGTTAG
*
4158485 TAAAAA-AATAAAA
1 TAAAAAGAAAAAAA
4158498 TAAAAAGTTAAAAAAA
1 TAAAAAG--AAAAAAA
4158514 TAAAAAG-AAAAAA
1 TAAAAAGAAAAAAA
4158527 -AAAAAGAAAAAAAGA
1 TAAAAAG-AAAAAA-A
*
4158542 AAAAAAGAAAAAAA
1 TAAAAAGAAAAAAA
4158556 ATTAAAGAGG
Statistics
Matches: 50, Mismatches: 1, Indels: 13
0.78 0.02 0.20
Matches are distributed among these distances:
12 6 0.12
13 12 0.24
14 6 0.12
15 7 0.14
16 19 0.38
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.08
Consensus pattern (14 bp):
TAAAAAGAAAAAAA
Found at i:4158517 original size:8 final size:8
Alignment explanation
Indices: 4158507--4158555 Score: 62
Period size: 8 Copynumber: 5.9 Consensus size: 8
4158497 ATAAAAAGTT
*
4158507 AAAAAAAT
1 AAAAAAAG
*
4158515 AAAAAGAAA
1 AAAAA-AAG
4158524 AAAAAAAAG
1 A-AAAAAAG
4158533 AAAAAAAG
1 AAAAAAAG
4158541 AAAAAAAG
1 AAAAAAAG
4158549 AAAAAAA
1 AAAAAAA
4158556 ATTAAAGAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
8 27 0.73
9 6 0.16
10 4 0.11
ACGTcount: A:0.90, C:0.00, G:0.08, T:0.02
Consensus pattern (8 bp):
AAAAAAAG
Found at i:4158530 original size:28 final size:28
Alignment explanation
Indices: 4158485--4158556 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 28
4158475 TCCAGGTTAG
*
4158485 TAAAAA-AATAAAATAAAAAGTTAAAAAA-A
1 TAAAAAGAA-AAAA-AAAAAG-AAAAAAAGA
4158514 TAAAAAGAAAAAAAAAAAGAAAAAAAGA
1 TAAAAAGAAAAAAAAAAAGAAAAAAAGA
*
4158542 AAAAAAGAAAAAAAA
1 TAAAAAGAAAAAAAA
4158557 TTAAAGAGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
27 6 0.15
28 21 0.54
29 10 0.26
30 2 0.05
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.08
Consensus pattern (28 bp):
TAAAAAGAAAAAAAAAAAGAAAAAAAGA
Found at i:4160488 original size:35 final size:37
Alignment explanation
Indices: 4160442--4160521 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
4160432 TTTGAGAATT
*
4160442 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
* *
4160477 TGGTGATGATATATGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
4160514 TGGTGATG
1 TGGTGATG
4160522 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 20 0.50
36 4 0.10
37 16 0.40
ACGTcount: A:0.28, C:0.04, G:0.36, T:0.33
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:4164547 original size:35 final size:37
Alignment explanation
Indices: 4164501--4164580 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
4164491 TTTGAGAATT
**
4164501 TGGTGATGATATAGGCGTGAT-A-TGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATTGAAGATGGACTA
*
4164536 TGGTGATGATATAGGCGTGATAATTGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATTGAAGATGGACTA
4164573 TGGTGATG
1 TGGTGATG
4164581 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 1 0.03
37 18 0.45
ACGTcount: A:0.28, C:0.04, G:0.36, T:0.33
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATTGAAGATGGACTA
Found at i:4171357 original size:19 final size:19
Alignment explanation
Indices: 4171333--4171377 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
4171323 TCGTTTGAAA
4171333 TTTTTTGAAATTTTGGTTT
1 TTTTTTGAAATTTTGGTTT
***
4171352 TTTTTTGTTTTTTTGGTTT
1 TTTTTTGAAATTTTGGTTT
4171371 TTTTTTG
1 TTTTTTG
4171378 GTTTTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.07, C:0.00, G:0.16, T:0.78
Consensus pattern (19 bp):
TTTTTTGAAATTTTGGTTT
Found at i:4171374 original size:12 final size:11
Alignment explanation
Indices: 4171343--4171387 Score: 69
Period size: 11 Copynumber: 4.4 Consensus size: 11
4171333 TTTTTTGAAA
4171343 TTTTGGTTTTT
1 TTTTGGTTTTT
4171354 TTTT-G--TTT
1 TTTTGGTTTTT
4171362 TTTTGGTTTTT
1 TTTTGGTTTTT
4171373 TTTTGGTTTTT
1 TTTTGGTTTTT
4171384 TTTT
1 TTTT
4171388 AAAATAGTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
8 7 0.23
9 1 0.03
10 1 0.03
11 22 0.71
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (11 bp):
TTTTGGTTTTT
Found at i:4171382 original size:19 final size:19
Alignment explanation
Indices: 4171343--4171384 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
4171333 TTTTTTGAAA
