Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold258
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: 5730937
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 25
Found at i:3187007 original size:9 final size:10
Alignment explanation
Indices: 3186959--3187016 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
3186949 GATGTAAATA
*
3186959 TATATTTATAT
1 TATA-TTATTT
3186970 TATATTATTAT
1 TATATTATT-T
*
3186981 TAT-TTTTTT
1 TATATTATTT
3186990 TAT-TATATTT
1 TATAT-TATTT
3187000 TA-ATTATTT
1 TATATTATTT
3187009 TATATTAT
1 TATATTAT
3187017 ATTTTTTTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
9 12 0.30
10 20 0.50
11 8 0.20
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TATATTATTT
Found at i:3187030 original size:23 final size:22
Alignment explanation
Indices: 3186957--3187030 Score: 78
Period size: 21 Copynumber: 3.3 Consensus size: 22
3186947 ATGATGTAAA
3186957 TATATATTTATATTATATTATTAT
1 TATAT-TTTATATTATATT-TTAT
* * *
3186981 TATTTTTTTTATTATATTTTAA
1 TATATTTTATATTATATTTTAT
*
3187003 T-TATTTTATATTATATTTTTT
1 TATATTTTATATTATATTTTAT
3187024 TCATATT
1 T-ATATT
3187031 AATATAATAG
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
21 17 0.41
22 4 0.10
23 16 0.39
24 4 0.10
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (22 bp):
TATATTTTATATTATATTTTAT
Found at i:3196472 original size:19 final size:21
Alignment explanation
Indices: 3196434--3196472 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
3196424 GAGAAAGAAA
*
3196434 TAAAAACAATAAATAAATTTT
1 TAAAAACAATAAAAAAATTTT
3196455 TAAAAA-AA-AAAAAAATTT
1 TAAAAACAATAAAAAAATTT
3196473 CGCTTAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 2 0.12
21 6 0.35
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAAAACAATAAAAAAATTTT
Found at i:3202355 original size:3 final size:3
Alignment explanation
Indices: 3202347--3202380 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3202337 AAAATGTGAA
3202347 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3202381 GAAGAGAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3210265 original size:2 final size:2
Alignment explanation
Indices: 3210258--3210293 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3210248 GATTGTTGAG
3210258 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3210294 TTAGAGAGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3210653 original size:21 final size:21
Alignment explanation
Indices: 3210620--3210659 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3210610 AGTTAAAAAG
3210620 GAGAGATTCAAAGAAGAGTGT
1 GAGAGATTCAAAGAAGAGTGT
*
3210641 GAGAGTATT-AAAGCAGAGT
1 GAGAG-ATTCAAAGAAGAGT
3210660 TAGCTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.42, C:0.05, G:0.33, T:0.20
Consensus pattern (21 bp):
GAGAGATTCAAAGAAGAGTGT
Found at i:3216224 original size:2 final size:2
Alignment explanation
Indices: 3216219--3216244 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3216209 GATATATATA
3216219 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
3216245 CCCGCCTGTG
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:3220099 original size:2 final size:2
Alignment explanation
Indices: 3220092--3220140 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
3220082 GCAAATATGA
* * *
3220092 AT AT AT AT AC AT AT AT AT AT AT AT AT GT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3220134 AT AT AT A
1 AT AT AT A
3220141 CAAGTAACAG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3220879 original size:2 final size:2
Alignment explanation
Indices: 3220874--3220903 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
3220864 ATAATATCCT
3220874 TA TA TA TCA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA T
3220904 TTACGTATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3221459 original size:16 final size:17
Alignment explanation
Indices: 3221417--3221459 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
3221407 TTTAATATAT
* *
3221417 ATAAAATTTTTACTTAA
1 ATAAAATTTATAATTAA
3221434 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
3221449 ATAAAATTTAT
1 ATAAAATTTAT
3221460 TTAAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 7 0.30
16 10 0.43
17 6 0.26
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:3221466 original size:27 final size:26
Alignment explanation
Indices: 3221436--3221522 Score: 70
Period size: 28 Copynumber: 3.1 Consensus size: 26
3221426 TTACTTAAAT
3221436 AAAATTATAATTAATAAAATTTATTTAA
1 AAAATT-TAATTAATAAAATTTATTT-A
* *
3221464 AAATATTTAATAAAT-AAATTTAAAGTT-
1 AAA-ATTTAATTAATAAAATTT--ATTTA
3221491 AAAATTTAATTATATAAAAAATTTATTTA
1 AAAATTTAATTA-AT--AAAATTTATTTA
3221520 AAA
1 AAA
3221523 TATAAGATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
26 8 0.17
27 11 0.23
28 13 0.28
29 9 0.19
30 6 0.13
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (26 bp):
AAAATTTAATTAATAAAATTTATTTA
Found at i:3221520 original size:28 final size:27
Alignment explanation
Indices: 3221435--3221523 Score: 85
Period size: 30 Copynumber: 3.2 Consensus size: 27
3221425 TTTACTTAAA
3221435 TAAAATTATAATTAAT--AAAATTTATT
1 TAAAATT-TAATTAATAAAAAATTTATT
* * *
3221461 TAAAA-ATATTTAATAAATAAATTTAAAGT
1 TAAAATTTAATTAATAAA-AAATTT--ATT
3221490 TAAAATTTAATTATATAAAAAATTTATT
1 TAAAATTTAATTA-ATAAAAAATTTATT
3221518 TAAAAT
1 TAAAAT
3221524 ATAAGATAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
24 7 0.14
26 6 0.12
27 6 0.12
28 8 0.16
29 7 0.14
30 11 0.22
31 5 0.10
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (27 bp):
TAAAATTTAATTAATAAAAAATTTATT
Found at i:3221614 original size:17 final size:18
Alignment explanation
Indices: 3221570--3221614 Score: 60
Period size: 16 Copynumber: 2.6 Consensus size: 18
3221560 AAAAAATAAT
3221570 TAAAATAAAATATGACACA
1 TAAAAT-AAATATGACACA
3221589 -AAAAT-AATATGA-ACA
1 TAAAATAAATATGACACA
3221604 TAAAATAAATA
1 TAAAATAAATA
3221615 CATACACATG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 3 0.12
16 12 0.50
17 4 0.17
18 5 0.21
ACGTcount: A:0.67, C:0.07, G:0.04, T:0.22
Consensus pattern (18 bp):
TAAAATAAATATGACACA
Found at i:3222534 original size:19 final size:18
Alignment explanation
Indices: 3222498--3222540 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
3222488 ATATATAATT
3222498 TTTTTTCTTTCCTTTTTCC
1 TTTTTTCTTTCCTTTTT-C
*
3222517 TTTTTTC-TTCTTTCTTTC
1 TTTTTTCTTTCCTT-TTTC
3222535 TTTTTT
1 TTTTTT
3222541 GATAGAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTTCTTTCCTTTTTC
Found at i:3223238 original size:75 final size:75
Alignment explanation
Indices: 3223145--3223289 Score: 281
Period size: 75 Copynumber: 1.9 Consensus size: 75
3223135 AAATTGAATC
*
3223145 ACGATGATTAACTATACAAAATATAACATGAATTGAGATATAATACAAACTCAACATATATATAT
1 ACGATGATTAACTATACAAAATATAACATGAATTGAAATATAATACAAACTCAACATATATATAT
3223210 ATATATATAT
66 ATATATATAT
3223220 ACGATGATTAACTATACAAAATATAACATGAATTGAAATATAATACAAACTCAACATATATATAT
1 ACGATGATTAACTATACAAAATATAACATGAATTGAAATATAATACAAACTCAACATATATATAT
3223285 ATATA
66 ATATA
3223290 ATTAAAACAC
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 69 1.00
ACGTcount: A:0.52, C:0.11, G:0.06, T:0.31
Consensus pattern (75 bp):
ACGATGATTAACTATACAAAATATAACATGAATTGAAATATAATACAAACTCAACATATATATAT
ATATATATAT
Found at i:3223755 original size:32 final size:34
Alignment explanation
Indices: 3223695--3223779 Score: 88
Period size: 32 Copynumber: 2.6 Consensus size: 34
3223685 AATATGTATG
* *
3223695 ATAATATGAATATATAAATATTTTAAAAT-T-TAT
1 ATAATAT-AATTTATAAATATTTTAAAATGTAAAT
*
3223728 ATAATATAATTTATTAAT-TTATTAAAATGTAAAT
