Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 299 of 335
Found at i:89046215 original size:2 final size:2
Alignment explanation
Indices: 89046210--89046246 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
89046200 AAAAAAAAAA
89046210 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
89046247 GACAGGATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:89047896 original size:30 final size:30
Alignment explanation
Indices: 89047860--89047922 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
89047850 ACTTATTTTA
89047860 TTGTTAACTTTGTTATTATTTTAAAGACAT
1 TTGTTAACTTTGTTATTATTTTAAAGACAT
* * * *
89047890 TTGTTAATTTTTTTATTATTTTAGAGGCAT
1 TTGTTAACTTTGTTATTATTTTAAAGACAT
89047920 TTG
1 TTG
89047923 CTTGTTAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.05, G:0.13, T:0.57
Consensus pattern (30 bp):
TTGTTAACTTTGTTATTATTTTAAAGACAT
Found at i:89048027 original size:19 final size:20
Alignment explanation
Indices: 89047998--89048045 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
89047988 TTGTTGGAAA
*
89047998 ATATTTA-TTTTGATGT-TT
1 ATATTTATTTTTTATGTATT
*
89048016 TTA-TTATTTTTTATGTATT
1 ATATTTATTTTTTATGTATT
89048035 ATATTTATTTT
1 ATATTTATTTT
89048046 AAATTTATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 3 0.12
18 10 0.42
19 4 0.17
20 7 0.29
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (20 bp):
ATATTTATTTTTTATGTATT
Found at i:89050417 original size:52 final size:52
Alignment explanation
Indices: 89050355--89050458 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 52
89050345 TATAGTTTAA
89050355 CCTATTTTTAAATAGTAAAACAAGTCCTGCAAAGTCAAGCCAAATTTAAACT
1 CCTATTTTTAAATAGTAAAACAAGTCCTGCAAAGTCAAGCCAAATTTAAACT
* *
89050407 CCTATTTTTAAATAGTAAAACAAGTCCTGCGAAGTCAATCCAAATTTAAACT
1 CCTATTTTTAAATAGTAAAACAAGTCCTGCAAAGTCAAGCCAAATTTAAACT
89050459 ATCTAAACCC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.30
Consensus pattern (52 bp):
CCTATTTTTAAATAGTAAAACAAGTCCTGCAAAGTCAAGCCAAATTTAAACT
Found at i:89050681 original size:21 final size:21
Alignment explanation
Indices: 89050657--89050720 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
89050647 ACCATAATCT
89050657 ATTTTTATAAAAATATTTAAA
1 ATTTTTATAAAAATATTTAAA
* * *
89050678 A-TTTAAAAGAAAATATATAAA
1 ATTTTTATA-AAAATATTTAAA
**
89050699 AAATTTATAAAAAT-TTTAAA
1 ATTTTTATAAAAATATTTAAA
89050719 AT
1 AT
89050721 ATAAAAGAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
20 11 0.33
21 18 0.55
22 4 0.12
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
ATTTTTATAAAAATATTTAAA
Found at i:89050738 original size:26 final size:27
Alignment explanation
Indices: 89050687--89050753 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 27
89050677 AATTTAAAAG
*
89050687 AAAATATATAAAAAATTTATAAAAATTTT
1 AAAATATA-AAAAAATTTAT-AAAATTAT
89050716 AAAATATAAAAGAAA-TTAT-AAATTAT
1 AAAATATAAAA-AAATTTATAAAATTAT
*
89050742 AAATTATAAAAA
1 AAAATATAAAAA
89050754 TATGTGTATC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
25 1 0.03
26 16 0.46
28 7 0.20
29 11 0.31
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (27 bp):
AAAATATAAAAAAATTTATAAAATTAT
Found at i:89050749 original size:42 final size:42
Alignment explanation
Indices: 89050661--89050756 Score: 126
Period size: 42 Copynumber: 2.3 Consensus size: 42
89050651 TAATCTATTT
* *
89050661 TTATAAAAATATTTAAAATTTAAAAGAAAATATATAAAAAAT
1 TTATAAAAATATTTAAAATATAAAAGAAAATATATAAAAAAA
89050703 TTATAAAAAT-TTTAAAATATAAAAG-AAAT-TATAAATTATAAA
1 TTATAAAAATATTTAAAATATAAAAGAAAATATATAAA--A-AAA
89050745 TTATAAAAATAT
1 TTATAAAAATAT
89050757 GTGTATCTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
39 6 0.12
40 4 0.08
41 15 0.31
42 22 0.46
43 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (42 bp):
TTATAAAAATATTTAAAATATAAAAGAAAATATATAAAAAAA
Found at i:89051539 original size:66 final size:66
Alignment explanation
Indices: 89051433--89051556 Score: 248
Period size: 66 Copynumber: 1.9 Consensus size: 66
89051423 TAACTTGTTC
89051433 TAAAAGCATGAGATGTCTTCCAAATGCAATGCATGCTGACATGTATGATATTTAAAAATGGCTTA
1 TAAAAGCATGAGATGTCTTCCAAATGCAATGCATGCTGACATGTATGATATTTAAAAATGGCTTA
89051498 T
66 T
89051499 TAAAAGCATGAGATGTCTTCCAAATGCAATGCATGCTGACATGTATGATATTTAAAAA
1 TAAAAGCATGAGATGTCTTCCAAATGCAATGCATGCTGACATGTATGATATTTAAAAA
89051557 GGGTTTAATG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.31
Consensus pattern (66 bp):
TAAAAGCATGAGATGTCTTCCAAATGCAATGCATGCTGACATGTATGATATTTAAAAATGGCTTA
T
Found at i:89056380 original size:20 final size:22
Alignment explanation
Indices: 89056354--89056397 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
89056344 CATAATCTAT
* *
89056354 TTTTTAAA-AAAATATTTAAAA
1 TTTTAAAAGAAAATATATAAAA
89056375 TTTTAAAAGAAAATATATAAAA
1 TTTTAAAAGAAAATATATAAAA
89056397 T
1 T
89056398 ATATAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
TTTTAAAAGAAAATATATAAAA
Found at i:89056398 original size:9 final size:9
Alignment explanation
Indices: 89056384--89056418 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
89056374 ATTTTAAAAG
89056384 AAAATATAT
1 AAAATATAT
89056393 AAAATATAT
1 AAAATATAT
* *
89056402 AAAATTTTT
1 AAAATATAT
89056411 AAAATATA
1 AAAATATA
89056419 AAAGAAATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
AAAATATAT
Found at i:89060275 original size:2 final size:2
Alignment explanation
Indices: 89060268--89060293 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
89060258 TATGCCCATA
89060268 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
89060294 TGTAGCACCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:89061247 original size:27 final size:26
Alignment explanation
Indices: 89061210--89061324 Score: 140
Period size: 27 Copynumber: 4.3 Consensus size: 26
89061200 AGCATGGCTG
* *
89061210 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
89061236 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
89061264 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
89061291 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
*
89061318 TCAGAAC
1 CCAGAAC
89061325 GCTTCCTCCA
Statistics
Matches: 79, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
26 5 0.06
27 57 0.72
28 17 0.22
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:89061274 original size:54 final size:54
Alignment explanation
Indices: 89061210--89061324 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 54
89061200 AGCATGGCTG
*
89061210 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
89061264 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
*
89061318 TCAGAAC
1 CCAGAAC
89061325 GCTTCCTCCA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 36 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:89062975 original size:26 final size:26
Alignment explanation
Indices: 89062938--89063046 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
89062928 CATGAAATTC
*
89062938 TTAT-ATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
89062963 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
*
89062989 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCCA
* *
89063015 TTATCATTGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCCA
89063041 TTATCA
1 TTATCA
89063047 ATTTGTACCA
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
25 4 0.05
26 76 0.95
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.35
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCCA
Found at i:89065821 original size:3 final size:3
Alignment explanation
Indices: 89065813--89065841 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
89065803 AGGTGAACCA
89065813 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
89065842 TTTTCTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:89071947 original size:21 final size:21
Alignment explanation
Indices: 89071921--89071961 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
89071911 ATCTGCTCAA
* *
89071921 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
89071942 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
89071962 TCGCTTGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:89082314 original size:2 final size:2
Alignment explanation
Indices: 89082307--89082339 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
89082297 ATCTATGCAC
89082307 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
89082340 AGGTATCTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:89083959 original size:2 final size:2
Alignment explanation
Indices: 89083952--89083994 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
89083942 ATTGAAAGGG
*
89083952 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
89083994 A
1 A
89083995 AAAGTATGTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:89085470 original size:26 final size:26
Alignment explanation
Indices: 89085434--89085543 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
89085424 TGATACAAAT
89085434 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
89085460 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
89085486 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
89085512 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
89085538 TGATAA
1 TGATAA
89085544 GAATTTCATG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:89087056 original size:26 final size:26
Alignment explanation
Indices: 89087026--89087078 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
89087016 TTTATAGTTT
89087026 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
89087052 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
89087078 T
1 T
89087079 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:89088988 original size:24 final size:24
Alignment explanation
Indices: 89088956--89089008 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
89088946 TAATTTGTGC
* *
89088956 ATATTAAAATAAAAACATATG-GAA
1 ATATCAAAAT-AAAACATATGAAAA
*
89088980 ATATCAAAATGAAACATATGAAAA
1 ATATCAAAATAAAACATATGAAAA
89089004 ATATC
1 ATATC
89089009 CAATTGGTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.25
Consensus pattern (24 bp):