*
4171343 TTTTGGTTTTTTTTTGTTT
1 TTTTGGTTTTTTTTTGGTT
4171362 TTTTGGTTTTTTTTTGGTT
1 TTTTGGTTTTTTTTTGGTT
4171381 TTTT
1 TTTT
4171385 TTTAAAATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (19 bp):
TTTTGGTTTTTTTTTGGTT
Found at i:4173317 original size:17 final size:18
Alignment explanation
Indices: 4173295--4173330 Score: 56
Period size: 17 Copynumber: 2.0 Consensus size: 18
4173285 CCTTAAATTC
4173295 TTTCTTCTA-CCTTTCTA
1 TTTCTTCTATCCTTTCTA
4173312 TTTCTTCTATTCCTTTCTA
1 TTTCTTCTA-TCCTTTCTA
4173331 CCCTAACCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
19 8 0.47
ACGTcount: A:0.11, C:0.28, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTCTTCTATCCTTTCTA
Found at i:4175993 original size:19 final size:20
Alignment explanation
Indices: 4175969--4176008 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
4175959 TCCCTTTTCT
4175969 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
4175988 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
4176008 T
1 T
4176009 ATTATTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:4179648 original size:19 final size:21
Alignment explanation
Indices: 4179624--4179675 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
4179614 CGACCAAGAG
*
4179624 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
4179643 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
4179664 CATGTATTTTCA
1 CATGTATTTTCA
4179676 AAGGGGTTCC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:4180114 original size:19 final size:20
Alignment explanation
Indices: 4180090--4180129 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
4180080 TCCCTTTTCT
4180090 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
4180109 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
4180129 T
1 T
4180130 ATTATTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:4181733 original size:28 final size:28
Alignment explanation
Indices: 4181701--4181789 Score: 100
Period size: 28 Copynumber: 3.4 Consensus size: 28
4181691 GAAATGATTT
4181701 ATAATGATGCTGCCTTGATGTATATATG
1 ATAATGATGCTGCCTTGATGTATATATG
***
4181729 ATAATGATGCT-TAAT-ATG-AT-T-T-
1 ATAATGATGCTGCCTTGATGTATATATG
*
4181751 ATAATGATGTTGCCTTGATGTATATATG
1 ATAATGATGCTGCCTTGATGTATATATG
4181779 ATAATGATGCT
1 ATAATGATGCT
4181790 TGATATGATT
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
22 10 0.21
23 2 0.04
24 4 0.09
25 4 0.09
26 4 0.09
27 2 0.04
28 21 0.45
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (28 bp):
ATAATGATGCTGCCTTGATGTATATATG
Found at i:4181752 original size:50 final size:50
Alignment explanation
Indices: 4181694--4181803 Score: 195
Period size: 50 Copynumber: 2.2 Consensus size: 50
4181684 AACTAATGAA
4181694 ATGATTTATAATGATGCTGCCTTGATGTATATATGATAATGATGCTTAAT
1 ATGATTTATAATGATGCTGCCTTGATGTATATATGATAATGATGCTTAAT
* *
4181744 ATGATTTATAATGATGTTGCCTTGATGTATATATGATAATGATGCTTGAT
1 ATGATTTATAATGATGCTGCCTTGATGTATATATGATAATGATGCTTAAT
4181794 ATGA-TTATAA
1 ATGATTTATAA
4181804 GACTATCCTA
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
49 6 0.10
50 52 0.90
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.43
Consensus pattern (50 bp):
ATGATTTATAATGATGCTGCCTTGATGTATATATGATAATGATGCTTAAT
Found at i:4181802 original size:28 final size:28
Alignment explanation
Indices: 4181716--4181802 Score: 80
Period size: 25 Copynumber: 3.3 Consensus size: 28
4181706 GATGCTGCCT
*
4181716 TGATGTATATATGATAATGATGCTTAATA
1 TGAT-TATATATGATAATGATGCTTGATA
* *
4181745 TGATT-TATA--ATGATGTTGCCTTG--A
1 TGATTATATATGATAATGATG-CTTGATA
4181769 TG--TATATATGATAATGATGCTTGATA
1 TGATTATATATGATAATGATGCTTGATA
4181795 TGATTATA
1 TGATTATA
4181803 AGACTATCCT
Statistics
Matches: 45, Mismatches: 5, Indels: 17
0.67 0.07 0.25
Matches are distributed among these distances:
22 1 0.02
23 4 0.09
24 7 0.16
25 14 0.31
26 6 0.13
27 4 0.09
28 5 0.11
29 4 0.09
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (28 bp):
TGATTATATATGATAATGATGCTTGATA
Done.