Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 77 of 182
Found at i:24329118 original size:26 final size:26
Alignment explanation
Indices: 24329085--24329145 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
24329075 AATTCATTAT
* *
24329085 GAGCACAGATAATATTTAGCTCATAC
1 GAGCACAGACAATATTTAGCCCATAC
24329111 GAGCACAGACAATATTTAGCCCATAC
1 GAGCACAGACAATATTTAGCCCATAC
*
24329137 GAGCCCAGA
1 GAGCACAGA
24329146 ATGGTTAGCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (26 bp):
GAGCACAGACAATATTTAGCCCATAC
Found at i:24329161 original size:24 final size:24
Alignment explanation
Indices: 24329134--24329219 Score: 145
Period size: 24 Copynumber: 3.6 Consensus size: 24
24329124 ATTTAGCCCA
24329134 TACGAGCCCAGAATGGTTAGCTCT
1 TACGAGCCCAGAATGGTTAGCTCT
24329158 TACGAGCCCAGAATGGTTAGCTCT
1 TACGAGCCCAGAATGGTTAGCTCT
* *
24329182 TACGAGCCTAGAATGATTAGCTCT
1 TACGAGCCCAGAATGGTTAGCTCT
*
24329206 TACGAGCCTAGAAT
1 TACGAGCCCAGAAT
24329220 CAGAGTAACG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (24 bp):
TACGAGCCCAGAATGGTTAGCTCT
Found at i:24329162 original size:50 final size:48
Alignment explanation
Indices: 24329100--24329212 Score: 136
Period size: 48 Copynumber: 2.3 Consensus size: 48
24329090 CAGATAATAT
* * *
24329100 TTAGCTCATACGAGCACAGACAATATTTAGCCCATACGAGCCCAGAATGG
1 TTAGCTCTTACGAGCACAG--AATAGTTAGCCCATACGAGCCCAGAATGA
* * * * *
24329150 TTAGCTCTTACGAGCCCAGAATGGTTAGCTCTTACGAGCCTAGAATGA
1 TTAGCTCTTACGAGCACAGAATAGTTAGCCCATACGAGCCCAGAATGA
24329198 TTAGCTCTTACGAGC
1 TTAGCTCTTACGAGC
24329213 CTAGAATCAG
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
48 38 0.69
50 17 0.31
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (48 bp):
TTAGCTCTTACGAGCACAGAATAGTTAGCCCATACGAGCCCAGAATGA
Found at i:24329247 original size:27 final size:27
Alignment explanation
Indices: 24329215--24329280 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
24329205 TTACGAGCCT
*
24329215 AGAATCAGAGTAACGCTCTTTTGAACC
1 AGAATCAGAATAACGCTCTTTTGAACC
*
24329242 AGAATCAGAATAACGCTCTTTTGAGCC
1 AGAATCAGAATAACGCTCTTTTGAACC
*
24329269 AGAATTAGAATA
1 AGAATCAGAATA
24329281 CTCCTCAAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (27 bp):
AGAATCAGAATAACGCTCTTTTGAACC
Found at i:24337574 original size:14 final size:14
Alignment explanation
Indices: 24337555--24337587 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
24337545 ACTCATCTTA
24337555 GAAGATCAATGCTG
1 GAAGATCAATGCTG
24337569 GAAGATCAATGCTG
1 GAAGATCAATGCTG
24337583 GAAGA
1 GAAGA
24337588 AGAATGCAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.39, C:0.12, G:0.30, T:0.18
Consensus pattern (14 bp):
GAAGATCAATGCTG
Found at i:24337593 original size:14 final size:14
Alignment explanation
Indices: 24337555--24337594 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
24337545 ACTCATCTTA
*
24337555 GAAGATCAATGCTG
1 GAAGAACAATGCTG
*
24337569 GAAGATCAATGCTG
1 GAAGAACAATGCTG
*
24337583 GAAGAAGAATGC
1 GAAGAACAATGC
24337595 AGCGACAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.40, C:0.12, G:0.30, T:0.17
Consensus pattern (14 bp):
GAAGAACAATGCTG
Found at i:24359303 original size:6 final size:6
Alignment explanation
Indices: 24359292--24359338 Score: 58
Period size: 6 Copynumber: 7.5 Consensus size: 6
24359282 TCACCGTTTA
* *
24359292 TTCTTT TTCTTT TTCTTT CTTCTTT TTCTCTT TTTTTT TTGTTT TTC
1 TTCTTT TTCTTT TTCTTT -TTCTTT TTCT-TT TTCTTT TTCTTT TTC
24359339 AAGTGACTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
6 25 0.69
7 11 0.31
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (6 bp):
TTCTTT
Found at i:24359316 original size:13 final size:12
Alignment explanation
Indices: 24359292--24359338 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 12
24359282 TCACCGTTTA
24359292 TTCTTTTTCTTT
1 TTCTTTTTCTTT
24359304 TTCTTTCTTCTTT
1 TTCTTT-TTCTTT
*
24359317 TTCTCTTTTTTTT
1 TTCT-TTTTCTTT
*
24359330 TTGTTTTTC
1 TTCTTTTTC
24359339 AAGTGACTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 10 0.33
13 18 0.60
14 2 0.07
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (12 bp):
TTCTTTTTCTTT
Found at i:24359316 original size:19 final size:19
Alignment explanation
Indices: 24359292--24359338 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
24359282 TCACCGTTTA
24359292 TTCTTTTTCT-TTTTCTTTC
1 TTCTTTTTCTCTTTT-TTTC
*
24359311 TTCTTTTTCTCTTTTTTTT
1 TTCTTTTTCTCTTTTTTTC
*
24359330 TTGTTTTTC
1 TTCTTTTTC
24359339 AAGTGACTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 21 0.84
20 4 0.16
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (19 bp):
TTCTTTTTCTCTTTTTTTC
Found at i:24360379 original size:12 final size:12
Alignment explanation
Indices: 24360358--24360390 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
24360348 CCTGAGCAGG
24360358 TTTT-TCTTCTT
1 TTTTCTCTTCTT
24360369 TTTTCTCTTCTT
1 TTTTCTCTTCTT
*
24360381 CTTTCTCTTC
1 TTTTCTCTTC
24360391 CTCGTCTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTCTCTTCTT
Found at i:24369461 original size:38 final size:38
Alignment explanation
Indices: 24369410--24369487 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 38
24369400 TGTCCGAAAA
*
24369410 TATTGTCATCATACACCTTTGGAATGTTGCTAGCGCAT
1 TATTGTCATCATACACCTCTGGAATGTTGCTAGCGCAT
* *
24369448 TATTGTCATCATACACCTCTGGAATGTTGTTGGCGCAT
1 TATTGTCATCATACACCTCTGGAATGTTGCTAGCGCAT
24369486 TA
1 TA
24369488 CACAACCCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (38 bp):
TATTGTCATCATACACCTCTGGAATGTTGCTAGCGCAT
Found at i:24390037 original size:18 final size:18
Alignment explanation
Indices: 24390014--24390057 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
24390004 GCAGCTTGAC
*
24390014 CAGATGCAATCACAAATT
1 CAGATGCAATCACAAACT
* * *
24390032 CAGATGTAATCGCATACT
1 CAGATGCAATCACAAACT
24390050 CAGATGCA
1 CAGATGCA
24390058 GCCACAGGTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.23
Consensus pattern (18 bp):
CAGATGCAATCACAAACT
Found at i:24396241 original size:18 final size:18
Alignment explanation
Indices: 24396200--24396250 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
24396190 ATTGAGGCAG
24396200 AGGAAGAAGAAAGAA-AAA
1 AGGAAGAAG-AAGAAGAAA
* *
24396218 AAGAAGAAGAAGAAGAGA
1 AGGAAGAAGAAGAAGAAA
*
24396236 AGGAAGAGGAAGAAG
1 AGGAAGAAGAAGAAG
24396251 GAATTGCCAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 5 0.18
18 23 0.82
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (18 bp):
AGGAAGAAGAAGAAGAAA
Found at i:24396662 original size:17 final size:16
Alignment explanation
Indices: 24396632--24396665 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
24396622 ATGCATTTTA
24396632 TTTTTTGTCATTGCAT
1 TTTTTTGTCATTGCAT
*
24396648 TTTTATTGTCCTTGCAT
1 TTTT-TTGTCATTGCAT
24396665 T
1 T
24396666 GTAGTTGCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.12, C:0.15, G:0.12, T:0.62
Consensus pattern (16 bp):
TTTTTTGTCATTGCAT
Found at i:24396673 original size:11 final size:11
Alignment explanation
Indices: 24396659--24396701 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
24396649 TTTATTGTCC
24396659 TTGCATTGTAG
1 TTGCATTGTAG
*
24396670 TTGCATTTTCATAG
1 TTGCA--TT-GTAG
24396684 TTGCATTGTAG
1 TTGCATTGTAG
24396695 TTGCATT
1 TTGCATT
24396702 TCCATTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
11 15 0.56
12 2 0.07
13 2 0.07
14 8 0.30
ACGTcount: A:0.19, C:0.12, G:0.21, T:0.49
Consensus pattern (11 bp):
TTGCATTGTAG
Found at i:24402545 original size:29 final size:30
Alignment explanation
Indices: 24402495--24402552 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
24402485 GAGGAATTTG
* *
24402495 GGGATCAAAATCGAAGTTTTTGGAAAATTC
1 GGGATCAAAATAGAAGCTTTTGGAAAATTC
24402525 GGGATCAAAATAGAA-CTTTTGGAAAATT
1 GGGATCAAAATAGAAGCTTTTGGAAAATT
24402553 TGAAGTTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (30 bp):
GGGATCAAAATAGAAGCTTTTGGAAAATTC
Found at i:24402670 original size:29 final size:29
Alignment explanation
Indices: 24402584--24402819 Score: 148
Period size: 30 Copynumber: 8.1 Consensus size: 29
24402574 TGGAAATTTA
* * * *
24402584 AGGG-AAATATGGTAATTTTTAGATGCTC
1 AGGGTAAAAATGGTAATTTTTGGAAGTTC
*
24402612 AAGGGT-GAAATGGTAA-TTTTGGAAAAGTTC
1 -AGGGTAAAAATGGTAATTTTTGG--AAGTTC
* *
24402642 AGGGTCAAAATGGTAATTTTTGGATGTTC
1 AGGGTAAAAATGGTAATTTTTGGAAGTTC
** **
24402671 GAGGGTAAAAAAAGTGTTTTTTGGAAGTT-
1 -AGGGTAAAAATGGTAATTTTTGGAAGTTC
* ** *
24402700 TGGGGCAAAATGGTAATTTTTGTGAAGTTTG
1 AGGGTAAAAATGGTAATTTTTG-GAAG-TTC
* *
24402731 AGGGTTAAAAT-GTGATTTTTGGAAGTTC
1 AGGGTAAAAATGGTAATTTTTGGAAGTTC
* *
24402759 GAGGGTAAAAAT-GTATTTTTTGAGAAATTC
1 -AGGGTAAAAATGGTAATTTTTG-GAAGTTC
*
24402789 -GGGTGAAAATGGTAA--TTTGGAAAGTTC
1 AGGGTAAAAATGGTAATTTTTGG-AAGTTC
24402816 AGGG
1 AGGG
24402820 GTCGAAATAT
Statistics
Matches: 161, Mismatches: 32, Indels: 29
0.73 0.14 0.13
Matches are distributed among these distances:
26 1 0.01
27 9 0.06
28 34 0.21
29 51 0.32
30 52 0.32
31 14 0.09
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.35
Consensus pattern (29 bp):
AGGGTAAAAATGGTAATTTTTGGAAGTTC
Found at i:24402711 original size:88 final size:86
Alignment explanation
Indices: 24402614--24402837 Score: 251
Period size: 88 Copynumber: 2.6 Consensus size: 86
24402604 AGATGCTCAA
*
24402614 GGGTG-AAATGGTAATTTTGGAAAAGTTCAGGGTCAAAATGGTAATTTTTGGATGTTCGAGGGTA
1 GGGTGAAAATGGTAATTTTGG-AAAGTTCAGGGTCAAAAT-GTAATTTTTGGAAGTTCGAGGGT-
* * *
24402678 AAAAAAGTGTTTTTTG-GAAGTTT
63 AAAAAAGTATTTTTTGAGAAATTC
* * *
24402701 GGG-GCAAAATGGTAATTTTTGTG-AAGTTTGAGGGTTAAAATGTGATTTTTGGAAGTTCGAGGG
1 GGGTG-AAAATGGTAA-TTTTG-GAAAG-TTCAGGGTCAAAATGTAATTTTTGGAAGTTCGAGGG
*
24402764 TAAAAATGTATTTTTTGAGAAATTC
62 TAAAAAAGTATTTTTTGAGAAATTC
* *
24402789 GGGTGAAAATGGTAA-TTTGGAAAGTTCAGGGGTCGAAATATAATTTTTG
1 GGGTGAAAATGGTAATTTTGGAAAGTTCA-GGGTCAAAATGTAATTTTTG
24402838 AAAACTTTAG
Statistics
Matches: 115, Mismatches: 13, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
85 4 0.03
86 24 0.21
87 17 0.15
88 51 0.44
89 18 0.16
90 1 0.01
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.36
Consensus pattern (86 bp):
GGGTGAAAATGGTAATTTTGGAAAGTTCAGGGTCAAAATGTAATTTTTGGAAGTTCGAGGGTAAA
AAAGTATTTTTTGAGAAATTC
Found at i:24402777 original size:58 final size:60
Alignment explanation
Indices: 24402636--24402789 Score: 174
Period size: 58 Copynumber: 2.6 Consensus size: 60
24402626 AATTTTGGAA
* *
24402636 AAGTTC-AGGGTCAAAATGGTAATTTTTGGATGTTCGAGGGTAAAAAAAGTGTTTTTTGG
1 AAGTTCGAGGGTCAAAATGGTAATTTTTGGAAGTTCGAGGGTAAAAAAAGTGATTTTTGG
* * * *
24402695 AAGTTTG-GGG-CAAAATGGTAATTTTTGTGAAGTTTGAGGGT-TAAAATGTGATTTTTGG
1 AAGTTCGAGGGTCAAAATGGTAATTTTTG-GAAGTTCGAGGGTAAAAAAAGTGATTTTTGG
* * *
24402753 AAGTTCGAGGGTAAAAAT-GTATTTTTTGAGAAATTCG
1 AAGTTCGAGGGTCAAAATGGTAATTTTTG-GAAGTTCG
24402790 GGTGAAAATG
Statistics
Matches: 79, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
58 37 0.47
59 37 0.47
60 5 0.06
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.37
Consensus pattern (60 bp):
AAGTTCGAGGGTCAAAATGGTAATTTTTGGAAGTTCGAGGGTAAAAAAAGTGATTTTTGG
Found at i:24404665 original size:36 final size:33
Alignment explanation
Indices: 24404608--24404693 Score: 109
Period size: 36 Copynumber: 2.5 Consensus size: 33
24404598 TTAAATTTTA
*
24404608 AATTCAAATTTAAAAATAAATTTAAACTCAAAAAAT
1 AATTTAAATTT-AAAATAAATTTAAACT--AAAAAT
*
24404644 AAGTTTAAATTTAAAATAAATTTAAACTTAAAAT
1 AA-TTTAAATTTAAAATAAATTTAAACTAAAAAT
*
24404678 AATTTAAATTTTAAAT
1 AATTTAAATTTAAAAT
24404694 TTTAAAATTG
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
33 13 0.28
34 7 0.15
36 18 0.39
37 8 0.17
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.37
Consensus pattern (33 bp):
AATTTAAATTTAAAATAAATTTAAACTAAAAAT
Found at i:24404693 original size:16 final size:16
Alignment explanation
Indices: 24404639--24404693 Score: 74
Period size: 17 Copynumber: 3.3 Consensus size: 16
24404629 TTAAACTCAA
24404639 AAAATAAGTTTAAATTT
1 AAAATAA-TTTAAATTT
*
24404656 AAAATAAATTTAAACTT
1 AAAAT-AATTTAAATTT
24404673 AAAATAATTTAAATTT
1 AAAATAATTTAAATTT
