Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 85 of 171
Found at i:28121132 original size:118 final size:118
Alignment explanation
Indices: 28120957--28121215 Score: 378
Period size: 118 Copynumber: 2.2 Consensus size: 118
28120947 CCAAAATTTT
* * *
28120957 CAAAAATTACAATTTTACCCCCCGAATCTTTTAAAATTCCATTTTTAACCTCGATTTCAACAAAA
1 CAAAAATTACCATTTTA-CCCCCGAAGCTTCTAAAATTCCATTTTTAACCTCGATTTCAACAAAA
* * *
28121022 ATTACCATTTTACCCCCGAAA-CTTACAGAATTCCGTTTTTAACCCCGATTTCAC
65 ATTACCATTTTA-CCCCGAAATCTTACAAAATTCCATTTTTAACCCCGATTACAC
* *
28121076 CAAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTTCATTTTTAACCTCGATTTCACCAAAAA
1 CAAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCTCGATTTCAACAAAAA
* * **
28121141 TTGCCATTTTACCCCTAAATCTTTTAAAATTCCATTTTTAACCCCGATTACAC
66 TTACCATTTTACCCCGAAATCTTACAAAATTCCATTTTTAACCCCGATTACAC
28121194 C-AAAATTACCATTTTACCCCCG
1 CAAAAATTACCATTTTACCCCCG
28121216 GGTATCCATA
Statistics
Matches: 127, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
117 28 0.22
118 83 0.65
119 16 0.13
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (118 bp):
CAAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCTCGATTTCAACAAAAA
TTACCATTTTACCCCGAAATCTTACAAAATTCCATTTTTAACCCCGATTACAC
Found at i:28121209 original size:29 final size:29
Alignment explanation
Indices: 28120989--28121215 Score: 85
Period size: 29 Copynumber: 7.7 Consensus size: 29
28120979 CGAATCTTTT
* * * *
28120989 AAAATTCCATTTTTAACCTCGATTTCAACA
1 AAAATTCCA-TTTTAACCCCGATTACTACC
* *
28121019 AAAATTACCATTTTACCCCCGA-AACTTA-C
1 AAAATT-CCATTTTAACCCCGATTAC-TACC
* * *
28121048 AGAATTCCGTTTTTAACCCCGATTTC-ACC
1 AAAATTCC-ATTTTAACCCCGATTACTACC
* * *
28121077 AAAAATTACCATTTTACCCCCGA--AGCTTCT
1 -AAAATT-CCATTTTAACCCCGATTA-CTACC
* * *
28121107 AAAATTTCATTTTTAACCTCGATTTC-ACC
1 AAAATTCCA-TTTTAACCCCGATTACTACC
* * ***
28121136 AAAAATTGCCATTTT-ACCCCTA-AATCTTTT
1 -AAAATT-CCATTTTAACCCCGATTA-CTACC
28121166 AAAATTCCATTTTTAACCCCGATTAC-ACC
1 AAAATTCCA-TTTTAACCCCGATTACTACC
*
28121195 AAAATTACCATTTTACCCCCG
1 AAAATT-CCATTTTAACCCCG
28121216 GGTATCCATA
Statistics
Matches: 140, Mismatches: 37, Indels: 41
0.64 0.17 0.19
Matches are distributed among these distances:
28 8 0.06
29 68 0.49
30 56 0.40
31 8 0.06
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (29 bp):
AAAATTCCATTTTAACCCCGATTACTACC
Found at i:28124340 original size:19 final size:19
Alignment explanation
Indices: 28124302--28124340 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
28124292 ATTATTTGTG
*
28124302 AAAATTTTAAAAATTATTA
1 AAAATTTAAAAAATTATTA
28124321 AAAATTTAAAATAATT-TTA
1 AAAATTTAAAA-AATTATTA
28124340 A
1 A
28124341 TATATTATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAATTTAAAAAATTATTA
Found at i:28124342 original size:9 final size:9
Alignment explanation
Indices: 28124302--28124340 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
28124292 ATTATTTGTG
28124302 AAAATTTTA
1 AAAATTTTA
28124311 AAAATTATTA
1 AAAATT-TTA
*
28124321 AAAATTTAA
1 AAAATTTTA
28124330 AATAATTTTA
1 AA-AATTTTA
28124340 A
1 A
28124341 TATATTATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
9 10 0.38
10 16 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
AAAATTTTA
Found at i:28125915 original size:3 final size:3
Alignment explanation
Indices: 28125907--28125936 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
28125897 GATTGAGCTT
28125907 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28125937 GATCACTTTT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28127401 original size:9 final size:10
Alignment explanation
Indices: 28127379--28127410 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
28127369 GGATCACCAC
28127379 AAAACGTTTA
1 AAAACGTTTA
28127389 AAAACGTTTA
1 AAAACGTTTA
28127399 AAAACG-TTA
1 AAAACGTTTA
28127408 AAA
1 AAA
28127411 CATCGGTCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 6 0.27
10 16 0.73
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.25
Consensus pattern (10 bp):
AAAACGTTTA
Found at i:28128476 original size:58 final size:59
Alignment explanation
Indices: 28128414--28128729 Score: 387
Period size: 59 Copynumber: 5.4 Consensus size: 59
28128404 TGATAAACGA
* * * * *
28128414 TGAAATCGGGGTGAAAAATGGGACTTTTGGATA-CAT-GGGGGCAAAATGGTAATTTTGG
1 TGAAATCGGGGTTAAAAATGGGAATTTTAGA-AGCTTCGGGGGTAAAATGGTAATTTTGG
* *
28128472 TGAAATCAGGGTTAAAAAT-GGAATTTTA-AGAGTTTCGGGGGTAAAATGGTAATTTTTGG
1 TGAAATCGGGGTTAAAAATGGGAATTTTAGA-AGCTTCGGGGGTAAAATGGTAA-TTTTGG
* *
28128531 TGAAATCAGGGTTAAAAA-AGGAATTTTAGAAGCTTCGGGGGTAAAATGGTAATTTTTGG
1 TGAAATCGGGGTTAAAAATGGGAATTTTAGAAGCTTCGGGGGTAAAATGGTAA-TTTTGG
*
28128590 TGAAATCGGGGTTAAAAAT-GAAATTTTAGAAGCTTCGGGGGTAAAATGGTAATTTTCGG
1 TGAAATCGGGGTTAAAAATGGGAATTTTAGAAGCTTCGGGGGTAAAATGGTAATTTT-GG
* * *
28128649 TAAAATCGGGGTTAAAAATGGG-ATTTTAAAAGCTTC-GGGGCAAAATGGTAAATTTTGG
1 TGAAATCGGGGTTAAAAATGGGAATTTTAGAAGCTTCGGGGGTAAAATGGT-AATTTTGG
* *
28128707 TGAAATCAGGGTTGAAAATGGGA
1 TGAAATCGGGGTTAAAAATGGGA
28128730 TTTAGGAAAG
Statistics
Matches: 230, Mismatches: 18, Indels: 19
0.86 0.07 0.07
Matches are distributed among these distances:
56 2 0.01
57 8 0.03
58 69 0.30
59 149 0.65
60 2 0.01
ACGTcount: A:0.34, C:0.06, G:0.30, T:0.30
Consensus pattern (59 bp):
TGAAATCGGGGTTAAAAATGGGAATTTTAGAAGCTTCGGGGGTAAAATGGTAATTTTGG
Found at i:28128496 original size:29 final size:30
Alignment explanation
Indices: 28128414--28128669 Score: 135
Period size: 29 Copynumber: 8.7 Consensus size: 30
28128404 TGATAAACGA
* * *
28128414 TGAAATCGGGGTGAAAAATGGGACTTTTGG
1 TGAAATCGGGGTTAAAAATGGTAATTTTGG
* **
28128444 AT-ACAT-GGGG-GCAAAATGGTAATTTTGG
1 -TGAAATCGGGGTTAAAAATGGTAATTTTGG
* *
28128472 TGAAATCAGGGTTAAAAATGG-AATTTT-A
1 TGAAATCGGGGTTAAAAATGGTAATTTTGG
* ** *
28128500 AGAGTTTCGGGGGT-AAAATGGTAATTTTTGG
1 TGA-AATCGGGGTTAAAAATGGTAA-TTTTGG
* *
28128531 TGAAATCAGGGTTAAAAAAGG-AATTTT--
1 TGAAATCGGGGTTAAAAATGGTAATTTTGG
* * *
28128558 AGAAGCTTCGGGGGT-AAAATGGTAATTTTTGG
1 TGAA--ATCGGGGTTAAAAATGGTAA-TTTTGG
*
28128590 TGAAATCGGGGTTAAAAAT-GAAATTTT--
1 TGAAATCGGGGTTAAAAATGGTAATTTTGG
* * *
28128617 AGAAGCTTCGGGGGT-AAAATGGTAATTTTCGG
1 TGAA--ATCGGGGTTAAAAATGGTAATTTT-GG
*
28128649 TAAAATCGGGGTTAAAAATGG
1 TGAAATCGGGGTTAAAAATGG
28128670 GATTTTAAAA
Statistics
Matches: 165, Mismatches: 38, Indels: 44
0.67 0.15 0.18
Matches are distributed among these distances:
27 7 0.04
28 38 0.23
29 51 0.31
30 43 0.26
31 21 0.13
32 5 0.03
ACGTcount: A:0.34, C:0.05, G:0.30, T:0.30
Consensus pattern (30 bp):
TGAAATCGGGGTTAAAAATGGTAATTTTGG
Found at i:28128554 original size:59 final size:59
Alignment explanation
Indices: 28128450--28128732 Score: 410
Period size: 59 Copynumber: 4.8 Consensus size: 59
28128440 TTGGATACAT
* *
28128450 GGGGGCAAAATGGTAA-TTTTGGTGAAATCAGGGTTAAAAATGGAATTTTA-AGAGTTTC
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAGA-AGCTTC
*
28128508 GGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAAAGGAATTTTAGAAGCTTC
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAGCTTC
* *
28128567 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGAAATTTTAGAAGCTTC
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAGCTTC
* * * * *
28128626 GGGGGTAAAATGGTAATTTTCGGTAAAATCGGGGTTAAAAATGGGATTTTAAAAGCTTC
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAGCTTC
* * * *
28128685 -GGGGCAAAATGGTAAATTTTGGTGAAATCAGGGTTGAAAATGGGATTT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTT
28128733 AGGAAAGTTT
Statistics
Matches: 206, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
58 57 0.28
59 148 0.72
60 1 0.00
ACGTcount: A:0.34, C:0.05, G:0.30, T:0.31
Consensus pattern (59 bp):
GGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAGCTTC
Found at i:28128772 original size:30 final size:30
Alignment explanation
Indices: 28128736--28128979 Score: 389
Period size: 30 Copynumber: 8.0 Consensus size: 30
28128726 GGGATTTAGG
28128736 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
* *
28128766 AAAGTTTTGGGGTCAAAATATAATTTTAGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
28128796 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
28128826 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
*
28128856 AAAGTTTTGGGATCAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
*
28128886 AAAGTTTTAGGGTCAAAATGTAATTTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAA-TTTTGGA
*
28128917 AAAGTGTTGGGGTCAAAATGTAATTTTCTGGA
1 AAAGTTTTGGGGTCAAAATGTAA-TTT-TGGA
* *
28128949 AGAGTGTTGGGGTCAAAATGTAATTTCTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTT-TGGA
28128980 CAATTTAGGG
Statistics
Matches: 202, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
30 136 0.67
31 40 0.20
32 26 0.13
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (30 bp):
AAAGTTTTGGGGTCAAAATGTAATTTTGGA
Found at i:28128824 original size:19 final size:19
Alignment explanation
Indices: 28128800--28128854 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
28128790 TTTAGAAAAG
28128800 TTTTGGGGTCAAAATGTAA
1 TTTTGGGGTCAAAATGTAA
28128819 TTTT--GG--AAAA-G---
1 TTTTGGGGTCAAAATGTAA
28128830 TTTTGGGGTCAAAATGTAA
1 TTTTGGGGTCAAAATGTAA
28128849 TTTTGG
1 TTTTGG
28128855 AAAAGTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
11 4 0.14
13 2 0.07
14 1 0.04
15 8 0.29
16 1 0.04
17 2 0.07
19 10 0.36
ACGTcount: A:0.29, C:0.04, G:0.27, T:0.40
Consensus pattern (19 bp):
TTTTGGGGTCAAAATGTAA
Found at i:28130552 original size:15 final size:15
Alignment explanation
Indices: 28130532--28130562 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28130522 ATGGTGGATG
28130532 GAGCTGGTGGTGGCA
1 GAGCTGGTGGTGGCA
28130547 GAGCTGGTGGTGGCA
1 GAGCTGGTGGTGGCA
28130562 G
1 G
28130563 CGGCACAGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.55, T:0.19
Consensus pattern (15 bp):
GAGCTGGTGGTGGCA
Found at i:28130725 original size:12 final size:12
Alignment explanation
Indices: 28130708--28130750 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 12
28130698 GGACTTTAAA
28130708 AATTTTTATGTT
1 AATTTTTATGTT
*
28130720 AATTTTAATGTTTT
1 AATTTTTATG--TT
28130734 AATTTTTAT-TT
1 AATTTTTATGTT
28130745 AATTTT
1 AATTTT
28130751 AAATTCAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 8 0.30
12 9 0.33
14 10 0.37
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (12 bp):
AATTTTTATGTT
Found at i:28130768 original size:17 final size:16
Alignment explanation
Indices: 28130748--28130817 Score: 81
Period size: 17 Copynumber: 4.4 Consensus size: 16
28130738 TTTATTTAAT
*
28130748 TTTAAATTCAAAGTAAA
1 TTTAAATTTAAA-TAAA
*
28130765 TTTAAA--TAATTAAA
1 TTTAAATTTAAATAAA
28130779 TTTAAATTTAACATAAA
1 TTTAAATTTAA-ATAAA
28130796 TTTAAATTTAAATAAA
1 TTTAAATTTAAATAAA
*
28130812 ATTAAA
1 TTTAAA
28130818 AATCAATTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
14 10 0.22
15 2 0.04
16 13 0.28
17 21 0.46
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:28130770 original size:6 final size:6
Alignment explanation
Indices: 28130741--28130808 Score: 61
Period size: 6 Copynumber: 11.3 Consensus size: 6
28130731 TTTAATTTTT
* * *
28130741 ATTTAA TTTTAA ATTCAA A-GTAA ATTTAA ATAATTAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT--TTAA ATTTAA ATTTAA