1 ATAATATAATTTATAAATATT-TTAAAATGTAAAT
*
3223762 ATAATATATTTTA-AAATA
1 ATAATATAATTTATAAATA
3223780 ATTATAATAC
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
31 2 0.05
32 16 0.37
33 11 0.26
34 14 0.33
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (34 bp):
ATAATATAATTTATAAATATTTTAAAATGTAAAT
Found at i:3229856 original size:26 final size:27
Alignment explanation
Indices: 3229811--3229863 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
3229801 GAAAAAAGTA
3229811 TTAAAAAATTATTTAAAATAATATAAAT
1 TTAAAAAATTATTTAAAATAATA-AAAT
*
3229839 TTAAAAAA-TA-TTAGAATAATAAAAT
1 TTAAAAAATTATTTAAAATAATAAAAT
3229864 CTTTTATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 4 0.17
26 10 0.42
27 2 0.08
28 8 0.33
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (27 bp):
TTAAAAAATTATTTAAAATAATAAAAT
Found at i:3235786 original size:46 final size:46
Alignment explanation
Indices: 3235713--3235804 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
3235703 TTATCACTTG
* * *
3235713 AACACTGAATCATTTACGAAAATAAATATAATCTAAACGATATATT
1 AACAATGAATCATTTACGAAAAGAAATAGAATCTAAACGATATATT
* *
3235759 AACAATGAATCATTTATGAAAAGAAATAGAATCTCAACGATATATT
1 AACAATGAATCATTTACGAAAAGAAATAGAATCTAAACGATATATT
3235805 TACCCGGCTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.29
Consensus pattern (46 bp):
AACAATGAATCATTTACGAAAAGAAATAGAATCTAAACGATATATT
Found at i:3238137 original size:22 final size:24
Alignment explanation
Indices: 3238108--3238159 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 24
3238098 AATTTTTAAA
*
3238108 ATTA-ATTAAAATAAT-TATTTTT
1 ATTATATTAAAATAATAAATTTTT
*
3238130 A-TATATTAAAATTATAAATTTTT
1 ATTATATTAAAATAATAAATTTTT
3238153 ATTATAT
1 ATTATAT
3238160 ATTACTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 2 0.08
22 11 0.44
23 7 0.28
24 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
ATTATATTAAAATAATAAATTTTT
Found at i:3240111 original size:23 final size:23
Alignment explanation
Indices: 3240055--3240118 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
3240045 ATTTTTTATT
*
3240055 TAAAT-TTAAAT-TTATATTAAA
1 TAAATATTAAATATTATTTTAAA
* * * *
3240076 TAATTAATCAATATTATTTTGAA
1 TAAATATTAAATATTATTTTAAA
3240099 TAAATATTAAATATATATTT
1 TAAATATTAAATAT-TATTT
3240119 AATTTAAATA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
21 4 0.12
22 4 0.12
23 19 0.59
24 5 0.16
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TAAATATTAAATATTATTTTAAA
Found at i:3241956 original size:35 final size:36
Alignment explanation
Indices: 3241899--3241967 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
3241889 TTGGTAAATT
3241899 TTATAATAATTATTATATTTAA-TGTAAAAATATTG
1 TTATAATAATTATTATATTTAATTGTAAAAATATTG
* * *
3241934 TTATAAGTGATTATTTTA-TTAATTTTAAAAATAT
1 TTATAA-TAATTATTATATTTAATTGTAAAAATAT
3241968 CTAAATTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 10 0.34
36 19 0.66
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (36 bp):
TTATAATAATTATTATATTTAATTGTAAAAATATTG
Found at i:3242069 original size:9 final size:9
Alignment explanation
Indices: 3242066--3242105 Score: 62
Period size: 9 Copynumber: 4.2 Consensus size: 9
3242056 ATTTTATTAA
3242066 TTTTAATTT
1 TTTTAATTT
3242075 TTTTAATTT
1 TTTTAATTT
3242084 TTTTAATTT
1 TTTTAATTT
3242093 ATTTATAATTT
1 -TTT-TAATTT
3242104 TT
1 TT
3242106 ATTCTTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
9 18 0.62
10 5 0.17
11 6 0.21
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTAATTT
Found at i:3242073 original size:15 final size:15
Alignment explanation
Indices: 3242055--3242084 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3242045 TATATAAATA
3242055 AATTTTATTAATTTT
1 AATTTTATTAATTTT
*
3242070 AATTTTTTTAATTTT
1 AATTTTATTAATTTT
3242085 TTTAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
AATTTTATTAATTTT
Found at i:3242724 original size:20 final size:18
Alignment explanation
Indices: 3242687--3242746 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
3242677 TTTTATAATT
3242687 TTTTATTTTTAAATAATAA
1 TTTTATTTTTAAA-AATAA
3242706 TTTTATTTATATAAAAATAA
1 TTTTATTT-T-TAAAAATAA
* *
3242726 ATTAATTTTTTAAAAA-AA
1 TTTTA-TTTTTAAAAATAA
3242744 TTT
1 TTT
3242747 AATTAAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
18 4 0.11
19 14 0.40
20 10 0.29
21 7 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTTATTTTTAAAAATAA
Found at i:3242827 original size:35 final size:34
Alignment explanation
Indices: 3242777--3242848 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 34
3242767 AGAATCAAAG
* * *
3242777 TTAAATTAAATATATAAATATATTTGATTATTAT-T
1 TTAAAGTAAAAATATAAATAT-TTTAATT-TTATAT
3242812 TTAAAGTAAAAATATAAATATTTTAATTTTATAT
1 TTAAAGTAAAAATATAAATATTTTAATTTTATAT
3242846 TTA
1 TTA
3242849 CTAATTTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 4 0.12
34 10 0.30
35 19 0.58
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (34 bp):
TTAAAGTAAAAATATAAATATTTTAATTTTATAT
Found at i:3245729 original size:2 final size:2
Alignment explanation
Indices: 3245722--3245762 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3245712 TAATTGGTTT
3245722 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA T
3245763 GAGAAACTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3247170 original size:66 final size:66
Alignment explanation
Indices: 3247056--3247246 Score: 242
Period size: 66 Copynumber: 2.9 Consensus size: 66
3247046 TTCCGCCGGT
* * * * *
3247056 GATGATTCGTCTAAATATGGTTTTGATGGAATACCG-GCTTACAACCCTCAGGCAAAGCCAAAGG
1 GATGATTCATCTAAATATGGTTTTGATGGAATA-AGAGCTGACAGCCCTCAAGCAAAGCCAAAGG
3247120 CC
65 CC
* * *
3247122 GATGATTCATCTAAATATGGCTTTGATGGAATAAGAGCTGACAGCCCTCAAGCAAAGCCAGATGC
1 GATGATTCATCTAAATATGGTTTTGATGGAATAAGAGCTGACAGCCCTCAAGCAAAGCCAAAGGC
*
3247187 T
66 C
* * *
3247188 GATGATTCATCTAAATATGGTTTTGATGGAAT-AGCAGCGGATAGCCCGCAAGCAAAGCC
1 GATGATTCATCTAAATATGGTTTTGATGGAATAAG-AGCTGACAGCCCTCAAGCAAAGCC
3247247 TGAAGGAGAA
Statistics
Matches: 110, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
65 3 0.03
66 107 0.97
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (66 bp):
GATGATTCATCTAAATATGGTTTTGATGGAATAAGAGCTGACAGCCCTCAAGCAAAGCCAAAGGC
C
Found at i:3250027 original size:21 final size:22
Alignment explanation
Indices: 3250003--3250045 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
3249993 AAAAAATAAA
*
3250003 TAAAATA-TGTAATATTTTTTT
1 TAAAATATTGTAAAATTTTTTT
3250024 TAAAATATTTGTAAAATTTTTT
1 TAAAATA-TTGTAAAATTTTTT
3250046 AAAAAATCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
23 12 0.63
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (22 bp):
TAAAATATTGTAAAATTTTTTT
Found at i:3253773 original size:3 final size:3
Alignment explanation
Indices: 3253759--3253790 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
3253749 TTCAAAGGAC
*
3253759 GAA GAT GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
3253791 GGATGAAGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.34, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:3254021 original size:3 final size:3
Alignment explanation
Indices: 3254013--3254305 Score: 243
Period size: 3 Copynumber: 96.0 Consensus size: 3
3254003 AAAGAGGCAG
* * *
3254013 AGA AGA AGAA AGG AGA AGA ATGA AGA AGG AGA GGA AG- AGA AGA AGA
1 AGA AGA AG-A AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA
*
3254059 AGA AGA AGGA AGAA AGAA AGAA AGAA AGA CGA AGA AGA AGA AGA AGA
1 AGA AGA A-GA AG-A AG-A AG-A AG-A AGA AGA AGA AGA AGA AGA AGA
* * * *
3254106 AGAA AGA CGG AGA AGA AGAA AGT AGA AGA AGA AGG AGA AGA AGA AGA