*
24404689 TAAAT
1 AAAAT
24404694 TTTAAAATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
16 14 0.41
17 18 0.53
18 2 0.06
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (16 bp):
AAAATAATTTAAATTT
Found at i:24405328 original size:86 final size:85
Alignment explanation
Indices: 24405219--24405429 Score: 273
Period size: 85 Copynumber: 2.5 Consensus size: 85
24405209 AAGATGATTG
* * *
24405219 CCTCACTTGTTTTAATCCGCTTCTCTGTATCTCATCAGGAAAACGGATTTGGTCCACTTCTTTAT
1 CCTCACTTGTTTTAATCCACTTCTCTGTATCTCATCAGGAAAAC-AATTTGGTCCACTTCTCTAT
24405284 ATCTCATCAGGAAGCTGACCA
65 ATCTCATCAGGAAGCTGACCA
* * * *
24405305 CCTCATTTGTTTTAATTCACTTCTCTGTATCTCATCAGGAAGACAATTTGGTCCACTTCTCTGTA
1 CCTCACTTGTTTTAATCCACTTCTCTGTATCTCATCAGGAAAACAATTTGGTCCACTTCTCTATA
24405370 TCTCATCAGGAAGCTGACCA
66 TCTCATCAGGAAGCTGACCA
** * * * *
24405390 TTTTA-TTGCTTCAA-CCTACTTCTCAGTATCTCATCAGGAA
1 CCTCACTTGTTTTAATCC-ACTTCTCTGTATCTCATCAGGAA
24405430 GCTAGGGTTC
Statistics
Matches: 110, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
83 1 0.01
84 29 0.26
85 40 0.36
86 40 0.36
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.36
Consensus pattern (85 bp):
CCTCACTTGTTTTAATCCACTTCTCTGTATCTCATCAGGAAAACAATTTGGTCCACTTCTCTATA
TCTCATCAGGAAGCTGACCA
Found at i:24405389 original size:85 final size:86
Alignment explanation
Indices: 24405179--24405429 Score: 283
Period size: 86 Copynumber: 2.9 Consensus size: 86
24405169 TGTTTCATTG
** * * * *** *
24405179 ATTTGGTATACTTCTCTGTATCTCACCAAGAAGATGATTGCCTCACTTGTTTTAATCCGCTTCTC
1 ATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTGACCACCTCACTTGTTTTAATCCACTTCTC
*
24405244 TGTATCTCATCAGGAAAACGG
66 TGTATCTCATCAGGAAAACGA
* * * *
24405265 ATTTGGTCCACTTCTTTATATCTCATCAGGAAGCTGACCACCTCATTTGTTTTAATTCACTTCTC
1 ATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTGACCACCTCACTTGTTTTAATCCACTTCTC
*
24405330 TGTATCTCATCAGGAAGAC-A
66 TGTATCTCATCAGGAAAACGA
** * * *
24405350 ATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTGACCATTTTA-TTGCTTCAA-CCTACTTCT
1 ATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTGACCACCTCACTTGTTTTAATCC-ACTTCT
*
24405413 CAGTATCTCATCAGGAA
65 CTGTATCTCATCAGGAA
24405430 GCTAGGGTTC
Statistics
Matches: 140, Mismatches: 24, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
83 1 0.01
84 29 0.21
85 40 0.29
86 70 0.50
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.37
Consensus pattern (86 bp):
ATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTGACCACCTCACTTGTTTTAATCCACTTCTC
TGTATCTCATCAGGAAAACGA
Found at i:24405584 original size:172 final size:171
Alignment explanation
Indices: 24405360--24405792 Score: 670
Period size: 172 Copynumber: 2.5 Consensus size: 171
24405350 ATTTGGTCCA
* *
24405360 CTTCTCTGTATCTCATCAGGAAGCTGACCATTTTATTGCTTCAACCTACTTCTCAGTATCTCATC
1 CTTCTCTGTATCTCATCAGGAAGCTGACCATTTTATTGCTTCGACCTACTTCTCAGTATCTTATC
*
24405425 AGGAAGCTAGGGTTCGAAGTTT-GACTCACATTGAGCTTTGTTTCATTAATTTGGTATACTTCTC
66 AGGAAGCT-GGGTTCGAAGTTTCG-CTCACATTGAGCTTTGTTTCATTAATTTGATATACTTCTC
24405489 TCTATCTCACCAGGAACATGACCGCCTCACTTGTTTTAATCCG
129 TCTATCTCACCAGGAACATGACCGCCTCACTTGTTTTAATCCG
* * * * *
24405532 CTTCTTTGTATCTCATCAGGAAGATGATCATTTTATTGCTTCGACTTACTTCTCAGTACCTTATC
1 CTTCTCTGTATCTCATCAGGAAGCTGACCATTTTATTGCTTCGACCTACTTCTCAGTATCTTATC
* *
24405597 AGGAAGCTGGGGTCCGAAGTTTCGCTCACATTGAGCTTTGTTTCATTGATTTGATATACTTCTCT
66 AGGAAGCT-GGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATTAATTTGATATACTTCTCT
* * * *
24405662 GTATCTCATCAGGAAGATGACCGCCTCACTTGTTTTAATCTG
130 CTATCTCACCAGGAACATGACCGCCTCACTTGTTTTAATCCG
* * *
24405704 CTTCTCTGTATCTCATCAAGAAGCTGACCATTTTATTACTTCGACCTGCTTCTCAGTATCTTATC
1 CTTCTCTGTATCTCATCAGGAAGCTGACCATTTTATTGCTTCGACCTACTTCTCAGTATCTTATC
24405769 AGGAAGCTGGAGTTCGAAGTTTCG
66 AGGAAGCTGG-GTTCGAAGTTTCG
24405793 AACTTCTCTT
Statistics
Matches: 235, Mismatches: 24, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
171 2 0.01
172 232 0.99
173 1 0.00
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.37
Consensus pattern (171 bp):
CTTCTCTGTATCTCATCAGGAAGCTGACCATTTTATTGCTTCGACCTACTTCTCAGTATCTTATC
AGGAAGCTGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATTAATTTGATATACTTCTCTC
TATCTCACCAGGAACATGACCGCCTCACTTGTTTTAATCCG
Found at i:24406732 original size:39 final size:40
Alignment explanation
Indices: 24406634--24406784 Score: 144
Period size: 39 Copynumber: 3.7 Consensus size: 40
24406624 AATTTAAGCT
* *
24406634 GCCCTTTACGGGTTTTCAACTCAAACTTTCTTTGGTTTCAAGAC
1 GCCCTTTACGGGTTTTCAACTCAATCCTT-TTT--TTTCAA-AC
* * *
24406678 GCCCTTTGCGGGTTTTCATCTCAATCCTTTTTTTT-AAAG
1 GCCCTTTACGGGTTTTCAACTCAATCCTTTTTTTTCAAAC
* *
24406717 GCCCTTTACGGGTTTTCAACTCGAA-CCTTTTTTTTGAGAC
1 GCCCTTTACGGGTTTTCAACTC-AATCCTTTTTTTTCAAAC
** * *
24406757 GCCCTTTGTGGGTTTTCATCTCATTCCT
1 GCCCTTTACGGGTTTTCAACTCAATCCT
24406785 AGGAAAAATA
Statistics
Matches: 91, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
39 32 0.35
40 28 0.31
41 3 0.03
43 3 0.03
44 25 0.27
ACGTcount: A:0.16, C:0.25, G:0.17, T:0.42
Consensus pattern (40 bp):
GCCCTTTACGGGTTTTCAACTCAATCCTTTTTTTTCAAAC
Found at i:24406775 original size:79 final size:82
Alignment explanation
Indices: 24406634--24406784 Score: 227
Period size: 79 Copynumber: 1.9 Consensus size: 82
24406624 AATTTAAGCT
*
24406634 GCCCTTTACGGGTTTTCAACTCAAACTTTCTTTGGTTTCAAGACGCCCTTTGCGGGTTTTCATCT
1 GCCCTTTACGGGTTTTCAACTCAAACCTTCTTT-GTTTCAAGACGCCCTTTGCGGGTTTTCATCT
24406699 CAATCCTTTTTTTTAAAG
65 CAATCCTTTTTTTTAAAG
* * *
24406717 GCCCTTTACGGGTTTTCAACTCGAACCTT-TTT-TTT-GAGACGCCCTTTGTGGGTTTTCATCTC
1 GCCCTTTACGGGTTTTCAACTCAAACCTTCTTTGTTTCAAGACGCCCTTTGCGGGTTTTCATCTC
*
24406779 ATTCCT
66 AATCCT
24406785 AGGAAAAATA
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
79 30 0.48
80 3 0.05
82 3 0.05
83 27 0.43
ACGTcount: A:0.16, C:0.25, G:0.17, T:0.42
Consensus pattern (82 bp):
GCCCTTTACGGGTTTTCAACTCAAACCTTCTTTGTTTCAAGACGCCCTTTGCGGGTTTTCATCTC
AATCCTTTTTTTTAAAG
Found at i:24412967 original size:309 final size:309
Alignment explanation
Indices: 24412408--24414263 Score: 3649
Period size: 309 Copynumber: 6.0 Consensus size: 309
24412398 TTCATTATCC
* *
24412408 CTCTTTCTGGGAGCAGGCCTTTGGGTGTTTTCTCCAGCCTCAATCTTACCATTTTTAATTGCATT
1 CTCTTTCTAGGAGCAGGCCTTTGGGTGTTTTCTCCAACCTCAATCTTACCATTTTTAATTGCATT
*
24412473 TTCGATCATCTCCCCCAATATGACTATATCCGAAAAAATTTTAGTGGCATTTCCTAACAAATAAT
66 TTCGATCATCTCCCCCAATATGACTATATCCGAAAAAAATTTAGTGGCATTTCCTAACAAATAAT
24412538 TGAGATAAGGTGCCTTGAGAGTGTTAACCAACAACATCGTTGTTTCTTTTTCTGTTAGTGGTGGC
131 TGAGATAAGGTGCCTTGAGAGTGTTAACCAACAACATCGTTGTTTCTTTTTCTGTTAGTGGTGGC
24412603 TGCACCTGAGTTACCACATCTCGCCACCTCTATTCATACTGTCTGAAACTCTCATTTGATCTTTT
196 TGCACCTGAGTTACCACATCTCGCCACCTCTATTCATACTGTCTGAAACTCTCATTTGATCTTTT
24412668 CTCCATGTTTTGTAGTGTAAGTCGGTCAGGAGCTATTTCTGTTACATGG
261 CTCCATGTTTTGTAGTGTAAGTCGGTCAGGAGCTATTTCTGTTACATGG
24412717 CTCTTTCTAGGAGCAGGCCTTTGGGTGTTTTCTCCAACCTCAATCTTACCATTTTTAATTGCATT
1 CTCTTTCTAGGAGCAGGCCTTTGGGTGTTTTCTCCAACCTCAATCTTACCATTTTTAATTGCATT
24412782 TTCGATCATCTCCCCCAATATGACTATATCCGAAAAAAATTTAGTGGCATTTCCTAACAAATAAT
66 TTCGATCATCTCCCCCAATATGACTATATCCGAAAAAAATTTAGTGGCATTTCCTAACAAATAAT
24412847 TGAGATAAGGTGCCTTGAGAGTGTTAACCAACAACATCGTTGTTTCTTTTTCTGTTAGTGGTGGC
131 TGAGATAAGGTGCCTTGAGAGTGTTAACCAACAACATCGTTGTTTCTTTTTCTGTTAGTGGTGGC
24412912 TGCACCTGAGTTACCACATCTCGCCACCTCTATTCATACTGTCTGAAACTCTCATTTGATCTTTT
196 TGCACCTGAGTTACCACATCTCGCCACCTCTATTCATACTGTCTGAAACTCTCATTTGATCTTTT
24412977 CTCCATGTTTTGTAGTGTAAGTCGGTCAGGAGCTATTTCTGTTACATGG
261 CTCCATGTTTTGTAGTGTAAGTCGGTCAGGAGCTATTTCTGTTACATGG
24413026 CTCTTTCTAGGAGCAGGCCTTTGGGTGTTTTCTCCAACCTCAATCTTACCATTTTTAATTGCATT
1 CTCTTTCTAGGAGCAGGCCTTTGGGTGTTTTCTCCAACCTCAATCTTACCATTTTTAATTGCATT
*
24413091 TTCGATCATCTCCCCCAATATGACTATATCCGAAAAAATTTTAGTGGCATTTCCTAACAAATAAT
66 TTCGATCATCTCCCCCAATATGACTATATCCGAAAAAAATTTAGTGGCATTTCCTAACAAATAAT
24413156 TGAGATAAGGTGCCTTGAGAGTGTTAACCAACAACATCGTTGTTTCTTTTTCTGTTAGTGGTGGC
131 TGAGATAAGGTGCCTTGAGAGTGTTAACCAACAACATCGTTGTTTCTTTTTCTGTTAGTGGTGGC
24413221 TGCACCTGAGTTACCACATCTCGCCACCTCTATTCATACTGTCTGAAACTCTCATTTGATCTTTT
196 TGCACCTGAGTTACCACATCTCGCCACCTCTATTCATACTGTCTGAAACTCTCATTTGATCTTTT
24413286 CTCCATGTTTTGTAGTGTAAGTCGGTCAGGAGCTATTTCTGTTACATGG
261 CTCCATGTTTTGTAGTGTAAGTCGGTCAGGAGCTATTTCTGTTACATGG
24413335 CTCTTTCTAGGAGCAGGCCTTTGGGTGTTTTCTCCAACCTCAATCTTACCATTTTTAATTGCATT
1 CTCTTTCTAGGAGCAGGCCTTTGGGTGTTTTCTCCAACCTCAATCTTACCATTTTTAATTGCATT
24413400 TTCGATCATCTCCCCCAATATGACTATATCCGAAAAAAATTTAGTGGCATTTCCTAACAAATAAT
66 TTCGATCATCTCCCCCAATATGACTATATCCGAAAAAAATTTAGTGGCATTTCCTAACAAATAAT
24413465 TGAGATAAGGTGCCTTGAGAGTGTTAACCAACAACATCGTTGTTTCTTTTTCTGTTAGTGGTGGC
131 TGAGATAAGGTGCCTTGAGAGTGTTAACCAACAACATCGTTGTTTCTTTTTCTGTTAGTGGTGGC
24413530 TGCACCTGAGTTACCACATCTCGCCACCTCTATTCATACTGTCTGAAACTCTCATTTGATCTTTT
196 TGCACCTGAGTTACCACATCTCGCCACCTCTATTCATACTGTCTGAAACTCTCATTTGATCTTTT
24413595 CTCCATGTTTTGTAGTGTAAGTCGGTCAGGAGCTATTTCTGTTACATGG
261 CTCCATGTTTTGTAGTGTAAGTCGGTCAGGAGCTATTTCTGTTACATGG
24413644 CTCTTTCTAGGAGCAGGCCTTTGGGTGTTTTCTCCAACCTCAATCTTACCATTTTTAATTGCATT
1 CTCTTTCTAGGAGCAGGCCTTTGGGTGTTTTCTCCAACCTCAATCTTACCATTTTTAATTGCATT
*
24413709 TTCGATCATCTCCCCTAATATGACTATATCCGAAAAAAATTTAGTGGCATTTCCTAACAAATAAT
66 TTCGATCATCTCCCCCAATATGACTATATCCGAAAAAAATTTAGTGGCATTTCCTAACAAATAAT
24413774 TGAGATAAGGTGCCTTGAGAGTGTTAACCAACAACATCGTTGTTTCTTTTTCTGTTAGTGGTGGC
131 TGAGATAAGGTGCCTTGAGAGTGTTAACCAACAACATCGTTGTTTCTTTTTCTGTTAGTGGTGGC
24413839 TGCACCTGAGTTACCACATCTCGCCACCTCTATTCATACTGTCTGAAACTCTCATTTGATCTTTT
196 TGCACCTGAGTTACCACATCTCGCCACCTCTATTCATACTGTCTGAAACTCTCATTTGATCTTTT
24413904 CTCCATGTTTTGTAGTGTAAGTCGGTCAGGAGCTATTTCTGTTACATGG
261 CTCCATGTTTTGTAGTGTAAGTCGGTCAGGAGCTATTTCTGTTACATGG
24413953 CTCTTTCTAGGAGCAGGCCTTTGGGTGTTTTCTCCAACCTCAATCTTACCATTTTTAATTGCATT
1 CTCTTTCTAGGAGCAGGCCTTTGGGTGTTTTCTCCAACCTCAATCTTACCATTTTTAATTGCATT
*
24414018 TTTGATCATCTCCCCCAATATGACTATATCCGAAAAAAATTTAGTGGCATTTCCTAACAAATAAT
66 TTCGATCATCTCCCCCAATATGACTATATCCGAAAAAAATTTAGTGGCATTTCCTAACAAATAAT
*
24414083 TGAGATAAGGTACCTTGAGAGTGTTAACCAACAACATCGTTGTTTCTTTTTCTGTTAGTGGTGGC
131 TGAGATAAGGTGCCTTGAGAGTGTTAACCAACAACATCGTTGTTTCTTTTTCTGTTAGTGGTGGC
24414148 TGCACCTGAGTTACCACATCTCGCCACCTCTATTCATACTGTCTGAAACTCTCATTTGATCTTTT
196 TGCACCTGAGTTACCACATCTCGCCACCTCTATTCATACTGTCTGAAACTCTCATTTGATCTTTT
24414213 CTCCATGTTTTGTAGTGTAAGTCGGTCAGGAGCTATTTCTGTTACATGG
261 CTCCATGTTTTGTAGTGTAAGTCGGTCAGGAGCTATTTCTGTTACATGG
24414262 CT
1 CT
24414264 ATATTTCTTT
Statistics
Matches: 1538, Mismatches: 9, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
309 1538 1.00
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.37
Consensus pattern (309 bp):
CTCTTTCTAGGAGCAGGCCTTTGGGTGTTTTCTCCAACCTCAATCTTACCATTTTTAATTGCATT
TTCGATCATCTCCCCCAATATGACTATATCCGAAAAAAATTTAGTGGCATTTCCTAACAAATAAT
TGAGATAAGGTGCCTTGAGAGTGTTAACCAACAACATCGTTGTTTCTTTTTCTGTTAGTGGTGGC
TGCACCTGAGTTACCACATCTCGCCACCTCTATTCATACTGTCTGAAACTCTCATTTGATCTTTT
CTCCATGTTTTGTAGTGTAAGTCGGTCAGGAGCTATTTCTGTTACATGG
Found at i:24418595 original size:29 final size:30
Alignment explanation
Indices: 24418539--24418604 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
24418529 ATTTTTGAGG
*
24418539 AATTTGGGGATAAAAATCAAAGTTTTTGGAA
1 AATTT-GGGATAAAAATCAAAGCTTTTGGAA
* *
24418570 AATTTGGGATCAAAATCGAA-CTTTTGGAA
1 AATTTGGGATAAAAATCAAAGCTTTTGGAA
24418599 AATTTG
1 AATTTG
24418605 AAGTTGAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 14 0.44
30 13 0.41
31 5 0.16
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.33
Consensus pattern (30 bp):
AATTTGGGATAAAAATCAAAGCTTTTGGAA
Found at i:24418653 original size:29 final size:30
Alignment explanation
Indices: 24418561--24418861 Score: 110
Period size: 29 Copynumber: 10.3 Consensus size: 30
24418551 AAAATCAAAG
* *
24418561 TTTTTGGAAAATTTG-GGATCAAAATCG-AA
1 TTTTTGG-AAATTTGAGGGTCAAAATGGTAA
* * * * *
24418590 CTTTTGGAAAATTTGAAGTTGAAAAT-GTGA
1 TTTTTGG-AAATTTGAGGGTCAAAATGGTAA
*
24418620 CTTTTGGAAATTTGAGGGT-AAAATGGTAA
1 TTTTTGGAAATTTGAGGGTCAAAATGGTAA