ATATCAAAATAAAACATATGAAAA
Found at i:89089611 original size:10 final size:10
Alignment explanation
Indices: 89089596--89089621 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
89089586 TATTTTTATT
89089596 TTTAAAAATA
1 TTTAAAAATA
89089606 TTTAAAAATA
1 TTTAAAAATA
89089616 TTTAAA
1 TTTAAA
89089622 TATTAGTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
TTTAAAAATA
Found at i:89089642 original size:26 final size:25
Alignment explanation
Indices: 89089613--89089697 Score: 68
Period size: 26 Copynumber: 3.3 Consensus size: 25
89089603 ATATTTAAAA
89089613 ATATTTAAATATTAGTATAAAATATT
1 ATATTTAAATATTA-TATAAAATATT
*
89089639 ATATTTTTTAATATTAT-TAAACATA-T
1 ATA--TTTAAATATTATATAAA-ATATT
* **
89089665 ATATTTAATTATTAATATAATTTATT
1 ATATTTAAATATT-ATATAAAATATT
89089691 AT-TTTAA
1 ATATTTAA
89089698 TAAATTATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
24 8 0.17
25 9 0.19
26 17 0.35
27 4 0.08
28 10 0.21
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (25 bp):
ATATTTAAATATTATATAAAATATT
Found at i:89092665 original size:47 final size:47
Alignment explanation
Indices: 89092600--89092893 Score: 482
Period size: 47 Copynumber: 6.3 Consensus size: 47
89092590 ATAAGATATG
* *
89092600 TATATGTGGTAAAGCCGAATGGCCAATGTGACGAATGTGAATGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAATGTGTA
*
89092647 TATATGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAATATGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAATGTGTA
*
89092694 TATATGTGATAAGGCCAAATGGCCAATGTGACGAATGTG-ATGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAATGTGTA
89092740 TATATGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAATGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAATGTGTA
* *
89092787 TATATGTGATACGGCCGAATGGCCAATGTGATGAATGTGAATGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAATGTGTA
* * * *
89092834 TATATGTGATAAGGCCAAATGGCCAATGTGATGGATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAATGTGTA
*
89092881 TAAATGTGATAAG
1 TATATGTGATAAG
89092894 TCCCGAAGGG
Statistics
Matches: 233, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
46 44 0.19
47 189 0.81
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.28
Consensus pattern (47 bp):
TATATGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAATGTGTA
Found at i:89092770 original size:22 final size:22
Alignment explanation
Indices: 89092743--89092865 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
89092733 ATGTGTATAT
89092743 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* * * **
89092765 ATGTGACGAATG-TGAATGTGTATA
1 ATGTGA-TAAGGCCGAATG-G-CCA
*
89092789 TATGTGATACGGCCGAATGGCCA
1 -ATGTGATAAGGCCGAATGGCCA
* * **
89092812 ATGTGATGAATG-TGAATGTGTATA
1 ATGTGAT-AAGGCCGAATG-G-CCA
*
89092836 TATGTGATAAGGCCAAATGGCCA
1 -ATGTGATAAGGCCGAATGGCCA
89092859 ATGTGAT
1 ATGTGAT
89092866 GGATGTGAAA
Statistics
Matches: 70, Mismatches: 21, Indels: 20
0.63 0.19 0.18
Matches are distributed among these distances:
22 30 0.43
23 9 0.13
24 9 0.13
25 22 0.31
ACGTcount: A:0.32, C:0.11, G:0.29, T:0.28
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:89092852 original size:140 final size:141
Alignment explanation
Indices: 89092600--89092893 Score: 500
Period size: 140 Copynumber: 2.1 Consensus size: 141
89092590 ATAAGATATG
* *
89092600 TATATGTGGTAAAGCCGAATGGCCAATGTGACGAATGTGAATGTGTATATATGTGATAAGGCCGA
1 TATATGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAATGTGTATATATGTGATAAGGCCGA
89092665 ATGGCCAATGTGACGAATGTGAATATGTATATATGTGATAAGGCCAAATGGCCAATGTGACGAAT
66 ATGGCCAATGTGACGAATGTGAATATGTATATATGTGATAAGGCCAAATGGCCAATGTGACGAAT
*
89092730 GTG-ATGTGTA
131 GTGAAAGTGTA
*
89092740 TATATGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAATGTGTATATATGTGATACGGCCGA
1 TATATGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAATGTGTATATATGTGATAAGGCCGA
* * * *
89092805 ATGGCCAATGTGATGAATGTGAATGTGTATATATGTGATAAGGCCAAATGGCCAATGTGATGGAT
66 ATGGCCAATGTGACGAATGTGAATATGTATATATGTGATAAGGCCAAATGGCCAATGTGACGAAT
89092870 GTGAAAGTGTA
131 GTGAAAGTGTA
*
89092881 TAAATGTGATAAG
1 TATATGTGATAAG
89092894 TCCCGAAGGG
Statistics
Matches: 144, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
140 126 0.88
141 18 0.12
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.28
Consensus pattern (141 bp):
TATATGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAATGTGTATATATGTGATAAGGCCGA
ATGGCCAATGTGACGAATGTGAATATGTATATATGTGATAAGGCCAAATGGCCAATGTGACGAAT
GTGAAAGTGTA
Found at i:89096159 original size:92 final size:93
Alignment explanation
Indices: 89096035--89096287 Score: 292
Period size: 92 Copynumber: 2.8 Consensus size: 93
89096025 TTAAAAAAAG
*
89096035 AAAAGCAATTAAG--TCTCCTTTTTTTTTTTTGCACTCAATTGGATAGC-TGAACTTTCAAGGTG
1 AAAAGCAATTAAGCCTCTCCTTTTTTTTTTTTGCACTCAATTGGATA-CTTGAACTTTCAAAGTG
*
89096097 TATCAAAAAGG-CTCTCAAACTTTTT-AAA
65 CATCAAAAAGGTC-CTCAAACTTTTTCAAA
* * * *
89096125 AAAAGTAATTAAGCCTCTGCTTTTTTTTTTTTGCACTCAATTGGGTACTTGAA-TATTCAAAATG
1 AAAAGCAATTAAGCCTCTCCTTTTTTTTTTTTGCACTCAATTGGATACTTGAACT-TTCAAAGTG
* *
89096189 CATTAAAAAGGTCCTCAAATTTTTTCAAA
65 CATCAAAAAGGTCCTCAAACTTTTTCAAA
** * *
89096218 AAAATGCAATTAA-CC-C-CCTACTTTTTTTTTGCACT-AACTGGATACTTGAACTGTCAAAGTG
1 AAAA-GCAATTAAGCCTCTCCTTTTTTTTTTTTGCACTCAATTGGATACTTGAACTTTCAAAGTG
89096279 CATCAAAAA
65 CATCAAAAA
89096288 AGCCCTGTGA
Statistics
Matches: 138, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
90 40 0.29
91 19 0.14
92 62 0.45
93 10 0.07
94 7 0.05
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (93 bp):
AAAAGCAATTAAGCCTCTCCTTTTTTTTTTTTGCACTCAATTGGATACTTGAACTTTCAAAGTGC
ATCAAAAAGGTCCTCAAACTTTTTCAAA
Found at i:89096418 original size:19 final size:19
Alignment explanation
Indices: 89096396--89096451 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
89096386 TAAAATCAAT
89096396 AAAATATATAAAAATTAGA
1 AAAATATATAAAAATTAGA
* *
89096415 AAAAT-TATAAAATTTTATA
1 AAAATATATAAAA-ATTAGA
*
89096434 AAAATCATAAAAAAATTA
1 AAAAT-ATATAAAAATTA
89096452 TAAATTGCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
18 7 0.23
19 14 0.47
20 3 0.10
21 6 0.20
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAATATATAAAAATTAGA
Found at i:89096443 original size:9 final size:9
Alignment explanation
Indices: 89096396--89096446 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
89096386 TAAAATCAAT
89096396 AAAATATATA
1 AAAAT-TATA
*
89096406 AAAATTAGA
1 AAAATTATA
89096415 AAAATTATA
1 AAAATTATA
*
89096424 AAATTTTATA
1 AAA-ATTATA
*
89096434 AAAATCATA
1 AAAATTATA
89096443 AAAA
1 AAAA
89096447 AATTATAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 22 0.63
10 13 0.37
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (9 bp):
AAAATTATA
Found at i:89096656 original size:21 final size:18
Alignment explanation
Indices: 89096635--89096707 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 18
89096625 GTACTATAAT
89096635 TTTTATATATTTTTTACGAA
1 TTTTATAT-TTTTTTAC-AA
* *
89096655 TTTTATATTTCTTTACATTT
1 TTTTATATTTTTTTACA--A
*
89096675 TTTTATAATTTTCTTACAA
1 TTTTAT-ATTTTTTTACAA
89096694 TTTTATATTTTTTT
1 TTTTATATTTTTTT
89096708 CTATTTTTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
18 8 0.18
19 13 0.30
20 14 0.32
21 9 0.20
ACGTcount: A:0.25, C:0.07, G:0.01, T:0.67
Consensus pattern (18 bp):
TTTTATATTTTTTTACAA
Found at i:89096686 original size:39 final size:39
Alignment explanation
Indices: 89096634--89096725 Score: 116
Period size: 39 Copynumber: 2.3 Consensus size: 39
89096624 GGTACTATAA
89096634 TTTTTATATATTTT-TTACGAATTTTATATTTCTTTAC-ATT
1 TTTTTATA-ATTTTCTTAC-AATTTTATATTT-TTTACTATT
*
89096674 TTTTTATAATTTTCTTACAATTTTATATTTTTTTCTATT
1 TTTTTATAATTTTCTTACAATTTTATATTTTTTACTATT
*
89096713 TTTATTAAAATTT
1 TTT-TTATAATTT
89096726 AATAATTTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
38 4 0.09
39 23 0.49
40 20 0.43
ACGTcount: A:0.26, C:0.07, G:0.01, T:0.66
Consensus pattern (39 bp):
TTTTTATAATTTTCTTACAATTTTATATTTTTTACTATT
Found at i:89096698 original size:29 final size:29
Alignment explanation
Indices: 89096666--89096725 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
89096656 TTTATATTTC
* *
89096666 TTTACATTTTTTTATAATTTTCTTACAAT
1 TTTACATTTTTTTATAATTTTATTAAAAT
* * *
89096695 TTTATATTTTTTTCTATTTTTATTAAAAT
1 TTTACATTTTTTTATAATTTTATTAAAAT
89096724 TT
1 TT
89096726 AATAATTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (29 bp):
TTTACATTTTTTTATAATTTTATTAAAAT
Found at i:89097068 original size:85 final size:86
Alignment explanation
Indices: 89096856--89097101 Score: 302
Period size: 86 Copynumber: 2.9 Consensus size: 86
89096846 GTCAAAAAGC
* * * * * ** * * *
89096856 CTTTTTGAAGCATTTTGATAGTTCAAGTATCCAACTGAGTG-AAAATTGGAGGGGTTTAATTGC-
1 CTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAATGCAAAAAAGAAGGGGCTTAATTACT
*
89096919 TTTTTTAAAAAAGTTAAGGGT
66 TTTTTTGAAAAAGTTAAGGGT
* *
89096940 CTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAA-AATGGGCTTAATTACT
1 CTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAATGCAAAAAAGAAGGGGCTTAATTACT
*
89097004 TTTTTTGAAAAAGTTTGAGGGT
66 TTTTTTGAAAAAG-TTAAGGGT
* * *
89097026 CTTTTTGATGTATTTTGAAAGTT-AAGTACCCAATTTAATGCAAAAAAGAAGGGGCTTAATTAAT
1 CTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAATGCAAAAAAGAAGGGGCTTAATTACT
89097090 TTTTTTGAAAAA
66 TTTTTTGAAAAA
89097102 AAATTGAGGA
Statistics
Matches: 141, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
84 48 0.34
85 38 0.27
86 55 0.39
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.38
Consensus pattern (86 bp):
CTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAATGCAAAAAAGAAGGGGCTTAATTACT
TTTTTTGAAAAAGTTAAGGGT
Found at i:89099829 original size:47 final size:44
Alignment explanation
Indices: 89099760--89099877 Score: 130
Period size: 46 Copynumber: 2.6 Consensus size: 44
89099750 GAGTTCTGAA
* *
89099760 CTCGTTGAGTTGAGCCCGAGTTCGTGA-GATGTAACTAGGCATCCGAG
1 CTCGTTGAGTTGAGTCCGAGTTCGTGAGGATGTAA--ACGC--CCGAG
* * *
89099807 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAAACGCGCGAG
1 CTCGTTGAGTTGAGTCCGAGTTC-GTGA-GGATGTAAACGCCCGAG
89099853 CTCGTTGAGTTGAGTCCGAGTTCGT