1 AG-A AGA AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * * * * * * *
3254153 AGA AGG A-A AGA AGG AGG AGA AGG AGA AGG AGA AGG AGA AGG AGA AGG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * * * * * *
3254200 AGA AGG AGA AGA AGG AGA AGG AGA AGG AGA AGG AGA AGG AGA AGG AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * *
3254248 AGG AGA AGG AGA AGG AGA AGA AG- AGA AGA AG- AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
3254294 AGA AGA AGA AGA
1 AGA AGA AGA AGA
3254306 CTCAACGTTG
Statistics
Matches: 230, Mismatches: 50, Indels: 20
0.77 0.17 0.07
Matches are distributed among these distances:
2 7 0.03
3 193 0.84
4 30 0.13
ACGTcount: A:0.58, C:0.01, G:0.41, T:0.01
Consensus pattern (3 bp):
AGA
Found at i:3254350 original size:51 final size:50
Alignment explanation
Indices: 3254286--3254385 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 50
3254276 AAGAGAAGAA
*
3254286 GAAGAAGAAGAAGAAGAAGACTCAACGT-TGCAATCATCATTTTTAACAGGG
1 GAAGAAGAAGAAGAAGAAGACTC-AC-TATGCAATCATCATTTTCAACAGGG
* * *
3254337 GAAGAAGATGAAGAAGAATATTCACTCATGCAATCATCATTTTCAACAG
1 GAAGAAGAAGAAGAAGAAGACTCACT-ATGCAATCATCATTTTCAACAG
3254386 AACAATATGA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
49 1 0.02
50 2 0.05
51 40 0.93
ACGTcount: A:0.43, C:0.15, G:0.20, T:0.22
Consensus pattern (50 bp):
GAAGAAGAAGAAGAAGAAGACTCACTATGCAATCATCATTTTCAACAGGG
Found at i:3254396 original size:48 final size:49
Alignment explanation
Indices: 3254314--3254409 Score: 122
Period size: 48 Copynumber: 1.9 Consensus size: 49
3254304 GACTCAACGT
* * * *
3254314 TGCAATCATCATTTTTAACAGGGGAAGAAGATGAAGAAGAATATTCACTCA
1 TGCAATCATCATTTTCAACA--GGAACAAGATGAAAAAGAAGATTCACTCA
*
3254365 TGCAATCATCATTTTCAACA-GAACAATATGAAAAAGAAGATTCAC
1 TGCAATCATCATTTTCAACAGGAACAAGATGAAAAAGAAGATTCAC
3254410 CAGGGAAACC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
48 21 0.52
51 19 0.47
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.25
Consensus pattern (49 bp):
TGCAATCATCATTTTCAACAGGAACAAGATGAAAAAGAAGATTCACTCA
Found at i:3260738 original size:23 final size:23
Alignment explanation
Indices: 3260708--3260753 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
3260698 TAAAAAGGAG
3260708 ACCATTGATTAGCACATTACTTA
1 ACCATTGATTAGCACATTACTTA
3260731 ACCATTGATTAGCACATTACTTA
1 ACCATTGATTAGCACATTACTTA
3260754 CTTTAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.35
Consensus pattern (23 bp):
ACCATTGATTAGCACATTACTTA
Found at i:3267690 original size:2 final size:2
Alignment explanation
Indices: 3267675--3267708 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
3267665 CTATTTTCTG
*
3267675 TA TA TA AA TCA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA T
3267709 GTCTGCAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3269059 original size:3 final size:3
Alignment explanation
Indices: 3269051--3269078 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3269041 CTGGATTAAG
3269051 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3269079 CCAGTTACAT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3277165 original size:6 final size:6
Alignment explanation
Indices: 3277151--3277192 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
3277141 CCCATTCCTT
*
3277151 AAAAA- AAAAAC AAAAAC AAAAAAAC CAAAAC AAAAAC AAAAA
1 AAAAAC AAAAAC AAAAAC --AAAAAC AAAAAC AAAAAC AAAAA
3277193 GGGAGTTAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
5 5 0.16
6 21 0.66
8 6 0.19
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:3277173 original size:14 final size:14
Alignment explanation
Indices: 3277154--3277186 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
3277144 ATTCCTTAAA
3277154 AAAAAAACAAAAAC
1 AAAAAAACAAAAAC
*
3277168 AAAAAAACCAAAAC
1 AAAAAAACAAAAAC
3277182 AAAAA
1 AAAAA
3277187 CAAAAAGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAACAAAAAC
Found at i:3277174 original size:20 final size:20
Alignment explanation
Indices: 3277151--3277192 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
3277141 CCCATTCCTT
3277151 AAAAAAAAAACAAAAACAAA
1 AAAAAAAAAACAAAAACAAA
**
3277171 AAAACCAAAACAAAAACAAA
1 AAAAAAAAAACAAAAACAAA
3277191 AA
1 AA
3277193 GGGAGTTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAACAAAAACAAA
Found at i:3282802 original size:2 final size:2
Alignment explanation
Indices: 3282795--3282820 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3282785 AATGCAACTG
3282795 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
3282821 CATCTAATTC
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:3284090 original size:2 final size:2
Alignment explanation
Indices: 3284083--3284108 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3284073 ATACACCAAT
3284083 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3284109 AAATAAAATA
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):
TA
Found at i:3284232 original size:2 final size:2
Alignment explanation
Indices: 3284225--3284255 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3284215 TAAGAGTATG
3284225 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 A
3284256 GACGGCTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3285262 original size:18 final size:19
Alignment explanation
Indices: 3285239--3285275 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3285229 CTGACGATAT
*
3285239 CTTTCTTCA-CTCTTCTTC
1 CTTTCTTCATCTCTCCTTC
3285257 CTTTCTTCATCTCTCCTTC
1 CTTTCTTCATCTCTCCTTC
3285276 TCTTGCAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.05, C:0.41, G:0.00, T:0.54
Consensus pattern (19 bp):
CTTTCTTCATCTCTCCTTC
Found at i:3287844 original size:2 final size:2
Alignment explanation
Indices: 3287837--3287864 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3287827 TTTTATACAA
3287837 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3287865 TGACTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3288113 original size:13 final size:13
Alignment explanation
Indices: 3288089--3288121 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3288079 TTACATTTAT
3288089 AATTAA-TAATAC
1 AATTAATTAATAC
3288101 AATTAATTAATAC
1 AATTAATTAATAC
*
3288114 TATTAATT
1 AATTAATT
3288122 TCTCATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (13 bp):
AATTAATTAATAC
Found at i:3290349 original size:40 final size:40
Alignment explanation
Indices: 3290299--3290379 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
3290289 TAAAATTATA
3290299 TAAATACATTAAAATTTTATGTAATCTCCTCATTTATTAG
1 TAAATACATTAAAATTTTATGTAATCTCCTCATTTATTAG
3290339 TAAATACATTAAAATTTTATGTAATCTCCTCATTTATTAG
1 TAAATACATTAAAATTTTATGTAATCTCCTCATTTATTAG
3290379 T
1 T
3290380 GATAGATTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.46
Consensus pattern (40 bp):
TAAATACATTAAAATTTTATGTAATCTCCTCATTTATTAG
Found at i:3290731 original size:24 final size:21
Alignment explanation
Indices: 3290680--3290731 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 21
3290670 GTTGTAATTT
3290680 AAATTTTTTATTTAAATTTAA
1 AAATTTTTTATTTAAATTTAA
3290701 ATTAATTTTATTATTTAAAATATTAA
1 A--AATTTT-TTATTT-AAAT-TTAA
3290727 AAATT
1 AAATT
3290732 AAAAATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
21 1 0.04
23 6 0.23
24 10 0.38
25 4 0.15
26 5 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
AAATTTTTTATTTAAATTTAA
Found at i:3290742 original size:33 final size:33
Alignment explanation
Indices: 3290705--3290809 Score: 83
Period size: 33 Copynumber: 3.2 Consensus size: 33
3290695 ATTTAAATTA
3290705 ATTTTATTATTTAAAATATTAAAAATTAAAAAT
1 ATTTTATTATTTAAAATATTAAAAATTAAAAAT