*** * * *
24418649 TTTTTGGATGCTCGGGGGT-GAAATGGTAA
1 TTTTTGGAAATTTGAGGGTCAAAATGGTAA
*
24418678 -TTTTGGAAAAGTTT-AGGGTCAAAATGGCAA
1 TTTTTGG-AAA-TTTGAGGGTCAAAATGGTAA
* ** * *
24418708 TTTTTAGATGTTCGAGGG-CAAAATTGG-GA
1 TTTTTGGAAATTTGAGGGTCAAAA-TGGTAA
* * *
24418737 TTTTTGGAAGTATGAGGGTAAAAAT-GTAA
1 TTTTTGGAAATTTGAGGGTCAAAATGGTAA
* ** *
24418766 TTTTTGAGAAGTTCAAGGGT-AAAATTGTAA
1 TTTTTG-GAAATTTGAGGGTCAAAATGGTAA
* * * * *
24418796 -TTTTGGAAAGTTCAGAGTCGAAAT-ATAA
1 TTTTTGGAAATTTGAGGGTCAAAATGGTAA
* * *
24418824 TTTCTGGAAAGTTTG-GAGGTCAAAA-CGTGA
1 TTTTTGGAAA-TTTGAG-GGTCAAAATGGTAA
24418854 TTTTTGGA
1 TTTTTGGA
24418862 CAGTTCAATG
Statistics
Matches: 203, Mismatches: 51, Indels: 35
0.70 0.18 0.12
Matches are distributed among these distances:
28 23 0.11
29 108 0.53
30 67 0.33
31 5 0.02
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.35
Consensus pattern (30 bp):
TTTTTGGAAATTTGAGGGTCAAAATGGTAA
Found at i:24418704 original size:59 final size:57
Alignment explanation
Indices: 24418621--24418807 Score: 182
Period size: 59 Copynumber: 3.2 Consensus size: 57
24418611 AAAATGTGAC
* * *
24418621 TTTTGGAAA-TTTGAGGGTAAAATGGTAATTTTTGGATGCTCGGGGGTGAAATGGTAA
1 TTTTGGAAAGTTT-AGGGTAAAATGGTAATTTTTGGATGTTCGAGGGTAAAATGGTAA
* * * * *
24418678 TTTTGGAAAAGTTTAGGGTCAAAATGGCAATTTTTAGATGTTCGAGGGCAAAATTGGGAT
1 TTTTGG-AAAGTTTAGGGT-AAAATGGTAATTTTTGGATGTTCGAGGGTAAAA-TGGTAA
* * * *
24418738 TTTTGG-AAGTATGAGGGTAAAAAT-GTAATTTTTGAGAAGTTCAAGGGTAAAATTGTAA
1 TTTTGGAAAGT-TTAGGGT-AAAATGGTAATTTTTG-GATGTTCGAGGGTAAAATGGTAA
24418796 TTTTGGAAAGTT
1 TTTTGGAAAGTT
24418808 CAGAGTCGAA
Statistics
Matches: 105, Mismatches: 18, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
57 6 0.06
58 30 0.29
59 59 0.56
60 10 0.10
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (57 bp):
TTTTGGAAAGTTTAGGGTAAAATGGTAATTTTTGGATGTTCGAGGGTAAAATGGTAA
Found at i:24420622 original size:6 final size:6
Alignment explanation
Indices: 24420585--24420692 Score: 53
Period size: 6 Copynumber: 18.3 Consensus size: 6
24420575 GACCTTTTAA
* * * * *
24420585 TTAAATT TTAAAT TCAAAT TCAAA- ATAAAT TTAAAT TTAAAA ATAAAT
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
** * * * * *
24420633 TTAAACT CAAAAA ATAAGT TTAAAT TTAAA- ATAAAT TTAAAC TTAAA-
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
24420680 ATAAA- TTAAAT TT
1 TTAAAT TTAAAT TT
24420693 TAAAATTTTA
Statistics
Matches: 75, Mismatches: 22, Indels: 9
0.71 0.21 0.08
Matches are distributed among these distances:
5 15 0.20
6 51 0.68
7 9 0.12
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.38
Consensus pattern (6 bp):
TTAAAT
Found at i:24420695 original size:17 final size:17
Alignment explanation
Indices: 24420593--24420698 Score: 115
Period size: 17 Copynumber: 6.1 Consensus size: 17
24420583 AATTAAATTT
* *
24420593 TAAATTCAAATTCAAAA
1 TAAATTTAAATTTAAAA
24420610 TAAATTTAAATTTAAAAA
1 TAAATTTAAATTT-AAAA
**
24420628 TAAATTTAAACTCAAAAAA
1 TAAATTTAAA-T-TTAAAA
*
24420647 TAAGTTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
24420664 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
24420681 TAAA-TTAAATTTTAAAA
1 TAAATTTAAA-TTTAAAA
24420698 T
1 T
24420699 TTTAAAATTG
Statistics
Matches: 75, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
16 5 0.07
17 41 0.55
18 15 0.20
19 14 0.19
ACGTcount: A:0.58, C:0.05, G:0.01, T:0.36
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:24422627 original size:16 final size:19
Alignment explanation
Indices: 24422576--24422627 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 19
24422566 CTTTGGCTTT
24422576 CTTCTTCTTCTTCTTTGCA
1 CTTCTTCTTCTTCTTTGCA
24422595 CTTCTTCTTCTTATCTTTGCA
1 CTTCTTCTTC-T-TCTTTGCA
24422616 CTT-TCTCTTCTT
1 CTTCT-TCTTCTT
24422628 GTCCTTCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 11 0.37
20 3 0.10
21 16 0.53
ACGTcount: A:0.06, C:0.31, G:0.04, T:0.60
Consensus pattern (19 bp):
CTTCTTCTTCTTCTTTGCA
Found at i:24432122 original size:71 final size:70
Alignment explanation
Indices: 24432006--24432139 Score: 196
Period size: 71 Copynumber: 1.9 Consensus size: 70
24431996 AAAACGGTCT
* *
24432006 GATGGTTGAGATCTTGCATTTGTTGCGGATTCACTACAGCATCGTGAGTCACTATAAAGTGAAAC
1 GATGGTTGAGATCCTACATTTGTTGCGGATTCACTACAGCATCGTGAGTCACTA-AAAGTGAAAC
24432071 TGGTTC
65 TGGTTC
* * * * *
24432077 GATGGTTGAGATCCTACATTTTTTGCTGATTCTCTACAGCATCGTGATTCACTAAATGTGAAA
1 GATGGTTGAGATCCTACATTTGTTGCGGATTCACTACAGCATCGTGAGTCACTAAAAGTGAAA
24432140 TGAATCCATG
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
70 8 0.14
71 48 0.86
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.34
Consensus pattern (70 bp):
GATGGTTGAGATCCTACATTTGTTGCGGATTCACTACAGCATCGTGAGTCACTAAAAGTGAAACT
GGTTC
Found at i:24433029 original size:21 final size:20
Alignment explanation
Indices: 24433005--24433043 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
24432995 TAAAAGAATG
*
24433005 ACTTGTATCGGTAGATGTCTC
1 ACTTATATCGGTAG-TGTCTC
24433026 ACTTATATCGGTAGTGTC
1 ACTTATATCGGTAGTGTC
24433044 ATAGGTATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (20 bp):
ACTTATATCGGTAGTGTCTC
Found at i:24434836 original size:16 final size:17
Alignment explanation
Indices: 24434810--24434841 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
24434800 ATTTTTTCTA
24434810 CTTTCTCTTTTTCTTTG
1 CTTTCTCTTTTTCTTTG
24434827 CTTTCT-TTTTTCTTT
1 CTTTCTCTTTTTCTTT
24434842 TTTTTATATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.00, C:0.22, G:0.03, T:0.75
Consensus pattern (17 bp):
CTTTCTCTTTTTCTTTG
Found at i:24435454 original size:17 final size:17
Alignment explanation
Indices: 24435429--24435471 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
24435419 AATTGAACTA
*
24435429 ACAAGTAAAATGCAACG
1 ACAACTAAAATGCAACG
*
24435446 ACAACTAAAATGCAATG
1 ACAACTAAAATGCAACG
*
24435463 ACAATTAAA
1 ACAACTAAA
24435472 TGAGATGCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.56, C:0.16, G:0.12, T:0.16
Consensus pattern (17 bp):
ACAACTAAAATGCAACG
Found at i:24435905 original size:18 final size:16
Alignment explanation
Indices: 24435870--24435914 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 16
24435860 GGGCAACATC
24435870 TTCTTCCTCTT-TGTT
1 TTCTTCCTCTTCTGTT
24435885 TTCTTCCTCTTCTGGTCT
1 TTCTTCCTCTTCT-GT-T
*
24435903 TTCTTCTTCTTC
1 TTCTTCCTCTTC
24435915 ATTCACCTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 11 0.42
16 1 0.04
17 2 0.08
18 12 0.46
ACGTcount: A:0.00, C:0.31, G:0.07, T:0.62
Consensus pattern (16 bp):
TTCTTCCTCTTCTGTT
Found at i:24441846 original size:18 final size:18
Alignment explanation
Indices: 24441811--24441846 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
24441801 ATCTTGTGGC
*
24441811 TGCATCTGGTTGTATGAT
1 TGCATCTGGTTCTATGAT
*
24441829 TGCATCTGGTTCTGTGAT
1 TGCATCTGGTTCTATGAT
24441847 CACATCTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.14, G:0.28, T:0.44
Consensus pattern (18 bp):
TGCATCTGGTTCTATGAT
Found at i:24447945 original size:13 final size:13
Alignment explanation
Indices: 24447927--24447959 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
24447917 AAATAATAAA
24447927 AAAATCACTTAAC
1 AAAATCACTTAAC
24447940 AAAATCACTTAAC
1 AAAATCACTTAAC
24447953 AAAATCA
1 AAAATCA
24447960 TCAAATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.58, C:0.21, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAATCACTTAAC
Found at i:24453548 original size:18 final size:18
Alignment explanation
Indices: 24453527--24453561 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
24453517 CAATTATTCT
24453527 TTTTTACTTAA-CTGTTTG
1 TTTTTAC-TAATCTGTTTG
24453545 TTTTTACTAATCTGTTT
1 TTTTTACTAATCTGTTT
24453562 TAACTTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.17, C:0.11, G:0.09, T:0.63
Consensus pattern (18 bp):
TTTTTACTAATCTGTTTG
Found at i:24468500 original size:559 final size:557
Alignment explanation
Indices: 24467427--24469180 Score: 2227
Period size: 559 Copynumber: 3.1 Consensus size: 557
24467417 ATGCGTTACA
* * * *
24467427 ACATGTAATTTAATTAAATCGCCAAGCAGATGAAGTTCTCTCTTGCATTTACATGCACTCATTAA
1 ACATGTAATTTAATGAAATCGCCAAGCAGATGAAGTCCTCTCTTGCAATTACATGTACTCATTAA
* * * * * * * *
24467492 ATTAATCGCCGAAATCCAAAAGCAACAATAAAAATACACTACCAATAATTA-AGAGAAAATGTTC
66 ATTACTCTCTGAAACCCAAAAGCAATAACAAAATTACACTACCAATAATTACA-AGAAAATGTTT
* * *
24467556 CAATCTTCCCCGGGATACAATGCATATCTACCACGAAGTAGAAGAAGAACATCACATGTAACAAA
130 CAATCTTCCCCGGGATACTATACATATCTACCACAAAGTAGAAGAAGAACATCACATGTAACAAA
** * * ** *** *
24467621 GCATATCAGGCCCTAAAATTTGTGACTATTTGCAGGTTTATGCAATCCAACTAGCAAACTTAAAA
195 GCATATCAATCCCTAAAATTAGTGTCTATTTGGTGGTTTATGCAATCTTGCTAGCCAACTTAAAA
* *
24467686 G-GTTTCCACAATATGGGTATGGAGCTCCCAAAGTCCAACATTGTTACCTACTCATGACAGATAA
260 GAG-TTCCACAATATGGGTATGGAGCTCCCAAAGCCCAACATTG---CCTACTTATGACAGATAA
* * *
24467750 TATCCCTTTTATCCATGGTGCTTGCTCCTGCAAGGTAGGTTTGCTTCTTAAAGCAACCTCCGAAT
321 TATCCCTTTTAGCCATGGTGCTTGCTCTTGCAAGGTAGGTTTGCTTATTAAAGCAACCT-CGAAT
* * *
24467815 G-TGGTAATTTTTGTTTCTTTTAGGGCCTGATATGCTGTGTTACATGTGATGTTCTTCTTCTACT
385 GCT-GTAATTATTGTTTCTTTTAGGGCTTGATATGCTTTGTTACATGTGATGTTCTTCTTCTACT
* * * ** *
24467879 TTGTTGTAGATATGTATAGTATCCCAGGGGAAGAGTGGAATATTTTCTCCAGATTTTTGGTAGTG
449 TTGTTGTAGATATGTATAGTATCCC-GAGGAAGACTGGAACATTTTCTCTTGATTATTGGTAGTG
* * *
24467944 TAATTTTATTGTTGCTTTTGGATTTCAGAGAGTAATTCAATGAGT
513 TAATTTTATTGTTGCTTTTGGGTTTCAGAGAGTAATTTAACGAGT
* * *
24467989 ACATGTAATTTAATGAAATCGCCAAGTAGAT-AATGTCCTTTCTTGCAATTACATGTAATCATTA
1 ACATGTAATTTAATGAAATCGCCAAGCAGATGAA-GTCCTCTCTTGCAATTACATGTACTCATTA
* *
24468053 AATTACTCTCTAAAACCCAAAAGCAATAGCAAAATTACACTACCAATAATTACAAGAAAATGTTT
65 AATTACTCTCTGAAACCCAAAAGCAATAACAAAATTACACTACCAATAATTACAAGAAAATGTTT
* * * * *
24468118 CAATCTTCCCCGAGGATACTATACATATCTACCACAAATTAAAAAAAGAACATCACAGGTAATAA
130 CAATCTTCCCCG-GGATACTATACATATCTACCACAAAGTAGAAGAAGAACATCACATGTAACAA
* * *
24468183 AGCATACCAATCCCTAAAATTGGTGTCAATTTGGTGGTTTATGCAATCTTGCTAGCCAACTTAAA
194 AGCATATCAATCCCTAAAATTAGTGTCTATTTGGTGGTTTATGCAATCTTGCTAGCCAACTTAAA
*
24468248 AGAGTTCCACAATATGGGTATGGAGCTCCCAAAGCCCAACATTG-CTGCTTATGACAGATAATAA
259 AGAGTTCCACAATATGGGTATGGAGCTCCCAAAGCCCAACATTGCCTACTTATGACAGATAAT-A
* * * **
24468312 T-CTTTTTAGCCATGGTGCTTGGTCTTGCAAGGTAGGTTTTCTTATTAAAGCTTCCATCGAATGC
323 TCCCTTTTAGCCATGGTGCTTGCTCTTGCAAGGTAGGTTTGCTTATTAAAGCAACC-TCGAATGC
* * * *
24468376 TGTAATTATTGTTTATTTTAGGGCTTTATATGCTTTGTTACATGTAATGTTCTTTTTCTACTTTG
387 TGTAATTATTGTTTCTTTTAGGGCTTGATATGCTTTGTTACATGTGATGTTCTTCTTCTACTTTG
*
24468441 TTGTAGATATGTATAGTATCACCGAGGAAGATTGGAACATTTTCTCTTGATTATTGGTAGTGTAA
452 TTGTAGATATGTATAGTATC-CCGAGGAAGACTGGAACATTTTCTCTTGATTATTGGTAGTGTAA
* *
24468506 TTTTATTGTTGCTTTTGGGTTTCGGAGTGTAATTTAACGAGT
516 TTTTATTGTTGCTTTTGGGTTTCAGAGAGTAATTTAACGAGT
** * * * *
24468548 ACATGTAATTTAATGAAATTTCAAAGCAGATAAAGTCCTCTCTTGGAATTACATGTATTCATTAA
1 ACATGTAATTTAATGAAATCGCCAAGCAGATGAAGTCCTCTCTTGCAATTACATGTACTCATTAA
*
24468613 ATTACTCTTTGAAACCCAAAAGCAATAACAAAATTACACTACCAATAA-T-CAAGTGAAAATGTT
66 ATTACTCTCTGAAACCCAAAAGCAATAACAAAATTACACTACCAATAATTACAA--GAAAATGTT
* * *
24468676 TCAATCTTCCTCGGGAATGCTATACATATCTACCACAAAGTAGAAGAATAACATCACATGT-ACA
129 TCAATCTTCCCCGGG-ATACTATACATATCTACCACAAAGTAGAAGAAGAACATCACATGTAACA
* * * * * *
24468740 AAGCATATCAAGT-CCTAAAATTACTATCTA-TTAGTATGTTTATGCAATCTTGCAAGCCGACTT
193 AAGCATATCAA-TCCCTAAAATTAGTGTCTATTTGGT-GGTTTATGCAATCTTGCTAGCCAACTT
* **
24468803 -AAAGAGTTCCACAATATGGGTGTGGAGCTCCCACTGCCCAACATTGTTGCCTACTTATGACAGA
256 AAAAGAGTTCCACAATATGGGTATGGAGCTCCCAAAGCCCAACA---TTGCCTACTTATGACAGA
* * * *
24468867 TAATATCCCTTTTAGCCATAGTGCTTGCTCTTGGAAGGCAGGCTTGCTTATTAAAGCAACCTCTG
318 TAATATCCCTTTTAGCCATGGTGCTTGCTCTTGCAAGGTAGGTTTGCTTATTAAAGCAACCTC-G
* ** *
24468932 AATGCGGTAATTATTGTTTCCATTAGGGATTGATATGCTTTGTTACATGTGATGTTCTTCTTCTA
382 AATGCTGTAATTATTGTTTCTTTTAGGGCTTGATATGCTTTGTTACATGTGATGTTCTTCTTCTA
* * * * * * * *
24468997 CTTTGTGGTAGATATGTATCGTATTCTCAACGAAGACTAGAACATTTTCTCTTGATTATTGGCAA
447 CTTTGTTGTAGATATGTATAGTA-TCCCGAGGAAGACTGGAACATTTTCTCTTGATTATTGGTAG