1 CTCGTTGAGTTGAGTCCGAGTTCGT
89099878 TTATGGGCGG
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
45 1 0.02
46 27 0.44
47 22 0.35
48 5 0.08
50 7 0.11
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.29
Consensus pattern (44 bp):
CTCGTTGAGTTGAGTCCGAGTTCGTGAGGATGTAAACGCCCGAG
Found at i:89104843 original size:93 final size:93
Alignment explanation
Indices: 89104731--89104902 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
89104721 GCCCATAAGT
* *
89104731 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
89104796 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
89104824 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
89104889 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
89104903 CAAATATCCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:89104898 original size:46 final size:46
Alignment explanation
Indices: 89104723--89104898 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
89104713 TGTAACCCGC
* * *
89104723 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
89104769 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
89104819 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
89104862 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
89104899 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:89112027 original size:19 final size:18
Alignment explanation
Indices: 89112005--89112044 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
89111995 AGAATAAAAC
89112005 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAA-AT
89112024 TTATCTACCTAAATAAAT
1 TTATCTACCTAAATAAAT
89112042 TTA
1 TTA
89112045 AAATGTATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (18 bp):
TTATCTACCTAAATAAAT
Found at i:89112993 original size:40 final size:40
Alignment explanation
Indices: 89112919--89112994 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
89112909 TCACACCATG
* **
89112919 TGGGAATAAAATCGACCCACCCATCCCTGTACACCAAATA
1 TGGGAATAAAATCGACCCACCCAACCCTAAACACCAAATA
* * *
89112959 TGGGGATAATATCGACCCATCCAACCCTAAACACCA
1 TGGGAATAAAATCGACCCACCCAACCCTAAACACCA
89112995 TAAGGTATCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.37, C:0.33, G:0.13, T:0.17
Consensus pattern (40 bp):
TGGGAATAAAATCGACCCACCCAACCCTAAACACCAAATA
Found at i:89123144 original size:46 final size:46
Alignment explanation
Indices: 89123092--89123498 Score: 582
Period size: 46 Copynumber: 8.8 Consensus size: 46
89123082 GAGTGTGCTC
*
89123092 CCTGATATGGAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
1 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
89123138 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
1 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
* *
89123184 CGTGATATGGAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
1 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
89123230 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
1 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
* *
89123276 CGTGATATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAA
1 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
* **
89123322 CGTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAA
1 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
* * *
89123368 CCTAACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAA
1 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
* *** **
89123414 CATGACGGGAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAA
1 CCTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
** * * * *
89123461 AATGATA-GAAAACGAGTAAAACCATAGTTGAAAGATAC
1 CCTGATATG-AAATGTGTAAGACCATGGTTGAAAGATAC
89123499 TATGACATCA
Statistics
Matches: 336, Mismatches: 24, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
46 296 0.88
47 40 0.12
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (46 bp):
CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
Found at i:89130237 original size:43 final size:44
Alignment explanation
Indices: 89130157--89130273 Score: 116
Period size: 43 Copynumber: 2.7 Consensus size: 44
89130147 TCGATGCCAC
*
89130157 TGTCCTAGACAA-GGTCTTATACG-AAATCAC-ATAACAATACCGA
1 TGTCCTAGA-AATGGTCTTATATGTAAA-CACAATAACAATACCGA
* *
89130200 TGTCCTAGAAATGGTCTTATATGTAAACACAAT-ACAATGCCTA
1 TGTCCTAGAAATGGTCTTATATGTAAACACAATAACAATACCGA
* * * * *
89130243 TGTCCCAGACATGATCTTACATGTAATCACA
1 TGTCCTAGAAATGGTCTTATATGTAAACACA
89130274 TCCCGGTAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
42 2 0.03
43 56 0.89
44 5 0.08
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (44 bp):
TGTCCTAGAAATGGTCTTATATGTAAACACAATAACAATACCGA
Found at i:89131182 original size:11 final size:11
Alignment explanation
Indices: 89131164--89131203 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
89131154 ACAATAACAA
89131164 CAAAATAATAG
1 CAAAATAATAG
*
89131175 CAACATAATAG
1 CAAAATAATAG
* *
89131186 TAAAATAGTAG
1 CAAAATAATAG
89131197 CAAAATA
1 CAAAATA
89131204 TGGAAAAAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.60, C:0.10, G:0.10, T:0.20
Consensus pattern (11 bp):
CAAAATAATAG
Found at i:89135297 original size:129 final size:129
Alignment explanation
Indices: 89135064--89135320 Score: 455
Period size: 129 Copynumber: 2.0 Consensus size: 129
89135054 AACTTTGGCC
89135064 CTCATAATTTCCATTAGTTGTTTGGAAAGCTCTGCTATCCCCTAATTGTGAACCACAACCATTGC
1 CTCATAATTTCCATTAGTTGTTTGGAAAGCTCTGCTATCCCCTAATTGTGAACCACAACCATTGC
* *
89135129 CACTCGTTTTTCTTCCATTTGTTAGTTTCTTATAGAGCTTCCAACACGTTTCTCGAGTGTGCCG
66 CACTCGTTTTTCTTCCATTTGTCAGTTTCTTATAAAGCTTCCAACACGTTTCTCGAGTGTGCCG
*
89135193 CTCATAATTTCCATTAGTTGTTTGGAAAGCTCTGCTATCCTCTAATTGT-AAGCCACAACCATTG
1 CTCATAATTTCCATTAGTTGTTTGGAAAGCTCTGCTATCCCCTAATTGTGAA-CCACAACCATTG
89135257 CCACTC-TTTTTCCTTCCATTTGTCAGTTTCTTATAAAGCTTCCAACACGTTTCTCGAGTGTGCC
65 CCACTCGTTTTT-CTTCCATTTGTCAGTTTCTTATAAAGCTTCCAACACGTTTCTCGAGTGTGCC
89135321 AATATTTTTT
Statistics
Matches: 123, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
128 7 0.06
129 116 0.94
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.38
Consensus pattern (129 bp):
CTCATAATTTCCATTAGTTGTTTGGAAAGCTCTGCTATCCCCTAATTGTGAACCACAACCATTGC
CACTCGTTTTTCTTCCATTTGTCAGTTTCTTATAAAGCTTCCAACACGTTTCTCGAGTGTGCCG
Found at i:89135492 original size:16 final size:16
Alignment explanation
Indices: 89135471--89135504 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
89135461 TTCTAACATC
89135471 AGAAAAAATCTCACGA
1 AGAAAAAATCTCACGA
89135487 AGAAAAAATCTCACGA
1 AGAAAAAATCTCACGA
89135503 AG
1 AG
89135505 TTTTGGAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.18, G:0.15, T:0.12
Consensus pattern (16 bp):
AGAAAAAATCTCACGA
Found at i:89136394 original size:19 final size:19
Alignment explanation
Indices: 89136370--89136413 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
89136360 TTAGAATATG
*
89136370 AATAAAACTTATTTATCTA
1 AATAAAACTTATTTACCTA
*
89136389 AATAAAATTTATTTACCTA
1 AATAAAACTTATTTACCTA
89136408 AATAAA
1 AATAAA
89136414 TTTAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (19 bp):
AATAAAACTTATTTACCTA
Found at i:89145156 original size:16 final size:16
Alignment explanation
Indices: 89145145--89145176 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
89145135 ATTGTAATTG
89145145 AATAGAGCTGTAATAA
1 AATAGAGCTGTAATAA
*
89145161 AATAGAGTTGTAATAA
1 AATAGAGCTGTAATAA
89145177 GTAATTTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.19, T:0.28
Consensus pattern (16 bp):
AATAGAGCTGTAATAA
Found at i:89145271 original size:16 final size:16
Alignment explanation
Indices: 89145236--89145291 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
89145226 GTTTGGTTCA
*
89145236 CTGTAATGAAATAG-G
1 CTGTAATTAAATAGAG
* *
89145251 ACTGTAATTGAATTGAG
1 -CTGTAATTAAATAGAG
89145268 CTGTAA-TAAATAGAG
1 CTGTAATTAAATAGAG
89145283 CTGTAATTA
1 CTGTAATTA
89145292 GTAATTTAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
15 13 0.39
16 19 0.58
17 1 0.03
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.32
Consensus pattern (16 bp):
CTGTAATTAAATAGAG
Found at i:89145333 original size:115 final size:116
Alignment explanation
Indices: 89145107--89145334 Score: 368
Period size: 115 Copynumber: 2.0 Consensus size: 116
89145097 TTACTTACGT
** * *
89145107 TACGTTTGGTTGGCTGTAATGAAATAGGATTGTAATTGAATAGAGCTGTAATAAAATAGAGTTGT
1 TACGTTTGGTTCACTGTAATGAAATAGGACTGTAATTGAATAGAGCTGTAATAAAATAGAGCTGT
89145172 AATAAGTAATTTAACTGTTTGGTTGAATAGAATGGAATAAAACTGTAACGG
66 AATAAGTAATTTAACTGTTTGGTTGAATAGAATGGAATAAAACTGTAACGG
*
89145223 TACGTTTGGTTCACTGTAATGAAATAGGACTGTAATTGAATTGAGCTGTAAT-AAATAGAGCTGT
1 TACGTTTGGTTCACTGTAATGAAATAGGACTGTAATTGAATAGAGCTGTAATAAAATAGAGCTGT
* * * *
89145287 AATTAGTAATTTAACTGTTTGGTTGAATGGAATGGAATAGAGCTGTAA
66 AATAAGTAATTTAACTGTTTGGTTGAATAGAATGGAATAAAACTGTAA
89145335 TAGAATTCTT
Statistics
Matches: 103, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
115 55 0.53
116 48 0.47
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.34
Consensus pattern (116 bp):
TACGTTTGGTTCACTGTAATGAAATAGGACTGTAATTGAATAGAGCTGTAATAAAATAGAGCTGT
AATAAGTAATTTAACTGTTTGGTTGAATAGAATGGAATAAAACTGTAACGG
Found at i:89145359 original size:44 final size:46
Alignment explanation
Indices: 89145276--89145364 Score: 139
Period size: 44 Copynumber: 2.0 Consensus size: 46
89145266 AGCTGTAATA
89145276 AATAGAGCTGTAATTAGTAATTTAACTGTTTGGTTGAATGGAATGG
1 AATAGAGCTGTAATTAGTAATTTAACTGTTTGGTTGAATGGAATGG
*
89145322 AATAGAGCTGTAA-TAG-AATTCTTA-TGTTTGGTTGAATGGAATG
1 AATAGAGCTGTAATTAGTAATT-TAACTGTTTGGTTGAATGGAATG
89145365 ATGTTGTAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
44 23 0.56
45 5 0.12
46 13 0.32
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (46 bp):
AATAGAGCTGTAATTAGTAATTTAACTGTTTGGTTGAATGGAATGG
Found at i:89145527 original size:61 final size:55
Alignment explanation
Indices: 89145445--89145593 Score: 140
Period size: 61 Copynumber: 2.5 Consensus size: 55
89145435 GATTATTATT
*
89145445 ATTAAATTTTAATA-AGATTATTGATACATATATTTTAATAAAAATAAAAATAAATAATTTA
1 ATTAAATTTTAATATA-ATTATT-ATA-ATATAATTTAAT-AAAAT---AATAAATAATTTA
* * *