* * * *
3290738 ATTTTATAATTTATAAT-TAAAATTAAATAAAAAT
1 ATTTTATTATTTAAAATATTAAA--AATTAAAAAT
* * *
3290772 ATTATT-TTA-TTAAATTAATAATAATT-AAAAT
1 ATT-TTATTATTTAAAATATTAAAAATTAAAAAT
*
3290803 TTTTTAT
1 ATTTTAT
3290810 ATAAATTAAA
Statistics
Matches: 55, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
30 2 0.04
31 8 0.15
32 7 0.13
33 20 0.36
34 16 0.29
35 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (33 bp):
ATTTTATTATTTAAAATATTAAAAATTAAAAAT
Found at i:3290801 original size:32 final size:34
Alignment explanation
Indices: 3290728--3290828 Score: 88
Period size: 34 Copynumber: 3.1 Consensus size: 34
3290718 AAATATTAAA
3290728 AATTAAAAATATTTTATAATTTATAATTAAAATT
1 AATTAAAAATATTTTATAATTTATAATTAAAATT
* *
3290762 AAATAAAAATATTATT-TTA-TTA-AATTAATAA-T
1 AATTAAAAATATT-TTATAATTTATAATTAA-AATT
* * *
3290794 AATTAAAATTTTTTATATAAATTA-AATT-AAATT
1 AATTAAAAATATTT-TATAATTTATAATTAAAATT
3290827 AA
1 AA
3290829 ATTTATTAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
31 1 0.02
32 20 0.36
33 11 0.20
34 21 0.38
35 2 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (34 bp):
AATTAAAAATATTTTATAATTTATAATTAAAATT
Found at i:3290821 original size:5 final size:5
Alignment explanation
Indices: 3290811--3290848 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
3290801 ATTTTTTATA
*
3290811 TAAAT TAAAT TAAAT TAAAT T-TAT TAAAT TAAA- TAAAT
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT
3290849 AATTCTACTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 7 0.24
5 22 0.76
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TAAAT
Found at i:3290826 original size:29 final size:31
Alignment explanation
Indices: 3290752--3290829 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 31
3290742 TATAATTTAT
*
3290752 AATTAAAATTAAATAAAAATATTATTTTATTA
1 AATT-AAATTAAATTAAAATATTATTTTATTA
*
3290784 AATT-AATAATAATT-AAA-ATT-TTTTATATA
1 AATTAAATTA-AATTAAAATATTATTTTAT-TA
3290813 AATTAAATTAAATTAAA
1 AATTAAATTAAATTAAA
3290830 TTTATTAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
28 6 0.15
29 13 0.33
30 13 0.33
31 3 0.08
32 4 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
AATTAAATTAAATTAAAATATTATTTTATTA
Found at i:3290843 original size:29 final size:29
Alignment explanation
Indices: 3290752--3290848 Score: 83
Period size: 28 Copynumber: 3.3 Consensus size: 29
3290742 TATAATTTAT
* *
3290752 AATTAAAATTAAATAAAAATATTATTTTATTA
1 AATT-AAATTAAAT-TAAAT-TTATTATATTA
* *
3290784 AATT-AATAATAATTAAAATTTTTTATA-TA
1 AATTAAATTA-AATT-AAATTTATTATATTA
*
3290813 AATTAAATTAAATTAAATTTATTAAATTA
1 AATTAAATTAAATTAAATTTATTATATTA
3290842 AA-TAAAT
1 AATTAAAT
3290849 AATTCTACTC
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
28 15 0.28
29 14 0.26
30 14 0.26
31 7 0.13
32 4 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
AATTAAATTAAATTAAATTTATTATATTA
Found at i:3294011 original size:21 final size:21
Alignment explanation
Indices: 3293972--3294029 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 21
3293962 TTTAAATACG
*
3293972 ATATTT-A-AAATA-TATAAT
1 ATATTTAATAAATATTAAAAT
3293990 ATATTTAATAAATATTAAAAT
1 ATATTTAATAAATATTAAAAT
**
3294011 A-ATAAAAATAAATATTAAA
1 ATAT-TTAATAAATATTAAA
3294030 TTTATTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 6 0.18
19 1 0.03
20 7 0.21
21 19 0.58
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATTTAATAAATATTAAAAT
Found at i:3294624 original size:20 final size:19
Alignment explanation
Indices: 3294580--3294625 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 19
3294570 ATTGATATAA
3294580 TTTATAT-TTATATAAATT
1 TTTATATATTATATAAATT
*
3294598 TTAATATATTA-ATAATATT
1 TTTATATATTATATAA-ATT
3294617 TATTATATA
1 T-TTATATA
3294626 AATTGTTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 10 0.43
19 7 0.30
20 6 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTATATATTATATAAATT
Found at i:3294924 original size:24 final size:24
Alignment explanation
Indices: 3294875--3294932 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 24
3294865 ATACTTTTAT
*
3294875 TATTAAAATAAAAATATTATATTA
1 TATTAAAATAAAAATATTATAATA
* *
3294899 TATTAAAA-ATAAATAATATAA-A
1 TATTAAAATAAAAATATTATAATA
3294921 TA-T-AAATAAAAA
1 TATTAAAATAAAAA
3294933 ATACCTTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
20 3 0.10
21 5 0.17
22 3 0.10
23 10 0.34
24 8 0.28
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (24 bp):
TATTAAAATAAAAATATTATAATA
Found at i:3295643 original size:11 final size:11
Alignment explanation
Indices: 3295627--3295679 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
3295617 AAAATATAAT
3295627 TATTTATTTAA
1 TATTTATTTAA
**
3295638 TATTTA-AAAA
1 TATTTATTTAA
3295648 TATTTATTTAA
1 TATTTATTTAA
***
3295659 TATTTAAAAAA
1 TATTTATTTAA
3295670 TATTTATTTA
1 TATTTATTTA
3295680 TCTTTTTAAG
Statistics
Matches: 31, Mismatches: 10, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
10 8 0.26
11 23 0.74
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TATTTATTTAA
Found at i:3295652 original size:21 final size:22
Alignment explanation
Indices: 3295627--3295679 Score: 99
Period size: 21 Copynumber: 2.5 Consensus size: 22
3295617 AAAATATAAT
3295627 TATTTATTTAATATTT-AAAAA
1 TATTTATTTAATATTTAAAAAA
3295648 TATTTATTTAATATTTAAAAAA
1 TATTTATTTAATATTTAAAAAA
3295670 TATTTATTTA
1 TATTTATTTA
3295680 TCTTTTTAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 16 0.52
22 15 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTTATTTAATATTTAAAAAA
Found at i:3295782 original size:14 final size:14
Alignment explanation
Indices: 3295765--3295795 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3295755 AAATATATAT
3295765 TTTATTAATTGTTA
1 TTTATTAATTGTTA
*
3295779 TTTATTAATTTTTA
1 TTTATTAATTGTTA
3295793 TTT
1 TTT
3295796 TATCATTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (14 bp):
TTTATTAATTGTTA
Found at i:3295945 original size:11 final size:11
Alignment explanation
Indices: 3295931--3295974 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
3295921 AAAATTAATT
3295931 AAAAAAATATG
1 AAAAAAATATG
3295942 AAAAAAATAAT-
1 AAAAAAAT-ATG
3295953 AAAAAAATATAG
1 AAAAAAATAT-G
*
3295965 AAAAATATAT
1 AAAAAAATAT
3295975 CTTATCTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 2 0.07
11 16 0.55
12 11 0.38
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (11 bp):
AAAAAAATATG
Found at i:3295947 original size:23 final size:23
Alignment explanation
Indices: 3295921--3295969 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
3295911 TAGTGATAAT
*
3295921 AAAATTAATTAAAAAAATAT-GAA
1 AAAAATAA-TAAAAAAATATAGAA
3295944 AAAAATAATAAAAAAATATAGAA
1 AAAAATAATAAAAAAATATAGAA
3295967 AAA
1 AAA
3295970 TATATCTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (23 bp):
AAAAATAATAAAAAAATATAGAA
Found at i:3302163 original size:53 final size:52
Alignment explanation
Indices: 3302088--3302188 Score: 125
Period size: 53 Copynumber: 1.9 Consensus size: 52
3302078 ATCTTAAAAT
* *
3302088 TATATTTAATTATTATTAATTTAATTATT-ATTCAATTATATTTTAATTGAAG
1 TATATTTAAATATTATTAATTT-ATTATTAATTCAATTATATATTAATTGAAG
* *
3302140 TATATATTAAATATT-TTAAATTTATTTTTAATTTAATTATATATTAATT
1 TATAT-TTAAATATTATT-AATTTATTATTAATTCAATTATATATTAATT
3302189 TTAAAATGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
52 12 0.29
53 30 0.71
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (52 bp):
TATATTTAAATATTATTAATTTATTATTAATTCAATTATATATTAATTGAAG
Found at i:3302536 original size:17 final size:18
Alignment explanation
Indices: 3302503--3302538 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