* *
24469062 TGTAATTTTATTGTTGTTTTTGGGTTTCAGAGATTAATTTAACGAGT
511 TGTAATTTTATTGTTGCTTTTGGGTTTCAGAGAGTAATTTAACGAGT
* * **
24469109 ACATGTAATTTAATGAAATCACTAAATAGATGAAGTCCTCTCTTGCAATTACATGTACTCATTAA
1 ACATGTAATTTAATGAAATCGCCAAGCAGATGAAGTCCTCTCTTGCAATTACATGTACTCATTAA
*
24469174 GTTACTC
66 ATTACTC
24469181 ATAAAATATA
Statistics
Matches: 1035, Mismatches: 136, Indels: 43
0.85 0.11 0.04
Matches are distributed among these distances:
557 47 0.05
558 52 0.05
559 379 0.37
560 15 0.01
561 281 0.27
562 121 0.12
563 139 0.13
564 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Consensus pattern (557 bp):
ACATGTAATTTAATGAAATCGCCAAGCAGATGAAGTCCTCTCTTGCAATTACATGTACTCATTAA
ATTACTCTCTGAAACCCAAAAGCAATAACAAAATTACACTACCAATAATTACAAGAAAATGTTTC
AATCTTCCCCGGGATACTATACATATCTACCACAAAGTAGAAGAAGAACATCACATGTAACAAAG
CATATCAATCCCTAAAATTAGTGTCTATTTGGTGGTTTATGCAATCTTGCTAGCCAACTTAAAAG
AGTTCCACAATATGGGTATGGAGCTCCCAAAGCCCAACATTGCCTACTTATGACAGATAATATCC
CTTTTAGCCATGGTGCTTGCTCTTGCAAGGTAGGTTTGCTTATTAAAGCAACCTCGAATGCTGTA
ATTATTGTTTCTTTTAGGGCTTGATATGCTTTGTTACATGTGATGTTCTTCTTCTACTTTGTTGT
AGATATGTATAGTATCCCGAGGAAGACTGGAACATTTTCTCTTGATTATTGGTAGTGTAATTTTA
TTGTTGCTTTTGGGTTTCAGAGAGTAATTTAACGAGT
Found at i:24475205 original size:36 final size:36
Alignment explanation
Indices: 24475154--24475254 Score: 123
Period size: 36 Copynumber: 2.8 Consensus size: 36
24475144 TGGTAACAGG
* * * *
24475154 CATGAACTTTGGGTCAACAGGGAATAAAATGAGCAT
1 CATGACCTTTAGGTCAATAGGGAATAAAATAAGCAT
*
24475190 CATGACCTTTAGGTCAATA-GGAAGTAAAGTAAGCAT
1 CATGACCTTTAGGTCAATAGGGAA-TAAAATAAGCAT
* *
24475226 CATGACCATTAGGTCAATAGGGAGTAAAA
1 CATGACCTTTAGGTCAATAGGGAATAAAA
24475255 CGAATAAAGA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
35 4 0.07
36 48 0.87
37 3 0.05
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.23
Consensus pattern (36 bp):
CATGACCTTTAGGTCAATAGGGAATAAAATAAGCAT
Found at i:24486048 original size:36 final size:36
Alignment explanation
Indices: 24486000--24486100 Score: 123
Period size: 36 Copynumber: 2.8 Consensus size: 36
24485990 TGGTAACAGG
* *
24486000 CATGACCTTTGGGTCAACAA-GAGGTAAAATGAGCAT
1 CATGACCTTTGGGTCAACAAGGA-ATAAAATGAGAAT
* *
24486036 TATGACCTTTGGGTCAACAAGGAATAAAGTGAGAAT
1 CATGACCTTTGGGTCAACAAGGAATAAAATGAGAAT
* * *
24486072 CATGACCTTTGGGTTAGCAAGGAGTAAAA
1 CATGACCTTTGGGTCAACAAGGAATAAAA
24486101 CGGATAAAGA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
36 53 0.96
37 2 0.04
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.24
Consensus pattern (36 bp):
CATGACCTTTGGGTCAACAAGGAATAAAATGAGAAT
Found at i:24496903 original size:2 final size:2
Alignment explanation
Indices: 24496896--24496920 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
24496886 TTTAGTATTT
24496896 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
24496921 TTGTGTGTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24499140 original size:17 final size:17
Alignment explanation
Indices: 24499118--24499157 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
24499108 TATTGTTTCT
24499118 TTATTTATTCATTTTTA
1 TTATTTATTCATTTTTA
*
24499135 TTATTTATTTATTTTTA
1 TTATTTATTCATTTTTA
24499152 TCTATT
1 T-TATT
24499158 CAACTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (17 bp):
TTATTTATTCATTTTTA
Found at i:24508464 original size:51 final size:51
Alignment explanation
Indices: 24508409--24508625 Score: 330
Period size: 51 Copynumber: 4.3 Consensus size: 51
24508399 ATGACATACT
* * * *
24508409 GTCATTGGACCTTTAATTCGTCATGGATTCATTTACTCATGATGACACTTA
1 GTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCATGATGACACTTA
*
24508460 GTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCATGATAACACTTA
1 GTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCATGATGACACTTA
*
24508511 GTCATCGGACCTTTAATCCGTAAAGGA--CAGTTACTCATGATGACACTTA
1 GTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCATGATGACACTTA
* *
24508560 GTCATCGGACCTTTAATCCGTAAACGATTCATTTACTCACGATGACACTTA
1 GTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCATGATGACACTTA
*
24508611 GTCACCGGACTCTTT
1 GTCATCGGAC-CTTT
24508626 CGTTTATAGC
Statistics
Matches: 152, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
49 46 0.30
51 102 0.67
52 4 0.03
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (51 bp):
GTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCATGATGACACTTA
Found at i:24508562 original size:100 final size:101
Alignment explanation
Indices: 24508409--24508625 Score: 328
Period size: 100 Copynumber: 2.1 Consensus size: 101
24508399 ATGACATACT
* * * * *
24508409 GTCATTGGACCTTTAATTCGTCATGGATTCATTTACTCATGATGACACTTAGTCATCGGACCTTT
1 GTCATCGGACCTTTAATCCGTAAAGGA-TCAGTTACTCATGATGACACTTAGTCATCGGACCTTT
* *
24508474 AATCCGTAAAGGATTCATTTACTCATGATAACACTTA
65 AATCCGTAAACGATTCATTTACTCACGATAACACTTA
24508511 GTCATCGGACCTTTAATCCGTAAAGGA-CAGTTACTCATGATGACACTTAGTCATCGGACCTTTA
1 GTCATCGGACCTTTAATCCGTAAAGGATCAGTTACTCATGATGACACTTAGTCATCGGACCTTTA
*
24508575 ATCCGTAAACGATTCATTTACTCACGATGACACTTA
66 ATCCGTAAACGATTCATTTACTCACGATAACACTTA
*
24508611 GTCACCGGACTCTTT
1 GTCATCGGAC-CTTT
24508626 CGTTTATAGC
Statistics
Matches: 105, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
100 78 0.74
101 4 0.04
102 23 0.22
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (101 bp):
GTCATCGGACCTTTAATCCGTAAAGGATCAGTTACTCATGATGACACTTAGTCATCGGACCTTTA
ATCCGTAAACGATTCATTTACTCACGATAACACTTA
Found at i:24512146 original size:10 final size:10
Alignment explanation
Indices: 24512126--24512157 Score: 50
Period size: 9 Copynumber: 3.4 Consensus size: 10
24512116 TATCAAATTT
24512126 TAAAA-TTAA
1 TAAAATTTAA
24512135 TAAAATTTAA
1 TAAAATTTAA
24512145 T-AAATTTAA
1 TAAAATTTAA
24512154 TAAA
1 TAAA
24512158 TACCGTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 14 0.67
10 7 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TAAAATTTAA
Found at i:24519351 original size:34 final size:34
Alignment explanation
Indices: 24519265--24519360 Score: 115
Period size: 34 Copynumber: 2.9 Consensus size: 34
24519255 TCAAATCAAT
* * *
24519265 AAAGCTTCTTTCTTTATTG-ATAA-TCAACCTAT
1 AAAGCTTCTTTCCTTATTGAAAAACTCAACCTAC
* * *
24519297 AAAACTACTTCCCTTATTGAAAAACTCAACCTAC
1 AAAGCTTCTTTCCTTATTGAAAAACTCAACCTAC
*
24519331 AAAGCTTCTTTCCTTCTTGAAAAACTCAAC
1 AAAGCTTCTTTCCTTATTGAAAAACTCAAC
24519361 TGATAAATCT
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
32 15 0.29
33 3 0.06
34 34 0.65
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.34
Consensus pattern (34 bp):
AAAGCTTCTTTCCTTATTGAAAAACTCAACCTAC
Found at i:24519430 original size:34 final size:34
Alignment explanation
Indices: 24519309--24519431 Score: 94
Period size: 34 Copynumber: 3.6 Consensus size: 34
24519299 AACTACTTCC
* *
24519309 CTTA-TTGAAAAACTCAACCTA-CAAAGCTTCTTT
1 CTTAGTTGAAAAACTCAACCTATC-AATCTTATTT
* * *
24519342 CCTT-CTTGAAAAACTCAA-CTGATAAATCTTTTTT
1 -CTTAGTTGAAAAACTCAACCT-ATCAATCTTATTT
* * *
24519376 CTTTGTT-AAGACACTTAACCTATCAATCTTATTT
1 CTTAGTTGAA-AAACTCAACCTATCAATCTTATTT
*
24519410 CTTAGTTGAAAGACTCAACCTA
1 CTTAGTTGAAAAACTCAACCTA
24519432 AAGCTTTTTC
Statistics
Matches: 71, Mismatches: 11, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
33 7 0.10
34 60 0.85
35 4 0.06
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.37
Consensus pattern (34 bp):
CTTAGTTGAAAAACTCAACCTATCAATCTTATTT
Found at i:24526198 original size:12 final size:12
Alignment explanation
Indices: 24526181--24526205 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24526171 ATTGGAATTT
24526181 CTATTCAGTCTG
1 CTATTCAGTCTG
24526193 CTATTCAGTCTG
1 CTATTCAGTCTG
24526205 C
1 C
24526206 AACCACAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.28, G:0.16, T:0.40
Consensus pattern (12 bp):
CTATTCAGTCTG
Found at i:24530531 original size:18 final size:17
Alignment explanation
Indices: 24530496--24530551 Score: 87
Period size: 17 Copynumber: 3.2 Consensus size: 17
24530486 AGTGTAGAGT
24530496 AGTTACATGCGAGTTCG
1 AGTTACATGCGAGTTCG
24530513 AGTTACTATG-GATGTTCG
1 AGTTAC-ATGCGA-GTTCG
24530531 AGTTACATGCGAGTTCG
1 AGTTACATGCGAGTTCG
24530548 AGTT
1 AGTT
24530552 TGAGAGCAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
17 20 0.56
18 16 0.44
ACGTcount: A:0.23, C:0.14, G:0.29, T:0.34
Consensus pattern (17 bp):
AGTTACATGCGAGTTCG
Found at i:24538837 original size:18 final size:18
Alignment explanation
Indices: 24538803--24538837 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
24538793 ACTTCTGTAG
*
24538803 CTCGAGGTCGTGGTAGTA
1 CTCGAGGTCGTGCTAGTA
*
24538821 CTCGAGGTGGTGCTAGT
1 CTCGAGGTCGTGCTAGT
24538838 GGTAGAGTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.17, G:0.40, T:0.29
Consensus pattern (18 bp):
CTCGAGGTCGTGCTAGTA
Found at i:24543734 original size:17 final size:17
Alignment explanation
Indices: 24543700--24543741 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
24543690 TTATGGGACA
*
24543700 AAAATGAGAATGATGTG
1 AAAATGAGAATGAAGTG
24543717 AAAAT-AGAATTGAAGTG
1 AAAATGAGAA-TGAAGTG
24543734 AAATATGA
1 AAA-ATGA
24543742 TTTTTACCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 4 0.19
17 14 0.67
18 2 0.10
19 1 0.05
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (17 bp):
AAAATGAGAATGAAGTG
Found at i:24543914 original size:58 final size:58
Alignment explanation
Indices: 24543824--24543959 Score: 272
Period size: 58 Copynumber: 2.3 Consensus size: 58
24543814 TTTTAGATCT
24543824 CCCCAATTCCCAGAGGGTCGAGGGAGAAAACCCCAAATTGGTCGGTTATTATTATTAG
1 CCCCAATTCCCAGAGGGTCGAGGGAGAAAACCCCAAATTGGTCGGTTATTATTATTAG
24543882 CCCCAATTCCCAGAGGGTCGAGGGAGAAAACCCCAAATTGGTCGGTTATTATTATTAG
1 CCCCAATTCCCAGAGGGTCGAGGGAGAAAACCCCAAATTGGTCGGTTATTATTATTAG
24543940 CCCCAATTCCCAGAGGGTCG
1 CCCCAATTCCCAGAGGGTCG
24543960 TGGGCAGTCC
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 78 1.00
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.23
Consensus pattern (58 bp):
CCCCAATTCCCAGAGGGTCGAGGGAGAAAACCCCAAATTGGTCGGTTATTATTATTAG
Found at i:24548445 original size:18 final size:18
Alignment explanation
Indices: 24548424--24548458 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
24548414 TACCTCTGCC
*
24548424 ACTAGCACCACCTCGAGT
1 ACTACCACCACCTCGAGT
*
24548442 ACTACCACGACCTCGAG
1 ACTACCACCACCTCGAG
24548459 CTGCAGAAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.40, G:0.17, T:0.14
Consensus pattern (18 bp):
ACTACCACCACCTCGAGT
Found at i:24568698 original size:13 final size:15
Alignment explanation
Indices: 24568656--24568698 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
24568646 ATTTAGGGTA
24568656 TTATAATGATTATTTT
1 TTATAAT-ATTATTTT
24568672 TTATGAATATTATTTT
1 TTAT-AATATTATTTT
24568688 TTATATATATT
1 TTATA-ATATT
24568699 CTGTATATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 1 0.04
16 21 0.84
17 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (15 bp):
TTATAATATTATTTT
Found at i:24570035 original size:18 final size:19
Alignment explanation
Indices: 24570012--24570047 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
24570002 ATTTGTATCT
24570012 TTTTATAACTT-ACTAAAC
1 TTTTATAACTTAACTAAAC
*
24570030 TTTTATATCTTAACTAAA
1 TTTTATAACTTAACTAAA
24570048 AGTGGTAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTTATAACTTAACTAAAC
Found at i:24573133 original size:23 final size:23
Alignment explanation
Indices: 24573107--24573151 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
24573097 GTTAAGCTTA
24573107 AAAACAATA-TTTGAAAACAATTG
1 AAAACAATAGTTTGAAAA-AATTG
**
24573130 AAAACTTTAGTTTGAAAAAATT
1 AAAACAATAGTTTGAAAAAATT
24573152 TTGCGTGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.31
Consensus pattern (23 bp):
AAAACAATAGTTTGAAAAAATTG
Found at i:24575191 original size:12 final size:12
Alignment explanation
Indices: 24575174--24575198 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24575164 TGCTATCATG
24575174 ATGAATGCTATT
1 ATGAATGCTATT
24575186 ATGAATGCTATT
1 ATGAATGCTATT
24575198 A
1 A