89145506 ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAATAATATATATTTTA
1 ATTAAATTTTAATATAATTATTA-T-AATATAATTTAATAAAATAATAAATAATTTA
89145563 A-TAACATTATTAATATAATTATTAATAATAT
1 ATTAA-ATT-TTAATATAATTATT-ATAATAT
89145594 TTAATAATAA
Statistics
Matches: 77, Mismatches: 5, Indels: 16
0.79 0.05 0.16
Matches are distributed among these distances:
56 2 0.03
57 20 0.26
58 15 0.19
59 1 0.01
60 6 0.08
61 31 0.40
62 2 0.03
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (55 bp):
ATTAAATTTTAATATAATTATTATAATATAATTTAATAAAATAATAAATAATTTA
Found at i:89145575 original size:12 final size:11
Alignment explanation
Indices: 89145514--89145611 Score: 51
Period size: 12 Copynumber: 8.5 Consensus size: 11
89145504 TAATTATATT
89145514 TTAATATAATTA
1 TTAATA-AATTA
*
89145526 TTATTAAATATAA
1 TTAATAAAT-T-A
*
89145539 TTTAATAAAATA
1 -TTAATAAATTA
* *
89145551 AT-ATATATT-
1 TTAATAAATTA
89145560 TTAATAACATTA
1 TTAATAA-ATTA
89145572 TTAATATAATTA
1 TTAATA-AATTA
89145584 TTAATAATATTTA
1 TTAATAA-A-TTA
*
89145597 ATAAT-AATT-
1 TTAATAAATTA
89145606 TTAATA
1 TTAATA
89145612 TAAAATTATT
Statistics
Matches: 66, Mismatches: 10, Indels: 22
0.67 0.10 0.22
Matches are distributed among these distances:
9 5 0.08
10 10 0.15
11 9 0.14
12 25 0.38
13 10 0.15
14 7 0.11
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (11 bp):
TTAATAAATTA
Found at i:89145599 original size:46 final size:47
Alignment explanation
Indices: 89145500--89145614 Score: 127
Period size: 46 Copynumber: 2.5 Consensus size: 47
89145490 AAAAATAAAT
*
89145500 AATTTAAT-TATATTTTAATATAATTATTATTAAATATAATTTAATA
1 AATTTAATATATATTTTAATATAATTATTAATAAATATAATTTAATA
*
89145546 AA-ATAATATATATTTTAATA-ACATTATTAATATAAT-T-A-TTAATA
1 AATTTAATATATATTTTAATATA-ATTATTAATA-AATATAATTTAATA
89145590 ATATTTAATA-ATAATTTTAATATAA
1 A-ATTTAATATAT-ATTTTAATATAA
89145615 AATTATTATT
Statistics
Matches: 59, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
44 7 0.12
45 9 0.15
46 39 0.66
47 4 0.07
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (47 bp):
AATTTAATATATATTTTAATATAATTATTAATAAATATAATTTAATA
Found at i:89156959 original size:5 final size:5
Alignment explanation
Indices: 89156949--89156979 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
89156939 ATTTACCTCC
89156949 TTATA TTATA TTATA TTATA TTATA TTATA T
1 TTATA TTATA TTATA TTATA TTATA TTATA T
89156980 ATTTTTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:89159946 original size:17 final size:17
Alignment explanation
Indices: 89159926--89159959 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
89159916 AAATAGATTT
89159926 TTAATTAAAAATTTTAA
1 TTAATTAAAAATTTTAA
*
89159943 TTAATTAAAATTTTTAA
1 TTAATTAAAAATTTTAA
89159960 ACCTAAACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAATTAAAAATTTTAA
Found at i:89160720 original size:94 final size:92
Alignment explanation
Indices: 89160584--89160774 Score: 235
Period size: 94 Copynumber: 2.1 Consensus size: 92
89160574 AAACTTTTTT
* * *
89160584 AAAAAAAATAATTAAGTCCCTCTCCTTTTTTTTGCACTCAATT-GAGCAATTTAACTTTCAAAAT
1 AAAAAAAAAAATTAAGTCCCTCTCCTTTTTTTTCCACTCAATTAG-GCAATTAAACTTTCAAAAT
* *
89160648 GCATCAAAAAGGCCCCCAAACTTCTTTAA
65 GCATCAAAAAGACCCCCAAAATT-TTTAA
* *
89160677 AAAAAAAAGAAATTAAG-CCCT-TGCCTGTTTTTTTCCACTCAATTAGGTACTTAAACTTTCAAA
1 AAAAAAAA-AAATTAAGTCCCTCT-CCT-TTTTTTTCCACTCAATTAGGCAATTAAACTTTCAAA
* *
89160740 ATGCATCAAAAAGACCCTCAAAATTTTTCA
63 ATGCATCAAAAAGACCCCCAAAATTTTTAA
89160770 AAAAA
1 AAAAA
89160775 GCAATTAAGC
Statistics
Matches: 85, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
92 1 0.01
93 24 0.28
94 59 0.69
95 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (92 bp):
AAAAAAAAAAATTAAGTCCCTCTCCTTTTTTTTCCACTCAATTAGGCAATTAAACTTTCAAAATG
CATCAAAAAGACCCCCAAAATTTTTAA
Found at i:89161108 original size:10 final size:10
Alignment explanation
Indices: 89161095--89161174 Score: 55
Period size: 10 Copynumber: 8.5 Consensus size: 10
89161085 CTTTATAAAA
89161095 TTTTATAATT
1 TTTTATAATT
89161105 TTTT-T-ATAT
1 TTTTATAAT-T
* *
89161114 TTCTAT-ATA
1 TTTTATAATT
89161123 TTTTATAATT
1 TTTTATAATT
*
89161133 TTTTATGA-T
1 TTTTATAATT
89161142 TTTTAT-A-T
1 TTTTATAATT
*
89161150 TTTTCTAATT
1 TTTTATAATT
* *
89161160 TTTAATAAAT
1 TTTTATAATT
89161170 TTTTA
1 TTTTA
89161175 ATATTTTAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 10
0.73 0.13 0.13
Matches are distributed among these distances:
8 9 0.16
9 18 0.33
10 28 0.51
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.68
Consensus pattern (10 bp):
TTTTATAATT
Found at i:89161128 original size:17 final size:18
Alignment explanation
Indices: 89161105--89161152 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
89161095 TTTTATAATT
89161105 TTTTTATATTTCTATAT-A
1 TTTTTATATTT-TATATGA
*
89161123 -TTTTATAATTTTTTATGA
1 TTTTTAT-ATTTTATATGA
89161141 TTTTTATATTTT
1 TTTTTATATTTT
89161153 TCTAATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 10 0.38
18 10 0.38
19 6 0.23
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTTTATATTTTATATGA
Found at i:89161130 original size:28 final size:28
Alignment explanation
Indices: 89161094--89161188 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
89161084 ACTTTATAAA
*
89161094 ATTTTATAATTTTTTTATATTTCTATAT
1 ATTTTATAATTTTTTTATATTTTTATAT
89161122 ATTTTATAA-TTTTTTATGATTTTTATAT
1 ATTTTATAATTTTTTTAT-ATTTTTATAT
* * *
89161150 -TTTTCTAATTTTTAATAAATTTTTA-AT
1 ATTTTATAATTTTT-TTATATTTTTATAT
89161177 ATTTTA-AATTTT
1 ATTTTATAATTTT
89161189 ATTAAGTTTA
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
27 23 0.40
28 33 0.57
29 2 0.03
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (28 bp):
ATTTTATAATTTTTTTATATTTTTATAT
Found at i:89161135 original size:9 final size:9
Alignment explanation
Indices: 89161095--89161254 Score: 73
Period size: 9 Copynumber: 17.6 Consensus size: 9
89161085 CTTTATAAAA
89161095 TTTTATAAT
1 TTTTATAAT
*
89161104 TTTTTTATAT
1 TTTTATA-AT
*
89161114 TTCTAT-AT
1 TTTTATAAT
89161122 ATTTTATAATT
1 -TTTTATAA-T
*
89161133 TTTTATGAT
1 TTTTATAAT
89161142 TTTTAT-AT
1 TTTTATAAT
*
89161150 TTTTCTAAT
1 TTTTATAAT
*
89161159 TTTTAATAAA
1 TTTT-ATAAT
89161169 TTTT-TAAT
1 TTTTATAAT
89161177 ATTTTA-AA-
1 -TTTTATAAT
*
89161185 TTTTATTAAG
1 TTTTA-TAAT
*
89161195 TTTAATAAT
1 TTTTATAAT
* **
89161204 ATTTATAGC
1 TTTTATAAT
* *
89161213 TTTAAT-TT
1 TTTTATAAT
89161221 ATTTTA-AATT
1 -TTTTATAA-T
89161231 TTTTATAATT
1 TTTTATAA-T
*
89161241 TTTTCTAAT
1 TTTTATAAT
89161250 TTTTA
1 TTTTA
89161255 ATAAAAAAAG
Statistics
Matches: 113, Mismatches: 23, Indels: 30
0.68 0.14 0.18
Matches are distributed among these distances:
7 5 0.04
8 12 0.11
9 58 0.51
10 37 0.33
11 1 0.01
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (9 bp):
TTTTATAAT
Found at i:89161153 original size:19 final size:18
Alignment explanation
Indices: 89161095--89161163 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 18
89161085 CTTTATAAAA
* *
89161095 TTTTATAATTTTTTTATAT
1 TTTTAT-ATTTTTATATTT
* *
89161114 TTCTATATATTTTATAATT
1 TTTTATAT-TTTTATATTT
89161133 TTTTATGATTTTTATATTT
1 TTTTAT-ATTTTTATATTT
*
89161152 TTCTA-ATTTTTA
1 TTTTATATTTTTA
89161164 ATAAATTTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
17 7 0.17
18 2 0.05
19 30 0.73
20 2 0.05
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.70
Consensus pattern (18 bp):
TTTTATATTTTTATATTT
Found at i:89161160 original size:17 final size:18
Alignment explanation
Indices: 89161102--89161163 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 18
89161092 AAATTTTATA
* *
89161102 ATTTTTTTATATTTCTAT
1 ATTTTTATATTTTTCTAT
89161120 ATATTTTATAATTTTT-TAT
1 AT-TTTTAT-ATTTTTCTAT
89161139 GATTTTTATATTTTTCTA-
1 -ATTTTTATATTTTTCTAT
89161157 ATTTTTA
1 ATTTTTA
89161164 ATAAATTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
17 7 0.18
18 8 0.21
19 16 0.42
20 7 0.18
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (18 bp):
ATTTTTATATTTTTCTAT
Found at i:89161182 original size:36 final size:37
Alignment explanation
Indices: 89161086--89161188 Score: 97
Period size: 38 Copynumber: 2.8 Consensus size: 37
89161076 TTCTTACGAC
* *
89161086 TTTATAAAATTTTATAAT-TTTTTTATATTTCTATATAT
1 TTTAT-AAATTTT-TAATATTTTATATTTTTCTATATAT
*
89161124 TTTAT-AATTTTTTATGATTTTTATATTTTTCTA-AT-T
1 TTTATAAATTTTTAAT-A-TTTTATATTTTTCTATATAT
*
89161160 TTTAATAAATTTTTAATATTTTAAATTTT
1 TTT-ATAAATTTTTAATATTTTATATTTT
89161189 ATTAAGTTTA
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
35 3 0.05
36 20 0.36
37 5 0.09
38 27 0.49
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (37 bp):
TTTATAAATTTTTAATATTTTATATTTTTCTATATAT
Found at i:89161251 original size:27 final size:26
Alignment explanation
Indices: 89161095--89161252 Score: 79
Period size: 28 Copynumber: 5.8 Consensus size: 26
89161085 CTTTATAAAA
* *
89161095 TTTTATAATTTTTTTATATTTCTATATA
1 TTTTATAATTTTTTTA-ATTT-TAAATT
* *
89161123 TTTTATAATTTTTTATGATTTT-TATAT
1 TTTTATAATTTTTT-TAATTTTAAAT-T
* * * *
89161150 TTTTCTAATTTTTAATAAATTTTTAATA
1 TTTTATAATTTTT--TTAATTTTAAATT
* * *
89161178 TTTTA-AATTTTATTAAGTTTAATAAT
1 TTTTATAATTTTTTTAATTTTAA-ATT
* * *
89161204 ATTTATAGCTTTAATTT-ATTTTAAATT
1 TTTTATA-ATTT-TTTTAATTTTAAATT
89161231 TTTTATAATTTTTTCTAATTTT
1 TTTTATAATTTTTT-TAATTTT
89161253 TAATAAAAAA
Statistics
Matches: 96, Mismatches: 23, Indels: 23
0.68 0.16 0.16
Matches are distributed among these distances:
25 9 0.09
26 12 0.12
27 33 0.34
28 36 0.38
29 6 0.06
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.65
Consensus pattern (26 bp):
TTTTATAATTTTTTTAATTTTAAATT
Found at i:89162982 original size:11 final size:11
Alignment explanation
Indices: 89162961--89162994 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
89162951 TTGTAGTTCA
89162961 AAAACAAAAAAG
1 AAAA-AAAAAAG
89162973 AAAAAAAAAAG
1 AAAAAAAAAAG
*
89162984 AAAAAGAAAAG
1 AAAAAAAAAAG
89162995 GCATGGCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:89163170 original size:130 final size:132
Alignment explanation
Indices: 89162917--89163170 Score: 352
Period size: 133 Copynumber: 1.9 Consensus size: 132
89162907 AGATTTGCGT
* * *