28130790 CA--TAA ATTTAA ATTTAA AT
1 -ATTTAA ATTTAA ATTTAA AT
28130809 AAAATTAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
4 1 0.02
5 6 0.12
6 36 0.72
7 1 0.02
8 6 0.12
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (6 bp):
ATTTAA
Found at i:28130786 original size:31 final size:31
Alignment explanation
Indices: 28130743--28130802 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
28130733 TAATTTTTAT
*
28130743 TTAATTTTAAATTCAA-AGTAAATTTAAATAA
1 TTAAATTTAAATTCAACA-TAAATTTAAATAA
*
28130774 TTAAATTTAAATTTAACATAAATTTAAAT
1 TTAAATTTAAATTCAACATAAATTTAAAT
28130803 TTAAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (31 bp):
TTAAATTTAAATTCAACATAAATTTAAATAA
Found at i:28131283 original size:38 final size:38
Alignment explanation
Indices: 28131236--28132040 Score: 172
Period size: 37 Copynumber: 23.4 Consensus size: 38
28131226 GGACGACGTT
*
28131236 ACTCTTACTTCAATTTCAGAGATCAAGCCTTGTTGTCCA
1 ACTC-TACTTCAATTTCAGAGATCAAGACTTGTTGTCCA
** *
28131275 ACTCTACTTCAATTTCA-AGAGGATGAC--GTTG--C-
1 ACTCTACTTCAATTTCAGAGATCAAGACTTGTTGTCCA
* *
28131307 TCT-TACTTCAATTTCAGAGATCAAGACTTGTTATCCA
1 ACTCTACTTCAATTTCAGAGATCAAGACTTGTTGTCCA
** * *
28131344 ACTCTACTTCAATTTCA-AGAAGATGGC--GTTG--C-
1 ACTCTACTTCAATTTCAGAGATCAAGACTTGTTGTCCA
* * * * * *
28131376 TCT-TACTTCAAATTCAAAGA-CAAGACCTGATATCCA
1 ACTCTACTTCAATTTCAGAGATCAAGACTTGTTGTCCA
** *
28131412 ACTCTACTTCAATTTCA-AGAGGATGAC--GTTG--C-
1 ACTCTACTTCAATTTCAGAGATCAAGACTTGTTGTCCA
* * *
28131444 TCT-TACTTCAATTTCAGAGATCAAGACGTGTTATCC-
1 ACTCTACTTCAATTTCAGAGATCAAGACTTGTTGTCCA
*** *
28131480 ACTCTACTTCAATTTCA-AGGGGATGAC--GTTG--C-
1 ACTCTACTTCAATTTCAGAGATCAAGACTTGTTGTCCA
* * * *
28131512 TCT-TACTTCAATTTCAGAGATGAAGACGTGTTATCC-
1 ACTCTACTTCAATTTCAGAGATCAAGACTTGTTGTCCA
*** * *
28131548 ACTCTACTTCAATTTCA-AGGGGGATGAC--ATTG--C-
1 ACTCTACTTCAATTTCAGA-GATCAAGACTTGTTGTCCA
* * * *
28131581 TCT-TACTTCAATTTCAGAGATGAAGACATGTTATCC-
1 ACTCTACTTCAATTTCAGAGATCAAGACTTGTTGTCCA
*** *
28131617 ACTCTACTTCAATTTCA-AGGGGATGAC--GTTG--C-
1 ACTCTACTTCAATTTCAGAGATCAAGACTTGTTGTCCA
* * *
28131649 TCT-TACTTCAATTTCAGAGATAAAGA-TGTGTTATCC-
1 ACTCTACTTCAATTTCAGAGATCAAGACT-TGTTGTCCA
*** *
28131685 ACTCTACTTCAATTTCA-AGGGGATGAC--GTTG--C-
1 ACTCTACTTCAATTTCAGAGATCAAGACTTGTTGTCCA
* * * *
28131717 TCT-TACTTCAATTTCAGAGATGAAGACGTGTTATCC-
1 ACTCTACTTCAATTTCAGAGATCAAGACTTGTTGTCCA
* *
28131753 ACTCTACTTCAATTTCAAGGGAT---GAC--ATTG--C-
1 ACTCTACTTCAATTTC-AGAGATCAAGACTTGTTGTCCA
* * * *
28131784 TCT-TACTTCAGTTTCAGAGATAAAGA-TGTGTTATCC-
1 ACTCTACTTCAATTTCAGAGATCAAGACT-TGTTGTCCA
*** *
28131820 ACTCTACTTCAATTTCA-AGGGGATGAC--GTTG--C-
1 ACTCTACTTCAATTTCAGAGATCAAGACTTGTTGTCCA
* * * *
28131852 TCT-TACTTCAATTTCAGAGATGAAGACGTGTTATCC-
1 ACTCTACTTCAATTTCAGAGATCAAGACTTGTTGTCCA
*** * *
28131888 ACTCTACTTCAATTTCA-AGGGGATGAC--ATTG--C-
1 ACTCTACTTCAATTTCAGAGATCAAGACTTGTTGTCCA
* * *
28131920 TCT-TACTTCAATTTCAGAGATCAAGACGTGTTATCC-
1 ACTCTACTTCAATTTCAGAGATCAAGACTTGTTGTCCA
*** *
28131956 ACTCTACTTCAATTTCA-AGGGGATGAC--GTTG--C-
1 ACTCTACTTCAATTTCAGAGATCAAGACTTGTTGTCCA
* * * *
28131988 TCT-TACTTCAATTTCAGAGATGAAGACGTGTTATCC-
1 ACTCTACTTCAATTTCAGAGATCAAGACTTGTTGTCCA
28132024 ACTCTACTTCAATTTCA
1 ACTCTACTTCAATTTCA
28132041 AGGGGATGAC
Statistics
Matches: 565, Mismatches: 124, Indels: 156
0.67 0.15 0.18
Matches are distributed among these distances:
29 5 0.01
30 11 0.02
31 122 0.22
32 101 0.18
33 11 0.02
34 44 0.08
35 15 0.03
36 70 0.12
37 151 0.27
38 31 0.05
39 4 0.01
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (38 bp):
ACTCTACTTCAATTTCAGAGATCAAGACTTGTTGTCCA
Found at i:28131442 original size:68 final size:68
Alignment explanation
Indices: 28131171--28132190 Score: 1593
Period size: 68 Copynumber: 15.0 Consensus size: 68
28131161 AAATGATCTC
* * * ** * *
28131171 GCTCTTACTTCAATTTC--AGA--AAGGCGTGTTGTCCAACTCTATTTTGATTTCAAGAGGACGA
1 GCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGATGA
28131232 CGTT
65 CGTT
* * * * * *
28131236 ACTCTTACTTCAATTTCAGAGATCAAGCCTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATGA
1 GCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGATGA
28131301 CGTT
65 CGTT
* * ** *
28131305 GCTCTTACTTCAATTTCAGAGATCAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAAGATGG
1 GCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGATGA
28131370 CGTT
65 CGTT
* * * * * *
28131374 GCTCTTACTTCAAATTCAAAGA-CAAGACCTGATATCCAACTCTACTTCAATTTCAAGAGGATGA
1 GCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGATGA
28131438 CGTT
65 CGTT
*
28131442 GCTCTTACTTCAATTTCAGAGATCAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
1 GCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
28131507 GTT
66 GTT
28131510 GCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGGATGA
1 GCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAA-GGGGATGA
*
28131575 CATT
65 CGTT
*
28131579 GCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
1 GCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
28131644 GTT
66 GTT
* *
28131647 GCTCTTACTTCAATTTCAGAGATAAAGATGTGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
1 GCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
28131712 GTT
66 GTT
28131715 GCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAA-GGGATGAC
1 GCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
*
28131779 ATT
66 GTT
* * *
28131782 GCTCTTACTTCAGTTTCAGAGATAAAGATGTGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
1 GCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
28131847 GTT
66 GTT
28131850 GCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
1 GCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
*
28131915 ATT
66 GTT
*
28131918 GCTCTTACTTCAATTTCAGAGATCAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
1 GCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
28131983 GTT
66 GTT
28131986 GCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
1 GCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
*
28132051 ATT
66 GTT
*
28132054 GCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
1 GCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
28132119 GTT
66 GTT
* * *
28132122 GCTCTTACTTCAGTTTCAGAGATAAAGATGTGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
1 GCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
28132187 GTT
66 GTT
28132190 G
1 G
28132191 AGACCTGCAG
Statistics
Matches: 897, Mismatches: 51, Indels: 11
0.94 0.05 0.01
Matches are distributed among these distances:
65 16 0.02
67 66 0.07
68 613 0.68
69 202 0.23
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (68 bp):
GCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
GTT
Found at i:28131583 original size:205 final size:204
Alignment explanation
Indices: 28131171--28132186 Score: 1585
Period size: 205 Copynumber: 5.0 Consensus size: 204
28131161 AAATGATCTC
* * * ** * *
28131171 GCTCTTACTTCAATTTC--AGA--AAGGCGTGTTGTCCAACTCTATTTTGATTTCAAGAGGACGA
1 GCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGATGA
* * * * *
28131232 CGTTACTCTTACTTCAATTTCAGAGATCAAGCCTTGTTGTCCAACTCTACTTCAATTTCAAGAGG
65 CGTTGCTCTTACTTCAATTTCAGAGATCAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGG
*
28131297 ATGACGTTGCTCTTACTTCAATTTCAGAGATCAAGACTTGTTATCCAACTCTACTTCAATTTCAA
129 ATGACGTTGCTCTTACTTCAATTTCAGAGATCAAGACGTGTTATCC-ACTCTACTTCAATTTCAA
** * *
28131362 GAAGATGGCGTT
193 GGGGATGACATT
* * * * * *
28131374 GCTCTTACTTCAAATTCAAAGA-CAAGACCTGATATCCAACTCTACTTCAATTTCAAGAGGATGA
1 GCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGATGA
28131438 CGTTGCTCTTACTTCAATTTCAGAGATCAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGA
65 CGTTGCTCTTACTTCAATTTCAGAGATCAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGA
*
28131503 TGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGG
130 TGACGTTGCTCTTACTTCAATTTCAGAGATCAAGACGTGTTATCCACTCTACTTCAATTTCAA-G
28131568 GGGATGACATT
194 GGGATGACATT
*
28131579 GCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
1 GCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
* *
28131644 GTTGCTCTTACTTCAATTTCAGAGATAAAGATGTGTTATCCACTCTACTTCAATTTCAAGGGGAT
66 GTTGCTCTTACTTCAATTTCAGAGATCAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGAT
*
28131709 GACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAA-GG
131 GACGTTGCTCTTACTTCAATTTCAGAGATCAAGACGTGTTATCCACTCTACTTCAATTTCAAGGG
28131773 GATGACATT
196 GATGACATT
* * *
28131782 GCTCTTACTTCAGTTTCAGAGATAAAGATGTGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
1 GCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
*
28131847 GTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGAT
66 GTTGCTCTTACTTCAATTTCAGAGATCAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGAT
*
28131912 GACATTGCTCTTACTTCAATTTCAGAGATCAAGACGTGTTATCCACTCTACTTCAATTTCAAGGG
131 GACGTTGCTCTTACTTCAATTTCAGAGATCAAGACGTGTTATCCACTCTACTTCAATTTCAAGGG
*
28131977 GATGACGTT
196 GATGACATT
28131986 GCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
1 GCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
* * *
28132051 ATTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGAT
66 GTTGCTCTTACTTCAATTTCAGAGATCAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGAT
* * *
28132116 GACGTTGCTCTTACTTCAGTTTCAGAGATAAAGATGTGTTATCCACTCTACTTCAATTTCAAGGG
131 GACGTTGCTCTTACTTCAATTTCAGAGATCAAGACGTGTTATCCACTCTACTTCAATTTCAAGGG
28132181 GATGAC
196 GATGAC
28132187 GTTGAGACCT
Statistics
Matches: 761, Mismatches: 46, Indels: 11
0.93 0.06 0.01
Matches are distributed among these distances:
203 211 0.28
204 220 0.29
205 247 0.32
206 83 0.11
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (204 bp):
GCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
GTTGCTCTTACTTCAATTTCAGAGATCAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGAT
GACGTTGCTCTTACTTCAATTTCAGAGATCAAGACGTGTTATCCACTCTACTTCAATTTCAAGGG
GATGACATT
Found at i:28143074 original size:9 final size:10
Alignment explanation
Indices: 28143052--28143083 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
28143042 GGATCACCAC
28143052 AAAACGTTTA
1 AAAACGTTTA
28143062 AAAACGTTTA
1 AAAACGTTTA
28143072 AAAACG-TTA
1 AAAACGTTTA
28143081 AAA
1 AAA
28143084 CATCGGTCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 6 0.27
10 16 0.73
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.25
Consensus pattern (10 bp):
AAAACGTTTA
Found at i:28144210 original size:59 final size:59
Alignment explanation
Indices: 28144122--28144403 Score: 423
Period size: 58 Copynumber: 4.8 Consensus size: 59
28144112 TTTGGATACC
* *
28144122 CGGGGGCAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTA-AGAGTTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGA-AGCTT
* *
28144180 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTAAAAAATAGAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
*
28144239 C-GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
*
28144297 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAAT-GAGATTTTAAAAGCTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGA-ATTTTAGAAGCTT
* * *
28144356 C-GGGGCAAAATGGTAAATTTTGGTGAAATCGGGGTT-AAAATGGGATTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTT
28144404 AGGAAAGTTT