24575199 ATTCTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
ATGAATGCTATT
Found at i:24577730 original size:47 final size:47
Alignment explanation
Indices: 24577661--24577754 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
24577651 TTTTATGCCT
24577661 CAAAAATATAGAAGTTGAAGCTCCCTTAGAAGATCCTCTTTCATCAG
1 CAAAAATATAGAAGTTGAAGCTCCCTTAGAAGATCCTCTTTCATCAG
24577708 CAAAAATATAGAA-TATGAAGCTCCCTTAGAAGATCCTCTTTCATCAG
1 CAAAAATATAGAAGT-TGAAGCTCCCTTAGAAGATCCTCTTTCATCAG
24577755 TATTTATCAA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
46 1 0.02
47 45 0.98
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (47 bp):
CAAAAATATAGAAGTTGAAGCTCCCTTAGAAGATCCTCTTTCATCAG
Found at i:24579566 original size:12 final size:13
Alignment explanation
Indices: 24579528--24579577 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 13
24579518 CCTTTCTTTT
24579528 TTCTTTC-CCTTC
1 TTCTTTCTCCTTC
* *
24579540 CTCTTCTCATTCTTC
1 TTCTT-TC-TCCTTC
24579555 TTCTTT-TCCTTC
1 TTCTTTCTCCTTC
24579567 TTCTTTCTCCT
1 TTCTTTCTCCT
24579578 CATCAATCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
12 15 0.50
13 6 0.20
14 1 0.03
15 8 0.27
ACGTcount: A:0.02, C:0.38, G:0.00, T:0.60
Consensus pattern (13 bp):
TTCTTTCTCCTTC
Found at i:24582566 original size:64 final size:64
Alignment explanation
Indices: 24582486--24582608 Score: 237
Period size: 64 Copynumber: 1.9 Consensus size: 64
24582476 CACAATGTCA
24582486 AATAATACTGTCGTTGCATACCTTGAATAGGTAAGGCTCATTCCAGTAGTATTTTGTGACGTTG
1 AATAATACTGTCGTTGCATACCTTGAATAGGTAAGGCTCATTCCAGTAGTATTTTGTGACGTTG
*
24582550 AATAATATTGTCGTTGCATACCTTGAATAGGTAAGGCTCATTCCAGTAGTATTTTGTGA
1 AATAATACTGTCGTTGCATACCTTGAATAGGTAAGGCTCATTCCAGTAGTATTTTGTGA
24582609 TGTCGCGAAG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 58 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.37
Consensus pattern (64 bp):
AATAATACTGTCGTTGCATACCTTGAATAGGTAAGGCTCATTCCAGTAGTATTTTGTGACGTTG
Found at i:24584155 original size:26 final size:26
Alignment explanation
Indices: 24584114--24584166 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
24584104 TTCTGAGAGT
*
24584114 AATTCTGGACACGTTCATGTAGCGAC
1 AATTCTGGACACGTTCATGCAGCGAC
* *
24584140 AATTCTGTACATGTTCATGCAGCGAC
1 AATTCTGGACACGTTCATGCAGCGAC
24584166 A
1 A
24584167 TTCCTGGGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (26 bp):
AATTCTGGACACGTTCATGCAGCGAC
Found at i:24584197 original size:37 final size:38
Alignment explanation
Indices: 24584156--24584243 Score: 117
Period size: 38 Copynumber: 2.3 Consensus size: 38
24584146 GTACATGTTC
*
24584156 ATGCAGCGACA-TTCCTGGGTGCAA-TTGAAGAATACTT
1 ATGCAGCGACAGTT-CTGGATGCAATTTGAAGAATACTT
* *
24584193 ATGCAGCGATAGTTCTGGATGCAATTTGAAGAATATTT
1 ATGCAGCGACAGTTCTGGATGCAATTTGAAGAATACTT
*
24584231 ATGCAGCGCCAGT
1 ATGCAGCGACAGT
24584244 CTTAGGTGCA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
37 19 0.43
38 25 0.57
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (38 bp):
ATGCAGCGACAGTTCTGGATGCAATTTGAAGAATACTT
Found at i:24589806 original size:13 final size:13
Alignment explanation
Indices: 24589788--24589812 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24589778 TAAGTTAAAA
24589788 ATGCTAAAAATGC
1 ATGCTAAAAATGC
24589801 ATGCTAAAAATG
1 ATGCTAAAAATG
24589813 ATAAAATGGG
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:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (13 bp):
ATGCTAAAAATGC
Found at i:24591889 original size:16 final size:16
Alignment explanation
Indices: 24591868--24591903 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
24591858 AAATAATCCC
*
24591868 AAAATTACAAGTCTCA
1 AAAATTAAAAGTCTCA
24591884 AAAATTAAAAGTCTCA
1 AAAATTAAAAGTCTCA
24591900 AAAA
1 AAAA
24591904 CTCTTTATTC
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:0.58, C:0.14, G:0.06, T:0.22
Consensus pattern (16 bp):
AAAATTAAAAGTCTCA
Found at i:24596683 original size:30 final size:30
Alignment explanation
Indices: 24596649--24596705 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
24596639 CCTCGGCAGG
*
24596649 TTCTTTTTCATCTTTAT-CTTCTTCCTTTCC
1 TTCTTTTTCATCTTGATCCTTC-TCCTTTCC
*
24596679 TTCTTTTTCTTCTTGATCCTTCTCCTT
1 TTCTTTTTCATCTTGATCCTTCTCCTT
24596706 CAATTGATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.05, C:0.30, G:0.02, T:0.63
Consensus pattern (30 bp):
TTCTTTTTCATCTTGATCCTTCTCCTTTCC
Found at i:24601548 original size:29 final size:30
Alignment explanation
Indices: 24601505--24601877 Score: 320
Period size: 30 Copynumber: 12.6 Consensus size: 30
24601495 TGTTTTATCT
24601505 AAAATTCACATTTTAACCCCTAAA-TTTTCC
1 AAAA-TCACATTTTAACCCCTAAACTTTTCC
* *
24601535 AAAATCATATTTTAACCCCTAAAC-TTTCTT
1 AAAATCACATTTTAACCCCTAAACTTTTC-C
* * *
24601565 AAAATCATATTTTGA--CCTAAAACTTTCCC
1 AAAATCACATTTTAACCCCT-AAACTTTTCC
* *
24601594 AAAATCACATTTTAACCTC-AAACTTTCCC
1 AAAATCACATTTTAACCCCTAAACTTTTCC
* * * *
24601623 AAAATCACATTTTGACTCGT-AAC-TTTCTT
1 AAAATCACATTTTAACCCCTAAACTTTTC-C
* *
24601652 AAAATCATATTTTAACCCCTAAACTCTTCC
1 AAAATCACATTTTAACCCCTAAACTTTTCC
** *
24601682 AAAATTTCA-TTTAGACCCCTAAACTTCTT-T
1 AAAATCACATTTTA-ACCCCTAAACTT-TTCC
* *
24601712 AAAATTACATTTTAA-TCCTAAACTTTTCC
1 AAAATCACATTTTAACCCCTAAACTTTTCC
* * *
24601741 AAAATTACATTTTAA-TCCTCAAACTTTTTC
1 AAAATCACATTTTAACCCCT-AAACTTTTCC
*
24601771 AAAATTACATTTTAACCCCTAAACTTTTCC
1 AAAATCACATTTTAACCCCTAAACTTTTCC
*
24601801 AAAATCACATTTTAACCCCTAAAC-TTTCTT
1 AAAATCACATTTTAACCCCTAAACTTTTC-C
* * * *
24601831 AAAATTACATTTCAACCCCTAAATTTTTCT
1 AAAATCACATTTTAACCCCTAAACTTTTCC
* * *
24601861 AAGATTATATTTTAACC
1 AAAATCACATTTTAACC
24601878 TTAAATTCTC
Statistics
Matches: 286, Mismatches: 39, Indels: 36
0.79 0.11 0.10
Matches are distributed among these distances:
28 8 0.03
29 119 0.42
30 142 0.50
31 17 0.06
ACGTcount: A:0.36, C:0.24, G:0.01, T:0.38
Consensus pattern (30 bp):
AAAATCACATTTTAACCCCTAAACTTTTCC
Found at i:24601873 original size:60 final size:60
Alignment explanation
Indices: 24601505--24601901 Score: 345
Period size: 59 Copynumber: 6.7 Consensus size: 60
24601495 TGTTTTATCT
* * * * *
24601505 AAAATTCACATTTTAACCCCTAAATTTTC-CAAAATCATATTTTAACCCCTAAAC-TTTCTT
1 AAAATT-ACATTTTAACCCCTAAACTTTCTTAAAATTACATTTTAACCCCTAAACTTTTC-C
* * * ** * * *
24601565 AAAATCATATTTTGA--CCTAAAACTTTCCCAAAATCACATTTTAACCTC-AAACTTTCCC
1 AAAATTACATTTTAACCCCT-AAACTTTCTTAAAATTACATTTTAACCCCTAAACTTTTCC
* * * * * * *
24601623 AAAATCACATTTTGACTCGT-AACTTTCTTAAAATCATATTTTAACCCCTAAACTCTTCC
1 AAAATTACATTTTAACCCCTAAACTTTCTTAAAATTACATTTTAACCCCTAAACTTTTCC
* *
24601682 AAAATTTCA-TTTAGACCCCTAAAC-TTCTTTAAAATTACATTTTAA-TCCTAAACTTTTCC
1 AAAATTACATTTTA-ACCCCTAAACTTTC-TTAAAATTACATTTTAACCCCTAAACTTTTCC
*
24601741 AAAATTACATTTTAA-TCCTCAAACTTT-TTCAAAATTACATTTTAACCCCTAAACTTTTCC
1 AAAATTACATTTTAACCCCT-AAACTTTCTT-AAAATTACATTTTAACCCCTAAACTTTTCC
* * * *
24601801 AAAATCACATTTTAACCCCTAAACTTTCTTAAAATTACATTTCAACCCCTAAATTTTTCT
1 AAAATTACATTTTAACCCCTAAACTTTCTTAAAATTACATTTTAACCCCTAAACTTTTCC
* * * *
24601861 AAGATTATATTTTAA-CCTTAAA-TTCTCTTAAACTT-CATTTT
1 AAAATTACATTTTAACCCCTAAACTT-TCTTAAAATTACATTTT
24601902 TTAACACCAT
Statistics
Matches: 281, Mismatches: 39, Indels: 36
0.79 0.11 0.10
Matches are distributed among these distances:
57 3 0.01
58 64 0.23
59 105 0.37
60 104 0.37
61 5 0.02
ACGTcount: A:0.36, C:0.24, G:0.01, T:0.39
Consensus pattern (60 bp):
AAAATTACATTTTAACCCCTAAACTTTCTTAAAATTACATTTTAACCCCTAAACTTTTCC
Found at i:24602772 original size:325 final size:324
Alignment explanation
Indices: 24602178--24602798 Score: 920
Period size: 325 Copynumber: 1.9 Consensus size: 324
24602168 AAACAATTTT
* * * * * * *
24602178 AAAACCGAGGCAATATCATTTCGTGTGAAAATTTCAAAAAATTGTGCCTTAACGTGTTGGGTGTG
1 AAAAACGAGGCAATACCATTTCGTGTGAAAACTTCAAAAAATTATGCCCTAACGTGCTAGGTGTG
* * * * ** **
24602243 ATTTTTCGTATAATTTGCACGATCGAATATTCTTTTTAAACCTTTTAAATGTCCTTCAATTTCAA
66 ATTTTTCATATAATTCGCACGATCGAATATCCTTTTAAAACCTTCAAAACATCCTTCAATTTCAA
*
24602308 AATTTCGAGAACATCATGCCCTAACGTGTTGGACACGACTTCAATTCTCCGAGAAATTTGAAACA
131 AATTTCGAGAACATCATGCCCTAACGTGTTGGACACGACTTCAATTCTCCGAGAAATTCGAAACA
* * *
24602373 CACAGGGCATTTTTCTTCAAATTCGTTTTTTGAAAATCATGCGAAATAAGTTATGTGTACAAGGA
196 CACAGGGCATTTTTCTTCAAATTCGATTTTTGAAAATCATGCGAAATAAGTTATGTGTAAAAAGA
24602438 TCATATTTTAAAATTCACTCGAGATTTC-AAGTTTTCAAAAAAAATACAAATAATTTTAAACCA
261 TCATATTTTAAAATTCACTCGAGATTTCAAAGTTTTCAAAAAAAATACAAATAATTTTAAACCA
* * *
24602501 AAAAACGAGGCAATACCCTTTCGTGTGAAAGCTTCGAAAAATTATGCCCTAACGTGCTAGGTGTG
1 AAAAACGAGGCAATACCATTTCGTGTGAAAACTTCAAAAAATTATGCCCTAACGTGCTAGGTGTG
**
24602566 ATTTTTCATATAATTCGCGTGATCGAATATCCTCTTTAAAACCCTTCAAAACATCCTTCAATTTC
66 ATTTTTCATATAATTCGCACGATCGAATATCCT-TTTAAAA-CCTTCAAAACATCCTTCAATTTC
* * * *
24602631 GAAATTTCGAGAACGTCGTGCCCTAACGTGTTGGACACGAGTTCAATTCTCCGAGAAATTCGAAA
129 AAAATTTCGAGAACATCATGCCCTAACGTGTTGGACACGACTTCAATTCTCCGAGAAATTCGAAA
* *
24602696 CACACGGGGCATTTTTCTTCAAATTTGATTTTTGAAAATCATGCGAAATAAGTTATGTGTAAAAA
194 CACACAGGGCATTTTTCTTCAAATTCGATTTTTGAAAATCATGCGAAATAAGTTATGTGTAAAAA
* * *
24602761 GATCGTATTTTAAACTTCACTTGAGATTTCAAAGTTTT
259 GATCATATTTTAAAATTCACTCGAGATTTCAAAGTTTT
24602799 AACAAATAAG
Statistics
Matches: 262, Mismatches: 33, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
323 83 0.32
324 6 0.02
325 166 0.63
326 7 0.03
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (324 bp):
AAAAACGAGGCAATACCATTTCGTGTGAAAACTTCAAAAAATTATGCCCTAACGTGCTAGGTGTG
ATTTTTCATATAATTCGCACGATCGAATATCCTTTTAAAACCTTCAAAACATCCTTCAATTTCAA
AATTTCGAGAACATCATGCCCTAACGTGTTGGACACGACTTCAATTCTCCGAGAAATTCGAAACA
CACAGGGCATTTTTCTTCAAATTCGATTTTTGAAAATCATGCGAAATAAGTTATGTGTAAAAAGA
TCATATTTTAAAATTCACTCGAGATTTCAAAGTTTTCAAAAAAAATACAAATAATTTTAAACCA
Found at i:24604652 original size:21 final size:20
Alignment explanation
Indices: 24604619--24604661 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
24604609 CATGTTATTT
*
24604619 ATTTTATGCTTTCATATTTAC
1 ATTTTATGATTTCATA-TTAC
* *
24604640 ATTTTATTATTTCTTATTAC
1 ATTTTATGATTTCATATTAC
24604660 AT
1 AT
24604662 CGCATATCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.26, C:0.12, G:0.02, T:0.60
Consensus pattern (20 bp):
ATTTTATGATTTCATATTAC
Found at i:24629433 original size:43 final size:41
Alignment explanation
Indices: 24629379--24629515 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
24629369 TAAAAAGTAA
* *
24629379 AGCAATAGCGGCGTTTATAGAAAAAAACGCTGCTAAAGGTCAG
1 AGCATTAGCGGCGTTTAT-G-AAAAAACGCCGCTAAAGGTCAG
** *
24629422 AGCATTAGCGGCGTTTATGGGAAAGCGCCGCTAAAGGTCAG
1 AGCATTAGCGGCGTTTATGAAAAAACGCCGCTAAAGGTCAG
* * * * * **
24629463 AGCATTAACGACGTTTCTTG-GAAAGCGCCGCTAAAGGTTGG
1 AGCATTAGCGGCGTTT-ATGAAAAAACGCCGCTAAAGGTCAG
24629504 AGCATTAGCGGC
1 AGCATTAGCGGC
24629516 CATAGCGGCA
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
41 61 0.75
42 3 0.04
43 17 0.21
ACGTcount: A:0.31, C:0.19, G:0.30, T:0.20
Consensus pattern (41 bp):
AGCATTAGCGGCGTTTATGAAAAAACGCCGCTAAAGGTCAG
Found at i:24629463 original size:41 final size:41
Alignment explanation
Indices: 24629410--24629650 Score: 173
Period size: 41 Copynumber: 5.7 Consensus size: 41
24629400 AAAAAACGCT
24629410 GCTAAAGGTCAGAGCATTAGCGGCGTTTATGGGAAAGCGCC
1 GCTAAAGGTCAGAGCATTAGCGGCGTTTATGGGAAAGCGCC
* * * *
24629451 GCTAAAGGTCAGAGCATTAACGACGTTTCTTGGAAAGCGCC
1 GCTAAAGGTCAGAGCATTAGCGGCGTTTATGGGAAAGCGCC
**
24629492 GCTAAAGGTTGGAGCATTAGCGGCCATAGCGGCATTTATGGGAAAGCGCC
1 GCTAAAGGTCAGAGCATTAGC-G-----GC-G--TTTATGGGAAAGCGCC
** ** * *
24629542 GCTAAAGGTC-GAAGCATTAGCAACACTTGTAGGAAAGCGCC
1 GCTAAAGGTCAG-AGCATTAGCGGCGTTTATGGGAAAGCGCC
* ** * ***
24629583 GCTAAAGATCAGAGCATTAATGGCGCTTTCTCATAAA-CGCC
1 GCTAAAGGTCAGAGCATTAGCGGCG-TTTATGGGAAAGCGCC
* *
24629624 GCTAAAGGTTA-AGCAATAGCGGCGTTT
1 GCTAAAGGTCAGAGCATTAGCGGCGTTT
24629651 TCCCATAAGC
Statistics
Matches: 155, Mismatches: 33, Indels: 26
0.72 0.15 0.12
Matches are distributed among these distances:
39 3 0.02
40 10 0.06
41 98 0.63
42 8 0.05
44 1 0.01
47 1 0.01
48 1 0.01
49 1 0.01
50 32 0.21
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (41 bp):