89162917 GCACTAGTGATGTTTATTGATTGGGTTTTACTTTTTGTAGTTCAAAAACAAAAAAGAAAAAAAAA
1 GCACTAATGATGTTTATTGATTGGATTTTACTTTTTATAGTTCAAAAACAAAAAAGAAAAAAAAA
*
89162982 AGAAAAAGAAAAGGCATGGCAATGATCTTCTAATTTTAACCCACCTAATAACAACAAGCACATGC
66 AG-AAAAGAAAAGGCATGGCAAAGATCTTCTAATTTTAACCCACCTAATAACAACAAGCACATGC
89163047 TAA
130 TAA
* * * * * *
89163050 GCACTAATGATGTTTATTGTTTGGATTTTACTTTTTATATTTTAAAAA-TAAATA-AAAAAGAAA
1 GCACTAATGATGTTTATTGATTGGATTTTACTTTTTATAGTTCAAAAACAAAAAAGAAAAAAAAA
* * *
89163113 AG-AAAGAAAAGGCATGGCAAAGATGCTTCTATTTTTAACCCACCTATTAACACCAAGC
66 AGAAAAGAAAAGGCATGGCAAAGAT-CTTCTAATTTTAACCCACCTAATAACAACAAGC
89163171 TCATAACAAT
Statistics
Matches: 107, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
129 21 0.20
130 30 0.28
131 10 0.09
132 4 0.04
133 42 0.39
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (132 bp):
GCACTAATGATGTTTATTGATTGGATTTTACTTTTTATAGTTCAAAAACAAAAAAGAAAAAAAAA
AGAAAAGAAAAGGCATGGCAAAGATCTTCTAATTTTAACCCACCTAATAACAACAAGCACATGCT
AA
Found at i:89163360 original size:40 final size:39
Alignment explanation
Indices: 89163312--89163390 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 39
89163302 CTAATTGGTA
* * *
89163312 GGTTAAAATTATAAATATATAAAAAGTGTTAAGGAGATTT
1 GGTTAAAATTAGAAACATATAAAAAGAG-TAAGGAGATTT
*
89163352 GGTTAAAATTAGATACATATAAAAAGAGTAAGGAGATTT
1 GGTTAAAATTAGAAACATATAAAAAGAGTAAGGAGATTT
89163391 AATTAACACC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
39 11 0.31
40 24 0.69
ACGTcount: A:0.48, C:0.01, G:0.19, T:0.32
Consensus pattern (39 bp):
GGTTAAAATTAGAAACATATAAAAAGAGTAAGGAGATTT
Found at i:89165058 original size:28 final size:28
Alignment explanation
Indices: 89165017--89165085 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
89165007 TTTAAAACCC
*
89165017 TAGGGGT-ATATCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
89165044 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
89165072 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
89165086 TGATCTACGC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 7 0.17
28 33 0.82
ACGTcount: A:0.19, C:0.10, G:0.28, T:0.43
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTGCTCTT
Found at i:89166917 original size:19 final size:18
Alignment explanation
Indices: 89166880--89166923 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
89166870 ATACATATAG
89166880 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
89166897 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
89166916 TACTAATT
1 TAATAATT
89166924 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:89167675 original size:59 final size:59
Alignment explanation
Indices: 89167583--89167700 Score: 218
Period size: 59 Copynumber: 2.0 Consensus size: 59
89167573 GTAGATGAAT
*
89167583 GCCTAGTTTAGGTATGCTTATCACAAAAATATTTTTGGGGAGAAGCTAAAATTTTGAGC
1 GCCTAGTTTAGGTATGCTTATCACAAAAATATTTTTGAGGAGAAGCTAAAATTTTGAGC
*
89167642 GCCTAGTTTAGGTATGCTTATCACAAAAATATTTTTGAGGAGAAGTTAAAATTTTGAGC
1 GCCTAGTTTAGGTATGCTTATCACAAAAATATTTTTGAGGAGAAGCTAAAATTTTGAGC
89167701 TTTTGAAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (59 bp):
GCCTAGTTTAGGTATGCTTATCACAAAAATATTTTTGAGGAGAAGCTAAAATTTTGAGC
Found at i:89168327 original size:14 final size:14
Alignment explanation
Indices: 89168290--89168327 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
89168280 TTTCCATTTC
89168290 TATTTCATTTAATT
1 TATTTCATTTAATT
*
89168304 TTTTTCATTTAAATT
1 TATTTCATTT-AATT
89168319 TATTT-ATTT
1 TATTTCATTT
89168328 CTCATTTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTTCATTTAATT
Found at i:89168348 original size:52 final size:55
Alignment explanation
Indices: 89168268--89168439 Score: 147
Period size: 58 Copynumber: 3.1 Consensus size: 55
89168258 TTTTCCTTTC
*
89168268 ATTTCATTTTCATTTCCATTTCTATTTCATTT-A-ATTT-TTTTCATTTAAATTT
1 ATTTCATTTTCATTTCAATTTCTATTTCATTTCAGATTTGTTTTCATTTAAATTT
* * *
89168320 ATTT-ATTTCTCATTTCAATTTTTTTTTCATTTCAGTTTTTGTTTTCATTTAAATTT
1 ATTTCATTT-TCATTTCAATTTCTATTTCATTTCAG-ATTTGTTTTCATTTAAATTT
* * * * **
89168376 ATAATTTATTTCCATTTAAACTTTC-ATTTCATTTCATATTCATATTTCATTTAACATTT
1 AT--TTCATTTTCATTTCAA-TTTCTATTTCATTTCAGATTTGT-TTTCATTTAA-ATTT
89168435 CATTT
1 -ATTT
89168440 TATTAATTTT
Statistics
Matches: 96, Mismatches: 12, Indels: 18
0.76 0.10 0.14
Matches are distributed among these distances:
51 4 0.04
52 24 0.25
53 1 0.01
55 3 0.03
56 17 0.18
57 3 0.03
58 31 0.32
59 11 0.11
60 2 0.02
ACGTcount: A:0.24, C:0.13, G:0.01, T:0.61
Consensus pattern (55 bp):
ATTTCATTTTCATTTCAATTTCTATTTCATTTCAGATTTGTTTTCATTTAAATTT
Found at i:89168364 original size:18 final size:17
Alignment explanation
Indices: 89168245--89168375 Score: 90
Period size: 17 Copynumber: 7.5 Consensus size: 17
89168235 AGGCCTATCC
*
89168245 TTTCAACTTTTATTTTTCC
1 TTTCAA-TTTT-TTTTTCA
**
89168264 TTTC-ATTTCATTTTCA
1 TTTCAATTTTTTTTTCA
* * *
89168280 TTTCCATTTCTATTTCA
1 TTTCAATTTTTTTTTCA
89168297 TTT-AA--TTTTTTTCA
1 TTTCAATTTTTTTTTCA
*
89168311 TTTAAATTTATTTATTTCTCA
1 TTTCAA-TT-TTT-TTT-TCA
89168332 TTTCAATTTTTTTTTCA
1 TTTCAATTTTTTTTTCA
*
89168349 TTTCAGTTTTTGTTTTCA
1 TTTCAATTTTT-TTTTCA
*
89168367 TTTAAATTT
1 TTTCAATTT
89168376 ATAATTTATT
Statistics
Matches: 91, Mismatches: 12, Indels: 19
0.75 0.10 0.16
Matches are distributed among these distances:
14 10 0.11
15 2 0.02
16 10 0.11
17 29 0.32
18 17 0.19
19 10 0.11
20 5 0.05
21 8 0.09
ACGTcount: A:0.20, C:0.14, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTCAATTTTTTTTTCA
Found at i:89168408 original size:17 final size:18
Alignment explanation
Indices: 89168362--89168439 Score: 51
Period size: 17 Copynumber: 4.4 Consensus size: 18
89168352 CAGTTTTTGT
*
89168362 TTTCATTTAAATTTATAA
1 TTTCATTTACATTTATAA
*
89168380 TTT-ATTTCCATTTA-AA
1 TTTCATTTACATTTATAA
89168396 CTTTCATTT-CATTTCAT-A
1 -TTTCATTTACATTT-ATAA
*
89168414 -TTCATATTTCATTTA-ACA
1 TTTCAT-TTACATTTATA-A
89168432 TTTCATTT
1 TTTCATTT
89168440 TATTAATTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
16 7 0.14
17 20 0.41
18 17 0.35
19 5 0.10
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTCATTTACATTTATAA
Found at i:89168442 original size:58 final size:57
Alignment explanation
Indices: 89168305--89168443 Score: 149
Period size: 58 Copynumber: 2.4 Consensus size: 57
89168295 CATTTAATTT
* * ** * **
89168305 TTTTCATTTAAATTTA-TTTATTTCTCATTTCAATTTTTTTTTCATTTCAGTTTTTG
1 TTTTCATTTAAATTTATTTTATTTCTCATTTAAACTTTCATTTCATTTCAGTATTCA
89168361 TTTTCATTTAAATTTATAATTTATTTC-CATTTAAACTTTCATTTCATTTCA-TATTCA
1 TTTTCATTTAAATTTAT--TTTATTTCTCATTTAAACTTTCATTTCATTTCAGTATTCA
89168418 TATTTCATTTAACATTTCATTTTATT
1 T-TTTCATTTAA-ATTT-ATTTTATT
89168444 AATTTTTTCA
Statistics
Matches: 70, Mismatches: 7, Indels: 10
0.80 0.08 0.11
Matches are distributed among these distances:
56 16 0.23
57 4 0.06
58 36 0.51
59 12 0.17
60 2 0.03
ACGTcount: A:0.25, C:0.12, G:0.01, T:0.61
Consensus pattern (57 bp):
TTTTCATTTAAATTTATTTTATTTCTCATTTAAACTTTCATTTCATTTCAGTATTCA
Found at i:89168556 original size:14 final size:14
Alignment explanation
Indices: 89168521--89168556 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 14
89168511 TCGTTTTAAG
89168521 TTATCTTTTTTCAAT
1 TTAT-TTTTTTCAAT
89168536 TTAATTTTTTTCAAT
1 TT-ATTTTTTTCAAT
89168551 TTATTT
1 TTATTT
89168557 CATATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 14 0.70
16 2 0.10
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATTTTTTTCAAT
Found at i:89168568 original size:11 final size:11
Alignment explanation
Indices: 89168539--89168573 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
89168529 TTTCAATTTA
89168539 ATTTTTTTCA-
1 ATTTTTTTCAT
*
89168549 ATTTATTTCAT
1 ATTTTTTTCAT
89168560 ATTTTTTTCAT
1 ATTTTTTTCAT
89168571 ATT
1 ATT
89168574 AATTAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.69
Consensus pattern (11 bp):
ATTTTTTTCAT
Found at i:89168878 original size:23 final size:20
Alignment explanation
Indices: 89168847--89168901 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 20
89168837 TGTAATTCCA
89168847 TTTTCATTTCATTTAAATTATT
1 TTTTCATTTCATTT-AATTA-T
*
89168869 TTTTCTATTTAAATTTAATTAT
1 TTTTC-ATTT-CATTTAATTAT
89168891 TTTTCATTTCA
1 TTTTCATTTCA
89168902 AAATTTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 1 0.03
21 4 0.14
22 11 0.38
23 9 0.31
24 4 0.14
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTCATTTCATTTAATTAT
Found at i:89168905 original size:23 final size:23
Alignment explanation
Indices: 89168857--89168921 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 23
89168847 TTTTCATTTC
89168857 ATTTAAATTATTTTTTCTATTT--AA
1 ATTT-AATTA-TTTTTC-ATTTCAAA
89168881 ATTTAATTATTTTTCATTTCAAA
1 ATTTAATTATTTTTCATTTCAAA
89168904 ATTT--TTA-TTTTCATTTCA
1 ATTTAATTATTTTTCATTTCA
89168922 GTTTTTGTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
20 11 0.28
21 7 0.18
22 6 0.15
23 11 0.28
24 4 0.10
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (23 bp):
ATTTAATTATTTTTCATTTCAAA
Found at i:89169055 original size:30 final size:29
Alignment explanation
Indices: 89168987--89169079 Score: 95
Period size: 28 Copynumber: 3.2 Consensus size: 29
89168977 TCATAATCAT
**
89168987 CATTTTATTTCATATTCATTTAACATTT--
1 CATTTTATTTCATATTC-TTTTTCATTTAA
*
89169015 CATTTCATTTCATATTCTTGTTTCATTTAA
1 CATTTTATTTCATATTCTT-TTTCATTTAA
89169045 CATTTTATTTCAATAATT-TTTTTCATTTAA
1 CATTTTATTTC-AT-ATTCTTTTTCATTTAA
89169075 -ATTTT
1 CATTTT
89169080 TTTTTCAATA
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
27 2 0.04
28 22 0.39
29 5 0.09
30 20 0.36
31 4 0.07
32 3 0.05
ACGTcount: A:0.27, C:0.13, G:0.01, T:0.59
Consensus pattern (29 bp):
CATTTTATTTCATATTCTTTTTCATTTAA
Found at i:89169096 original size:19 final size:17
Alignment explanation
Indices: 89169061--89169109 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 17
89169051 ATTTCAATAA
*
89169061 TTTTTTTCATTTAAATT
1 TTTTTTTCATATAAATT
89169078 TTTTTTTCAATATACAATTT
1 TTTTTTTC-ATATA-AA-TT
89169098 TTTTTTTCATAT
1 TTTTTTTCATAT
89169110 TAATCACAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 8 0.29
18 4 0.14
19 6 0.21
20 10 0.36