Statistics
Matches: 207, Mismatches: 12, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
57 9 0.04
58 107 0.52
59 90 0.43
60 1 0.00
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.31
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
Found at i:28144264 original size:117 final size:116
Alignment explanation
Indices: 28144124--28144403 Score: 458
Period size: 117 Copynumber: 2.4 Consensus size: 116
28144114 TGGATACCCG
*
28144124 GGGGCAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTA-AGAGTTTCGGGGGTA
1 GGGGCAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGA-AGCTTCGGGGGTA
*
28144188 AAATGGTAATTTTTGGTGAAATCGGGGTAAAAAAT-AGAATTTTAGAAGCTTC
65 AAATGGTAATTTTTGGTGAAATCGGGGTAAAAAATGAG-ATTTTAAAAGCTTC
*
28144240 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTTCGGGGGTA
1 GGGGCAAAATGGTAATTTT-GGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTTCGGGGGTA
*
28144305 AAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGAGATTTTAAAAGCTTC
65 AAATGGTAATTTTTGGTGAAATCGGGGTAAAAAATGAGATTTTAAAAGCTTC
*
28144357 GGGGCAAAATGGTAAATTTTGGTGAAATCGGGGTT-AAAATGGGATTT
1 GGGGCAAAATGGT-AATTTTGGTGAAATCGGGGTTAAAAATGGAATTT
28144404 AGGAAAGTTT
Statistics
Matches: 154, Mismatches: 6, Indels: 8
0.92 0.04 0.05
Matches are distributed among these distances:
116 29 0.19
117 116 0.75
118 9 0.06
ACGTcount: A:0.34, C:0.05, G:0.30, T:0.31
Consensus pattern (116 bp):
GGGGCAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTTCGGGGGTAA
AATGGTAATTTTTGGTGAAATCGGGGTAAAAAATGAGATTTTAAAAGCTTC
Found at i:28144443 original size:30 final size:30
Alignment explanation
Indices: 28144407--28144618 Score: 325
Period size: 30 Copynumber: 7.0 Consensus size: 30
28144397 GGGATTTAGG
28144407 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
*
28144437 AAAGTTTTGGGGTCAAAATATAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
*
28144467 AAAGTTTTGGGGTCGAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
* *
28144497 AAAGTTTTAGGGTTAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
* *
28144527 AAAGATTTGGGGTTAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
*
28144557 AAAGTTTTGGGGTCAAAATGTTATTTTTGGA
1 AAAGTTTTGGGGTCAAAATG-TAATTTTGGA
* *
28144588 AGAGTGTTGGGGTCAAAATGTAATTTCTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTT-TGGA
28144619 CAATTTAGGG
Statistics
Matches: 166, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
30 135 0.81
31 31 0.19
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (30 bp):
AAAGTTTTGGGGTCAAAATGTAATTTTGGA
Found at i:28145422 original size:15 final size:16
Alignment explanation
Indices: 28145392--28145424 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
28145382 GATTTTTTCG
28145392 AAACCCAGATCTTGGA
1 AAACCCAGATCTTGGA
28145408 AAACCCAGATC-TGGA
1 AAACCCAGATCTTGGA
28145423 AA
1 AA
28145425 CGTTTTGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.15
Consensus pattern (16 bp):
AAACCCAGATCTTGGA
Found at i:28146189 original size:15 final size:15
Alignment explanation
Indices: 28146169--28146199 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28146159 ATGGTGGATG
28146169 GAGCTGGTGGTGGCA
1 GAGCTGGTGGTGGCA
28146184 GAGCTGGTGGTGGCA
1 GAGCTGGTGGTGGCA
28146199 G
1 G
28146200 CGGCACAGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.55, T:0.19
Consensus pattern (15 bp):
GAGCTGGTGGTGGCA
Found at i:28146402 original size:14 final size:14
Alignment explanation
Indices: 28146383--28146409 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28146373 AAATTCAAAG
28146383 TAAATTTAAATAAT
1 TAAATTTAAATAAT
28146397 TAAATTTAAATAA
1 TAAATTTAAATAA
28146410 AATTAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAATTTAAATAAT
Found at i:28147703 original size:61 final size:61
Alignment explanation
Indices: 28147571--28147692 Score: 235
Period size: 61 Copynumber: 2.0 Consensus size: 61
28147561 CAATTTATTC
28147571 AAAAAGAAATTTATCAAATGTTTTGTTATATCAAAAAGGAAGATTGCTAAACTAAACTCTA
1 AAAAAGAAATTTATCAAATGTTTTGTTATATCAAAAAGGAAGATTGCTAAACTAAACTCTA
*
28147632 AAAAAGAAATTTATCAAATGTTTTGTTATATCAAAAAGGGAGATTGCTAAACTAAACTCTA
1 AAAAAGAAATTTATCAAATGTTTTGTTATATCAAAAAGGAAGATTGCTAAACTAAACTCTA
28147693 TTTGATAAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (61 bp):
AAAAAGAAATTTATCAAATGTTTTGTTATATCAAAAAGGAAGATTGCTAAACTAAACTCTA
Found at i:28148936 original size:3 final size:3
Alignment explanation
Indices: 28148923--28148967 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
28148913 GGTTGAGCTT
* *
28148923 TTA TCA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28148968 GATCACTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:28149666 original size:745 final size:725
Alignment explanation
Indices: 28148251--28149725 Score: 2244
Period size: 745 Copynumber: 2.0 Consensus size: 725
28148241 CTTCTAAAGA
* *
28148251 TCCTACAACAATAAGAAAGCATATTCACGCAAAATCATCAATCGAACAACTTTCGTGTCCAATTC
1 TCCTACAACAATAAGAAAGCATATTCAAGCAAAATCATCAATCAAACAACTTTCGTGTCCAATTC
* *
28148316 TTTCATACTTTTCTTATACGCACTTGTAAGTTTTTATTGTTACTCTTTAACTTAAGTGTTTTCTT
66 TTTCATACTTTTCTTATACACACTTGTAAGTTTTTATTGTTACTCTTTAACTCAAGTGTTTTCTT
* * *
28148381 GTTTATTTGTGTTTAATTGACAAACATTTTGACTTTGTGAGGATTATTTCTTTGTTTGTTTCTCT
131 GTTTATTTGTGCTTAATTGACAAACATTCTGAATTTGTGAGGATTATTTCTTTGTTTGTTTCTCT
* *
28148446 GTAATTCTTTACGAGGATTTGTGTCTTAAGATTTGGATAGAAATTTTACAGGAGTTCTAAGGTTA
196 GTAATTCTTTACGAGGATTTGTGTCTTAAGATTTGGATAGAAATCTTACAGGAATTCTAAGGTTA
* ** * *
28148511 CATTTTGTCCTCAAAGGTTGAACAAATTAGTGAATTTGAGAAAATCCTTAGTTGTGTAAAGCTAA
261 AACATTGTCCTCAAAAGTTGAACAAATTAATGAATTTGAGAAAATCCTTAGTTGTGTAAAGCTAA
* * *
28148576 GGTAGTGGGTCGAACCACTCTAAATTATTATGTTCATTGTTCTATATTTATTTTCTAGTTTTCCT
326 GGTAATGGGTCGAACCACTCTAAATTATTATGTTCATTGTTCTATATATATTTTCTAATTTTCCT
** * *
28148641 AAAAATTTTAAAAGTTAATTCACCCCCTATTAGTAATTCGATTTGATCATTTGAGGTAACATGTA
391 AAAAATTTTAAAAGCCAATTCACCCCCTATTAGCAATTCGATTTGATCATTTGAGCTAACATGTA
28148706 TATTGAGCCATAAATTATGTTTTAAATCTTCATCATTTGCTCTATCCTTACTTCTTACTTGGAGA
456 TATTGAGCCATAAATTATGTTTTAAATCTTCATCATTTGCTCTATCCTTACTTCTTACTTGGAGA
*
28148771 AATTCTTAATTAATTCTCGAAATTAGATGAGTGTTGGATTTGGTATTCGTTCAATAGGGGTGTAA
521 AATTCTTAATTAATTCTCGAAATTAGATGAGTGTTGGATTTGGTATGCGTTCAATAGGGGTGTAA
28148836 ATGAGGCACTTGTGCTCACAGATTATTCAAAAGAAATTCGAATTCGATTCAATCAAAGTCGAGCC
586 ATGAGGCACTTGTGCTCACAGATTATTCAAAAGAAATTCGAATTCGATTCAATCAAAGTCGAGCC
* * *
28148901 AAGCCCTAGCTTGGTTGAGCTTTTATCATTATTATTATTATTATTA-TA-ATTATTATTATTATT
651 AAGCCCAAGCTTGATTGAGCTTTTATCATTATTATTATTATTACTAGTACA-T-TT-TTA--A-T
28148964 ATTAGATCACTTTTGT
710 ATTAGATCACTTTTGT
*
28148980 TCCTACAACAATAAGAAAGTATATTCAAGCAAAATCATCAATCAAACAACCTTT-GTGTCCAATT
1 TCCTACAACAATAAGAAAGCATATTCAAGCAAAATCATCAATCAAACAA-CTTTCGTGTCCAATT
* * *
28149044 CTTTCATATTTTTCTTATACACACTTGTGAGCTTTTT-TTGTTATTCTTTAACTCAAGTGTTTTT
65 CTTTCATACTTTTCTTATACACACTTGTAAG-TTTTTATTGTTACTCTTTAACTCAAGTG-TTTT
28149108 CTTGTTTATTTGTGCTTAATTGACAAACATTCTGAATTTGTGAGGATTATTTCTTTGTTTGTTTC
128 CTTGTTTATTTGTGCTTAATTGACAAACATTCTGAATTTGTGAGGATTATTTCTTTGTTTGTTTC
* * *
28149173 TCTGTAATTCTTTGA-GAGGGTTTGTGTCTTAAGATTTGGATGGAAATCTTACAGGAATTGTAAG
193 TCTGTAATTCTTT-ACGAGGATTTGTGTCTTAAGATTTGGATAGAAATCTTACAGGAATTCTAAG
*
28149237 GTTAAACATTGTCCTCAAAAGTTGAACAAATTAATGAATTTGGGAAAATCCTTAGTTGTGTAAAG
257 GTTAAACATTGTCCTCAAAAGTTGAACAAATTAATGAATTTGAGAAAATCCTTAGTTGTGTAAAG
* *
28149302 CTAAGGTAATGGAGTAGACAATTAGGAACGAGCCACTCTAAATTGTTGTGTTCATTGTTCTATAT
322 CTAAGGTAATGG-GT---C------G-A--A-CCACTCTAAATTATTATGTTCATTGTTCTATAT
** * *
28149367 ATATTTTTCTAATTTTCCTAAATGTTTTAAAAGCCAATTCACCGCCTA-TGGCAATTTCGATTTG
373 ATA-TTTTCTAATTTTCCTAAAAATTTTAAAAGCCAATTCACCCCCTATTAGCAA-TTCGATTTG
*
28149431 ATCATTTGAGCTAACATGTATTTTGAGCCATAAATTATGTTTTAAATCTTCATCATTTGCTCTAT
436 ATCATTTGAGCTAACATGTATATTGAGCCATAAATTATGTTTTAAATCTTCATCATTTGCTCTAT
*
28149496 CCTTACTTCTTACTTGGAGAAATTTTTAATTAATTCTCGAAATTAGATGAGTGTTGGATTTGGTA
501 CCTTACTTCTTACTTGGAGAAATTCTTAATTAATTCTCGAAATTAGATGAGTGTTGGATTTGGTA
* **
28149561 TGCGTTCAATAGGGTTGTAAATGAGGCACTTGTGCTCGTAGATTATTCAAAAGAAATTCGAATTC
566 TGCGTTCAATAGGGGTGTAAATGAGGCACTTGTGCTCACAGATTATTCAAAAGAAATTCGAATTC
* *
28149626 GATTCAAGT-AAAGTCGAGCCAAGCCCAAGCTTGATTGAGCTTTTATTATTATTATTTTTATTAC
631 GATTCAA-TCAAAGTCGAGCCAAGCCCAAGCTTGATTGAGCTTTTATCATTATTATTATTATTAC
28149690 TAGTACATTTTTAATATTAGATCACTTTTGT
695 TAGTACATTTTTAATATTAGATCACTTTTGT
28149721 TCCTA
1 TCCTA
28149726 TTTTGATAAA
Statistics
Matches: 677, Mismatches: 46, Indels: 34
0.89 0.06 0.04
Matches are distributed among these distances:
729 104 0.15
730 202 0.30
731 3 0.00
734 1 0.00
740 1 0.00
741 23 0.03
742 1 0.00
743 1 0.00
744 40 0.06
745 296 0.44
746 4 0.01
747 1 0.00
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (725 bp):
TCCTACAACAATAAGAAAGCATATTCAAGCAAAATCATCAATCAAACAACTTTCGTGTCCAATTC
TTTCATACTTTTCTTATACACACTTGTAAGTTTTTATTGTTACTCTTTAACTCAAGTGTTTTCTT
GTTTATTTGTGCTTAATTGACAAACATTCTGAATTTGTGAGGATTATTTCTTTGTTTGTTTCTCT
GTAATTCTTTACGAGGATTTGTGTCTTAAGATTTGGATAGAAATCTTACAGGAATTCTAAGGTTA
AACATTGTCCTCAAAAGTTGAACAAATTAATGAATTTGAGAAAATCCTTAGTTGTGTAAAGCTAA
GGTAATGGGTCGAACCACTCTAAATTATTATGTTCATTGTTCTATATATATTTTCTAATTTTCCT
AAAAATTTTAAAAGCCAATTCACCCCCTATTAGCAATTCGATTTGATCATTTGAGCTAACATGTA
TATTGAGCCATAAATTATGTTTTAAATCTTCATCATTTGCTCTATCCTTACTTCTTACTTGGAGA
AATTCTTAATTAATTCTCGAAATTAGATGAGTGTTGGATTTGGTATGCGTTCAATAGGGGTGTAA
ATGAGGCACTTGTGCTCACAGATTATTCAAAAGAAATTCGAATTCGATTCAATCAAAGTCGAGCC
AAGCCCAAGCTTGATTGAGCTTTTATCATTATTATTATTATTACTAGTACATTTTTAATATTAGA
TCACTTTTGT
Found at i:28150784 original size:6 final size:6
Alignment explanation
Indices: 28150773--28150808 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
28150763 ATAGGAGACT
28150773 CAACTC CAACTC CAACTC CAACTC CAACTC CAACTC
1 CAACTC CAACTC CAACTC CAACTC CAACTC CAACTC
28150809 TAACATAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.50, G:0.00, T:0.17
Consensus pattern (6 bp):
CAACTC
Found at i:28150872 original size:29 final size:29
Alignment explanation
Indices: 28150839--28150894 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
28150829 TGTTTTATTT
* *
28150839 TTATTTTGAAGCAAATAAAATTTTTTTAA
1 TTATTTTAAAGAAAATAAAATTTTTTTAA
*
28150868 TTATTTTAAAGAAAATAAGATTTTTTT
1 TTATTTTAAAGAAAATAAAATTTTTTT
28150895 TAGTTTAGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (29 bp):
TTATTTTAAAGAAAATAAAATTTTTTTAA
Found at i:28151185 original size:21 final size:21
Alignment explanation
Indices: 28151156--28151209 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
28151146 TATATGTATT
*
28151156 ATTTGATTTTTAAATTAATTC
1 ATTTAATTTTTAAATTAATTC
*
28151177 ATTTAATTTTTTTAATTAATTC
1 ATTTAA-TTTTTAAATTAATTC
* *
28151199 AATTATTTTTT
1 ATTTAATTTTT
28151210 CAATCTAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 10 0.36
22 18 0.64
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (21 bp):
ATTTAATTTTTAAATTAATTC
Found at i:28151193 original size:18 final size:19
Alignment explanation
Indices: 28151170--28151208 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
28151160 GATTTTTAAA
* *
28151170 TTAATTCATTTAATT-TTT
1 TTAATTAATTCAATTATTT
28151188 TTAATTAATTCAATTATTT
1 TTAATTAATTCAATTATTT
28151207 TT
1 TT
28151209 TCAATCTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (19 bp):