GCTAAAGGTCAGAGCATTAGCGGCGTTTATGGGAAAGCGCC
Found at i:24629598 original size:91 final size:91
Alignment explanation
Indices: 24629427--24629601 Score: 244
Period size: 91 Copynumber: 1.9 Consensus size: 91
24629417 GTCAGAGCAT
* * ** *
24629427 TAGCGGCGTTTATGGGAAAGCGCCGCTAAAGGTCAGAGCATTAACGACGTTTCTTGGAAAGCGCC
1 TAGCGGCATTTATGGGAAAGCGCCGCTAAAGGTCAGAGCATTAACAACACTTCTAGGAAAGCGCC
* **
24629492 GCTAAAGGTTGGAGCATTAGCGGCCA
66 GCTAAAGATCAGAGCATTAGCGGCCA
* *
24629518 TAGCGGCATTTATGGGAAAGCGCCGCTAAAGGTC-GAAGCATTAGCAACACTTGTAGGAAAGCGC
1 TAGCGGCATTTATGGGAAAGCGCCGCTAAAGGTCAG-AGCATTAACAACACTTCTAGGAAAGCGC
24629582 CGCTAAAGATCAGAGCATTA
65 CGCTAAAGATCAGAGCATTA
24629602 ATGGCGCTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
90 1 0.01
91 72 0.99
ACGTcount: A:0.30, C:0.21, G:0.30, T:0.20
Consensus pattern (91 bp):
TAGCGGCATTTATGGGAAAGCGCCGCTAAAGGTCAGAGCATTAACAACACTTCTAGGAAAGCGCC
GCTAAAGATCAGAGCATTAGCGGCCA
Found at i:24629665 original size:40 final size:41
Alignment explanation
Indices: 24629576--24629668 Score: 107
Period size: 40 Copynumber: 2.3 Consensus size: 41
24629566 ACTTGTAGGA
* * *
24629576 AAGCGCCGCTAAAGATCAGAGCATTAATGGCGCTTTCTCAT
1 AAGCGCCGCTAAAGATCAGAGCAATAACGGCGCTTTCCCAT
* * * * *
24629617 AAACGCCGCTAAAGGTTA-AGCAATAGCGGCGTTTTCCCAT
1 AAGCGCCGCTAAAGATCAGAGCAATAACGGCGCTTTCCCAT
24629657 AAGCGCCGCTAA
1 AAGCGCCGCTAA
24629669 TTTATTTAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
40 28 0.65
41 15 0.35
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.22
Consensus pattern (41 bp):
AAGCGCCGCTAAAGATCAGAGCAATAACGGCGCTTTCCCAT
Found at i:24630700 original size:18 final size:18
Alignment explanation
Indices: 24630677--24630720 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
24630667 AAATACGAAA
24630677 AAAATTATTA-ACATTTCT
1 AAAATTATTAGA-ATTTCT
*
24630695 AAAATTTTTAGTAATTTCT
1 AAAATTATTAG-AATTTCT
24630714 AAAATTA
1 AAAATTA
24630721 ACATTATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 9 0.41
19 12 0.55
20 1 0.05
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (18 bp):
AAAATTATTAGAATTTCT
Found at i:24632231 original size:41 final size:41
Alignment explanation
Indices: 24632155--24632479 Score: 436
Period size: 41 Copynumber: 7.9 Consensus size: 41
24632145 AATATGAGAA
* * *
24632155 AGAGCATTACCGGCGCTTA-GAGAAAGCGCCGCTAAAGGTC
1 AGAGCATTAGCGGCGCTTATAAGAAAGCGCCGCTAAAGATC
* *
24632195 AGAGCATTAGCGGCGCTTATGAGAAAGCGCCACTAAAGATC
1 AGAGCATTAGCGGCGCTTATAAGAAAGCGCCGCTAAAGATC
* *
24632236 AGAGCATTAGCGGCGCTTATGAGAAAGCGCCACTAAAGATC
1 AGAGCATTAGCGGCGCTTATAAGAAAGCGCCGCTAAAGATC
* *
24632277 AGAGCATTAGCGGCGCTTATAAGAAAGCGCCGCTAAAGGTT
1 AGAGCATTAGCGGCGCTTATAAGAAAGCGCCGCTAAAGATC
* * *
24632318 AGAGTATTAGCGGTGCTTATAAGAAAGCACCGCTAAAGATC
1 AGAGCATTAGCGGCGCTTATAAGAAAGCGCCGCTAAAGATC
*
24632359 AGTGCATTAGCGGCGCTTATAAAGAAAGCGCCGCTAAAGATC
1 AGAGCATTAGCGGCGCTTAT-AAGAAAGCGCCGCTAAAGATC
* ** *
24632401 AGAGCATTAGAGGAACTTATAAGAAAGCGCCGCTAAAGGTC
1 AGAGCATTAGCGGCGCTTATAAGAAAGCGCCGCTAAAGATC
* ** *
24632442 AGAGCATTAGCGGGGCTTATTGGAAAAACGCCGCTAAA
1 AGAGCATTAGCGGCGCTTATAAG-AAAGCGCCGCTAAA
24632480 AGTTAAGCAA
Statistics
Matches: 255, Mismatches: 27, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
40 18 0.07
41 188 0.74
42 49 0.19
ACGTcount: A:0.34, C:0.20, G:0.27, T:0.18
Consensus pattern (41 bp):
AGAGCATTAGCGGCGCTTATAAGAAAGCGCCGCTAAAGATC
Found at i:24632598 original size:28 final size:28
Alignment explanation
Indices: 24632567--24632651 Score: 93
Period size: 27 Copynumber: 3.1 Consensus size: 28
24632557 ATTAACAATT
24632567 ATTTTAAAACTTATATAAACTAAAA-AA
1 ATTTTAAAACTTATATAAACTAAAATAA
* * * * ** *
24632594 AATTTAAAA-TTTTAAAAAATCTATTAA
1 ATTTTAAAACTTATATAAACTAAAATAA
24632621 ATTTTAAAACTTATATAAACTAAAATAA
1 ATTTTAAAACTTATATAAACTAAAATAA
24632649 ATT
1 ATT
24632652 AAATTATTTT
Statistics
Matches: 42, Mismatches: 14, Indels: 3
0.71 0.24 0.05
Matches are distributed among these distances:
26 9 0.21
27 18 0.43
28 15 0.36
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (28 bp):
ATTTTAAAACTTATATAAACTAAAATAA
Found at i:24632610 original size:17 final size:19
Alignment explanation
Indices: 24632590--24632629 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
24632580 TATAAACTAA
24632590 AAAAAAT-T-TAAAATTTT
1 AAAAAATCTATAAAATTTT
*
24632607 AAAAAATCTATTAAATTTT
1 AAAAAATCTATAAAATTTT
24632626 AAAA
1 AAAA
24632630 CTTATATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 1 0.05
19 12 0.60
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAAATCTATAAAATTTT
Found at i:24634293 original size:23 final size:22
Alignment explanation
Indices: 24634251--24634295 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
24634241 GTTTTCCTAC
*
24634251 CTTTTTAGTATGTGCTTTCTTT
1 CTTTTTAGTATGTGCATTCTTT
*
24634273 CTTTTTAGTATGTTCAATTCTTT
1 CTTTTTAGTATGTGC-ATTCTTT
24634296 TTAAATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.13, C:0.13, G:0.11, T:0.62
Consensus pattern (22 bp):
CTTTTTAGTATGTGCATTCTTT
Found at i:24636571 original size:43 final size:43
Alignment explanation
Indices: 24636510--24636798 Score: 409
Period size: 43 Copynumber: 6.7 Consensus size: 43
24636500 TCTGTTAATA
*
24636510 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCGTGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* **
24636553 TTAGCGGCGTTTGTGGGAAAAGCGCCTCTAAAGACTGTGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
*
24636596 TTAGCGGCGTTTGAGGGAAAAAGCGCCGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGG-AAAAGCGCCGCTAAAGACCATGTTCT
* *
24636640 TTAGCGCCGTTTGTGGGAAAAGCGTCGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* * * *
24636683 TTAGCAGCGTTTGTGGGGAAAGCACCGCTAAAGACCATGTTCA
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* *
24636726 TTAGCGGCGTTTATGGG-AAAGCGCCGCTAAAGATCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* * *
24636768 ATAGCGGCGTTTATGAGGAAAAACGCCGCTA
1 TTAGCGGCGTTTGTG-GGAAAAGCGCCGCTA
24636799 TTTTTAGCGG
Statistics
Matches: 221, Mismatches: 22, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
42 36 0.16
43 136 0.62
44 49 0.22
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
Found at i:24636655 original size:87 final size:86
Alignment explanation
Indices: 24636510--24636798 Score: 386
Period size: 87 Copynumber: 3.3 Consensus size: 86
24636500 TCTGTTAATA
* *
24636510 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCGTGTTCTTTAGCGGCGTTTGTGGGAAAAG
1 TTAGCGGCGTTTGAGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGGAAAAG
* *
24636575 CGCCTCTAAAGACTGTGTTCT
66 CGCCGCTAAAGACTATGTTCT
*
24636596 TTAGCGGCGTTTGAGGGAAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGCCGTTTGTGGGAAAA
1 TTAGCGGCGTTTGAGGG-AAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGGAAAA
* *
24636661 GCGTCGCTAAAGACCATGTTCT
65 GCGCCGCTAAAGACTATGTTCT
* * * * * *
24636683 TTAGCAGCGTTTGTGGGGAAAGCACCGCTAAAGACCATGTTCATTAGCGGCGTTTATGGG-AAAG
1 TTAGCGGCGTTTGAGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGGAAAAG
24636747 CGCCGCTAAAGA-TCATGTTCT
66 CGCCGCTAAAGACT-ATGTTCT
* *
24636768 ATAGCGGCGTTT-ATGAGGAAAAACGCCGCTA
1 TTAGCGGCGTTTGA-G-GGAAAAGCGCCGCTA
24636799 TTTTTAGCGG
Statistics
Matches: 177, Mismatches: 22, Indels: 8
0.86 0.11 0.04
Matches are distributed among these distances:
85 33 0.19
86 66 0.37
87 78 0.44
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (86 bp):
TTAGCGGCGTTTGAGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGGAAAAG
CGCCGCTAAAGACTATGTTCT
Found at i:24636744 original size:130 final size:128
Alignment explanation
Indices: 24636510--24636798 Score: 409
Period size: 130 Copynumber: 2.2 Consensus size: 128
24636500 TCTGTTAATA
* *
24636510 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCGTGTTCTTTAGCGGCGTTTGTGGGAAAAG
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCAGCGTTTGTGGGAAAAG
* * ** *
24636575 CGCCTCTAAAGACTGTGTTCTTTAGCGGCGTTTGAGGGAAAAAGCGCCGCTAAAGACCATGTTCT
66 CACCGCTAAAGACCATGTTCATTAGCGGCGTTTGAGGG--AAAGCGCCGCTAAAGACCATGTTCT
* * *
24636640 TTAGCGCCGTTTGTGGGAAAAGCGTCGCTAAAGACCATGTTCTTTAGCAGCGTTTGTGGGGAAAG
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCAGCGTTTGTGGGAAAAG
*
24636705 CACCGCTAAAGACCATGTTCATTAGCGGCGTTT-ATGGGAAAGCGCCGCTAAAGATCATGTTCT
66 CACCGCTAAAGACCATGTTCATTAGCGGCGTTTGA-GGGAAAGCGCCGCTAAAGACCATGTTCT
* * *
24636768 ATAGCGGCGTTTATGAGGAAAAACGCCGCTA
1 TTAGCGGCGTTTGTG-GGAAAAGCGCCGCTA
24636799 TTTTTAGCGG
Statistics
Matches: 141, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
128 36 0.26
129 14 0.10
130 91 0.65
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (128 bp):
TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCAGCGTTTGTGGGAAAAG
CACCGCTAAAGACCATGTTCATTAGCGGCGTTTGAGGGAAAGCGCCGCTAAAGACCATGTTCT
Found at i:24638334 original size:99 final size:99
Alignment explanation
Indices: 24638205--24638402 Score: 378
Period size: 99 Copynumber: 2.0 Consensus size: 99
24638195 TGATTATAAT
24638205 TTTTTTTTTAAATCTATTTCATGTTCTAGAAATATTTACATTAAAAACATATTATAATAGAAAGA
1 TTTTTTTTTAAATCTATTTCATGTTCTAGAAATATTTACATTAAAAACATATTATAATAGAAAGA
24638270 TCAACTTTCTTTTATTTTTATAGAAGAATCCTAA
66 TCAACTTTCTTTTATTTTTATAGAAGAATCCTAA
* *
24638304 TTTTTTTTTAAATCTATTTCATGTTGTAGAAATATTTACATTAAAAACATATTATAATCGAAAGA
1 TTTTTTTTTAAATCTATTTCATGTTCTAGAAATATTTACATTAAAAACATATTATAATAGAAAGA
24638369 TCAACTTTCTTTTATTTTTATAGAAGAATCCTAA
66 TCAACTTTCTTTTATTTTTATAGAAGAATCCTAA
24638403 CCCCTCTACT
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 97 1.00
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (99 bp):
TTTTTTTTTAAATCTATTTCATGTTCTAGAAATATTTACATTAAAAACATATTATAATAGAAAGA
TCAACTTTCTTTTATTTTTATAGAAGAATCCTAA
Found at i:24641359 original size:31 final size:33
Alignment explanation
Indices: 24641302--24641368 Score: 93
Period size: 31 Copynumber: 2.1 Consensus size: 33
24641292 CGATATTATT
*
24641302 TTTTAATTTTTTAAAAATATTTATATTGTTTTA
1 TTTTAATTATTTAAAAATATTTATATTGTTTTA
* *
24641335 TTTTAA-TATTTAATAAT-TTTATATTTTTTTA
1 TTTTAATTATTTAAAAATATTTATATTGTTTTA
24641366 TTT
1 TTT
24641369 ATTGAACATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 16 0.52
32 9 0.29
33 6 0.19
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (33 bp):
TTTTAATTATTTAAAAATATTTATATTGTTTTA
Found at i:24641701 original size:3 final size:3
Alignment explanation
Indices: 24641693--24641720 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
24641683 ACAGGTCTAC
24641693 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
24641721 GCTTAACTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:24642572 original size:19 final size:21
Alignment explanation
Indices: 24642548--24642587 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
24642538 TTTATCATGC
*
24642548 CATATACTA-ACATTT-AATT
1 CATATACCATACATTTCAATT
24642567 CATATACCATACATTTCAATT
1 CATATACCATACATTTCAATT
24642588 TCATGAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 6 0.33
21 4 0.22
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (21 bp):
CATATACCATACATTTCAATT
Found at i:24646727 original size:105 final size:105
Alignment explanation
Indices: 24646535--24646728 Score: 273
Period size: 105 Copynumber: 1.8 Consensus size: 105
24646525 CTTCTTTTTT
* * * * **
24646535 TTAAGAATATATTGGTCCTTTTGACGTGAAATGGAATAACAATTCAAGCACCCCATCCCGGTTAC
1 TTAAAAATATATTGGCCCTTTTGACGCGAAATGCAATAACAACCCAAGCACCCCATCCCGGTTAC
24646600 TCAGCCCAACACACTCTCAATTTATTACAATCATTTTTAC
66 TCAGCCCAACACACTCTCAATTTATTACAATCATTTTTAC
* * * * *
24646640 TTAAAAATGTATTGGCCCTTTTGATGCGAAATGCAATGACAACCCAAGCACTCCATCCTGGTTAC
1 TTAAAAATATATTGGCCCTTTTGACGCGAAATGCAATAACAACCCAAGCACCCCATCCCGGTTAC
24646705 TCAGCCCAACACACTC-CTAATTTA
66 TCAGCCCAACACACTCTC-AATTTA
24646729 CTTTTTCCAT
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
104 1 0.01
105 76 0.99
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.29
Consensus pattern (105 bp):
TTAAAAATATATTGGCCCTTTTGACGCGAAATGCAATAACAACCCAAGCACCCCATCCCGGTTAC
TCAGCCCAACACACTCTCAATTTATTACAATCATTTTTAC