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTTTCATATAAATT
Found at i:89169257 original size:21 final size:21
Alignment explanation
Indices: 89169215--89169257 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
89169205 TATTAAGGAC
*
89169215 ATTTAAATTTTTTCATATTTT
1 ATTTAAATTTTTTCATAATTT
89169236 ATTTAAATTTTTTC-TCAATTT
1 ATTTAAATTTTTTCAT-AATTT
89169257 A
1 A
89169258 AATATCATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTTAAATTTTTTCATAATTT
Found at i:89169535 original size:49 final size:47
Alignment explanation
Indices: 89169479--89169748 Score: 305
Period size: 47 Copynumber: 5.6 Consensus size: 47
89169469 CTTCGATTTC
*
89169479 ATTTAATTTGTATTTC-CATTTCATTTAAATTATCTTTATTCCCATTTTA
1 ATTTAATTT-T-TTTCTCATTTCATTTAAATTATCTTT-TTTCCATTTTA
* * *
89169528 ATTTAATTTTTTTTGTCATTTCATTTAAATTAT-TATTTTTTCATTTAA
1 ATTTAA-TTTTTTTCTCATTTCATTTAAATTATCT-TTTTTCCATTTTA
* * * * *
89169576 ATCTAATTTTGTTCTCAGTTCATTTAAATTATCTTTCTTCCCATCTTA
1 ATTTAATTTTTTTCTCATTTCATTTAAATTATCTTT-TTTCCATTTTA
* * *
89169624 ATTTAAATTTTTTTCTTATTTCATTTAAATTAT-TTTTTTCAATTTAA
1 ATTT-AATTTTTTTCTCATTTCATTTAAATTATCTTTTTTCCATTTTA
* *
89169671 ATTTAATTTTTATCCTCATTTCATTCAAATTATCTTTCTTTCCATTTTA
1 ATTTAATTTTT-TTCTCATTTCATTTAAATTATCTTT-TTTCCATTTTA
89169720 ATTT-ATTTTTTTCTCATTTCATTTAAATT
1 ATTTAATTTTTTTCTCATTTCATTTAAATT
89169749 TAATTTTTTC
Statistics
Matches: 185, Mismatches: 27, Indels: 20
0.80 0.12 0.09
Matches are distributed among these distances:
46 7 0.04
47 71 0.38
48 40 0.22
49 64 0.35
50 3 0.02
ACGTcount: A:0.26, C:0.13, G:0.01, T:0.60
Consensus pattern (47 bp):
ATTTAATTTTTTTCTCATTTCATTTAAATTATCTTTTTTCCATTTTA
Found at i:89169554 original size:22 final size:22
Alignment explanation
Indices: 89169451--89169771 Score: 123
Period size: 24 Copynumber: 13.5 Consensus size: 22
89169441 CATCTTTTTT
* **
89169451 TTTCATTTTATTTCATTTCTTCGA
1 TTTCATTTAATTTTTTTTC-TC-A
*
89169475 TTTCATTTAATTTGTATTTC-CA
1 TTTCATTTAATTT-TTTTTCTCA
*
89169497 TTTCATTTAAATTATCTTTATTCCCA
1 TTTCATTT-AATT-T-TTT-TTCTCA
* *
89169523 TTTTAATTTAATTTTTTTTGTCA
1 -TTTCATTTAATTTTTTTTCTCA
*
89169546 TTTCATTTAAATTATTATTTTTTCA
1 TTTCATTT-AATT-TT-TTTTCTCA
* * *
89169571 TTTAAATCTAA-TTTTGTTCTCA
1 TTT-CATTTAATTTTTTTTCTCA
* *
89169593 GTTCATTTAAATTATCTTTCTTCCCA
1 TTTCATTT-AATT-T-TTT-TTCTCA
* * *
89169619 TCTTAATTTAAATTTTTTTCTTA
1 T-TTCATTTAATTTTTTTTCTCA
89169642 TTTCATTTAAATTATTTTTT-TCAA
1 TTTCATTT-AATT-TTTTTTCTC-A
* * *
89169666 TTTAAATTTAATTTTTATCCTCA
1 TTT-CATTTAATTTTTTTTCTCA
*
89169689 TTTCATTCAAATTATCTTTCTT-TCCA
1 TTTCATT-TAATT-T-TTT-TTCT-CA
*
89169715 TTTTAATTT-A-TTTTTTTCTCA
1 -TTTCATTTAATTTTTTTTCTCA
*
89169736 TTTCATTTAAATTTAATTTTTTCTCT
1 TTTCATTT-AA-TT--TTTTTTCTCA
89169762 TTTCATTTAA
1 TTTCATTTAA
89169772 ATTACCTTTC
Statistics
Matches: 226, Mismatches: 37, Indels: 67
0.68 0.11 0.20
Matches are distributed among these distances:
20 7 0.03
21 7 0.03
22 40 0.18
23 38 0.17
24 44 0.19
25 34 0.15
26 37 0.16
27 19 0.08
ACGTcount: A:0.25, C:0.13, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTCATTTAATTTTTTTTCTCA
Found at i:89169554 original size:27 final size:25
Alignment explanation
Indices: 89169537--89169775 Score: 68
Period size: 26 Copynumber: 9.9 Consensus size: 25
89169527 AATTTAATTT
89169537 TTTTTGTCATTTCATTTAAATTATTA
1 TTTTT-TCATTTCATTTAAATTATTA
* *
89169563 TTTTTTCATTTAAATCT-AA-T-TT-
1 TTTTTTCATTT-CATTTAAATTATTA
* * *
89169585 TGTTCTCAGTTCATTTAAATTATCT-
1 TTTTTTCATTTCATTTAAATTAT-TA
** *
89169610 TTCTTCCCATCTTAATTTAAATT-TT-
1 TT-TTTTCAT-TTCATTTAAATTATTA
*
89169635 TTTCTT-ATTTCATTTAAATTA-T-
1 TTTTTTCATTTCATTTAAATTATTA
*
89169657 TTTTTTCAATTTAAATTT-AATT-TT-
1 TTTTTTC-ATTT-CATTTAAATTATTA
* ** *
89169681 TATCCTCATTTCA-TTCAA--ATTA
1 TTTTTTCATTTCATTTAAATTATTA
* *
89169703 -TCTTTC-TTTCCATTTTAATTTATT-
1 TTTTTTCATTT-CA-TTTAAATTATTA
89169727 TTTTTCTCATTTCATTTAAATTTAATT-
1 TTTTT-TCATTTCATTTAAA-TT-ATTA
* *
89169754 TTTTCTCTTTTCATTTAAATTA
1 TTTTTTCATTTCATTTAAATTA
89169776 CCTTTCTTTC
Statistics
Matches: 157, Mismatches: 31, Indels: 52
0.65 0.13 0.22
Matches are distributed among these distances:
20 3 0.02
21 11 0.07
22 30 0.19
23 12 0.08
24 17 0.11
25 30 0.19
26 33 0.21
27 21 0.13
ACGTcount: A:0.26, C:0.13, G:0.01, T:0.60
Consensus pattern (25 bp):
TTTTTTCATTTCATTTAAATTATTA
Found at i:89169609 original size:96 final size:97
Alignment explanation
Indices: 89169498--89169758 Score: 365
Period size: 96 Copynumber: 2.7 Consensus size: 97
89169488 GTATTTCCAT
* *
89169498 TTCATTTAAATTATCTTTATTCCCATTTTAATTTAATTTTTTTTGTCATTTCATTTAAATTATTA
1 TTCATTTAAATTATCTTTCTTCCCATTTTAATTTAA-TTTTTTTCTCATTTCATTTAAATTATTA
89169563 TTTTTTC-ATTTAAATCTAATTTTGT-T-CTCAG
65 TTTTTTCAATTTAAATCTAATTTT-TATCCTCAG
* *
89169594 TTCATTTAAATTATCTTTCTTCCCATCTTAATTTAAATTTTTTTCTTATTTCATTTAAATTA-T-
1 TTCATTTAAATTATCTTTCTTCCCATTTTAATTT-AATTTTTTTCTCATTTCATTTAAATTATTA
* *
89169657 TTTTTTCAATTTAAATTTAATTTTTATCCTCAT
65 TTTTTTCAATTTAAATCTAATTTTTATCCTCAG
* * *
89169690 TTCATTCAAATTATCTTTCTTTCCATTTTAATTT-ATTTTTTTCTCATTTCATTTAAATT-TAAT
1 TTCATTTAAATTATCTTTCTTCCCATTTTAATTTAATTTTTTTCTCATTTCATTTAAATTATTAT
89169753 TTTTTC
66 TTTTTC
89169759 TCTTTTCATT
Statistics
Matches: 148, Mismatches: 11, Indels: 13
0.86 0.06 0.08
Matches are distributed among these distances:
94 32 0.22
95 24 0.16
96 90 0.61
97 2 0.01
ACGTcount: A:0.26, C:0.13, G:0.01, T:0.60
Consensus pattern (97 bp):
TTCATTTAAATTATCTTTCTTCCCATTTTAATTTAATTTTTTTCTCATTTCATTTAAATTATTAT
TTTTTCAATTTAAATCTAATTTTTATCCTCAG
Found at i:89169789 original size:73 final size:77
Alignment explanation
Indices: 89169660--89169807 Score: 232
Period size: 73 Copynumber: 2.0 Consensus size: 77
89169650 AAATTATTTT
*
89169660 TTTCAATTTAAATTTAATTTTTATCCTCATTTCATTCAAATTATCTTTCTTTCCATTTTAATTTA
1 TTTCAATTTAAATTTAATTTTTATCCTCATTTCATTCAAATTACCTTTCTTTCCATTTTAATTTA
89169725 -TTTTTTTCTCA
66 CTTTTTTTCTCA
* *
89169736 TTTC-ATTTAAATTTAATTTTT-T-CTCTTTTCATTTAAATTACCTTTCTTTCCATTTTAATTTA
1 TTTCAATTTAAATTTAATTTTTATCCTCATTTCATTCAAATTACCTTTCTTTCCATTTTAATTTA
89169798 CGTTTTTTTC
66 C-TTTTTTTC
89169808 ATATTAATTT
Statistics
Matches: 67, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
73 37 0.55
74 1 0.01
75 25 0.37
76 4 0.06
ACGTcount: A:0.23, C:0.16, G:0.01, T:0.61
Consensus pattern (77 bp):
TTTCAATTTAAATTTAATTTTTATCCTCATTTCATTCAAATTACCTTTCTTTCCATTTTAATTTA
CTTTTTTTCTCA
Found at i:89169798 original size:22 final size:22
Alignment explanation
Indices: 89169759--89169817 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 22
89169749 TAATTTTTTC
*
89169759 TCTTTTCA-TTTAAATTACCTT
1 TCTTTTCATTTTAATTTACCTT
* *
89169780 TCTTTCCATTTTAATTTACGTT
1 TCTTTTCATTTTAATTTACCTT
*
89169802 T-TTTTCATATTAATTT
1 TCTTTTCATTTTAATTT
89169818 TTCTCTTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 20 0.62
22 12 0.38
ACGTcount: A:0.22, C:0.15, G:0.02, T:0.61
Consensus pattern (22 bp):
TCTTTTCATTTTAATTTACCTT
Found at i:89173636 original size:25 final size:25
Alignment explanation
Indices: 89173566--89173636 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 25
89173556 CAGCTCTCTT
* *
89173566 GAGCTTCTCGATATTTGGCTCACAA
1 GAGCTTCCCGATATATGGCTCACAA
** * *
89173591 GAGCTTCCCGATATACAGCTCATAT
1 GAGCTTCCCGATATATGGCTCACAA
89173616 GAGCTTCCC-ATTATATGGCTC
1 GAGCTTCCCGA-TATATGGCTC
89173637 GAAAAAGCTT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
24 1 0.03
25 36 0.97
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (25 bp):
GAGCTTCCCGATATATGGCTCACAA
Found at i:89174849 original size:3 final size:3
Alignment explanation
Indices: 89174843--89174992 Score: 58
Period size: 3 Copynumber: 48.0 Consensus size: 3
89174833 ATAACATGAC
* * * * *
89174843 AAT AAT AAT AAC AGT AGT AAT AAAT AAAT AAAT AAAT AAT GAT AAT AAA
1 AAT AAT AAT AAT AAT AAT AAT -AAT -AAT -AAT -AAT AAT AAT AAT AAT
* * * *
89174892 AAT AAT AGT AAAT AA- AAT AA- AGAT AA- AATT AAT AAT GAT AGT AACG
1 AAT AAT AAT -AAT AAT AAT AAT A-AT AAT AA-T AAT AAT AAT AAT AA-T
* * *
89174938 AAT -AT AAAT AAT AAT AGT AAA AAT AAT AAT AAT GAT AAT ACA- AATT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AA-T
89174984 AAT AAT AAT
1 AAT AAT AAT
89174993 GATGATATAA
Statistics
Matches: 112, Mismatches: 22, Indels: 26
0.70 0.14 0.16
Matches are distributed among these distances:
2 8 0.07
3 77 0.69
4 27 0.24
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:89174887 original size:22 final size:22
Alignment explanation
Indices: 89174862--89174995 Score: 57
Period size: 22 Copynumber: 6.1 Consensus size: 22
89174852 AACAGTAGTA
89174862 ATAAATAAATAAATAAATAATG
1 ATAAATAAATAAATAAATAATG
* *
89174884 ATAATAAAAATAATAGTAAATAA-A
1 ATAA-ATAAATAA-A-TAAATAATG
* * *
89174908 ATAAAGATA-AAATTAATAATG
1 ATAAATAAATAAATAAATAATG
* ** *
89174929 AT-AGTAACGAATATAAATAATA
1 ATAAATAAATAA-ATAAATAATG
89174951 ATAGTAA-AAAT-AAT-AATAATG
1 ATA--AATAAATAAATAAATAATG
* *
89174972 ATAATACAAATTAAT-AATAATG
1 ATAA-ATAAATAAATAAATAATG
89174994 AT
1 AT
89174996 GATATAAGTA
Statistics
Matches: 84, Mismatches: 16, Indels: 24
0.68 0.13 0.19
Matches are distributed among these distances:
19 1 0.01
20 9 0.11
21 18 0.21
22 30 0.36
23 11 0.13
24 7 0.08
25 8 0.10
ACGTcount: A:0.63, C:0.01, G:0.07, T:0.28
Consensus pattern (22 bp):
ATAAATAAATAAATAAATAATG
Found at i:89175133 original size:3 final size:3
Alignment explanation
Indices: 89175125--89175314 Score: 72
Period size: 3 Copynumber: 62.7 Consensus size: 3
89175115 GGTAGAAAAG
* * *
89175125 ATA ATA ATA ACGTA CTA ATA AGA ATA AAA AT- ATA ATA ATA ATA ATA
1 ATA ATA ATA A--TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
89175171 ATA ATA AT- ATT TTAA ATA A-G ATA ATA ATA ATA GAT- AGA AT- GTA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA
* * * * * *
89175214 GTA GTA ATA ATA CGTTA ATA A-A AGTA AGA GTA ATA ATA ATA AAA ATA
1 ATA ATA ATA ATA --ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA
* * *
89175261 AAA ATA ATA GTA A-A TATA ATA A-A TATA ATA ATA AAA GATA ATA ATA
1 ATA ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA -ATA ATA ATA
*
89175307 AAA ATA AT
1 ATA ATA AT
89175315 TAATTGGAAA
Statistics