TTAATTAATTCAATTATTT
Found at i:28151193 original size:22 final size:21
Alignment explanation
Indices: 28151162--28151209 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 21
28151152 TATTATTTGA
*
28151162 TTTTTAAATTAATTCATTTAAT
1 TTTTTAAATTAATTCAATT-AT
*
28151184 TTTTTTAATTAATTCAATTAT
1 TTTTTAAATTAATTCAATTAT
28151205 TTTTT
1 TTTTT
28151210 CAATCTAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTTAAATTAATTCAATTAT
Found at i:28157250 original size:22 final size:22
Alignment explanation
Indices: 28157237--28157291 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
28157227 TATTTTAATC
28157237 TTAAATTTACTTTAAATTCAAT
1 TTAAATTTACTTTAAATTCAAT
* * *
28157259 TTAAATTTAAATTTGAATTTAAT
1 TTAAATTT-ACTTTAAATTCAAT
28157282 TTAAAATTTA
1 TT-AAATTTA
28157292 ATATTATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.29
23 14 0.50
24 6 0.21
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (22 bp):
TTAAATTTACTTTAAATTCAAT
Found at i:28157267 original size:6 final size:6
Alignment explanation
Indices: 28157220--28157292 Score: 57
Period size: 6 Copynumber: 12.7 Consensus size: 6
28157210 CATTTGAAAA
* * *
28157220 TTAAAT TT--AT TTTAAT CTTAAAT TT-ACT TTAAA- TTCAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT -TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
28157265 TTAAAT TTGAAT TT-AAT TTAAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TT-AAAT TTAA
28157293 TATTATTATA
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
4 4 0.07
5 13 0.24
6 27 0.50
7 10 0.19
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (6 bp):
TTAAAT
Found at i:28157267 original size:17 final size:17
Alignment explanation
Indices: 28157240--28157286 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
28157230 TTTAATCTTA
*
28157240 AATTTACTTTAAA-TTC
1 AATTTAATTTAAATTTC
*
28157256 AATTTAAATTTAAATTTG
1 AATTT-AATTTAAATTTC
28157274 AATTTAATTTAAA
1 AATTTAATTTAAA
28157287 ATTTAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 5 0.19
17 15 0.56
18 7 0.26
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (17 bp):
AATTTAATTTAAATTTC
Found at i:28157277 original size:12 final size:12
Alignment explanation
Indices: 28157220--28157292 Score: 57
Period size: 11 Copynumber: 6.3 Consensus size: 12
28157210 CATTTGAAAA
28157220 TTAAATTT--AT
1 TTAAATTTAAAT
*
28157230 TTTAATCTTAAAT
1 TTAAAT-TTAAAT
*
28157243 TT-ACTTTAAA-
1 TTAAATTTAAAT
*
28157253 TTCAATTTAAAT
1 TTAAATTTAAAT
*
28157265 TTAAATTTGAAT
1 TTAAATTTAAAT
28157277 TT-AATTTAAAAT
1 TTAAATTT-AAAT
28157289 TTAA
1 TTAA
28157293 TATTATTATA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
10 7 0.14
11 19 0.38
12 19 0.38
13 5 0.10
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (12 bp):
TTAAATTTAAAT
Found at i:28157293 original size:12 final size:11
Alignment explanation
Indices: 28157217--28157293 Score: 75
Period size: 12 Copynumber: 6.8 Consensus size: 11
28157207 AACCATTTGA
*
28157217 AAATTAAATTT
1 AAATTTAATTT
*
28157228 -ATTTTAATCTT
1 AAATTTAAT-TT
*
28157239 AAATTTACTTT
1 AAATTTAATTT
*
28157250 AAATTCAATTT
1 AAATTTAATTT
28157261 AAATTTAAATTT
1 AAATTT-AATTT
*
28157273 GAATTTAATTT
1 AAATTTAATTT
28157284 AAAATTTAAT
1 -AAATTTAAT
28157294 ATTATTATAA
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
10 6 0.11
11 23 0.43
12 24 0.45
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:28157355 original size:12 final size:14
Alignment explanation
Indices: 28157321--28157377 Score: 77
Period size: 12 Copynumber: 4.3 Consensus size: 14
28157311 AAGAAAAAGT
28157321 CCAATTACAATGGC
1 CCAATTACAATGGC
28157335 CCAAATTA-AA-GGC
1 CC-AATTACAATGGC
28157348 CCAATTA-AA-GGC
1 CCAATTACAATGGC
28157360 CCAATTACAATGGC
1 CCAATTACAATGGC
28157374 CCAA
1 CCAA
28157378 ATAGGCCCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
12 17 0.43
13 7 0.17
14 11 0.28
15 5 0.12
ACGTcount: A:0.40, C:0.28, G:0.14, T:0.18
Consensus pattern (14 bp):
CCAATTACAATGGC
Found at i:28157455 original size:15 final size:15
Alignment explanation
Indices: 28157435--28157465 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28157425 CGTGCCTCTG
28157435 CTGCCACCACCAGCT
1 CTGCCACCACCAGCT
28157450 CTGCCACCACCAGCT
1 CTGCCACCACCAGCT
28157465 C
1 C
28157466 CATCCACCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.55, G:0.13, T:0.13
Consensus pattern (15 bp):
CTGCCACCACCAGCT
Found at i:28158339 original size:24 final size:23
Alignment explanation
Indices: 28158310--28158360 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
28158300 GAAAATCAAT
*
28158310 AAAGAACACAAAAAATGAA-GAATA
1 AAAGAACA-AAAAAAGGAAGGAA-A
28158334 AAAGAACAAAAAAAGGAAGGAAA
1 AAAGAACAAAAAAAGGAAGGAAA
28158357 AAAG
1 AAAG
28158361 GGGAAGAGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.73, C:0.06, G:0.18, T:0.04
Consensus pattern (23 bp):
AAAGAACAAAAAAAGGAAGGAAA
Found at i:28159099 original size:30 final size:30
Alignment explanation
Indices: 28159053--28159229 Score: 273
Period size: 30 Copynumber: 5.9 Consensus size: 30
28159043 CCCTAAATTA
* *
28159053 TCCAGAAATTATATTTTGACCCTAAAACTTT
1 TCCA-AAATTACATTTTGACCCCAAAACTTT
28159084 TCCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
28159114 TCCAAAATTATATTTTTACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
28159144 TCCAAAATTATATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
28159174 TCCAAGATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
28159204 TCCAAAATTACATTTTAACCCAAAAA
1 TCCAAAATTACATTTTGACCCCAAAA
28159230 ATCTCCTAAA
Statistics
Matches: 136, Mismatches: 10, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
30 132 0.97
31 4 0.03
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (30 bp):
TCCAAAATTACATTTTGACCCCAAAACTTT
Found at i:28159211 original size:90 final size:91
Alignment explanation
Indices: 28159053--28159229 Score: 302
Period size: 90 Copynumber: 2.0 Consensus size: 91
28159043 CCCTAAATTA
*
28159053 TCCAGAAATTATATTTTGACCCTAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCA
1 TCCAGAAATTATATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCA
* * *
28159118 AAATTATATTTTTACCCCAAAACTTT
66 AAATTACATTTTAACCCAAAAACTTT
*
28159144 TCCA-AAATTATATTTTGACCCCAAAACTTTTCCAAGATTACATTTTGACCCCAAAACTTTTCCA
1 TCCAGAAATTATATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCA
28159208 AAATTACATTTTAACCCAAAAA
66 AAATTACATTTTAACCCAAAAA
28159230 ATCTCCTAAA
Statistics
Matches: 81, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
90 77 0.95
91 4 0.05
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (91 bp):
TCCAGAAATTATATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCA
AAATTACATTTTAACCCAAAAACTTT
Found at i:28159278 original size:90 final size:90
Alignment explanation
Indices: 28159065--28159313 Score: 233
Period size: 90 Copynumber: 2.8 Consensus size: 90
28159055 CAGAAATTAT
* *
28159065 ATTTTGAC-CCTAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTATATTT
1 ATTTTGACACC-AAAACTTTACCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTT
* ** * * *
28159129 TTACCCCAAAACTTTTCCAAAATTAT
65 TTAACCCAAAAAATCTCCAAAATCAC
* * *
28159155 ATTTTGACCCCAAAACTTTTCCAAGATTACATTTTGACCCCAAAACTTTTCCAAAATTACA-TTT
1 ATTTTGACACCAAAACTTTACCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTT
* *
28159219 TAACCCAAAAAATCTCCTAAATCCC
66 TAACCCAAAAAATCTCCAAAATCAC
* ** * * *
28159244 ATTTTTA-ACCACGA-TTTCACCAAAATTTACCATTTT-ACCCCCGAAACCTTT--AAAATTGCA
1 ATTTTGACACCAAAACTTT-ACCAAAA-TTA-CATTTTGA-CCCCAAAACTTTTCCAAAATTACA
28159304 TTTTTAACCC
62 TTTTTAACCC
28159314 CGATATCACC
Statistics
Matches: 134, Mismatches: 19, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
87 3 0.02
88 17 0.13
89 39 0.29
90 73 0.54
91 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (90 bp):
ATTTTGACACCAAAACTTTACCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTT
TAACCCAAAAAATCTCCAAAATCAC
Found at i:28159336 original size:30 final size:30
Alignment explanation
Indices: 28159242--28159338 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
28159232 CTCCTAAATC
* *
28159242 CCATTTTTAACCACGATTTCACCAAAATTTA
1 CCATTTTTAACCCCGATATCACCAAAA-TTA
* * * ***
28159273 CCA-TTTTACCCCCGAAACCTTTAAAATT-
1 CCATTTTTAACCCCGATATCACCAAAATTA
*
28159301 GCATTTTTAACCCCGATATCACCAAAATTA
1 CCATTTTTAACCCCGATATCACCAAAATTA
28159331 CCATTTTT
1 CCATTTTT
28159339 CCCCCGAGTA
Statistics
Matches: 48, Mismatches: 16, Indels: 5
0.70 0.23 0.07
Matches are distributed among these distances:
28 2 0.04
29 21 0.44
30 22 0.46
31 3 0.06
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (30 bp):
CCATTTTTAACCCCGATATCACCAAAATTA
Found at i:28159343 original size:29 final size:29
Alignment explanation
Indices: 28159255--28159350 Score: 77
Period size: 29 Copynumber: 3.2 Consensus size: 29
28159245 TTTTTAACCA
* *
28159255 CGATTTCACCAAAATTTACCATTTTACCCC
1 CGATATCACCAAAA-TTACCATTTTTCCCC
* * *** * *
28159285 CGAAACCTTTAAAATT-GCATTTTTAACCC
1 CGATATCACCAAAATTACCATTTTT-CCCC
28159314 CGATATCACCAAAATTACCATTTTTCCCC
1 CGATATCACCAAAATTACCATTTTTCCCC
28159343 CGAGTATC
1 CGA-TATC
28159351 CATAAGTCCC
Statistics
Matches: 47, Mismatches: 16, Indels: 6
0.68 0.23 0.09
Matches are distributed among these distances:
28 6 0.13
29 22 0.47
30 19 0.40
ACGTcount: A:0.31, C:0.30, G:0.06, T:0.32
Consensus pattern (29 bp):
CGATATCACCAAAATTACCATTTTTCCCC
Found at i:28160380 original size:10 final size:10
Alignment explanation
Indices: 28160358--28160389 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
28160348 TAGACCGATG
28160358 TTTTAAA-GT
1 TTTTAAACGT
28160367 TTTTAAACGT
1 TTTTAAACGT
28160377 TTTTAAACGT
1 TTTTAAACGT
28160387 TTT
1 TTT
28160390 GTGGTGATCC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 7 0.32
10 15 0.68
ACGTcount: A:0.28, C:0.06, G:0.09, T:0.56
Consensus pattern (10 bp):
TTTTAAACGT
Found at i:28170578 original size:68 final size:68
Alignment explanation
Indices: 28170469--28171117 Score: 1104
Period size: 68 Copynumber: 9.5 Consensus size: 68
28170459 CTGCAGGTCT
* * *
28170469 CAACGTCATCCCCTTGAAATTGAAGTAGAGTAGATAACACGTCTTCTTCTCCGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
28170534 GAG
66 GAG
28170537 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
28170602 GAG
66 GAG
* *
28170605 CAACATCATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
28170670 GAG
66 GAG
28170673 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
28170738 GAG
66 GAG
* *
28170741 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
28170806 GAG
66 GAG
* *
28170809 CAATGTCATCCCCTTGAAATTGAAGTAGAGTGGTTAACACG-CTTTCATCTCTGAAATTGAAGTA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTC-TTCATCTCTGAAATTGAAGTA
28170873 AGAG
65 AGAG
* *
28170877 CAATGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTTTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
28170942 GAG
66 GAG
* *
28170945 CAATGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACG-CTTTCATCTCTAAAATTGAAGTA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTC-TTCATCTCTGAAATTGAAGTA
28171009 AGAG
65 AGAG
* *
28171013 CAACGTCATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTTTTCATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