Found at i:24650363 original size:24 final size:24
Alignment explanation
Indices: 24650330--24650377 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
24650320 ATTCATCTTC
*
24650330 TATTAATTTGCTCTGACAT-TTTA
1 TATTAATTTGCACTGACATATTTA
24650353 TATTATATTTGCACTGACATATTTA
1 TATTA-ATTTGCACTGACATATTTA
24650378 ATTCTTAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.23
24 13 0.59
25 4 0.18
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.50
Consensus pattern (24 bp):
TATTAATTTGCACTGACATATTTA
Found at i:24654874 original size:76 final size:76
Alignment explanation
Indices: 24654746--24654899 Score: 290
Period size: 76 Copynumber: 2.0 Consensus size: 76
24654736 GGATAATTCG
* *
24654746 TGACATTTTAGTAGATGTTCCCATAGACGACACCAACATTGATGTTAGTTTTATAAGGTTGGGTT
1 TGACATGTTAGTAGATGTTCCCATAGACGACACCAACATTGATGTTAATTTTATAAGGTTGGGTT
24654811 GAAATGATCAT
66 GAAATGATCAT
24654822 TGACATGTTAGTAGATGTTCCCATAGACGACACCAACATTGATGTTAATTTTATAAGGTTGGGTT
1 TGACATGTTAGTAGATGTTCCCATAGACGACACCAACATTGATGTTAATTTTATAAGGTTGGGTT
24654887 GAAATGATCAT
66 GAAATGATCAT
24654898 TG
1 TG
24654900 TTAAGTTGTA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (76 bp):
TGACATGTTAGTAGATGTTCCCATAGACGACACCAACATTGATGTTAATTTTATAAGGTTGGGTT
GAAATGATCAT
Found at i:24658559 original size:31 final size:30
Alignment explanation
Indices: 24658519--24658576 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
24658509 ATTCATTATT
* *
24658519 TTTAAATTAAAAATAGTTACTTAAAAAGTA
1 TTTAAATTAAAAATAATTACATAAAAAGTA
*
24658549 TTTAATATTAAATATAATTACATAAAAA
1 TTTAA-ATTAAAAATAATTACATAAAAA
24658577 TTTAATTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 5 0.21
31 19 0.79
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (30 bp):
TTTAAATTAAAAATAATTACATAAAAAGTA
Found at i:24660617 original size:30 final size:29
Alignment explanation
Indices: 24660573--24660773 Score: 219
Period size: 30 Copynumber: 6.8 Consensus size: 29
24660563 ACAAGTTCCT
* *
24660573 AAACTATCCAAAAATTATATTTTGAGCCCC
1 AAACT-TCCAAAAATTACATTTTTAGCCCC
* * * *
24660603 AAACTTCTCCAAAATTTCATTTTTAACCTCA
1 AAACTTC-CAAAAATTACATTTTTAGCC-CC
24660634 AAACTTCCAAAAATTACATTTTT-GCCCTC
1 AAACTTCCAAAAATTACATTTTTAGCCC-C
* *
24660663 GAACTTCCAAAAATTCCATTTTTAGCCCC
1 AAACTTCCAAAAATTACATTTTTAGCCCC
24660692 GAAACTTCCAAAAATTACATTTTTA-CCCTC
1 -AAACTTCCAAAAATTACATTTTTAGCCC-C
*
24660722 AAACTTCCAAAAATTTCATTTTT-GACCCC
1 AAACTTCCAAAAATTACATTTTTAG-CCCC
*
24660751 AAAACCTCCAAAAATTACATTTT
1 -AAACTTCCAAAAATTACATTTT
24660774 ACCCCCGGAT
Statistics
Matches: 145, Mismatches: 17, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
28 1 0.01
29 52 0.36
30 84 0.58
31 8 0.06
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTTAGCCCC
Found at i:24660700 original size:59 final size:59
Alignment explanation
Indices: 24660573--24660832 Score: 274
Period size: 59 Copynumber: 4.4 Consensus size: 59
24660563 ACAAGTTCCT
* * * * *
24660573 AAACTATCCAAAAATTATATTTTGAGCCC-CAAACTTCTCCAAAATTTCATTTTTAACCTCA
1 AAACT-TCCAAAAATTACATTTTTA-CCCTCAAACTTC-CAAAAATTCCATTTTTAACCCCA
* * * *
24660634 AAACTTCCAAAAATTACATTTTTGCCCTCGAACTTCCAAAAATTCCATTTTTAGCCCCG
1 AAACTTCCAAAAATTACATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCCCA
* *
24660693 AAACTTCCAAAAATTACATTTTTACCCTCAAACTTCCAAAAATTTCATTTTTGACCCCA
1 AAACTTCCAAAAATTACATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCCCA
* * ** * * *
24660752 AAACCTCCAAAAATTACA-TTTTACCCCCGGA-TGTCTAAAAACTCCATTTTTAACCCCG
1 AAACTTCCAAAAATTACATTTTTACCCTCAAACT-TCCAAAAATTCCATTTTTAACCCCA
**
24660810 AAACTTTTAAAAATTACCATTTT
1 AAACTTCCAAAAATTA-CATTTT
24660833 ATCCTTGAAT
Statistics
Matches: 168, Mismatches: 27, Indels: 9
0.82 0.13 0.04
Matches are distributed among these distances:
57 1 0.01
58 43 0.26
59 93 0.55
60 26 0.15
61 5 0.03
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (59 bp):
AAACTTCCAAAAATTACATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCCCA
Found at i:24660779 original size:29 final size:29
Alignment explanation
Indices: 24660573--24660832 Score: 218
Period size: 30 Copynumber: 8.8 Consensus size: 29
24660563 ACAAGTTCCT
* * *
24660573 AAACTATCCAAAAATTATATTTTGAGCCCC
1 AAACT-TCCAAAAATTACATTTTTACCCCC
* * * *
24660603 AAACTTCTCCAAAATTTCATTTTTAACCTCA
1 AAACTTC-CAAAAATTACATTTTT-ACCCCC
* *
24660634 AAACTTCCAAAAATTACATTTTTGCCCTC
1 AAACTTCCAAAAATTACATTTTTACCCCC
* * *
24660663 GAACTTCCAAAAATTCCATTTTTAGCCCCG
1 AAACTTCCAAAAATTACATTTTTA-CCCCC
*
24660693 AAACTTCCAAAAATTACATTTTTACCCTC
1 AAACTTCCAAAAATTACATTTTTACCCCC
* *
24660722 AAACTTCCAAAAATTTCATTTTTGACCCCA
1 AAACTTCCAAAAATTACATTTTT-ACCCCC
*
24660752 AAACCTCCAAAAATTACA-TTTTACCCCC
1 AAACTTCCAAAAATTACATTTTTACCCCC
** * * * *
24660780 GGA-TGTCTAAAAACTCCATTTTTAACCCCG
1 AAACT-TCCAAAAATTACATTTTT-ACCCCC
**
24660810 AAACTTTTAAAAATTACCATTTT
1 AAACTTCCAAAAATTA-CATTTT
24660833 ATCCTTGAAT
Statistics
Matches: 181, Mismatches: 40, Indels: 17
0.76 0.17 0.07
Matches are distributed among these distances:
28 16 0.09
29 58 0.32
30 90 0.50
31 17 0.09
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTTACCCCC
Found at i:24660847 original size:29 final size:28
Alignment explanation
Indices: 24660814--24660892 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 28
24660804 ACCCCGAAAC
24660814 TTTTAAAAATTACCATTTTATCCTT-GAAT
1 TTTTAAAAATTACCATTTTAT--TTCGAAT
* * *
24660843 TTTTAAAAATTTCGATTTTGATTTCGATT
1 TTTTAAAAATTACCATTTT-ATTTCGAAT
*
24660872 TTTCTAAAAATCACCATTTTA
1 TTT-TAAAAATTACCATTTTA
24660893 CCCTCAAACA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
28 2 0.05
29 24 0.59
30 15 0.37
ACGTcount: A:0.33, C:0.13, G:0.05, T:0.49
Consensus pattern (28 bp):
TTTTAAAAATTACCATTTTATTTCGAAT
Found at i:24660969 original size:28 final size:28
Alignment explanation
Indices: 24660934--24661009 Score: 127
Period size: 28 Copynumber: 2.7 Consensus size: 28
24660924 CCAAATTTTC
24660934 CTAAAATTACCATTTTGCCCTCGAGAGT
1 CTAAAATTACCATTTTGCCCTCGAGAGT
*
24660962 -TCAAAATTACCATTTTACCCTCGAGAGT
1 CT-AAAATTACCATTTTGCCCTCGAGAGT
24660990 CTAAAATTACCATTTTGCCC
1 CTAAAATTACCATTTTGCCC
24661010 CCGGGTATCC
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
27 1 0.02
28 42 0.95
29 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (28 bp):
CTAAAATTACCATTTTGCCCTCGAGAGT
Found at i:24662223 original size:14 final size:13
Alignment explanation
Indices: 24662206--24662250 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
24662196 CAAATTATTT
24662206 TTCTCGATTTCTTA
1 TTCTCGATTT-TTA
* *
24662220 TTCTCAATTTTCAA
1 TTCTCGATTTT-TA
24662234 TTCTCGATTTTTA
1 TTCTCGATTTTTA
24662247 TTCT
1 TTCT
24662251 AAATTCTCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 6 0.23
14 20 0.77
ACGTcount: A:0.18, C:0.20, G:0.04, T:0.58
Consensus pattern (13 bp):
TTCTCGATTTTTA
Found at i:24662224 original size:28 final size:27
Alignment explanation
Indices: 24662193--24662255 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 27
24662183 AACTCTTAAC
*
24662193 TCTCAAATTATT-TTTCTCGATTTCTTAT
1 TCTCAAATT-TTAATTCTCGATTT-TTAT
24662221 TCTC-AATTTTCAATTCTCGATTTTTAT
1 TCTCAAATTTT-AATTCTCGATTTTTAT
24662248 TCT-AAATT
1 TCTCAAATT
24662256 CTCAATTCCC
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
26 2 0.06
27 15 0.48
28 14 0.45
ACGTcount: A:0.24, C:0.17, G:0.03, T:0.56
Consensus pattern (27 bp):
TCTCAAATTTTAATTCTCGATTTTTAT
Found at i:24662247 original size:27 final size:28
Alignment explanation
Indices: 24662206--24662263 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 28
24662196 CAAATTATTT
* *
24662206 TTCTCGATTTCTTATTCTCAATTTTCAA
1 TTCTCGATTTCTTATTCTAAATTCTCAA
24662234 TTCTCGATTT-TTATTCTAAATTCTCAA
1 TTCTCGATTTCTTATTCTAAATTCTCAA
24662261 TTC
1 TTC
24662264 CCAAATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 18 0.64
28 10 0.36
ACGTcount: A:0.22, C:0.21, G:0.03, T:0.53
Consensus pattern (28 bp):
TTCTCGATTTCTTATTCTAAATTCTCAA
Found at i:24664981 original size:217 final size:217
Alignment explanation
Indices: 24664606--24665040 Score: 861
Period size: 217 Copynumber: 2.0 Consensus size: 217
24664596 TTTTATTACT
24664606 TAAATGATATTTTAGTACATCAAGTGACAGACAAATAAGTTAGTGTTATTATAATACGAGTTAGT
1 TAAATGATATTTTAGTACATCAAGTGACAGACAAATAAGTTAGTGTTATTATAATACGAGTTAGT
24664671 CTTTTAATTGGCTCCTCTCATAGATGCTTCTGGGTTGTGTGGACATCTTGGCTTCGTATGACTTG
66 CTTTTAATTGGCTCCTCTCATAGATGCTTCTGGGTTGTGTGGACATCTTGGCTTCGTATGACTTG
24664736 GGTTTTTACAGTAATTGTATAACCTTGGTTGGTCTCCTCGCTCTTGAATATCCATACTGCCTCAT
131 GGTTTTTACAGTAATTGTATAACCTTGGTTGGTCTCCTCGCTCTTGAATATCCATACTGCCTCAT
*
24664801 ATCCAATTTGAGGTCGAGTGAC
196 ATCCAAGTTGAGGTCGAGTGAC
24664823 TAAATGATATTTTAGTACATCAAGTGACAGACAAATAAGTTAGTGTTATTATAATACGAGTTAGT
1 TAAATGATATTTTAGTACATCAAGTGACAGACAAATAAGTTAGTGTTATTATAATACGAGTTAGT
24664888 CTTTTAATTGGCTCCTCTCATAGATGCTTCTGGGTTGTGTGGACATCTTGGCTTCGTATGACTTG
66 CTTTTAATTGGCTCCTCTCATAGATGCTTCTGGGTTGTGTGGACATCTTGGCTTCGTATGACTTG
24664953 GGTTTTTACAGTAATTGTATAACCTTGGTTGGTCTCCTCGCTCTTGAATATCCATACTGCCTCAT
131 GGTTTTTACAGTAATTGTATAACCTTGGTTGGTCTCCTCGCTCTTGAATATCCATACTGCCTCAT
24665018 ATCCAAGTTGAGGTCGAGTGAC
196 ATCCAAGTTGAGGTCGAGTGAC
24665040 T
1 T
24665041 TTTCGGCTTG
Statistics
Matches: 217, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
217 217 1.00
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (217 bp):
TAAATGATATTTTAGTACATCAAGTGACAGACAAATAAGTTAGTGTTATTATAATACGAGTTAGT
CTTTTAATTGGCTCCTCTCATAGATGCTTCTGGGTTGTGTGGACATCTTGGCTTCGTATGACTTG
GGTTTTTACAGTAATTGTATAACCTTGGTTGGTCTCCTCGCTCTTGAATATCCATACTGCCTCAT
ATCCAAGTTGAGGTCGAGTGAC
Found at i:24666895 original size:12 final size:11
Alignment explanation
Indices: 24666856--24666906 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
24666846 GGAAATTGTT
* *
24666856 TTAAATTATTT
1 TTAAATAATTA
24666867 TTAAA-AATTA
1 TTAAATAATTA
24666877 TTAAAATAATTAA
1 TT-AAATAATT-A
24666890 TTAAATATATTA
1 TTAAATA-ATTA
24666902 TTAAA
1 TTAAA
24666907 ACTTTTCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
10 5 0.15
11 8 0.24
12 15 0.44
13 6 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TTAAATAATTA
Found at i:24670483 original size:14 final size:15
Alignment explanation
Indices: 24670462--24670492 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
24670452 TATTTTTATA
*
24670462 ATTTTTTTACAATTG
1 ATTTTTTAACAATTG
24670477 ATTTTTTAACAATTG
1 ATTTTTTAACAATTG
24670492 A
1 A
24670493 ACCATTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (15 bp):
ATTTTTTAACAATTG
Found at i:24678765 original size:29 final size:29
Alignment explanation
Indices: 24678732--24678791 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
24678722 TAATTTTGAA
24678732 GTATTTGGACTTAAAGCTGCAATTTATAG
1 GTATTTGGACTTAAAGCTGCAATTTATAG
*
24678761 GTATTTGGACTTAATGCTGCAATTTATAG
1 GTATTTGGACTTAAAGCTGCAATTTATAG
24678790 GT
1 GT
24678792 GGTCTTACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.40
Consensus pattern (29 bp):
GTATTTGGACTTAAAGCTGCAATTTATAG
Found at i:24684934 original size:24 final size:24
Alignment explanation
Indices: 24684907--24684964 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
24684897 ATTATTTTTT
*
24684907 TATTTTTTTAAAATATTCAT-ATTA
1 TATTTTTTTAAAAT-TTAATAATTA
* * *
24684931 TATTATTTTAATATTTAATAATTT
1 TATTTTTTTAAAATTTAATAATTA
24684955 TATTTTTTTA
1 TATTTTTTTA
24684965 TTTATTGAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (24 bp):
TATTTTTTTAAAATTTAATAATTA
Found at i:24686163 original size:13 final size:13
Alignment explanation
Indices: 24686142--24686173 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
24686132 TGATTTATTT
*
24686142 TTTACATATTTTA
1 TTTAAATATTTTA
24686155 TTTAAATATTTTA
1 TTTAAATATTTTA
24686168 TTTAAA
1 TTTAAA
24686174 AAATATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTAAATATTTTA
Found at i:24689042 original size:15 final size:16
Alignment explanation
Indices: 24689024--24689056 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
24689014 AAATTAAAAT
*
24689024 AAATTT-ATTTAATTG
1 AAATTTAATATAATTG