Matches: 138, Mismatches: 31, Indels: 36
0.67 0.15 0.18
Matches are distributed among these distances:
2 11 0.08
3 114 0.83
4 9 0.07
5 4 0.03
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:89175272 original size:27 final size:27
Alignment explanation
Indices: 89175230--89175313 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 27
89175220 ATAATACGTT
* *
89175230 AATAAAAGTAAGAGTAATAATAATAAA
1 AATAAAAATAAAAGTAATAATAATAAA
*
89175257 AATAAAAATAATAGTAA-ATATAATAAA
1 AATAAAAATAAAAGTAATA-ATAATAAA
* *
89175284 TATAATAATAAAAG--ATAATAATAAA
1 AATAAAAATAAAAGTAATAATAATAAA
89175309 AATAA
1 AATAA
89175314 TTAATTGGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
25 13 0.27
26 2 0.04
27 34 0.69
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (27 bp):
AATAAAAATAAAAGTAATAATAATAAA
Found at i:89175330 original size:34 final size:32
Alignment explanation
Indices: 89175245--89175314 Score: 90
Period size: 34 Copynumber: 2.2 Consensus size: 32
89175235 AAGTAAGAGT
*
89175245 AATAAT-AATA-AAAATAAAAATAATAGTAAA
1 AATAATAAATATAAAATAAAAATAATAATAAA
*
89175275 TATAATAAATATAATAATAAAAGATAATAATAAA
1 AATAATAAATATAA-AATAAAA-ATAATAATAAA
89175309 AATAAT
1 AATAAT
89175315 TAATTGGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 5 0.15
31 4 0.12
32 2 0.06
33 7 0.21
34 15 0.45
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (32 bp):
AATAATAAATATAAAATAAAAATAATAATAAA
Found at i:89184979 original size:49 final size:49
Alignment explanation
Indices: 89184922--89185020 Score: 171
Period size: 49 Copynumber: 2.0 Consensus size: 49
89184912 AATTTAAAGT
* *
89184922 TAGGAAAATTATCTTTAAAAAGACGAAAATGAGTTCATAAGATATGTAG
1 TAGGAAAATTATCTTTAAAAAGACGAAAAGGAGTTAATAAGATATGTAG
*
89184971 TAGGAAAATTATCTTTAGAAAGACGAAAAGGAGTTAATAAGATATGTAG
1 TAGGAAAATTATCTTTAAAAAGACGAAAAGGAGTTAATAAGATATGTAG
89185020 T
1 T
89185021 TGTTAATAAG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.46, C:0.05, G:0.20, T:0.28
Consensus pattern (49 bp):
TAGGAAAATTATCTTTAAAAAGACGAAAAGGAGTTAATAAGATATGTAG
Found at i:89186997 original size:19 final size:19
Alignment explanation
Indices: 89186973--89187018 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
89186963 TCCTAGAAAA
89186973 TAAATAAAACTTATCTATC
1 TAAATAAAACTTATCTATC
* *
89186992 TAAATAAGATTTATCTATC
1 TAAATAAAACTTATCTATC
89187011 TAAATAAA
1 TAAATAAA
89187019 TATATAAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.37
Consensus pattern (19 bp):
TAAATAAAACTTATCTATC
Found at i:89191614 original size:61 final size:61
Alignment explanation
Indices: 89191504--89191688 Score: 275
Period size: 61 Copynumber: 3.0 Consensus size: 61
89191494 GTGATGTAGT
* * ** *
89191504 AATTTTAAAATTATTTTTTGAAAAA-AATTTGAGGTTACTTACTACTGAAGTGCCTAATTA
1 AATTTTAAAATTATTTTTTGAAAAAGAAATTGAGGTTACTTAATGTTGAAGTACCTAATTA
89191564 AATTTTAAAATTATTTTTTGAAAAAGAAATTGAGGTTACTTAATGTTGAAGTACCTAATTA
1 AATTTTAAAATTATTTTTTGAAAAAGAAATTGAGGTTACTTAATGTTGAAGTACCTAATTA
* * *
89191625 AATTTTAAAATTATATTTTAAAAAAGAAATTGAGGTTACTTCA-GATTGAAGTACCTAATTA
1 AATTTTAAAATTATTTTTTGAAAAAGAAATTGAGGTTACTTAATG-TTGAAGTACCTAATTA
89191686 AAT
1 AAT
89191689 ATTTGTTTTT
Statistics
Matches: 115, Mismatches: 8, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
60 26 0.23
61 89 0.77
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.40
Consensus pattern (61 bp):
AATTTTAAAATTATTTTTTGAAAAAGAAATTGAGGTTACTTAATGTTGAAGTACCTAATTA
Found at i:89192003 original size:22 final size:22
Alignment explanation
Indices: 89191975--89192021 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
89191965 TAAAAGATAC
89191975 TTTGATATCCATACGTTAAGAA
1 TTTGATATCCATACGTTAAGAA
89191997 TTTGATATCCATACGTTAAGAA
1 TTTGATATCCATACGTTAAGAA
89192019 TTT
1 TTT
89192022 TCTTTCATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (22 bp):
TTTGATATCCATACGTTAAGAA
Found at i:89208292 original size:60 final size:61
Alignment explanation
Indices: 89208155--89208283 Score: 224
Period size: 60 Copynumber: 2.1 Consensus size: 61
89208145 GTGATGTAGT
*
89208155 AATTTTAAAATTATTTTTTGAAAAAGAAATTGAGGTTACTTAATCTTGAAGTACCTAATTA
1 AATTTTAAAATTATTTTTTGAAAAAGAAATTGAGGTTACTTAATATTGAAGTACCTAATTA
*
89208216 AATTTTAAAATTATTTTTT-AAAAAGAAATTGAGGTTACTTCATATTGAAGTACCTAATTA
1 AATTTTAAAATTATTTTTTGAAAAAGAAATTGAGGTTACTTAATATTGAAGTACCTAATTA
89208276 AATATTTA
1 AAT-TTTA
89208284 TTTTATTTTA
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
60 42 0.65
61 23 0.35
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (61 bp):
AATTTTAAAATTATTTTTTGAAAAAGAAATTGAGGTTACTTAATATTGAAGTACCTAATTA
Found at i:89209028 original size:15 final size:16
Alignment explanation
Indices: 89209008--89209037 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
89208998 GATTAAATTG
89209008 TATATT-TTTATAATC
1 TATATTATTTATAATC
89209023 TATATTATTTATAAT
1 TATATTATTTATAAT
89209038 TTTTAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
TATATTATTTATAATC
Found at i:89209254 original size:278 final size:272
Alignment explanation
Indices: 89208750--89209429 Score: 761
Period size: 278 Copynumber: 2.5 Consensus size: 272
89208740 TTTAATAGTT
* *
89208750 TATATATTTATAATTTTTAAAAAATTAAATTAATTTTTTATCATTTTCTAGAGTTAAAGTGTAAT
1 TATATATTTATAATTTTT-AAAAATTAAATTAA-TTTTTATCATTTT-TAGAATTAAAGTATAAT
* * ***
89208815 TTCATTATTATTAACTTAAAATTTTATAAATTATAAAAT-ATTTAAA--AAAAAATT-ATTTTAG
63 TT-ATTATTATTAATTTAAAATTTTATAAATTAT-AAATGACTTAAATGAAATTTTTCATTTTAG
* * * *
89208876 GAGGTCGAGACATTTGCCAGTCACCTCTTGCTCCACCACTAGCTAATGAATCTATTTCTAGTACC
126 GAGGTCAAGACATCTGCCAGTCACCTCTAGCTCCACCACTAGCTAATGAATCTATTTATAGTACC
* *
89208941 AAAATTTACTTTTTACTTATTAGGAAGGCTAAGAGCTAAGAAAATTTT-TGTGAG-TAGG-ATTA
191 AAAATTTACTTTTTACTTATTAGGAAGGCTAAGAGCCAA-AAAATTTTATGAG-GCT-GGAATTA
89209003 AATTGTATATTTTTATAATC
253 AATTGTATATTTTTATAATC
* * *
89209023 TATATTATTTATAATTTTTAAATAATTAAATCAGATTTTTATCATTTTTAGAATTAATGTACAAT
1 TATA-TATTTATAATTTTTAAA-AATTAAATTA-ATTTTTATCATTTTTAGAATTAAAGTATAAT
* *
89209088 CTTATCATTATTAATTTAAAATTTTATAAATTATAAATGGCTTAAATGATAATTTTTCATTTTAG
63 -TTATTATTATTAATTTAAAATTTTATAAATTATAAATGACTTAAATGA-AATTTTTCATTTTAG
* * * ** * *
89209153 AGAGGTTAAGGC-TCCTGCCAG-CAACCTCTAGCTCCATCGTTGGCTAATGAATCTATTTATATT
126 -GAGGTCAAGACAT-CTGCCAGTC-ACCTCTAGCTCCACCACTAGCTAATGAATCTATTTATAGT
* *
89209216 ACCAAAATTTACTTTTTACTTATTAGGAAGGTTAAGAGCCAATAAATTTTATGAGGCTGGAATTA
188 ACCAAAATTTACTTTTTACTTATTAGGAAGGCTAAGAGCCAAAAAATTTTATGAGGCTGGAATTA
* * *
89209281 AATTGTATGTTTTTATAGTT
253 AATTGTATATTTTTATAATC
* * * * * **
89209301 TATATCTTTATAATTTTT--AGATGAAATTATTTTTTATTATTTTTTTAATGTCAAAGTATAATT
1 TATATATTTATAATTTTTAAAAATTAAATTAATTTTTATCATTTTTAGAAT-T-AAAGTATAA-T
89209364 TTATTATTATTAATTTAAAATTTTATAAATTATAAATGACTTAAATAGAAAATTTTTCATTTTAG
63 TTATTATTATTAATTTAAAATTTTATAAATTATAAATGACTTAAAT-G-AAATTTTTCATTTTAG
89209429 G
126 G
89209430 CTTACCAGCC
Statistics
Matches: 345, Mismatches: 42, Indels: 38
0.81 0.10 0.09
Matches are distributed among these distances:
272 4 0.01
273 70 0.20
274 46 0.13
275 55 0.16
276 21 0.06
277 33 0.10
278 116 0.34
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.44
Consensus pattern (272 bp):
TATATATTTATAATTTTTAAAAATTAAATTAATTTTTATCATTTTTAGAATTAAAGTATAATTTA
TTATTATTAATTTAAAATTTTATAAATTATAAATGACTTAAATGAAATTTTTCATTTTAGGAGGT
CAAGACATCTGCCAGTCACCTCTAGCTCCACCACTAGCTAATGAATCTATTTATAGTACCAAAAT
TTACTTTTTACTTATTAGGAAGGCTAAGAGCCAAAAAATTTTATGAGGCTGGAATTAAATTGTAT
ATTTTTATAATC
Found at i:89209904 original size:34 final size:34
Alignment explanation
Indices: 89209862--89209932 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
89209852 AAAAGATACG
*
89209862 TTTAATTAATTCATATTTTTTATATATATAATAT
1 TTTAATTAATTCATATTTTCTATATATATAATAT
89209896 TTTAATTAATTCATATTTTCTATATATATAATAT
1 TTTAATTAATTCATATTTTCTATATATATAATAT
89209930 TTT
1 TTT
89209933 GACTTTAAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (34 bp):
TTTAATTAATTCATATTTTCTATATATATAATAT
Found at i:89209911 original size:16 final size:16
Alignment explanation
Indices: 89209862--89209914 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
89209852 AAAAGATACG
89209862 TTTAATTAATTCATAT
1 TTTAATTAATTCATAT
* *
89209878 TTT-TTATATATATAATAT
1 TTTAAT-TA-AT-TCATAT
89209896 TTTAATTAATTCATAT
1 TTTAATTAATTCATAT
89209912 TTT
1 TTT
89209915 CTATATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
15 1 0.03
16 13 0.45
17 4 0.14
18 10 0.34
19 1 0.03
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTAATTAATTCATAT
Found at i:89209931 original size:18 final size:17
Alignment explanation
Indices: 89209878--89209932 Score: 60
Period size: 16 Copynumber: 3.2 Consensus size: 17
89209868 TAATTCATAT
89209878 TTTTTATATATATAATA
1 TTTTTATATATATAATA
* *
89209895 TTTTAAT-TA-ATTCATA
1 TTTTTATATATA-TAATA
89209911 TTTTCTATATATATAATA
1 TTTT-TATATATATAATA
89209929 TTTT
1 TTTT
89209933 GACTTTAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
15 1 0.03
16 10 0.33
17 8 0.27
18 10 0.33
19 1 0.03
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTTATATATATAATA
Found at i:89210093 original size:23 final size:23
Alignment explanation
Indices: 89210067--89210113 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
89210057 CTGAACCCGA
89210067 ACTCTTTTTCTATCAACAAAATT
1 ACTCTTTTTCTATCAACAAAATT
89210090 ACTCTTTTTCTATCAACAAAATT
1 ACTCTTTTTCTATCAACAAAATT
89210113 A
1 A
89210114 GTAGAGCGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.43
Consensus pattern (23 bp):
ACTCTTTTTCTATCAACAAAATT
Found at i:89210810 original size:21 final size:21
Alignment explanation
Indices: 89210786--89210828 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
89210776 ATCCTAGGGG
89210786 TGGCCTGAGTTCTAGTCGCCC
1 TGGCCTGAGTTCTAGTCGCCC
89210807 TGGCCTGAGTTCTAGTCGCCC
1 TGGCCTGAGTTCTAGTCGCCC
89210828 T
1 T
89210829 AATCGTGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.09, C:0.33, G:0.28, T:0.30
Consensus pattern (21 bp):
TGGCCTGAGTTCTAGTCGCCC
Found at i:89213575 original size:3 final size:3
Alignment explanation
Indices: 89213567--89213660 Score: 72
Period size: 3 Copynumber: 31.3 Consensus size: 3
89213557 TCCATTTCGG
*