3302493 TAACATGATA
3302503 ATAATTAAAAATAATTTT
1 ATAATTAAAAATAATTTT
3302521 ATAATTAAAAAT-ATTTT
1 ATAATTAAAAATAATTTT
3302538 A
1 A
3302539 AATAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAATTAAAAATAATTTT
Found at i:3303262 original size:13 final size:13
Alignment explanation
Indices: 3303227--3303278 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
3303217 AATTAAGATT
*
3303227 AAATTTTTTATAAA
1 AAATTGTTTA-AAA
*
3303241 AAA-TATTTAAAA
1 AAATTGTTTAAAA
*
3303253 AAATTGTTTAAAG
1 AAATTGTTTAAAA
*
3303266 AAATTGATTAAAA
1 AAATTGTTTAAAA
3303279 TCAAATAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
12 6 0.19
13 23 0.72
14 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (13 bp):
AAATTGTTTAAAA
Found at i:3310365 original size:2 final size:2
Alignment explanation
Indices: 3310358--3310391 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3310348 ATTGGATTTA
*
3310358 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CG CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3310392 TTTTAACTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.03, T:0.47
Consensus pattern (2 bp):
CT
Found at i:3314752 original size:18 final size:18
Alignment explanation
Indices: 3314731--3314783 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
3314721 TATATTATAA
3314731 TTATATTTTAAAAATATT
1 TTATATTTTAAAAATATT
3314749 TTATA-TTTAAATAA-ATT
1 TTATATTTTAAA-AATATT
* *
3314766 TTAATATATTAATAATAT
1 TT-ATATTTTAAAAATAT
3314784 ATATTATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
17 11 0.38
18 12 0.41
19 6 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTATATTTTAAAAATATT
Found at i:3318253 original size:21 final size:21
Alignment explanation
Indices: 3318227--3318268 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3318217 CATCTTCCTT
* **
3318227 CTTCTCTGCTCTTTCACTCTC
1 CTTCTCCGCTCTCCCACTCTC
3318248 CTTCTCCGCTCTCCCACTCTC
1 CTTCTCCGCTCTCCCACTCTC
3318269 ACTGTCTTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.05, C:0.50, G:0.05, T:0.40
Consensus pattern (21 bp):
CTTCTCCGCTCTCCCACTCTC
Found at i:3319398 original size:2 final size:2
Alignment explanation
Indices: 3319391--3319429 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3319381 TTCTTCTTCT
3319391 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3319430 GTGGCCATAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3323562 original size:2 final size:2
Alignment explanation
Indices: 3323555--3323592 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3323545 ACACTTTCTT
3323555 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3323593 AAACTCTCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3324745 original size:2 final size:2
Alignment explanation
Indices: 3324738--3324766 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3324728 GTGGAGTGTT
3324738 TA TA 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 TA TA T
3324767 TAAAGGTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3332790 original size:3 final size:3
Alignment explanation
Indices: 3332782--3332807 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3332772 CTTCCTCTTC
3332782 CTA CTA CTA CTA CTA CTA CTA CTA CT
1 CTA CTA CTA CTA CTA CTA CTA CTA CT
3332808 GCGGTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
CTA
Found at i:3339257 original size:3 final size:3
Alignment explanation
Indices: 3339249--3339278 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3339239 AGGGAAAAAG
3339249 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
3339279 GCATACAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:3343096 original size:22 final size:22
Alignment explanation
Indices: 3343071--3343140 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
3343061 CCAACCTTGC
3343071 TTAAGATTCAAAACATTTTTAA
1 TTAAGATTCAAAACATTTTTAA
* * ** **
3343093 TTAAAGAGTTC-CACCA-CCTTGC
1 TT-AAGA-TTCAAAACATTTTTAA
3343115 TTAAGATTCAAAACATTTTTAA
1 TTAAGATTCAAAACATTTTTAA
3343137 TTAA
1 TTAA
3343141 AGAGTTCCAC
Statistics
Matches: 32, Mismatches: 12, Indels: 8
0.62 0.23 0.15
Matches are distributed among these distances:
20 3 0.09
21 7 0.22
22 12 0.38
23 7 0.22
24 3 0.09
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (22 bp):
TTAAGATTCAAAACATTTTTAA
Found at i:3343124 original size:44 final size:45
Alignment explanation
Indices: 3343046--3343176 Score: 239
Period size: 44 Copynumber: 3.0 Consensus size: 45
3343036 TTAGCCATAA
*
3343046 AATTAAAGAATTCCACCAACCTTGCTTAAGATTCAAAACATTTTT
1 AATTAAAGAGTTCCACCAACCTTGCTTAAGATTCAAAACATTTTT
3343091 AATTAAAGAGTTCCACC-ACCTTGCTTAAGATTCAAAACATTTTT
1 AATTAAAGAGTTCCACCAACCTTGCTTAAGATTCAAAACATTTTT
3343135 AATTAAAGAGTTCCACCAACCTTGCTTAAGATTC-AAACATTT
1 AATTAAAGAGTTCCACCAACCTTGCTTAAGATTCAAAACATTT
3343177 ATAAGATCAA
Statistics
Matches: 84, Mismatches: 1, Indels: 3
0.95 0.01 0.03
Matches are distributed among these distances:
44 52 0.62
45 32 0.38
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (45 bp):
AATTAAAGAGTTCCACCAACCTTGCTTAAGATTCAAAACATTTTT
Found at i:3346144 original size:21 final size:20
Alignment explanation
Indices: 3346127--3346168 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
3346117 CATAACTTTG
3346127 AAATTGT-TATTTTCAACTT
1 AAATTGTATATTTTCAACTT
*
3346146 AAATTTTATATTTTCAA-TT
1 AAATTGTATATTTTCAACTT
3346165 AAAT
1 AAAT
3346169 CAATGAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.52
Consensus pattern (20 bp):
AAATTGTATATTTTCAACTT
Found at i:3346620 original size:3 final size:3
Alignment explanation
Indices: 3346612--3346660 Score: 64
Period size: 3 Copynumber: 16.3 Consensus size: 3
3346602 TTAAGATGTA
* *
3346612 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAG AAT -AT AAT AAT CAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
3346657 AAT A
1 AAT A
3346661 TTATTTTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.90
4 2 0.05
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3354156 original size:2 final size:2
Alignment explanation
Indices: 3354151--3354179 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3354141 TGTGAGTGTG
3354151 TA TA 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 TA TA T
3354180 GTCCACCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3356901 original size:3 final size:3
Alignment explanation
Indices: 3356893--3356917 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3356883 CAGAATGTCC
3356893 CCA CCA CCA CCA CCA CCA CCA CCA C
1 CCA CCA CCA CCA CCA CCA CCA CCA C
3356918 TCTCTCTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:3358766 original size:15 final size:16
Alignment explanation
Indices: 3358748--3358781 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3358738 AAAAGTAAAA
*
3358748 TTTTAAA-AAATTAAT
1 TTTTAAATAAAATAAT
3358763 TTTTAAATAAAATAAT
1 TTTTAAATAAAATAAT
3358779 TTT
1 TTT
3358782 ATTATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTTAAATAAAATAAT
Found at i:3358810 original size:18 final size:18
Alignment explanation
Indices: 3358780--3358826 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
3358770 TAAAATAATT
3358780 TTATTATTTTATATTATT-A
1 TTATTA-TTTATATT-TTAA
3358799 TTATTATTTATATTTTAA
1 TTATTATTTATATTTTAA
*
3358817 TTTTTATTTA
1 TTATTATTTA
3358827 AAAAATTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 2 0.08
18 18 0.69
19 6 0.23
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTATTATTTATATTTTAA
Found at i:3359700 original size:11 final size:12
Alignment explanation
Indices: 3359669--3359699 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3359659 TTCTTTCTTT