28171078 GAG
66 GAG
* *
28171081 CAACGTCATCCTCTTGAAATTGAAGTAAAGTTGGATA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAG-TGGATA
28171118 GCAAAGTCTT
Statistics
Matches: 554, Mismatches: 22, Indels: 9
0.95 0.04 0.02
Matches are distributed among these distances:
67 1 0.00
68 547 0.99
69 6 0.01
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (68 bp):
CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAA
GAG
Found at i:28171440 original size:22 final size:22
Alignment explanation
Indices: 28171427--28171481 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
28171417 TATTTTAATC
28171427 TTAAATTTACTTTAAATTCAAT
1 TTAAATTTACTTTAAATTCAAT
* * *
28171449 TTAAATTTAAATTTGAATTTAAT
1 TTAAATTT-ACTTTAAATTCAAT
28171472 TTAAAATTTA
1 TT-AAATTTA
28171482 ATATTATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.29
23 14 0.50
24 6 0.21
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (22 bp):
TTAAATTTACTTTAAATTCAAT
Found at i:28171457 original size:6 final size:6
Alignment explanation
Indices: 28171410--28171482 Score: 57
Period size: 6 Copynumber: 12.7 Consensus size: 6
28171400 CATTTGAAAA
* * *
28171410 TTAAAT TT--AT TTTAAT CTTAAAT TT-ACT TTAAA- TTCAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT -TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
28171455 TTAAAT TTGAAT TT-AAT TTAAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TT-AAAT TTAA
28171483 TATTATTATA
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
4 4 0.07
5 13 0.24
6 27 0.50
7 10 0.19
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (6 bp):
TTAAAT
Found at i:28171457 original size:17 final size:17
Alignment explanation
Indices: 28171430--28171476 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
28171420 TTTAATCTTA
*
28171430 AATTTACTTTAAA-TTC
1 AATTTAATTTAAATTTC
*
28171446 AATTTAAATTTAAATTTG
1 AATTT-AATTTAAATTTC
28171464 AATTTAATTTAAA
1 AATTTAATTTAAA
28171477 ATTTAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 5 0.19
17 15 0.56
18 7 0.26
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (17 bp):
AATTTAATTTAAATTTC
Found at i:28171467 original size:12 final size:12
Alignment explanation
Indices: 28171410--28171482 Score: 57
Period size: 11 Copynumber: 6.3 Consensus size: 12
28171400 CATTTGAAAA
28171410 TTAAATTT--AT
1 TTAAATTTAAAT
*
28171420 TTTAATCTTAAAT
1 TTAAAT-TTAAAT
*
28171433 TT-ACTTTAAA-
1 TTAAATTTAAAT
*
28171443 TTCAATTTAAAT
1 TTAAATTTAAAT
*
28171455 TTAAATTTGAAT
1 TTAAATTTAAAT
28171467 TT-AATTTAAAAT
1 TTAAATTT-AAAT
28171479 TTAA
1 TTAA
28171483 TATTATTATA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
10 7 0.14
11 19 0.38
12 19 0.38
13 5 0.10
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (12 bp):
TTAAATTTAAAT
Found at i:28171483 original size:12 final size:11
Alignment explanation
Indices: 28171407--28171483 Score: 75
Period size: 12 Copynumber: 6.8 Consensus size: 11
28171397 AACCATTTGA
*
28171407 AAATTAAATTT
1 AAATTTAATTT
*
28171418 -ATTTTAATCTT
1 AAATTTAAT-TT
*
28171429 AAATTTACTTT
1 AAATTTAATTT
*
28171440 AAATTCAATTT
1 AAATTTAATTT
28171451 AAATTTAAATTT
1 AAATTT-AATTT
*
28171463 GAATTTAATTT
1 AAATTTAATTT
28171474 AAAATTTAAT
1 -AAATTTAAT
28171484 ATTATTATAA
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
10 6 0.11
11 23 0.43
12 24 0.45
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:28171554 original size:14 final size:14
Alignment explanation
Indices: 28171511--28171555 Score: 67
Period size: 14 Copynumber: 3.3 Consensus size: 14
28171501 AAGAAAAAGT
28171511 CCAATTACAATGGCC
1 CCAATTACAATGG-C
28171526 CCAATTA-AA-GGC
1 CCAATTACAATGGC
28171538 CCAATTACAATGGC
1 CCAATTACAATGGC
28171552 CCAA
1 CCAA
28171556 ATAGGCCCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 8 0.29
13 4 0.14
14 9 0.32
15 7 0.25
ACGTcount: A:0.38, C:0.31, G:0.13, T:0.18
Consensus pattern (14 bp):
CCAATTACAATGGC
Found at i:28171633 original size:15 final size:15
Alignment explanation
Indices: 28171613--28171643 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28171603 CGTGCCTCTG
28171613 CTGCCACCACCAGCT
1 CTGCCACCACCAGCT
28171628 CTGCCACCACCAGCT
1 CTGCCACCACCAGCT
28171643 C
1 C
28171644 CATCCACCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.55, G:0.13, T:0.13
Consensus pattern (15 bp):
CTGCCACCACCAGCT
Found at i:28172517 original size:24 final size:23
Alignment explanation
Indices: 28172488--28172538 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
28172478 GAAAATCAAT
*
28172488 AAAGAACACAAAAAATGAA-GAATA
1 AAAGAACA-AAAAAAGGAAGGAA-A
28172512 AAAGAACAAAAAAAGGAAGGAAA
1 AAAGAACAAAAAAAGGAAGGAAA
28172535 AAAG
1 AAAG
28172539 GGGAAGAGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.73, C:0.06, G:0.18, T:0.04
Consensus pattern (23 bp):
AAAGAACAAAAAAAGGAAGGAAA
Found at i:28173273 original size:30 final size:30
Alignment explanation
Indices: 28173232--28173315 Score: 123
Period size: 30 Copynumber: 2.8 Consensus size: 30
28173222 CTCTAAATTA
* *
28173232 TCCAGAAATTATATTTTTACCCCAAAACTTT
1 TCCA-AAATTACATTTTGACCCCAAAACTTT
*
28173263 TCCAAAATTATATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
28173293 TCCAAAATCACATTTTGACCCCA
1 TCCAAAATTACATTTTGACCCCA
28173316 TATTTTGACC
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
30 46 0.92
31 4 0.08
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.35
Consensus pattern (30 bp):
TCCAAAATTACATTTTGACCCCAAAACTTT
Found at i:28173320 original size:43 final size:43
Alignment explanation
Indices: 28173272--28173358 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
28173262 TTCCAAAATT
28173272 ATATTTTGACCCCAAAACTTTTCCAAAATCACATTTTGACCCC
1 ATATTTTGACCCCAAAACTTTTCCAAAATCACATTTTGACCCC
* *
28173315 ATATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCC
1 ATATTTTGACCCCAAAACTTTTCCAAAATCACATTTTGACCCC
28173358 A
1 A
28173359 AAACTTTTCC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (43 bp):
ATATTTTGACCCCAAAACTTTTCCAAAATCACATTTTGACCCC
Found at i:28173322 original size:13 final size:13
Alignment explanation
Indices: 28173304--28173328 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28173294 CCAAAATCAC
28173304 ATTTTGACCCCAT
1 ATTTTGACCCCAT
28173317 ATTTTGACCCCA
1 ATTTTGACCCCA
28173329 AAACTTTTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.32, G:0.08, T:0.36
Consensus pattern (13 bp):
ATTTTGACCCCAT
Found at i:28173329 original size:73 final size:73
Alignment explanation
Indices: 28173242--28173388 Score: 276
Period size: 73 Copynumber: 2.0 Consensus size: 73
28173232 TCCAGAAATT
*
28173242 ATATTTTTACCCCAAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTCCAAAATCACATT
1 ATATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTCCAAAATCACATT
28173307 TTGACCCC
66 TTGACCCC
*
28173315 ATATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTCCAAAATTACATT
1 ATATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTCCAAAATCACATT
28173380 TTGACCCC
66 TTGACCCC
28173388 A
1 A
28173389 AAACTTTTCC
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (73 bp):
ATATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTCCAAAATCACATT
TTGACCCC
Found at i:28173350 original size:30 final size:30
Alignment explanation
Indices: 28173317--28173510 Score: 354
Period size: 30 Copynumber: 6.5 Consensus size: 30
28173307 TTGACCCCAT
*
28173317 ATTTTGACCCCAAAACTTTTCCAAAATTAT
1 ATTTTGACCCCAAAACTTTTCCAAAATTAC
28173347 ATTTTGACCCCAAAACTTTTCCAAAATTAC
1 ATTTTGACCCCAAAACTTTTCCAAAATTAC
28173377 ATTTTGACCCCAAAACTTTTCCAAAATTAC
1 ATTTTGACCCCAAAACTTTTCCAAAATTAC
*
28173407 ATTTTAACCCCAAAACTTTTCCAAAATTAC
1 ATTTTGACCCCAAAACTTTTCCAAAATTAC
28173437 A-TTTGACCCCAAAACTTTTCCAAAATTAC
1 ATTTTGACCCCAAAACTTTTCCAAAATTAC
28173466 ATTTTGACCCCAAAACTTTTCCAAAATTAC
1 ATTTTGACCCCAAAACTTTTCCAAAATTAC
*
28173496 ATTTTGACCCAAAAA
1 ATTTTGACCCCAAAA
28173511 ATCTCCTAAA
Statistics
Matches: 159, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
29 28 0.18
30 131 0.82
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.33
Consensus pattern (30 bp):
ATTTTGACCCCAAAACTTTTCCAAAATTAC
Found at i:28173616 original size:30 final size:30
Alignment explanation
Indices: 28173523--28173619 Score: 99
Period size: 30 Copynumber: 3.3 Consensus size: 30
28173513 CTCCTAAATC
* *
28173523 CCATTTTTAACCACGATTTCACCAAAATTTA
1 CCATTTTTAACCCCGATATCACCAAAA-TTA
* * * ***
28173554 CCA-TTTTACCCCCGAAACCTTTAAAATT-
1 CCATTTTTAACCCCGATATCACCAAAATTA
28173582 CCATTTTTAACCCCGATATCACCAAAATTA
1 CCATTTTTAACCCCGATATCACCAAAATTA
28173612 CCATTTTT
1 CCATTTTT
28173620 CCCTCGGGTA
Statistics
Matches: 50, Mismatches: 14, Indels: 5
0.72 0.20 0.07
Matches are distributed among these distances:
28 3 0.06
29 21 0.42
30 23 0.46
31 3 0.06
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (30 bp):
CCATTTTTAACCCCGATATCACCAAAATTA
Found at i:28174658 original size:10 final size:10
Alignment explanation
Indices: 28174639--28174670 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
28174629 TAGACCGATG
28174639 TTTT-AACGT
1 TTTTAAACGT
28174648 TTTTAAACGT
1 TTTTAAACGT
28174658 TTTTAAACGT
1 TTTTAAACGT
28174668 TTT
1 TTT
28174671 GTGGTGATCC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.25, C:0.09, G:0.09, T:0.56
Consensus pattern (10 bp):
TTTTAAACGT
Found at i:28177720 original size:22 final size:22
Alignment explanation
Indices: 28177694--28177751 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
28177684 TATACTAAAT
28177694 TTTAATTCAATAATTAAAATTC
1 TTTAATTCAATAATTAAAATTC
28177716 TTTAATTCAATAATTAAAATTC
1 TTTAATTCAATAATTAAAATTC
28177738 TTTAATTCAA-AATT
1 TTTAATTCAATAATT
28177752 CCATATAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 4 0.11
22 32 0.89
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.47
Consensus pattern (22 bp):
TTTAATTCAATAATTAAAATTC
Found at i:28178542 original size:2 final size:2
Alignment explanation
Indices: 28178535--28178561 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28178525 AGTATTCAAT
28178535 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 T
28178562 CATTTTAGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28180292 original size:21 final size:21
Alignment explanation
Indices: 28180268--28180319 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
28180258 TGAAACAATA
28180268 CTACCGATACAAGT-ATGACTT
1 CTACCGATACAAGTGAT-ACTT
* *
28180289 CTACCGAAACATGTGATACTT
1 CTACCGATACAAGTGATACTT
28180310 CTACCGATAC
1 CTACCGATAC
28180320 TAAAAACTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 25 0.93
22 2 0.07
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (21 bp):
CTACCGATACAAGTGATACTT
Found at i:28180390 original size:21 final size:21
Alignment explanation
Indices: 28180360--28180411 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
28180350 CCTACAACTT
28180360 CTACCGATACAAGTATTCAGA
1 CTACCGATACAAGTATTCAGA
*
28180381 CTACCAATACAAGTATTCAGA
1 CTACCGATACAAGTATTCAGA
28180402 CTACCGATAC
1 CTACCGATAC
28180412 TACTATGAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.38, C:0.27, G:0.12, T:0.23
Consensus pattern (21 bp):
CTACCGATACAAGTATTCAGA
Found at i:28181476 original size:201 final size:194
Alignment explanation
Indices: 28181060--28181495 Score: 470