89213567 GAA GAA GAA -AA GAAA GAA GGA GAA GAA GAA -AA GGAA GAA TG-A GAA
1 GAA GAA GAA GAA G-AA GAA GAA GAA GAA GAA GAA -GAA GAA -GAA GAA
* * *
89213612 GAA GGAA GGA GAA TAA GAA -AA GGAA GAA G-A GAA GAA GAA GAA GGA
1 GAA -GAA GAA GAA GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA
89213657 GAA G
1 GAA G
89213661 GAGTCGGCTG
Statistics
Matches: 73, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
2 9 0.12
3 53 0.73
4 11 0.15
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:89213593 original size:21 final size:21
Alignment explanation
Indices: 89213567--89213615 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
89213557 TCCATTTCGG
89213567 GAAGAAGAAAAGAAAGAAGGA
1 GAAGAAGAAAAGAAAGAAGGA
* *
89213588 GAAGAAGAAAAGGAAGAATGA
1 GAAGAAGAAAAGAAAGAAGGA
89213609 GAAGAAG
1 GAAGAAG
89213616 GAAGGAGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.63, C:0.00, G:0.35, T:0.02
Consensus pattern (21 bp):
GAAGAAGAAAAGAAAGAAGGA
Found at i:89213655 original size:21 final size:22
Alignment explanation
Indices: 89213608--89213656 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 22
89213598 AGGAAGAATG
*
89213608 AGAAGAAGGAAG---GAGAATA
1 AGAAGAAGGAAGAATGAGAAGA
89213627 AGAA-AAGGAAGAA-GAGAAGA
1 AGAAGAAGGAAGAATGAGAAGA
89213647 AGAAGAAGGA
1 AGAAGAAGGA
89213657 GAAGGAGTCG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 7 0.27
19 4 0.15
20 10 0.38
21 5 0.19
ACGTcount: A:0.61, C:0.00, G:0.37, T:0.02
Consensus pattern (22 bp):
AGAAGAAGGAAGAATGAGAAGA
Found at i:89214125 original size:9 final size:9
Alignment explanation
Indices: 89214102--89214181 Score: 56
Period size: 9 Copynumber: 8.7 Consensus size: 9
89214092 CTACTCTTAT
89214102 TAAACATTTA
1 TAAA-ATTTA
*
89214112 AAAAATTTA
1 TAAAATTTA
* *
89214121 TAAAAATTG
1 TAAAATTTA
89214130 TAAAATTTTA
1 TAAAA-TTTA
89214140 TAAAATTGTA
1 TAAAATT-TA
*
89214150 -AAATTTTA
1 TAAAATTTA
*
89214158 TAATAA-TCA
1 TAA-AATTTA
*
89214167 TAAAAATTA
1 TAAAATTTA
89214176 TAAAAT
1 TAAAAT
89214182 ACATTAAAAA
Statistics
Matches: 54, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
8 4 0.07
9 37 0.69
10 13 0.24
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (9 bp):
TAAAATTTA
Found at i:89214134 original size:19 final size:19
Alignment explanation
Indices: 89214112--89214180 Score: 79
Period size: 18 Copynumber: 3.7 Consensus size: 19
89214102 TAAACATTTA
89214112 AAAAATTTATAAAAATTGT
1 AAAAATTTATAAAAATTGT
*
89214131 AAAATTTTAT-AAAATTGT
1 AAAAATTTATAAAAATTGT
* * **
89214149 AAAATTTTATAATAATCAT
1 AAAAATTTATAAAAATTGT
89214168 AAAAA-TTATAAAA
1 AAAAATTTATAAAA
89214181 TACATTAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
18 25 0.58
19 18 0.42
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (19 bp):
AAAAATTTATAAAAATTGT
Found at i:89214465 original size:18 final size:18
Alignment explanation
Indices: 89214444--89214490 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
89214434 ATTGTATAAT
*
89214444 TTTTTATATTTCTATA-TA
1 TTTTTATATTT-TATACGA
*
89214462 -TTTTATATTTTTTACGA
1 TTTTTATATTTTATACGA
89214479 TTTTTATATTTT
1 TTTTTATATTTT
89214491 TTTCTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 3 0.12
17 11 0.44
18 11 0.44
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTTTATATTTTATACGA
Found at i:89214491 original size:9 final size:9
Alignment explanation
Indices: 89214442--89214492 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 9
89214432 AAATTGTATA
89214442 ATTTTTTAT
1 ATTTTTTAT
*
89214451 A-TTTCTAT
1 ATTTTTTAT
*
89214459 ATATTTTAT
1 ATTTTTTAT
*
89214468 ATTTTTTACG
1 ATTTTTTA-T
89214478 A-TTTTTAT
1 ATTTTTTAT
89214486 ATTTTTT
1 ATTTTTT
89214493 TCTAAATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
8 8 0.24
9 24 0.73
10 1 0.03
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71
Consensus pattern (9 bp):
ATTTTTTAT
Found at i:89214501 original size:20 final size:20
Alignment explanation
Indices: 89214452--89214513 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 20
89214442 ATTTTTTATA
*
89214452 TTTCTATATATTTTATATTTT
1 TTTCTAAAT-TTTTATATTTT
* *
89214473 TTAC--GATTTTTATATTTT
1 TTTCTAAATTTTTATATTTT
*
89214491 TTTCTAAATTTTAATAATTTT
1 TTTCTAAATTTTTAT-ATTTT
89214512 TT
1 TT
89214514 AAATATTTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
18 14 0.42
19 2 0.06
20 7 0.21
21 10 0.30
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.68
Consensus pattern (20 bp):
TTTCTAAATTTTTATATTTT
Found at i:89214522 original size:19 final size:19
Alignment explanation
Indices: 89214489--89214544 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 19
89214479 TTTTTATATT
89214489 TTTTTCTAAAT-TTTAATAA
1 TTTTT-TAAATATTTAATAA
89214508 TTTTTTAAATATTTAAT-A
1 TTTTTTAAATATTTAATAA
* *
89214526 TTTATTAAA-ATCTAATAA
1 TTTTTTAAATATTTAATAA
89214544 T
1 T
89214545 ATTTATAGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
17 6 0.18
18 16 0.48
19 11 0.33
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTTTTAAATATTTAATAA
Found at i:89214528 original size:18 final size:18
Alignment explanation
Indices: 89214459--89214534 Score: 64
Period size: 19 Copynumber: 4.1 Consensus size: 18
89214449 ATATTTCTAT
* *
89214459 ATATTTTATATTTTTTACG
1 ATATTTAATATTTTTTA-A
* *
89214478 ATTTTTATATTTTTTTCTAA
1 ATATTTA-ATATTTTT-TAA
89214498 AT-TTTAATAATTTTTTAA
1 ATATTTAAT-ATTTTTTAA
*
89214516 ATATTTAATATTTATTAA
1 ATATTTAATATTTTTTAA
89214534 A
1 A
89214535 ATCTAATAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
18 16 0.34
19 20 0.43
20 9 0.19
21 2 0.04
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (18 bp):
ATATTTAATATTTTTTAA
Found at i:89214581 original size:10 final size:10
Alignment explanation
Indices: 89214566--89214598 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
89214556 TTATTGATTT
*
89214566 TAATTTTTAA
1 TAATTTTTTA
89214576 TAATTTTTTA
1 TAATTTTTTA
89214586 TAATTTTTTA
1 TAATTTTTTA
89214596 TAA
1 TAA
89214599 AAGCAGGGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TAATTTTTTA
Found at i:89217696 original size:50 final size:50
Alignment explanation
Indices: 89217630--89217806 Score: 273
Period size: 50 Copynumber: 3.5 Consensus size: 50
89217620 CCATGGCAAC
*
89217630 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGGCAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * * *
89217680 AAGTGATAAGTAATAGCTTCGGCTACACTTATCTAATCAATGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
*
89217730 AAGTGATAAGTGATAGCTTCGGCTGCACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
89217780 CAAGTGAAAAGTGGTAGCTTCGGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
89217807 CTGATCGGTG
Statistics
Matches: 113, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 90 0.80
51 23 0.20
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.26
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:89217821 original size:31 final size:31
Alignment explanation
Indices: 89217782--89217930 Score: 226
Period size: 31 Copynumber: 4.8 Consensus size: 31
89217772 ACAAATGACA
89217782 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
89217813 GGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
89217844 AGTGAAAAGTGGTAGCTCCGGCTACCTAATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* * *
89217875 AGTGAAAAATGGTAGCTCCGGCTATCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
89217906 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
89217931 AAGTGACAAG
Statistics
Matches: 105, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 105 1.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:89218018 original size:47 final size:46
Alignment explanation
Indices: 89217948--89218162 Score: 152
Period size: 47 Copynumber: 4.7 Consensus size: 46
89217938 AAGTAATTTC
* * * *
89217948 CGTATAAGATCAGATCTGGGATATGGCATCAGTGTGATATATGCTA
1 CGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
* * * *
89217994 CTGTATAAGACCATATCTGAGATATAGCATCAGTGAGATATGTGATT
1 C-GTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
* * * * * *
89218041 CGTGTAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTA
1 CGTATAAGACCATATCTGGGATATGGCATC-A-GTGAGATATATGA-TA
* * * *
89218090 CGTGTAAGACCATAGCTAGGCTATGGCATC-----GATATATGAATA
1 CGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATG-ATA
* * * *
89218132 TGTGTAAGACCATAGCTGGGCTATGGCATCA
1 CGTATAAGACCATATCTGGGATATGGCATCA
89218163 TTATATGAAG
Statistics
Matches: 143, Mismatches: 20, Indels: 15
0.80 0.11 0.08
Matches are distributed among these distances:
42 37 0.26
43 1 0.01
46 25 0.17
47 39 0.27
48 11 0.08
49 30 0.21
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (46 bp):
CGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
Found at i:89218100 original size:49 final size:48
Alignment explanation
Indices: 89218030--89218205 Score: 198
Period size: 42 Copynumber: 3.9 Consensus size: 48
89218020 GCATCAGTGA
*
89218030 GATATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATCGATATGT
1 GATATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATCGATATAT
*
89218078 GATATGTGATTACGTGTAAGACCATAGCTAGGCTATGGCATCGATATAT
1 GATATGTGATT-CGTGTAAGACCATAGCTGGGCTATGGCATCGATATAT
89218127 GA-A--T-A-T-GTGTAAGACCATAGCTGGGCTATGGCATC-ATTATAT
1 GATATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATCGA-TATAT
* **
89218169 GA-A---GA-T-GTGTAAGACCATAGTTGAACTATGGCATCGA
1 GATATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATCGA
89218206 GAAAACGAAG
Statistics
Matches: 118, Mismatches: 6, Indels: 13
0.86 0.04 0.09
Matches are distributed among these distances:
41 1 0.01
42 64 0.54
43 1 0.01
44 1 0.01
45 1 0.01
46 1 0.01
48 12 0.10
49 37 0.31
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (48 bp):
GATATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATCGATATAT
Found at i:89221680 original size:2 final size:2
Alignment explanation
Indices: 89221673--89221697 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
89221663 CCAAAGTGAG
89221673 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
89221698 AAAGTTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.