3359669 AATAAAAATTGA
1 AATAAAAATTGA
3359681 AATAAAAATTGA
1 AATAAAAATTGA
*
3359693 AGTAAAA
1 AATAAAA
3359700 TAAAACAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.23
Consensus pattern (12 bp):
AATAAAAATTGA
Found at i:3359931 original size:17 final size:17
Alignment explanation
Indices: 3359909--3359948 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3359899 AGGTATTAAA
*
3359909 AAATTAATATATTATTT
1 AAATTAATAAATTATTT
*
3359926 AAATTAATAAATTTTTT
1 AAATTAATAAATTATTT
3359943 ATAATT
1 A-AATT
3359949 TACTTTAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AAATTAATAAATTATTT
Found at i:3360178 original size:8 final size:8
Alignment explanation
Indices: 3360165--3360197 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
3360155 TGCTCTCTCC
3360165 TTTCTTTT
1 TTTCTTTT
3360173 TTTCTTTTT
1 TTTC-TTTT
3360182 TTTCTTTT
1 TTTCTTTT
3360190 TTT-TTTT
1 TTTCTTTT
3360197 T
1 T
3360198 ACAAATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 5 0.21
8 11 0.46
9 8 0.33
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (8 bp):
TTTCTTTT
Found at i:3360184 original size:10 final size:9
Alignment explanation
Indices: 3360165--3360197 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
3360155 TGCTCTCTCC
3360165 TTTC-TTTT
1 TTTCTTTTT
3360173 TTTCTTTTT
1 TTTCTTTTT
3360182 TTTCTTTTT
1 TTTCTTTTT
3360191 TTT-TTTT
1 TTTCTTTT
3360198 ACAAATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:3360187 original size:17 final size:16
Alignment explanation
Indices: 3360165--3360197 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
3360155 TGCTCTCTCC
3360165 TTTCTTTTTTTCTTTTT
1 TTTCTTTTTTT-TTTTT
3360182 TTTCTTTTTTTTTTTT
1 TTTCTTTTTTTTTTTT
3360198 ACAAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (16 bp):
TTTCTTTTTTTTTTTT
Found at i:3366646 original size:56 final size:56
Alignment explanation
Indices: 3366546--3366661 Score: 142
Period size: 56 Copynumber: 2.1 Consensus size: 56
3366536 GAATTCCTTG
* * * * * * * *
3366546 CAGTTCAGGCTATGATACATCCCATGATGCAAAATGCTAGAAGGCCGGATTGTATT
1 CAGTCCAGCCTATAATACATCCCATGATACAAAACGCTACAAGGCCGGATTCTATC
* *
3366602 CAGTCCAGCCTATAATACATCCCTTGATACACAACGCTACAAGGCCGGATTCTATC
1 CAGTCCAGCCTATAATACATCCCATGATACAAAACGCTACAAGGCCGGATTCTATC
3366658 CAGT
1 CAGT
3366662 AATAAAGGAG
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (56 bp):
CAGTCCAGCCTATAATACATCCCATGATACAAAACGCTACAAGGCCGGATTCTATC
Found at i:3368553 original size:18 final size:18
Alignment explanation
Indices: 3368496--3368554 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 18
3368486 TAAACGATCA
*
3368496 TAAAT-ATATATTTAAAT
1 TAAATAATATTTTTAAAT
* * *
3368513 TAATTAATA-TATT-ATT
1 TAAATAATATTTTTAAAT
3368529 TATAATAATATTTTTAAAT
1 TA-AATAATATTTTTAAAT
3368548 TAAATAA
1 TAAATAA
3368555 AATAATTCAT
Statistics
Matches: 31, Mismatches: 7, Indels: 7
0.69 0.16 0.16
Matches are distributed among these distances:
16 4 0.13
17 12 0.39
18 11 0.35
19 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAAATAATATTTTTAAAT
Found at i:3369801 original size:3 final size:3
Alignment explanation
Indices: 3369793--3369818 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3369783 CACAATTGAA
3369793 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
3369819 AGAGAGGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3371605 original size:26 final size:26
Alignment explanation
Indices: 3371575--3371635 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 26
3371565 TCGAAAATTT
3371575 TTAATATT-TATAAATATGT-AATTAAA
1 TTAATATTATATAAAT-T-TAAATTAAA
3371601 TTAATAATTATATAAATTTAAATTAAA
1 TTAAT-ATTATATAAATTTAAATTAAA
3371628 TT-ATATTA
1 TTAATATTA
3371636 AGTAATTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
25 4 0.12
26 8 0.25
27 13 0.41
28 7 0.22
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
TTAATATTATATAAATTTAAATTAAA
Found at i:3371756 original size:5 final size:5
Alignment explanation
Indices: 3371714--3371795 Score: 51
Period size: 5 Copynumber: 16.0 Consensus size: 5
3371704 ATTAAATCAT
* * * * *
3371714 TATAA TAAAA TATAA AAAAA T-TAA TAGAGA TATGA TATAA TATAAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATA-A TATAA TATAA TAT-AA TATAA
* *
3371765 T-TAAA TATAA TATAA AATAAA AATAA TATAA
1 TAT-AA TATAA TATAA TAT-AA TATAA TATAA
3371796 ACATCATATA
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
4 4 0.07
5 41 0.69
6 14 0.24
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.32
Consensus pattern (5 bp):
TATAA
Found at i:3371769 original size:10 final size:11
Alignment explanation
Indices: 3371748--3371784 Score: 60
Period size: 10 Copynumber: 3.5 Consensus size: 11
3371738 TAGAGATATG
3371748 ATATAATATAA
1 ATATAATATAA
3371759 ATATAAT-TAA
1 ATATAATATAA
3371769 ATATAATATAA
1 ATATAATATAA
3371780 A-ATAA
1 ATATAA
3371785 AAATAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 14 0.56
11 11 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
ATATAATATAA
Found at i:3371792 original size:21 final size:21
Alignment explanation
Indices: 3371748--3371795 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3371738 TAGAGATATG
* *
3371748 ATATAATATAAATATAATTAA
1 ATATAATATAAATAAAAATAA
3371769 ATATAATATAAAATAAAAAT-A
1 ATATAATAT-AAATAAAAATAA
3371790 ATATAA
1 ATATAA
3371796 ACATCATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
ATATAATATAAATAAAAATAA
Found at i:3371806 original size:16 final size:16
Alignment explanation
Indices: 3371752--3371796 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
3371742 GATATGATAT
*
3371752 AATATAA-ATATAATTA
1 AATATAATATA-AAATA
3371768 AATATAATATAAAATA
1 AATATAATATAAAATA
*
3371784 AAAATAATATAAA
1 AATATAATATAAA
3371797 CATCATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 23 0.88
17 3 0.12
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AATATAATATAAAATA
Found at i:3372185 original size:27 final size:27
Alignment explanation
Indices: 3372126--3372187 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
3372116 TAAAGATATG
3372126 AATATGTTAAAAATTATATAATATTATT
1 AATAT-TTAAAAATTATATAATATTATT
*
3372154 TATATTTAAAAATTTATATAA-ATT-TAT
1 AATATTTAAAAA-TTATATAATATTAT-T
3372181 AATATTT
1 AATATTT
3372188 TGAATACAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
26 1 0.03
27 17 0.57
28 12 0.40
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (27 bp):
AATATTTAAAAATTATATAATATTATT
Found at i:3372375 original size:5 final size:5
Alignment explanation
Indices: 3372360--3372429 Score: 58
Period size: 5 Copynumber: 14.2 Consensus size: 5
3372350 TCGAAACATG
* * *
3372360 ATATAA ATATA ATATA ATATA ATAAAA ATTAAA ATATA ATATA A-AAA
1 ATAT-A ATATA ATATA ATATA AT-ATA A-TATA ATATA ATATA ATATA
3372407 ATA-A ATATA ATATA A-AT- ATATA A
1 ATATA ATATA ATATA ATATA ATATA A
3372430 ATTTATTAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
3 1 0.02
4 11 0.20
5 31 0.56
6 11 0.20
7 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (5 bp):
ATATA
Found at i:3372376 original size:11 final size:11
Alignment explanation
Indices: 3372337--3372426 Score: 74
Period size: 11 Copynumber: 8.1 Consensus size: 11
3372327 TTGTGTACAA
*
3372337 AATATAAATAG
1 AATATAAATAT
** *
3372348 AATCGAAACAT
1 AATATAAATAT
*
3372359 GATATAAATAT
1 AATATAAATAT
3372370 AATAT-AATAT
1 AATATAAATAT
* *
3372380 AATAAAAATTAA
1 AATATAAA-TAT
*
3372392 AATATAATATAA
1 AATATAA-ATAT
*
3372404 AAAATAAATAT
1 AATATAAATAT
3372415 AATATAAATAT
1 AATATAAATAT
3372426 A
1 A
3372427 TAAATTTATT
Statistics
Matches: 61, Mismatches: 15, Indels: 6