Period size: 201 Copynumber: 2.2 Consensus size: 194
28181050 CTCATACGAT
* * * * * *
28181060 CTGTCGAGGACTCGCAACGTATGCGGTACCCCAACCATCGATAGGGTGCCTGTCTGTACTATACA
1 CTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCATCGATACGGTACCTG-CTGCACTATACA
* * *
28181125 CTGTTCCCTAACGATGCTACTCACACGAGCTATAAAGAGTATGCAATAAGCATAGTCCTAGCCAT
65 CTATTCCCCAACGATGCTACTCACACGAGCTATAAAGAGTATGCAATAAGCATAATCCTAGCCAT
*
28181190 CATAAGGCCTGTAATCCATTTAGGATCCATATCTCTTTCCCGAGTCACGATATTGCTCACACGAG
130 CATAAGGCCTGTAATCCATTTAGGATCCATATCTCTTTCCCGAGTCACGATATTGCTCACACAAG
* * *
28181255 CTGTCGAGGACTCACAACATATGCGGTACCTTAGCCATCGATACGGTATCTG-TGCA-TATA-AC
1 CTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCATCGATACGGTACCTGCTGCACTATACAC
* * * * * *
28181317 TATTCCCCAATGATGCTGCTCACACGAGCTGTCAAGAAG-ATGCACTTATGCATAAAT-CTCAGC
66 TATTCCCCAACGATGCTACTCACACGAGCTATAAAG-AGTATGCA-ATAAGCAT-AATCCT-AGC
* * * *
28181380 CATCGTAAGGTCTGTAATCCATTTAGGATCCATATTTCTTTTCTCATTTCCCGATTCACGATGCT
127 CATCATAAGGCCTGTAATCCATTTAGGATCCATA-------TCTC-TTTCCCGAGTCACGAT-AT
*
28181445 T-CTCGCACAAG
183 TGCTCACACAAG
* *
28181456 CTGTCGAGGACTCGCAACATATACGGTACCTCAGCTATCG
1 CTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCATCG
28181496 CGTCGGTTTC
Statistics
Matches: 200, Mismatches: 28, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
191 37 0.19
192 14 0.07
193 40 0.20
195 44 0.22
200 4 0.02
201 59 0.29
202 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (194 bp):
CTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCATCGATACGGTACCTGCTGCACTATACAC
TATTCCCCAACGATGCTACTCACACGAGCTATAAAGAGTATGCAATAAGCATAATCCTAGCCATC
ATAAGGCCTGTAATCCATTTAGGATCCATATCTCTTTCCCGAGTCACGATATTGCTCACACAAG
Found at i:28183566 original size:15 final size:15
Alignment explanation
Indices: 28183546--28183577 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
28183536 CCAAGTGTGG
28183546 GATGTGTTTCTATAT
1 GATGTGTTTCTATAT
28183561 GATGTGTTTCTATAT
1 GATGTGTTTCTATAT
28183576 GA
1 GA
28183578 AAACCCACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.22, C:0.06, G:0.22, T:0.50
Consensus pattern (15 bp):
GATGTGTTTCTATAT
Found at i:28186953 original size:2 final size:2
Alignment explanation
Indices: 28186946--28187021 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
28186936 GTTTATATTA
28186946 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
28186988 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
28187022 ATCTATCTAT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:28188149 original size:18 final size:18
Alignment explanation
Indices: 28188100--28188150 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 18
28188090 AGTATTTTGT
*
28188100 TTAATATTATTTTTTATC
1 TTAAAATTATTTTTTATC
*
28188118 TTAAAAATATTTTTTTAT-
1 TTAAAATTA-TTTTTTATC
*
28188136 TCTAAAGTTATTTTT
1 T-TAAAATTATTTTT
28188151 GAAAGGTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (18 bp):
TTAAAATTATTTTTTATC
Found at i:28188460 original size:34 final size:34
Alignment explanation
Indices: 28188412--28188479 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
28188402 TTTCTTAACC
*
28188412 TTCTCTTCAAAAACAACTTTTGTTCTCTCGAAAG
1 TTCTCTTCAAAAACAACATTTGTTCTCTCGAAAG
* *
28188446 TTCTTTTCAAAAACATCATTTGTTCTCTCGAAAG
1 TTCTCTTCAAAAACAACATTTGTTCTCTCGAAAG
28188480 AACTCTCTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (34 bp):
TTCTCTTCAAAAACAACATTTGTTCTCTCGAAAG
Found at i:28190815 original size:13 final size:11
Alignment explanation
Indices: 28190783--28190825 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
28190773 CCATTTTCTA
*
28190783 AATAAAATAAT
1 AATAAAATATT
28190794 AAT-AAATATTT
1 AATAAAATA-TT
28190805 AAGTAAAATATT
1 AA-TAAAATATT
28190817 AATAAAATA
1 AATAAAATA
28190826 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 5 0.18
13 5 0.18
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (11 bp):
AATAAAATATT
Found at i:28191206 original size:3 final size:3
Alignment explanation
Indices: 28191198--28191247 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
28191188 CTACTTCTTA
*
28191198 ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
28191246 AT
1 AT
28191248 ACTCCTCAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:28197459 original size:96 final size:96
Alignment explanation
Indices: 28197275--28197466 Score: 239
Period size: 96 Copynumber: 2.0 Consensus size: 96
28197265 AATTTTTAAG
* ** * * *
28197275 AAGGATATTTGATTATCTTGATTTGAAGAAATGTTGCACCTAGTGAGTTAAGGCGCAAATTTTCA
1 AAGGATATTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACGCAAAATTTCA
*
28197340 TAACCGAAGATAAGGAAACATTGCCTCGATT
66 TAACCGAAGATAAAGAAACATTGCCTCGATT
*
28197371 AAGGGTATTCGATTAT-TTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACGCAAAATTTC
1 AAGGATATTCGATTATCTT-GATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACGCAAAATTTC
*
28197435 GA-AACTCGAA-ATAAA-AGAATATTGCCTCGATT
65 -ATAAC-CGAAGATAAAGA-AACATTGCCTCGATT
28197467 TTAAAGTTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
95 3 0.04
96 75 0.90
97 5 0.06
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (96 bp):
AAGGATATTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACGCAAAATTTCA
TAACCGAAGATAAAGAAACATTGCCTCGATT
Found at i:28197765 original size:59 final size:57
Alignment explanation
Indices: 28197701--28197860 Score: 160
Period size: 58 Copynumber: 2.7 Consensus size: 57
28197691 ACCCGAGGGC
* * * *
28197701 AAAATGGTAATTTTAGACTCTCGAGGGTAAAATGGTAATTTTGGGAAAATTTGGGGTTA
1 AAAATGG-AATTTTAGACT-TCGAGGGTAAAATGGTAATTTTGGGAAAAATCGGGATAA
* *
28197760 AAAATGAAATTTTAGACATTC-AGGGGTAAAATGGTAATTTTTGGAAAAATCGGGATAA
1 AAAATGGAATTTTAGAC-TTCGA-GGGTAAAATGGTAATTTTGGGAAAAATCGGGATAA
* * * * *
28197818 AAAACGGAGTTTTTGGACAATCGAGGGTAGAATGGTAATTTTG
1 AAAATGGA-ATTTTAGAC-TTCGAGGGTAAAATGGTAATTTTG
28197861 AAAGTTTCAT
Statistics
Matches: 84, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
57 1 0.01
58 48 0.57
59 34 0.40
60 1 0.01
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.31
Consensus pattern (57 bp):
AAAATGGAATTTTAGACTTCGAGGGTAAAATGGTAATTTTGGGAAAAATCGGGATAA
Found at i:28197798 original size:28 final size:27
Alignment explanation
Indices: 28197701--28197800 Score: 87
Period size: 28 Copynumber: 3.5 Consensus size: 27
28197691 ACCCGAGGGC
28197701 AAAATGGTAATTTTAGAC-TCTCGAGGGT
1 AAAATGGTAATTTTAGACAT-TCG-GGGT
* * *
28197729 AAAATGGTAATTTTGGGAAAATTTGGGGTT
1 AAAATGGTAATTTT-AG-ACATTCGGGG-T
*
28197759 AAAAAT-GAAATTTTAGACATTCAGGGGT
1 -AAAATGGTAATTTTAGACATTC-GGGGT
28197787 AAAATGGTAATTTT
1 AAAATGGTAATTTT
28197801 TGGAAAAATC
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
27 5 0.09
28 26 0.46
29 9 0.16
30 11 0.19
31 6 0.11
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (27 bp):
AAAATGGTAATTTTAGACATTCGGGGT
Found at i:28197914 original size:58 final size:57
Alignment explanation
Indices: 28197852--28197984 Score: 140
Period size: 58 Copynumber: 2.3 Consensus size: 57
28197842 GGGTAGAATG
* * * *
28197852 GTAATTTTGAAAGTTTCATGGTCAAAAATGGAAAATTTGTAAGTTTGGGGGTAAAAAT
1 GTAATTTTGAAAGTTTCA-GGGCAAAAATGGAAAATTTGGAAATTTGAGGGTAAAAAT
* * ** * *
28197910 GTAATTTTTGGAAGTTTCAGGGCAAAAATGTAATTTTTGGAAATTTTAGGGTTAAAAT
1 GTAA-TTTTGAAAGTTTCAGGGCAAAAATGGAAAATTTGGAAATTTGAGGGTAAAAAT
28197968 GTAATTTCTGAGAAGTT
1 GTAATTT-TGA-AAGTT
28197985 CGTGGGTTAA
Statistics
Matches: 61, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
57 3 0.05
58 40 0.66
59 18 0.30
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.38
Consensus pattern (57 bp):
GTAATTTTGAAAGTTTCAGGGCAAAAATGGAAAATTTGGAAATTTGAGGGTAAAAAT
Found at i:28197919 original size:29 final size:29
Alignment explanation
Indices: 28197852--28198015 Score: 125
Period size: 29 Copynumber: 5.6 Consensus size: 29
28197842 GGGTAGAATG
* *
28197852 GTAA-TTTTGAAAGTTTCATGGTCAAAAAT
1 GTAATTTTTGGAAGTTTCAGGGT-AAAAAT
* ** * **
28197881 GGAAAATTTGTAAGTTTGGGGGTAAAAAT
1 GTAATTTTTGGAAGTTTCAGGGTAAAAAT
*
28197910 GTAATTTTTGGAAGTTTCAGGGCAAAAAT
1 GTAATTTTTGGAAGTTTCAGGGTAAAAAT
* * *
28197939 GTAATTTTTGGAAATTTTAGGGTTAAAAT
1 GTAATTTTTGGAAGTTTCAGGGTAAAAAT
* * *
28197968 GTAATTTCTGAGAAG-TTCGTGGGTTAAAAT
1 GTAATTTTTG-GAAGTTTC-AGGGTAAAAAT
**
28197998 ACAATTTTTGGACAGTTT
1 GTAATTTTTGGA-AGTTT
28198016 AGGAACTTTC
Statistics
Matches: 106, Mismatches: 24, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
29 69 0.65
30 35 0.33
31 2 0.02
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.38
Consensus pattern (29 bp):
GTAATTTTTGGAAGTTTCAGGGTAAAAAT
Found at i:28197997 original size:59 final size:58
Alignment explanation
Indices: 28197900--28198018 Score: 132
Period size: 59 Copynumber: 2.0 Consensus size: 58
28197890 GTAAGTTTGG
* ** *
28197900 GGGTAAAAATGTAATTTTTGGAAGTTTCAGGGCAAAAATGTAATTTTTGGAAATTTTA
1 GGGTAAAAATGTAATTTCTGGAAGTTTCAGGGCAAAAATACAATTTTTGGAAAGTTTA
* * ** *
28197958 GGGTTAAAATGTAATTTCTGAGAAG-TTCGTGGGTTAAAATACAATTTTTGGACAGTTTA
1 GGGTAAAAATGTAATTTCTG-GAAGTTTC-AGGGCAAAAATACAATTTTTGGAAAGTTTA
28198017 GG
1 GG
28198019 AACTTTCATG
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
58 21 0.42
59 29 0.58
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (58 bp):
GGGTAAAAATGTAATTTCTGGAAGTTTCAGGGCAAAAATACAATTTTTGGAAAGTTTA
Found at i:28199052 original size:18 final size:18
Alignment explanation
Indices: 28199004--28199046 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
28198994 ATTTCCTTTT
*
28199004 TTTAATAATTATTAATTA
1 TTTAATAAATATTAATTA
28199022 TTTAATAAATATT-ATTA
1 TTTAATAAATATTAATTA
28199039 TTT-ATAAA
1 TTTAATAAA
28199047 AGTATTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 5 0.21
17 7 0.29
18 12 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAATAAATATTAATTA
Found at i:28199833 original size:17 final size:17
Alignment explanation
Indices: 28199811--28199845 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
28199801 TTGATTTAAT
28199811 TTTAATTTAAAAATAAA
1 TTTAATTTAAAAATAAA
* *
28199828 TTTAATTTTAAGATAAA
1 TTTAATTTAAAAATAAA
28199845 T
1 T
28199846 CCAAACTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
TTTAATTTAAAAATAAA
Found at i:28200622 original size:201 final size:200
Alignment explanation
Indices: 28200301--28200687 Score: 587
Period size: 201 Copynumber: 1.9 Consensus size: 200
28200291 GAGTCGTTTG
* * * *
28200301 TTTCAATCCACTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCGCTTCTTAGTATCTCATTA
1 TTTCAATCCACTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTATCAGTATCTCATCA
* * *
28200366 GGAAGCTAACCATTTTATTTCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGG-GTTTAGA
66 AGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGAG-TTAGA
* * *
28200430 AGATTTGCTCGTATTGAGCCTCGAGTTGGCATACTTCTCTGTATCTCATTAGGAAGATAGCCGCC
130 AGATTTGCTCATATCGAGCCT-GAGTTGGCATACTTCTCTGTATCTCATCAGGAAGATAGCCGCC
28200495 TCACTTA
194 TCACTTA
* * *
28200502 TTTCAATTCACTTCTCTGTATCTCATTAGGAAGACGAATTTGGTTCACTTATCAGTATCTCATCA
1 TTTCAATCCACTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTATCAGTATCTCATCA
*
28200567 AGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGAGTTCGAA
66 AGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGAGTTAGAA
* * * *
28200632 GATTTTCTCATATCGAGCGTGGGTTGGCGTACTTCTCTGTATCTCATCAGGAAGAT