24689039 AAATTTAATATAATTG
1 AAATTTAATATAATTG
24689055 AA
1 AA
24689057 GGATCAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
AAATTTAATATAATTG
Found at i:24691388 original size:80 final size:79
Alignment explanation
Indices: 24691255--24691548 Score: 318
Period size: 80 Copynumber: 3.8 Consensus size: 79
24691245 TTGTACGAAC
* * ** *
24691255 CCCTATGATGGTTGAGATCCTGCATATGTTGCATATTCTTGACAGCTTGTGTGAGCAGCATCGCG
1 CCCTACGATGGCTGAGATCCTGCATATGTTGCGGATTCTTGATAGCTTGTGTGAGCAGCATCGC-
24691320 AGTGGCTAATATGGA
65 AGTGGCTAATATGGA
* *
24691335 CCCTACAATGGCTGAGATCCTGCATATGTTGCGGATTCTTGATAGCTTGTGT--G-AG--TAGCA
1 CCCTACGATGGCTGAGATCCTGCATATGTTGCGGATTCTTGATAGCTTGTGTGAGCAGCATCGCA
24691395 -T--CTAATATGGA
66 GTGGCTAATATGGA
* * * * * *
24691406 CCCTACGATGGCTGAGATCCTGTATGTGTTGCGGATTCTTGATAGCTTGTGTAAGTAGCATTGTA
1 CCCTACGATGGCTGAGATCCTGCATATGTTGCGGATTCTTGATAGCTTGTGTGAGCAGCATCGCA
* *
24691471 GTGGGTACTATGGA
66 GTGGCTAATATGGA
* * * * *
24691485 CCATATCGATGGTTGAGATCCTGCATATGTTACGGATTC-TCATCAACTTGTGTGAGCAGCATCG
1 CCCTA-CGATGGCTGAGATCCTGCATATGTTGCGGATTCTTGAT-AGCTTGTGTGAGCAGCATCG
24691549 TATACTGGTT
Statistics
Matches: 180, Mismatches: 24, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
71 59 0.33
73 2 0.01
74 3 0.02
75 3 0.02
76 3 0.02
77 3 0.02
78 1 0.01
79 15 0.08
80 91 0.51
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.32
Consensus pattern (79 bp):
CCCTACGATGGCTGAGATCCTGCATATGTTGCGGATTCTTGATAGCTTGTGTGAGCAGCATCGCA
GTGGCTAATATGGA
Found at i:24691417 original size:71 final size:71
Alignment explanation
Indices: 24691325--24691547 Score: 250
Period size: 71 Copynumber: 3.0 Consensus size: 71
24691315 TCGCGAGTGG
*
24691325 CTAATATGGACCCTACAATGGCTGAGATCCTGCATATGTTGCGGATTCTTGATAGCTTGTGTGAG
1 CTAATATGGACCCTACGATGGCTGAGATCCTGCATATGTTGCGGATTCTTGATAGCTTGTGTGAG
24691390 TAGCAT
66 TAGCAT
* * *
24691396 CTAATATGGACCCTACGATGGCTGAGATCCTGTATGTGTTGCGGATTCTTGATAGCTTGTGTAAG
1 CTAATATGGACCCTACGATGGCTGAGATCCTGCATATGTTGCGGATTCTTGATAGCTTGTGTGAG
24691461 TAGCATT
66 TAGCA-T
* * * * * *
24691468 GTAGTGGGTACTATGGACCATATCGATGGTTGAGATCCTGCATATGTTACGGATTC-TCATCAAC
1 CTA------A-TATGGACCCTA-CGATGGCTGAGATCCTGCATATGTTGCGGATTCTTGAT-AGC
*
24691532 TTGTGTGAGCAGCAT
57 TTGTGTGAGTAGCAT
24691547 C
1 C
24691548 GTATACTGGT
Statistics
Matches: 127, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
71 66 0.52
72 3 0.02
78 1 0.01
79 14 0.11
80 43 0.34
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (71 bp):
CTAATATGGACCCTACGATGGCTGAGATCCTGCATATGTTGCGGATTCTTGATAGCTTGTGTGAG
TAGCAT
Found at i:24691535 original size:151 final size:151
Alignment explanation
Indices: 24691255--24691547 Score: 374
Period size: 151 Copynumber: 1.9 Consensus size: 151
24691245 TTGTACGAAC
* * * *
24691255 CCCTATGATGGTTGAGATCCTGCATATGTTGCATATTCTTGACAGCTTGTGTGAGCAGCATCGCG
1 CCCTACGATGGCTGAGATCCTGCATATGTTGCAGATTCTTGACAGCTTGTGTAAGCAGCATCGCG
* * * *
24691320 AGTGGCTAATATGGACCCTACAATGGCTGAGATCCTGCATATGTTGCGGATTCTTGATAGCTTGT
66 AGTGGCTAATATGGACCATACAATGGCTGAGATCCTGCATATGTTACGGATTCTTCATAACTTGT
*
24691385 GTGAGTAGCATCTAATATGGA
131 GTGAGCAGCATCTAATATGGA
* * * * * * *
24691406 CCCTACGATGGCTGAGATCCTGTATGTGTTGCGGATTCTTGATAGCTTGTGTAAGTAGCATTG-T
1 CCCTACGATGGCTGAGATCCTGCATATGTTGCAGATTCTTGACAGCTTGTGTAAGCAGCATCGCG
* * * *
24691470 AGTGGGTACTATGGACCATATCGATGGTTGAGATCCTGCATATGTTACGGATTC-TCATCAACTT
66 AGTGGCTAATATGGACCATA-CAATGGCTGAGATCCTGCATATGTTACGGATTCTTCAT-AACTT
24691534 GTGTGAGCAGCATC
129 GTGTGAGCAGCATC
24691548 GTATACTGGT
Statistics
Matches: 120, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
150 20 0.17
151 100 0.83
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (151 bp):
CCCTACGATGGCTGAGATCCTGCATATGTTGCAGATTCTTGACAGCTTGTGTAAGCAGCATCGCG
AGTGGCTAATATGGACCATACAATGGCTGAGATCCTGCATATGTTACGGATTCTTCATAACTTGT
GTGAGCAGCATCTAATATGGA
Found at i:24693913 original size:30 final size:30
Alignment explanation
Indices: 24693879--24694039 Score: 166
Period size: 30 Copynumber: 5.4 Consensus size: 30
24693869 GCCAAATTCA
* * * *
24693879 AATTTTTGGAAAGTTTAGGGGTTAAAATAT
1 AATTTTTGGAAAATTTAAGGGTCAAAACAT
24693909 AATTTTTGGAAAATTTAAGGGTCAAAACAT
1 AATTTTTGGAAAATTTAAGGGTCAAAACAT
*
24693939 AATTTTTGGAAAATTTAAGCGTCAAAACAT
1 AATTTTTGGAAAATTTAAGGGTCAAAACAT
* **
24693969 AATTTTTAGAAAATTTGGGGGTCAAATA-AT
1 AATTTTTGGAAAATTTAAGGGTCAAA-ACAT
* **
24693999 -ATTTTT-AAAAAGTTCGAGGGTCAAAACAT
1 AATTTTTGGAAAA-TTTAAGGGTCAAAACAT
* *
24694028 ATTTTTTAGAAA
1 AATTTTTGGAAA
24694040 GCTCGGGGGG
Statistics
Matches: 112, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
28 5 0.04
29 19 0.17
30 84 0.75
31 4 0.04
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.36
Consensus pattern (30 bp):
AATTTTTGGAAAATTTAAGGGTCAAAACAT
Found at i:24694019 original size:29 final size:29
Alignment explanation
Indices: 24693959--24694068 Score: 116
Period size: 29 Copynumber: 3.7 Consensus size: 29
24693949 AAATTTAAGC
*
24693959 GTCAAAACATAATTTTTAGAAAA-TTTGGGG
1 GTCAAAACAT-ATTTTTA-AAAAGTTCGGGG
*
24693989 GTCAAATA-ATATTTTTAAAAAGTTCGAGG
1 GTCAAA-ACATATTTTTAAAAAGTTCGGGG
* *
24694018 GTCAAAACATATTTTTTAGAAAGCTCGGGGG
1 GTCAAAACATA-TTTTTAAAAAGTTC-GGGG
24694049 GTCAAAACATCATTTTTAAA
1 GTCAAAACAT-ATTTTTAAA
24694069 TGAAACATGA
Statistics
Matches: 68, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
28 5 0.07
29 21 0.31
30 20 0.29
31 21 0.31
32 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (29 bp):
GTCAAAACATATTTTTAAAAAGTTCGGGG
Found at i:24694425 original size:32 final size:32
Alignment explanation
Indices: 24694375--24694436 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
24694365 CAAAATCCTT
* *
24694375 AAAAAAATCACTTTATCC-TCTTATTTTTTTTA
1 AAAAAAACCACTTCATCCTTCTT-TTTTTTTTA
*
24694407 AAAAAAACCCCTTCATCCTTCTTTTTTTTT
1 AAAAAAACCACTTCATCCTTCTTTTTTTTT
24694437 CTATCCATGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 22 0.85
33 4 0.15
ACGTcount: A:0.31, C:0.21, G:0.00, T:0.48
Consensus pattern (32 bp):
AAAAAAACCACTTCATCCTTCTTTTTTTTTTA
Found at i:24694738 original size:22 final size:23
Alignment explanation
Indices: 24694713--24694769 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
24694703 ATTTTTTTAT
24694713 GTTTTTATTTCTTTTTTA-T-TTC
1 GTTTTTATTT-TTTTTTACTCTTC
**
24694735 GTTTTTAGGTTTTTTTACTCTTC
1 GTTTTTATTTTTTTTTACTCTTC
24694758 -TTTTTATTTTTT
1 GTTTTTATTTTTT
24694770 GCAGATTGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 7 0.24
22 19 0.66
23 3 0.10
ACGTcount: A:0.09, C:0.09, G:0.07, T:0.75
Consensus pattern (23 bp):
GTTTTTATTTTTTTTTACTCTTC
Found at i:24696412 original size:13 final size:14
Alignment explanation
Indices: 24696377--24696411 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
24696367 GAAAAGTAAG
24696377 TCATTTTTCAAATA
1 TCATTTTTCAAATA
24696391 TCATTTTTCGAAA-A
1 TCATTTTTC-AAATA
24696405 TCATTTT
1 TCATTTT
24696412 CAATGAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 17 0.85
15 3 0.15
ACGTcount: A:0.31, C:0.14, G:0.03, T:0.51
Consensus pattern (14 bp):
TCATTTTTCAAATA
Found at i:24698111 original size:42 final size:42
Alignment explanation
Indices: 24698041--24698189 Score: 120
Period size: 42 Copynumber: 3.5 Consensus size: 42
24698031 CTCGATTAGG
* * * *
24698041 GGTAAAAGATTGGAT-GATGGGTTCAATCTGCCCCATGGTCGA
1 GGTAAGAGATTGGATAG-TGGCTTAAATCTGCCCCATGATCGA
* * **
24698083 GGTAAGAGATTGGATAGTGTCTTAAATCTGCCCCTCTTGATTTA
1 GGTAAGAGATTGGATAGTGGCTTAAATCTG-CCC-CATGATCGA
* * * * *
24698127 GGAGTAAAAGAATGGATGGTGGCTTCAATCTGCCCCATGATCGG
1 -G-GTAAGAGATTGGATAGTGGCTTAAATCTGCCCCATGATCGA
*
24698171 GGTAAGAAATTGGATAGTG
1 GGTAAGAGATTGGATAGTG
24698190 CTATCTTTAA
Statistics
Matches: 81, Mismatches: 21, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
42 38 0.47
43 5 0.06
44 10 0.12
45 4 0.05
46 24 0.30
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.28
Consensus pattern (42 bp):
GGTAAGAGATTGGATAGTGGCTTAAATCTGCCCCATGATCGA
Found at i:24698157 original size:46 final size:46
Alignment explanation
Indices: 24698018--24698330 Score: 263
Period size: 46 Copynumber: 6.9 Consensus size: 46
24698008 AGATAGTAGT
* * *
24698018 TTCAA-CTGCCCCTCTCGA-TTAGGGGTAAAAGATTGGATGATGGG
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGGC
* * * * * * *
24698062 TTCAATCTG-CCC-CATG--GTCGAGGTAAGAGATTGGATAGTGTC
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGGC
* * * *
24698104 TTAAATCTGCCCCTCTTGATTTAGGAGTAAAAGAATGGATGGTGGC
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGGC
* * *
24698150 TTCAATCTG-CCC-CATGA--TCGGGGTAAGAA-ATTGGATAGT-GC
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAA-AAGATTGGATGGTGGC
* * * *
24698191 TATCTTTAATCCGCCTCTCTTGACTTAGAGGTAAAAGATTGGATGGTGAC
1 T-TC---AATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGGC
* *
24698241 TTCAATCTGCCCCACTTGACTTAGGGGTAAAAGATTAGATGGTGATGTC
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTG--G-C
24698290 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATG
1 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATG
24698331 ATGATGTAAC
Statistics
Matches: 209, Mismatches: 41, Indels: 33
0.74 0.14 0.12
Matches are distributed among these distances:
41 3 0.01
42 43 0.21
43 7 0.03
44 15 0.07
45 11 0.05
46 64 0.31
47 4 0.02
48 2 0.01
49 58 0.28
50 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (46 bp):
TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGGC
Found at i:24698185 original size:88 final size:88
Alignment explanation
Indices: 24698023--24698330 Score: 325
Period size: 88 Copynumber: 3.4 Consensus size: 88
24698013 GTAGTTTCAA
* * * * * *
24698023 CTGCCCCTCTCGA-TTAGGGGTAAAAGATTGGATGATGGGTTCAATCTGCCCCATGGTCGAGGTA
1 CTGCCCCTCTTGACTTAGGAGTAAAAGATTGGATGGTGGCTTCAATCTGCCCCATGATCGGGGTA
*
24698087 AGAGATTGGATAGTGTCTTAAAT
66 AGAAATTGGATAGTGTCTTAAAT
* *
24698110 CTGCCCCTCTTGATTTAGGAGTAAAAGAATGGATGGTGGCTTCAATCTGCCCCATGATCGGGGTA
1 CTGCCCCTCTTGACTTAGGAGTAAAAGATTGGATGGTGGCTTCAATCTGCCCCATGATCGGGGTA
*
24698175 AGAAATTGGATAGTGCTATCTTTAAT
66 AGAAATTGGATAGTG---TCTTAAAT
* * * *
24698201 CCGCCTCTCTTGACTTA-GAGGTAAAAGATTGGATGGTGACTTCAATCTGCCCCACTTGACTTAG
1 CTGCCCCTCTTGACTTAGGA-GTAAAAGATTGGATGGTGGCTTCAATCTGCCCCA--TGA--TCG
* * *
24698265 GGGTAA-AAGATTAGATGGTGATGTCTTCAAT
61 GGGTAAGAA-ATTGGAT--AG-TGTCTTAAAT
*
24698296 CTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATG
1 CTGCCCCTCTTGACTTAGGAGTAAAAGATTGGATG
24698331 ATGATGTAAC
Statistics
Matches: 186, Mismatches: 21, Indels: 20
0.82 0.09 0.09
Matches are distributed among these distances:
87 12 0.06
88 59 0.32
90 2 0.01
91 53 0.28
93 3 0.02
94 2 0.01
95 51 0.27
96 1 0.01
97 1 0.01
98 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (88 bp):
CTGCCCCTCTTGACTTAGGAGTAAAAGATTGGATGGTGGCTTCAATCTGCCCCATGATCGGGGTA
AGAAATTGGATAGTGTCTTAAAT
Found at i:24698312 original size:49 final size:49
Alignment explanation
Indices: 24698100--24698337 Score: 246
Period size: 49 Copynumber: 5.1 Consensus size: 49
24698090 GATTGGATAG
* * * *
24698100 TGTCTTAAATCTGCCCCTCTTGATTTAGGAGTAAAAGAATGGATGGTG-
1 TGTCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGA
* * * *
24698148 -G-CTTCAATCTG-CCC-CATGA--TCGGGGTAAGAA-ATTGGATAGTGC
1 TGTCTTCAATCTGCCCCTCTTGACTTAGGGGTAA-AAGATTGGATGGTGA
* * * * *
24698191 TATCTTTAATCCGCCTCTCTTGACTTAGAGGTAAAAGATTGGATGGTGA
1 TGTCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGA
* *
24698240 ---CTTCAATCTGCCCCACTTGACTTAGGGGTAAAAGATTAGATGGTGA
1 TGTCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGA
*
24698286 TGTCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGATGA
1 TGTCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGA
24698335 TGT
1 TGT
24698338 AACTTCACTC
Statistics
Matches: 154, Mismatches: 24, Indels: 23
0.77 0.12 0.11
Matches are distributed among these distances:
42 16 0.10
43 2 0.01
44 4 0.03
45 11 0.07
46 51 0.33
47 5 0.03
48 2 0.01
49 63 0.41
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.32
Consensus pattern (49 bp):
TGTCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGA
Done.