0.74 0.18 0.07
Matches are distributed among these distances:
10 9 0.15
11 34 0.56
12 17 0.28
13 1 0.02
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.30
Consensus pattern (11 bp):
AATATAAATAT
Found at i:3372413 original size:13 final size:14
Alignment explanation
Indices: 3372364--3372426 Score: 51
Period size: 13 Copynumber: 4.5 Consensus size: 14
3372354 AACATGATAT
3372364 AAATATAATATAATA
1 AAATATAATATAA-A
* * *
3372379 TAATA-AAAAT-TA
1 AAATATAATATAAA
3372391 AAATATAATATAAA
1 AAATATAATATAAA
3372405 AAATA-AATATAATA
1 AAATATAATATAA-A
3372419 TAAATATA
1 -AAATATA
3372427 TAAATTTATT
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
12 5 0.14
13 11 0.30
14 11 0.30
15 9 0.24
16 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
AAATATAATATAAA
Found at i:3372521 original size:11 final size:11
Alignment explanation
Indices: 3372493--3372554 Score: 55
Period size: 11 Copynumber: 6.1 Consensus size: 11
3372483 TTATATATTT
3372493 TAAATAT-ATA
1 TAAATATAATA
*
3372503 -AAAAATAATA
1 TAAATATAATA
*
3372513 TAAATATAAAA
1 TAAATATAATA
3372524 TAAA-ATTAAT-
1 TAAATA-TAATA
3372534 TAAA-AT-ATA
1 TAAATATAATA
3372543 TAAATATAATA
1 TAAATATAATA
3372554 T
1 T
3372555 GTTATAAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
8 2 0.05
9 10 0.24
10 11 0.26
11 19 0.45
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
TAAATATAATA
Found at i:3372525 original size:16 final size:16
Alignment explanation
Indices: 3372504--3372569 Score: 73
Period size: 16 Copynumber: 4.2 Consensus size: 16
3372494 AAATATATAA
3372504 AAAATAATATAAATAT
1 AAAATAATATAAATAT
* *
3372520 AAAATAAAATTAAT-T
1 AAAATAATATAAATAT
3372535 AAAAT-ATATAAATAT
1 AAAATAATATAAATAT
* **
3372550 AATATGTTATAAATAT
1 AAAATAATATAAATAT
3372566 AAAA
1 AAAA
3372570 ATATCAAAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
14 6 0.15
15 11 0.27
16 24 0.59
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (16 bp):
AAAATAATATAAATAT
Found at i:3373370 original size:13 final size:14
Alignment explanation
Indices: 3373335--3373372 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3373325 TAATTTAATT
*
3373335 TAATAATTTTTTTA
1 TAATAAATTTTTTA
*
3373349 TAATTAATTTTTTA
1 TAATAAATTTTTTA
3373363 -AATAAATTTT
1 TAATAAATTTT
3373373 AAATTAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TAATAAATTTTTTA
Found at i:3373814 original size:15 final size:16
Alignment explanation
Indices: 3373778--3373815 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
3373768 ATAAGTGTAG
*
3373778 TTAAATAAAATATAAA
1 TTAAATTAAATATAAA
*
3373794 TTAAATTAAAT-TAAT
1 TTAAATTAAATATAAA
3373809 TTAAATT
1 TTAAATT
3373816 TTAAATGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTAAATTAAATATAAA
Found at i:3376865 original size:6 final size:6
Alignment explanation
Indices: 3376854--3376878 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3376844 TCTCTCTCTA
3376854 GAAGCC GAAGCC GAAGCC GAAGCC G
1 GAAGCC GAAGCC GAAGCC GAAGCC G
3376879 CAGTCATGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.32, G:0.36, T:0.00
Consensus pattern (6 bp):
GAAGCC
Found at i:3380730 original size:18 final size:18
Alignment explanation
Indices: 3380703--3380745 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
3380693 AATGGCGTAG
*
3380703 AAAAAA-AATAATTTTTA
1 AAAAAATAATAAATTTTA
*
3380720 AGAAAATAATAAATTTTA
1 AAAAAATAATAAATTTTA
3380738 AAAAAATA
1 AAAAAATA
3380746 TTAGAGTTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
AAAAAATAATAAATTTTA
Found at i:3380823 original size:17 final size:17
Alignment explanation
Indices: 3380793--3380825 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3380783 TATCATAAAT
3380793 TATATAATATTTGATAA
1 TATATAATATTTGATAA
3380810 TATATTAATA-TTGATA
1 TATA-TAATATTTGATA
3380826 GAAAGATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (17 bp):
TATATAATATTTGATAA
Found at i:3380939 original size:32 final size:31
Alignment explanation
Indices: 3380903--3380972 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 31
3380893 TTAAAAAATA
*
3380903 TAAAATAATTATCAAAGATAATTTCTTTATTT
1 TAAAATAATTATCAAAAATAATTT-TTTATTT
*
3380935 TAAAAT--TT-TTAAAAATAATTTTTTATTT
1 TAAAATAATTATCAAAAATAATTTTTTATTT
*
3380963 TTAAA-AATTA
1 TAAAATAATTA
3380973 ATTATTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
28 11 0.34
29 13 0.41
30 2 0.06
32 6 0.19
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (31 bp):
TAAAATAATTATCAAAAATAATTTTTTATTT
Found at i:3380964 original size:20 final size:22
Alignment explanation
Indices: 3380939--3380994 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 22
3380929 TTATTTTAAA
3380939 ATTTTTAAAAAT-A-ATTTTTT
1 ATTTTTAAAAATAATATTTTTT
3380959 ATTTTTAAAAATTAATTATTTTTT
1 ATTTTTAAAAA-TAA-TATTTTTT
*
3380983 ATTTTTTAAAAT
1 ATTTTTAAAAAT
3380995 TTTGTTATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 11 0.35
21 1 0.03
22 1 0.03
23 1 0.03
24 17 0.55
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTTTTAAAAATAATATTTTTT
Found at i:3381532 original size:2 final size:2
Alignment explanation
Indices: 3381525--3381549 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3381515 CTCCTACATT
3381525 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
3381550 TGTCATCTAC
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:3387563 original size:91 final size:91
Alignment explanation
Indices: 3387408--3387583 Score: 343
Period size: 91 Copynumber: 1.9 Consensus size: 91
3387398 AAGAAAAGTA
3387408 CATGTAGACCCCTCGCTTTAAAGAGTCCAGAATTCTAAACACGATCAAGTTCCAAAAAATGGGTG
1 CATGTAGACCCCTCGCTTTAAAGAGTCCAGAATTCTAAACACGATCAAGTTCCAAAAAATGGGTG
3387473 GCAATAAAATAAAGCAATAAAGAGTC
66 GCAATAAAATAAAGCAATAAAGAGTC
*
3387499 CATGTAGACCCCTCGCTTTAAAGAGTCCAGAATTCTAACCACGATCAAGTTCCAAAAAATGGGTG
1 CATGTAGACCCCTCGCTTTAAAGAGTCCAGAATTCTAAACACGATCAAGTTCCAAAAAATGGGTG
3387564 GCAATAAAATAAAGCAATAA
66 GCAATAAAATAAAGCAATAA
3387584 GCTATTGTCT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 84 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.21
Consensus pattern (91 bp):
CATGTAGACCCCTCGCTTTAAAGAGTCCAGAATTCTAAACACGATCAAGTTCCAAAAAATGGGTG
GCAATAAAATAAAGCAATAAAGAGTC
Found at i:3394344 original size:17 final size:15
Alignment explanation
Indices: 3394324--3394375 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 15
3394314 TTAGGTAAAA
3394324 AAGAAAGAAAGAAGATG
1 AAGAAAGAAAGAA-A-G
3394341 AAG-AAGAAAGAAAG
1 AAGAAAGAAAGAAAG
3394355 AA-AAAGAAA-AAA-
1 AAGAAAGAAAGAAAG
3394367 AA-AAAGAAA
1 AAGAAAGAAA
3394376 AAAATATGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
12 9 0.26
13 3 0.09
14 9 0.26
15 1 0.03
16 9 0.26
17 3 0.09
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (15 bp):
AAGAAAGAAAGAAAG
Found at i:3394372 original size:12 final size:12
Alignment explanation
Indices: 3394344--3394379 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 12
3394334 GAAGATGAAG
3394344 AAGAAAGAAAGAAA
1 AAGAAA-AAA-AAA
3394358 AAGAAAAAAAAA
1 AAGAAAAAAAAA
3394370 AAGAAAAAAA
1 AAGAAAAAAA
3394380 TATGAAATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 13 0.59
13 3 0.14
14 6 0.27
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAAA
Found at i:3405101 original size:21 final size:20
Alignment explanation
Indices: 3405077--3405120 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
3405067 TTTCAAAAAA
*
3405077 TAACTTCTCATTTATATTTTT
1 TAACTTATCATTTAT-TTTTT
* *
3405098 TAACTTATTATTTCTTTTTT
1 TAACTTATCATTTATTTTTT
3405118 TAA
1 TAA
3405121 ATACTATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.25, C:0.11, G:0.00, T:0.64