131 GATTTGCTCATATCGAGCCTGAGTTGGCATACTTCTCTGTATCTCATCAGGAAGAT
28200688 GACTGCTTTA
Statistics
Matches: 167, Mismatches: 18, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
200 33 0.20
201 133 0.80
202 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.35
Consensus pattern (200 bp):
TTTCAATCCACTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTATCAGTATCTCATCA
AGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGAGTTAGAA
GATTTGCTCATATCGAGCCTGAGTTGGCATACTTCTCTGTATCTCATCAGGAAGATAGCCGCCTC
ACTTA
Found at i:28201065 original size:205 final size:207
Alignment explanation
Indices: 28200694--28201434 Score: 1040
Period size: 205 Copynumber: 3.6 Consensus size: 207
28200684 AGATGACTGC
* * * * **
28200694 TTTATTGCTTTGACCTGCTTCTCAGTATCTCATTAAGAAGCTGGGGGTTAGAAGATTTGCTTATA
1 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-GGGGTTCGAAGATTTGCTTGCA
* * * * *
28200759 TATCGAGCATGAGTTTGATTTGGTCTTCTTCTCAGTATGTCATGAAGAAGATGACCGCA-C-CGT
65 TATCGAGCCTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCAC-T
*
28200822 TCGTTTTAATTCGCTTCTCTG-TATCTCATCAGGAAGACGAATTTGGTCCACTTCTCTA-TATCT
129 T-GTTTTAATTCGCTTCTCTGATATC-C-TCAGGAAGACGAATTTGGTCCACTTCTC-AGTGTCT
28200885 CATTAAGAAGCTAACCAT
190 CATTAAGAAGCTAACCAT
*
28200903 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-GGGTTCGAAGATTTGATTGCAT
1 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTTGCAT
* *
28200967 -T-GAGCCTAGGTTTGATTTGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTG
66 ATCGAGCCTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTG
* *
28201030 TTTTAATTCGCTTCTCTAGATATCCTCAAGAAGACGAATTTGGTACACTTCTCAGTGTCTCATTA
131 TTTTAATTCGCTTCTCT-GATATCCTCAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATTA
* *
28201095 GGAAACTAACCAT
195 AGAAGCTAACCAT
* * *
28201108 TTTATTGCCTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCT-GGGTTCGAAGATTTGCTCGCAT
1 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTTGCAT
* *
28201172 -T-GAGCCTGGGTTTGATTTGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGACTGCATCACTTG
66 ATCGAGCCTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTG
* * *
28201235 TTTTAATTCGCTTCTCTGGATCTCCTCAGGAAGATGAATTTGGTCCACTTCTCAGTGTCTCATCA
131 TTTTAATTCGCTTCTCT-GATATCCTCAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATTA
28201300 AGAAGCTAACCA-
195 AGAAGCTAACCAT
*
28201312 TTTATTGCTTCGACCTACTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGC-T-CAT
1 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTTGCAT
** *
28201375 ATCGAGTGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGTCCGCATC
66 ATCGAGCCTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATC
28201435 GTTTGTTTCA
Statistics
Matches: 482, Mismatches: 42, Indels: 20
0.89 0.08 0.04
Matches are distributed among these distances:
203 3 0.01
204 41 0.09
205 370 0.77
206 6 0.01
207 23 0.05
209 39 0.08
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (207 bp):
TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTTGCAT
ATCGAGCCTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTG
TTTTAATTCGCTTCTCTGATATCCTCAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATTAA
GAAGCTAACCAT
Found at i:28201855 original size:49 final size:49
Alignment explanation
Indices: 28201802--28202213 Score: 402
Period size: 49 Copynumber: 8.4 Consensus size: 49
28201792 GTTCACCATT
* * **
28201802 GCGACTTAAACCTTTCCCTTCAAATCTTCGTGGTACTGGATCCGCCGTC
1 GCGACTTAGATCTTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTC
* *
28201851 GCGACTTAGATCTTTCTCTTCATGTCTTCGTGGTACTGGATCCGACGTC
1 GCGACTTAGATCTTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTC
*
28201900 GCGACTTAGATCTTTCCCTTCATGTCTTCGTGGTACTGGATCCGACGTC
1 GCGACTTAGATCTTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTC
* *
28201949 GC-AATTAGATCTTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTT
1 GCGACTTAGATCTTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTC
* * * * * *
28201997 GCGGCTTAAAAT-TTTCCTTTGATGTCTTCGTGGTACTAGATCCGCCGTT
1 GCGACTT-AGATCTTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTC
* * * * *
28202046 GCGGCTTAGATATTTCCCTT-ATGTCTTCGCGGTACTGGATCCGCCTTT
1 GCGACTTAGATCTTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTC
* * * * * * * * *
28202094 GTGGTCTTAGATCTTTCCCGTCGTGTCTTTTGAGGTACACGG-TCTGCCGTT
1 G-CGACTTAGATCTTTCCCTTCATGTC-TTCGTGGTAC-TGGATCCGCCGTC
* * * * * *
28202145 GCGACTTAGACCTTTCCCTT-TTGTATCTTTGCGGTACTGGATCCGCTGTT
1 GCGACTTAGATCTTTCCCTTCATG--TCTTCGTGGTACTGGATCCGCCGTC
*
28202195 GCGGTCTTAGATCTTTCCC
1 GC-GACTTAGATCTTTCCC
28202214 GTTGTGTTTC
Statistics
Matches: 310, Mismatches: 42, Indels: 20
0.83 0.11 0.05
Matches are distributed among these distances:
48 74 0.24
49 162 0.52
50 40 0.13
51 32 0.10
52 2 0.01
ACGTcount: A:0.14, C:0.27, G:0.22, T:0.37
Consensus pattern (49 bp):
GCGACTTAGATCTTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTC
Found at i:28202013 original size:97 final size:98
Alignment explanation
Indices: 28201800--28202090 Score: 390
Period size: 97 Copynumber: 3.0 Consensus size: 98
28201790 GGGTTCACCA
** **
28201800 TTGCGACTTAAACCTTTCCCTTCAAATCTTCGTGGTACTGGATCCGCCGTCGCGACTTAGATCTT
1 TTGCGACTTAAAATTTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTCGCGACTTAGATCTT
* *
28201865 TCTCTTCATGTCTTCGTGGTACTGGATCCGACG
66 TCCCTTCATGTCTTCGTGGTACTGGATCCGCCG
* * * *
28201898 TCGCGACTT-AGATCTTTCCCTTCATGTCTTCGTGGTACTGGATCCGACGTCGC-AATTAGATCT
1 TTGCGACTTAAAAT-TTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTCGCGACTTAGATCT
28201961 TTCCCTTCATGTCTTCGTGGTACTGGATCCGCCG
65 TTCCCTTCATGTCTTCGTGGTACTGGATCCGCCG
* * * * * * *
28201995 TTGCGGCTTAAAATTTTCCTTTGATGTCTTCGTGGTACTAGATCCGCCGTTGCGGCTTAGATATT
1 TTGCGACTTAAAATTTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTCGCGACTTAGATCTT
*
28202060 TCCCTT-ATGTCTTCGCGGTACTGGATCCGCC
66 TCCCTTCATGTCTTCGTGGTACTGGATCCGCC
28202091 TTTGTGGTCT
Statistics
Matches: 168, Mismatches: 22, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
97 107 0.64
98 61 0.36
ACGTcount: A:0.15, C:0.27, G:0.22, T:0.36
Consensus pattern (98 bp):
TTGCGACTTAAAATTTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTCGCGACTTAGATCTT
TCCCTTCATGTCTTCGTGGTACTGGATCCGCCG
Found at i:28202029 original size:146 final size:145
Alignment explanation
Indices: 28201813--28202088 Score: 403
Period size: 146 Copynumber: 1.9 Consensus size: 145
28201803 CGACTTAAAC
*
28201813 CTTTCCCTTCAAATCTTCGTGGTACTGGATCCGCCGTCGCGACTTAGATCTTTCTCTTCATGTCT
1 CTTTCCCTTCAAATCTTCGTGGTACTGGATCCGCCGTCGCGACTTAAATCTTTCTCTTCATGTCT
* * *
28201878 TCGTGGTACTGGATCCGACGTCGCGACTTAGATCTTTCCCTTCATGTCTTCGTGGTACTGGATCC
66 TCGTGGTACTAGATCCGACGTCGCGACTTAGATATTTCCCTT-ATGTCTTCGCGGTACTGGATCC
28201943 GACGTCGCAATTAGAT
130 GACGTCGCAATTAGAT
** * * *
28201959 CTTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTTGCGGCTTAAAAT-TTTC-CTTTGATGT
1 CTTTCCCTTCAAATCTTCGTGGTACTGGATCCGCCGTCGCGACTT-AAATCTTTCTC-TTCATGT
* * *
28202022 CTTCGTGGTACTAGATCCGCCGTTGCGGCTTAGATATTTCCCTTATGTCTTCGCGGTACTGGATC
64 CTTCGTGGTACTAGATCCGACGTCGCGACTTAGATATTTCCCTTATGTCTTCGCGGTACTGGATC
28202087 CG
129 CG
28202089 CCTTTGTGGT
Statistics
Matches: 116, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
145 23 0.20
146 90 0.78
147 3 0.03
ACGTcount: A:0.14, C:0.27, G:0.22, T:0.36
Consensus pattern (145 bp):
CTTTCCCTTCAAATCTTCGTGGTACTGGATCCGCCGTCGCGACTTAAATCTTTCTCTTCATGTCT
TCGTGGTACTAGATCCGACGTCGCGACTTAGATATTTCCCTTATGTCTTCGCGGTACTGGATCCG
ACGTCGCAATTAGAT
Found at i:28202208 original size:101 final size:99
Alignment explanation
Indices: 28201845--28202220 Score: 281
Period size: 97 Copynumber: 3.8 Consensus size: 99
28201835 TACTGGATCC
* * * * * * *
28201845 GCCGTCGCGACTTAGATC-TTTCTCTTCATGTCTTCGTGGTACTGGATCCGACGTCGC-GACTTA
1 GCCGTTGCGACTTAGA-CATTTCCCTT-ATGTCTTCGCGGTACTGGATCCGCCTTTGCGGTCTTA
* * * * * *
28201908 GATCTTTCCCTTCATGTC-TTCGTGGTAC-TGGATCC
64 GATCTTTCCCGTCGTGTCTTTTGAGGTACACGG-TCT
* * * * *
28201943 GACGTCGC-AATTAGATC-TTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTTGCGG-CTTA
1 GCCGTTGCGACTTAGA-CATTTCCCTT-ATGTCTTCGCGGTACTGGATCCGCCTTTGCGGTCTT-
* * * * * * *
28202005 AAAT-TTT-CCTTTGATGTC-TTCGTGGTACTA-GATCC
63 AGATCTTTCCCGTCG-TGTCTTTTGAGGTAC-ACGGTCT
* * *
28202040 GCCGTTGCGGCTTAGATATTTCCCTTATGTCTTCGCGGTACTGGATCCGCCTTTGTGGTCTTAGA
1 GCCGTTGCGACTTAGACATTTCCCTTATGTCTTCGCGGTACTGGATCCGCCTTTGCGGTCTTAGA
28202105 TCTTTCCCGTCGTGTCTTTTGAGGTACACGGTCT
66 TCTTTCCCGTCGTGTCTTTTGAGGTACACGGTCT
* * *
28202139 GCCGTTGCGACTTAGACCTTTCCCTTTTGTATCTTTGCGGTACTGGATCCG-CTGTTGCGGTCTT
1 GCCGTTGCGACTTAGACATTTCCCTTATG--TCTTCGCGGTACTGGATCCGCCT-TTGCGGTCTT
*
28202203 AGATCTTTCCCGTTGTGT
63 AGATCTTTCCCGTCGTGT
28202221 TTCATGGTAC
Statistics
Matches: 232, Mismatches: 31, Indels: 27
0.80 0.11 0.09
Matches are distributed among these distances:
96 4 0.02
97 105 0.45
98 36 0.16
99 40 0.17
100 2 0.01
101 45 0.19
ACGTcount: A:0.13, C:0.26, G:0.23, T:0.38
Consensus pattern (99 bp):
GCCGTTGCGACTTAGACATTTCCCTTATGTCTTCGCGGTACTGGATCCGCCTTTGCGGTCTTAGA
TCTTTCCCGTCGTGTCTTTTGAGGTACACGGTCT
Found at i:28203152 original size:1 final size:1
Alignment explanation
Indices: 28203142--28203195 Score: 54
Period size: 1 Copynumber: 54.0 Consensus size: 1
28203132 TCGACCTCTC
* * * * * *
28203142 TTTTTCTTTTTTTTTTCTTTTTTTTTTCTTTTTTTTTTCTTTTTCTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
28203196 ATTCATTGAA
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (1 bp):
T
Found at i:28203158 original size:11 final size:11
Alignment explanation
Indices: 28203142--28203195 Score: 99
Period size: 11 Copynumber: 4.9 Consensus size: 11
28203132 TCGACCTCTC
28203142 TTTTTCTTTTT
1 TTTTTCTTTTT
28203153 TTTTTCTTTTT
1 TTTTTCTTTTT
28203164 TTTTTCTTTTT
1 TTTTTCTTTTT
28203175 TTTTTCTTTTT
1 TTTTTCTTTTT
*
28203186 CTTTTCTTTT
1 TTTTTCTTTT
28203196 ATTCATTGAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
11 42 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:28203162 original size:17 final size:17
Alignment explanation
Indices: 28203140--28203195 Score: 80
Period size: 17 Copynumber: 3.4 Consensus size: 17
28203130 CCTCGACCTC
28203140 TCTTTTTCTTTTTTTTT
1 TCTTTTTCTTTTTTTTT
28203157 TCTTTTT-TTTTTCTTTT
1 TCTTTTTCTTTTT-TTTT
*
28203174 T-TTTTTCTTTTTCTTT
1 TCTTTTTCTTTTTTTTT
28203190 TCTTTT
1 TCTTTT
28203196 ATTCATTGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
16 14 0.40
17 21 0.60
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (17 bp):
TCTTTTTCTTTTTTTTT
Found at i:28208172 original size:29 final size:29
Alignment explanation
Indices: 28208140--28208204 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
28208130 AAAAAGAGAT
*
28208140 TTTTTGGA-TACTCGGGGGCAAAATGGTAA
1 TTTTTGGACT-CTCGAGGGCAAAATGGTAA
* *
28208169 -TTTTAGACTCTCGAGGGTAAAATGGTAA
1 TTTTTGGACTCTCGAGGGCAAAATGGTAA
28208197 TTTTTGGA
1 TTTTTGGA
28208205 AAAATCGGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 23 0.77
29 7 0.23
ACGTcount: A:0.28, C:0.09, G:0.28, T:0.35
Consensus pattern (29 bp):
TTTTTGGACTCTCGAGGGCAAAATGGTAA
Found at i:28208334 original size:59 final size:59
Alignment explanation
Indices: 28208239--28208488 Score: 288
Period size: 59 Copynumber: 4.2 Consensus size: 59