Consensus pattern (20 bp):
TAACTTATCATTTATTTTTT
Found at i:3405503 original size:3 final size:3
Alignment explanation
Indices: 3405497--3405551 Score: 64
Period size: 3 Copynumber: 19.3 Consensus size: 3
3405487 TTTTCTTTAA
*
3405497 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AATA ATT ATT -TT -TT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT
3405541 ATT -TT -TT ATT A
1 ATT ATT ATT ATT A
3405552 GGTATAGATT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 8 0.17
3 37 0.79
4 2 0.04
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3405617 original size:18 final size:18
Alignment explanation
Indices: 3405575--3405619 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
3405565 AATTTATTTG
*
3405575 AATG-GATAATAAAATTA
1 AATGTGATAATAAAAATA
* *
3405592 ATTATGATAATAAAAATA
1 AATGTGATAATAAAAATA
3405610 AATGTGATAA
1 AATGTGATAA
3405620 ATTAATTATT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.58, C:0.00, G:0.11, T:0.31
Consensus pattern (18 bp):
AATGTGATAATAAAAATA
Found at i:3405818 original size:36 final size:35
Alignment explanation
Indices: 3405775--3405880 Score: 123
Period size: 36 Copynumber: 3.0 Consensus size: 35
3405765 TATTTAATAA
3405775 ATTATTAAAATTATACTTT-T-TTAAATAATAAAAT
1 ATTATTAAAATTATA-TTTATATTAAATAATAAAAT
3405809 ATAATATT-AAATTATATTTATATTAAATAATAATAAGT
1 AT--TATTAAAATTATATTTATATTAAATAATAA-AA-T
*
3405847 ATTATTAAAA-TATATTTATGTTAAA-AATAAAAT
1 ATTATTAAAATTATATTTATATTAAATAATAAAAT
3405880 A
1 A
3405881 ATAAATAACT
Statistics
Matches: 64, Mismatches: 1, Indels: 15
0.80 0.01 0.19
Matches are distributed among these distances:
33 2 0.03
34 7 0.11
35 14 0.22
36 33 0.52
37 5 0.08
38 3 0.05
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (35 bp):
ATTATTAAAATTATATTTATATTAAATAATAAAAT
Found at i:3420306 original size:26 final size:24
Alignment explanation
Indices: 3420253--3420315 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 24
3420243 TTTTATGATT
**
3420253 TTTATAATTTAAAAAATATATATT
1 TTTATAATTTAAAAAATATATAAA
3420277 TTTATAATTTAAAAGTAATATA-AGAA
1 TTTATAATTTAAAA--AATATATA-AA
*
3420303 TTTAAAATTTAAA
1 TTTATAATTTAAA
3420316 TTTAAATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 14 0.42
25 1 0.03
26 18 0.55
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (24 bp):
TTTATAATTTAAAAAATATATAAA
Found at i:3420798 original size:33 final size:33
Alignment explanation
Indices: 3420756--3420818 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
3420746 ACTAAGCAAG
*
3420756 CATTTTGCTTCTATATATTTATATATATATATA
1 CATTTTGCTTCTATATATATATATATATATATA
3420789 CATTTTGCTTCTATATATATATATATATAT
1 CATTTTGCTTCTATATATATATATATATAT
3420819 TATGAGAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.54
Consensus pattern (33 bp):
CATTTTGCTTCTATATATATATATATATATATA
Found at i:3425186 original size:50 final size:50
Alignment explanation
Indices: 3425127--3425334 Score: 290
Period size: 50 Copynumber: 4.2 Consensus size: 50
3425117 TTGTTTAGAA
* * *
3425127 TCAACAATTACGACCACATCTCTCTATTGTCAAAGGTTGGTGAAGAATAG
1 TCAACAATTACGATCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAG
* * * *
3425177 TCAACAATTATGGTCACCTCTCTCTATTGTCAAAGGTTGGAGAAGAATAG
1 TCAACAATTACGATCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAG
* * * *
3425227 TCAACAATTATGATCATCTTTCTCGATTGTCTAAGGTTGGTGAAGAATAG
1 TCAACAATTACGATCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAG
* * *
3425277 TCAATAATTACGGTTACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAG
1 TCAACAATTACGATCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAG
3425327 TCAACAAT
1 TCAACAAT
3425335 GACAATACCT
Statistics
Matches: 139, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 139 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Consensus pattern (50 bp):
TCAACAATTACGATCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAG
Found at i:3429802 original size:52 final size:50
Alignment explanation
Indices: 3429708--3429845 Score: 195
Period size: 52 Copynumber: 2.7 Consensus size: 50
3429698 AGTTGCTTAG
*
3429708 AGTCAATAATTACGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAAAAT
1 AGTCAACAATTACGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAAAAT
*
3429758 AGTCAACAATTACGACCGTCTCTCTCTCTATTGTCAAAGGTTGGTGAAAAAT
1 AGTCAACAATTACGACC-AC-CTCTCTCTATTGTCAAAGGTTGGTGAAAAAT
* *** *
3429810 AGTTAACAATTACGGTTACCTCTCTCAATTGTCAAA
1 AGTCAACAATTACGACCACCTCTCTCTATTGTCAAA
3429846 AATTAGTAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
50 32 0.41
51 2 0.03
52 44 0.56
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (50 bp):
AGTCAACAATTACGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAAAAT
Found at i:3442261 original size:271 final size:269
Alignment explanation
Indices: 3441780--3442271 Score: 903
Period size: 271 Copynumber: 1.8 Consensus size: 269
3441770 AGTTGGTTAT
3441780 GTTTGTAATTTGGTGATATCTTGTTTTGTTGAGACTGCTACTGGCCTGAGATCAGGGACATTACT
1 GTTTGTAATTTGGTGATATCTTGTTTTGTTGAGACTGCTACTGGCCTGAGATCAGGGACATTACT
* *
3441845 GGGTGGCCCCTTTTTTCCTTTTTTATTTGTACTAAGTTTTTCTTCTCTGAAATGCAACAATTATC
66 GAGTGGCCCCCTTTTTCCTTTTTTATTTGTACTAAGTTTTTCTTCTCTGAAATGCAACAATTATC
*
3441910 GGATTTGAACACCAGTAGAGGATGCAATGGCTGTTTGGCAATTTATAAAGGGAATTTCTGAATAT
131 GGATTTGAACACCAATAGAGGATGCAATGGCTGTTTGGCAATTTATAAAGGGAATTTCTGAATAT
*
3441975 GAGGTGGTTTGTTGTTAACATGCCTGAGTGTTAACATTCCTGCTCAACAATTATCTTGTTTGTAA
196 GAGGTGATTTGTTGTTAACATGCCTGAGTGTTAACATTCCTGCTCAACAATTATCTTGTTTGTAA
3442040 TTTGGTAAC
261 TTTGGTAAC
3442049 GTTTGTAATTTGGTGATATCTTGTTTTGTTTGAGACTGCTACTGGCCTGAGATCAGGGACATTAC
1 GTTTGTAATTTGGTGATATCTTGTTTTG-TTGAGACTGCTACTGGCCTGAGATCAGGGACATTAC
3442114 TGAGTGGCCCCCTTTTTCCTTTTTTTATTTGTACTAAGTTTTTCTTCTCTGAAATGCAACAATTA
65 TGAGTGGCCCCCTTTTTCC-TTTTTTATTTGTACTAAGTTTTTCTTCTCTGAAATGCAACAATTA
* *
3442179 TCTGCTTTGAACACCAATAGAGGATGCAATGGCTGTTTGGCAATTTATAAAGGGAATTTCTGAAT
129 TCGGATTTGAACACCAATAGAGGATGCAATGGCTGTTTGGCAATTTATAAAGGGAATTTCTGAAT
*
3442244 ATGAGGTGATTTGTTGTTAACATTCCTG
194 ATGAGGTGATTTGTTGTTAACATGCCTG
3442272 CTCAACCTAT
Statistics
Matches: 214, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
269 28 0.13
270 53 0.25
271 133 0.62
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.40
Consensus pattern (269 bp):
GTTTGTAATTTGGTGATATCTTGTTTTGTTGAGACTGCTACTGGCCTGAGATCAGGGACATTACT
GAGTGGCCCCCTTTTTCCTTTTTTATTTGTACTAAGTTTTTCTTCTCTGAAATGCAACAATTATC
GGATTTGAACACCAATAGAGGATGCAATGGCTGTTTGGCAATTTATAAAGGGAATTTCTGAATAT
GAGGTGATTTGTTGTTAACATGCCTGAGTGTTAACATTCCTGCTCAACAATTATCTTGTTTGTAA
TTTGGTAAC
Found at i:3446032 original size:2 final size:2
Alignment explanation
Indices: 3446025--3446075 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
3446015 TTCAGTTAAG
3446025 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3446067 AT AT AT AT A
1 AT AT AT AT A
3446076 AAACCTAACA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3456375 original size:2 final size:2
Alignment explanation
Indices: 3456368--3456407 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3456358 GAAAGAAGTA
3456368 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3456408 GCAGTTCAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3459910 original size:2 final size:2
Alignment explanation
Indices: 3459903--3459944 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
3459893 ACGGTGTATC
* *
3459903 TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA T- TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3459944 T
1 T
3459945 GATTAGCATC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Done.