28208229 TTTGGACAAC
* * * *
28208239 CGAGGGTAGAATTGTAA-TTTTGAAAGTTTTGTGGTCAAAAATAAAATTTTTGGAAGTT
1 CGAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTCAAAAATAAAATTTTTGGAAGTT
* *
28208297 CGAGGGTAAAAATGTAATTTTTGGAAGTTTTGCGGTCAAAAATAGAATTTTTGGAAGTT
1 CGAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTCAAAAATAAAATTTTTGGAAGTT
* * * * **
28208356 CGAGAGCAAAAATGTAATTTTTGGAAGTTTCGGGGGCAAAAATTTAATTTTTGGAAGTT
1 CGAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTCAAAAATAAAATTTTTGGAAGTT
** * * * *
28208415 TTAGGGTCAAAAAAGTAATTTTTGGAAATTTTGGGGTTAAAAATGTAAA-TTTTGAGAAGTT
1 CGAGGGT-AAAAATGTAATTTTTGGAAGTTTTGGGGTCAAAAAT-AAAATTTTTG-GAAGTT
*
28208476 CGAGGGTCAAAAT
1 CGAGGGTAAAAAT
28208489 TCAATTTCTA
Statistics
Matches: 162, Mismatches: 26, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
58 15 0.09
59 93 0.57
60 40 0.25
61 14 0.09
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (59 bp):
CGAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTCAAAAATAAAATTTTTGGAAGTT
Found at i:28208488 original size:30 final size:30
Alignment explanation
Indices: 28208271--28208487 Score: 221
Period size: 30 Copynumber: 7.3 Consensus size: 30
28208261 AAAGTTTTGT
**
28208271 GGTCAAAAATAAAATTTTTGGAAGTTCGAG
1 GGTCAAAAATGTAATTTTTGGAAGTTCGAG
* *
28208301 GGT-AAAAATGTAATTTTTGGAAGTTTTG-C
1 GGTCAAAAATGTAATTTTTGGAAG-TTCGAG
28208330 GGTCAAAAATAG-AATTTTTGGAAGTTCGAG
1 GGTCAAAAAT-GTAATTTTTGGAAGTTCGAG
*
28208360 AG-CAAAAATGTAATTTTTGGAAGTTTCG-G
1 GGTCAAAAATGTAATTTTTGGAAG-TTCGAG
* * **
28208389 GGGCAAAAATTTAATTTTTGGAAGTTTTAG
1 GGTCAAAAATGTAATTTTTGGAAGTTCGAG
* * *
28208419 GGTCAAAAAAGTAATTTTTGGAAATTTTG-G
1 GGTCAAAAATGTAATTTTTGG-AAGTTCGAG
* *
28208449 GGTTAAAAATGTAAATTTTGAGAAGTTCGAG
1 GGTCAAAAATGTAATTTTTG-GAAGTTCGAG
28208480 GGTCAAAA
1 GGTCAAAA
28208488 TTCAATTTCT
Statistics
Matches: 154, Mismatches: 22, Indels: 21
0.78 0.11 0.11
Matches are distributed among these distances:
28 1 0.01
29 47 0.31
30 91 0.59
31 15 0.10
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.34
Consensus pattern (30 bp):
GGTCAAAAATGTAATTTTTGGAAGTTCGAG
Found at i:28209532 original size:18 final size:17
Alignment explanation
Indices: 28209488--28209535 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
28209478 TCCTTTTTTT
*
28209488 ATAATTATTAATTATTTA
1 ATAAATATT-ATTATTTA
28209506 ATAAATATTATTA-TTA
1 ATAAATATTATTATTTA
*
28209522 ATAAA-AGTATTATT
1 ATAAATATTATTATT
28209536 GTTATTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 6 0.22
16 9 0.33
17 4 0.15
18 8 0.30
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
ATAAATATTATTATTTA
Found at i:28209535 original size:21 final size:22
Alignment explanation
Indices: 28209513--28209556 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
28209503 TTAATAAATA
28209513 TTATTATTAATAAAAGTATTATT
1 TTATTATTAATAAAAGTATTA-T
*
28209536 GTTATTATTAATAAAATTATT
1 -TTATTATTAATAAAAGTATT
28209557 TAATATATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (22 bp):
TTATTATTAATAAAAGTATTAT
Found at i:28210366 original size:17 final size:17
Alignment explanation
Indices: 28210294--28210368 Score: 60
Period size: 17 Copynumber: 4.4 Consensus size: 17
28210284 ATTTAATTTT
*
28210294 AATTTAAAAATAAATTTA
1 AATTT-AAAATAAATTCA
* * *
28210312 ATTTTAAGATAAATCCA
1 AATTTAAAATAAATTCA
* * * **
28210329 GATTCAAAATGAATTTG
1 AATTTAAAATAAATTCA
28210346 AATTTAAAATAAATTCA
1 AATTTAAAATAAATTCA
28210363 AATTTA
1 AATTTA
28210369 TTTAAAATTT
Statistics
Matches: 40, Mismatches: 17, Indels: 1
0.69 0.29 0.02
Matches are distributed among these distances:
17 36 0.90
18 4 0.10
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.37
Consensus pattern (17 bp):
AATTTAAAATAAATTCA
Found at i:28210380 original size:7 final size:7
Alignment explanation
Indices: 28210368--28210392 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28210358 ATTCAAATTT
28210368 ATTTAAA
1 ATTTAAA
28210375 ATTTAAA
1 ATTTAAA
28210382 ATTTAAA
1 ATTTAAA
28210389 ATTT
1 ATTT
28210393 GAATGCAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
ATTTAAA
Found at i:28211263 original size:23 final size:23
Alignment explanation
Indices: 28211222--28211265 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
28211212 TTAAATTATT
28211222 TTTATTATTTTAAATATAAAATA
1 TTTATTATTTTAAATATAAAATA
*
28211245 TTTATT-TTTTACATCATAAAA
1 TTTATTATTTTAAAT-ATAAAA
28211266 ATTAAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTATTATTTTAAATATAAAATA
Found at i:28225089 original size:24 final size:25
Alignment explanation
Indices: 28225060--28225108 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
28225050 ATTTAAAATA
*
28225060 AATTTAAAA-ATATTTTTAATTTTT
1 AATTTAAAAGAGATTTTTAATTTTT
28225084 AATTTAAAAGAGATTTTTAATTTTT
1 AATTTAAAAGAGATTTTTAATTTTT
28225109 CACAATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (25 bp):
AATTTAAAAGAGATTTTTAATTTTT
Found at i:28232677 original size:24 final size:24
Alignment explanation
Indices: 28232617--28232703 Score: 95
Period size: 24 Copynumber: 3.6 Consensus size: 24
28232607 TTTCAGAAAT
**
28232617 TTAGCTCATACGAGCCCAGACAAAA
1 TTAGCTCATACGAGCCCAGA-AAGG
*
28232642 TTAGCTCATACGAGCCCAGATAGG
1 TTAGCTCATACGAGCCCAGAAAGG
* *
28232666 TTAGCTCTTACGAACCCA-AAATGG
1 TTAGCTCATACGAGCCCAGAAA-GG
*
28232690 TTAGCTCTTACGAG
1 TTAGCTCATACGAG
28232704 TTCAGAATCA
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
23 2 0.04
24 32 0.59
25 20 0.37
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (24 bp):
TTAGCTCATACGAGCCCAGAAAGG
Found at i:28232738 original size:27 final size:27
Alignment explanation
Indices: 28232706--28232835 Score: 181
Period size: 27 Copynumber: 4.8 Consensus size: 27
28232696 CTTACGAGTT
* *
28232706 CAGAATCAGAATAATGCTCTTTTGAGC
1 CAGAATCAGAATAACGCTCTTTCGAGC
28232733 CAGAATCAGAATAACGCTCTTTCGAGC
1 CAGAATCAGAATAACGCTCTTTCGAGC
28232760 CAGAATCAGAATAACGCTCTTTCGAGC
1 CAGAATCAGAATAACGCTCTTTCGAGC
* *
28232787 CGGAATCA-AATTTACGCTCTTTCGAGC
1 CAGAATCAGAA-TAACGCTCTTTCGAGC
* * *
28232814 TAGAATCAGATTAATGCTCTTT
1 CAGAATCAGAATAACGCTCTTT
28232836 ATAGCCAACC
Statistics
Matches: 92, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
26 2 0.02
27 89 0.97
28 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (27 bp):
CAGAATCAGAATAACGCTCTTTCGAGC
Found at i:28235338 original size:37 final size:37
Alignment explanation
Indices: 28235259--28235339 Score: 110
Period size: 37 Copynumber: 2.2 Consensus size: 37
28235249 TTAAAGTGAA
*
28235259 ATAAGTGATTATGCGAGCATATCTATATGCCTAAGTG
1 ATAAGTGATTATGCGAGCATATCTATATGCCGAAGTG
* *
28235296 ATAAGTGATTATGTGAGCATAT-TCATATGCCGATGTG
1 ATAAGTGATTATGCGAGCATATCT-ATATGCCGAAGTG
*
28235333 TTAAGTG
1 ATAAGTG
28235340 TATATTGCCA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
36 1 0.03
37 38 0.97
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.35
Consensus pattern (37 bp):
ATAAGTGATTATGCGAGCATATCTATATGCCGAAGTG
Found at i:28235479 original size:45 final size:45
Alignment explanation
Indices: 28235429--28235546 Score: 139
Period size: 45 Copynumber: 2.6 Consensus size: 45
28235419 TAACTGCATA
* * *
28235429 TCAACATATGTGAGCTATCATT-TCCGGGCAACTCGGGGTAACAAT
1 TCAACATAAGTGAACTATCATTGT-CGGGCAACTCGAGGTAACAAT
*
28235474 TCAACATAAGTGAACTATCATTGTCGGGCAACTCGAGGTAGCAAT
1 TCAACATAAGTGAACTATCATTGTCGGGCAACTCGAGGTAACAAT
** * * *
28235519 TCAATTTAAGTGAGCCATCGTTGTCGGG
1 TCAACATAAGTGAACTATCATTGTCGGG
28235547 AAACCCGGAG
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
45 62 0.98
46 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (45 bp):
TCAACATAAGTGAACTATCATTGTCGGGCAACTCGAGGTAACAAT
Found at i:28235900 original size:19 final size:19
Alignment explanation
Indices: 28235845--28235902 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
28235835 GATATGAAAC
28235845 TATGTGGAATT--TGTGAA
1 TATGTGGAATTGATGTGAA
*
28235862 CATGT-GACATTGATGTGAA
1 TATGTGGA-ATTGATGTGAA
28235881 TATGTGGAATTGATGTGAA
1 TATGTGGAATTGATGTGAA
28235900 TAT
1 TAT
28235903 CAAATGTGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 2 0.06
17 7 0.20
19 24 0.69
20 2 0.06
ACGTcount: A:0.31, C:0.03, G:0.28, T:0.38
Consensus pattern (19 bp):
TATGTGGAATTGATGTGAA
Found at i:28244598 original size:20 final size:21
Alignment explanation
Indices: 28244562--28244600 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28244552 CATTTGTTTA
*
28244562 TTTACTTTTATTTGTTTCACT
1 TTTACTTTTAGTTGTTTCACT
28244583 TTTACTTTT-GTTGTTTCA
1 TTTACTTTTAGTTGTTTCA
28244601 AATTCCTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.13, C:0.13, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTACTTTTAGTTGTTTCACT
Found at i:28244848 original size:17 final size:17
Alignment explanation
Indices: 28244826--28244858 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
28244816 AACGCCTAGG
28244826 TTATAAATCCTCTTTCC
1 TTATAAATCCTCTTTCC
28244843 TTATAAATCCTCTTTC
1 TTATAAATCCTCTTTC
28244859 TTGCAGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.48
Consensus pattern (17 bp):
TTATAAATCCTCTTTCC
Found at i:28246469 original size:15 final size:15
Alignment explanation
Indices: 28246441--28246479 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
28246431 ATGACCTGCT
28246441 GAAG-AAAA-AGGAA
1 GAAGAAAAAGAGGAA
28246454 GAAGAAAAAGAGGAA
1 GAAGAAAAAGAGGAA
*
28246469 GAAGACAAAGA
1 GAAGAAAAAGA
28246480 AGACAAAGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 4 0.17
14 4 0.17
15 15 0.65
ACGTcount: A:0.67, C:0.03, G:0.31, T:0.00
Consensus pattern (15 bp):
GAAGAAAAAGAGGAA
Found at i:28247592 original size:18 final size:18
Alignment explanation
Indices: 28247546--28247595 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
28247536 CAGTCATTTG
* * *
28247546 AAAAAGAAACAAAATGAG
1 AAAAAGAAAGAAAAAGAA
* *
28247564 AATAAGGAAGAAAAAGAA
1 AAAAAGAAAGAAAAAGAA
28247582 AAAAAGAAAGAAAA
1 AAAAAGAAAGAAAA
28247596 TTTTCATAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (18 bp):
AAAAAGAAAGAAAAAGAA
Found at i:28250499 original size:4 final size:4
Alignment explanation
Indices: 28250490--28250514 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
28250480 TTATTATCTT
28250490 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
28250515 CATTAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:28250818 original size:29 final size:29
Alignment explanation
Indices: 28250751--28250818 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
28250741 TTAACTAATA
* * *
28250751 TTTATTGCA-TTATTACTATGATTATATT
1 TTTATTGTATTTAATACTATAATTATATT
*
28250779 GTTACTT-TATTTAATACTATAATTATATT
1 TTTA-TTGTATTTAATACTATAATTATATT
28250808 TTTATTGTATT
1 TTTATTGTATT
28250819 AATTGTTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
28 6 0.19
29 26 0.81
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (29 bp):
TTTATTGTATTTAATACTATAATTATATT
Found at i:28251638 original size:26 final size:26
Alignment explanation
Indices: 28251600--28251689 Score: 87
Period size: 26 Copynumber: 3.5 Consensus size: 26
28251590 AAATTTAAAA
* * *
28251600 TTTG-ATTTAATTTAATTTGTGATTC
1 TTTGCATTTTATTTAATATGTGATAC
28251625 TTTGCATTTTATTTATATATGT--TAC
1 TTTGCATTTTATTTA-ATATGTGATAC
* * *
28251650 TTTGCATTTTATTTTATATATGATGC
1 TTTGCATTTTATTTAATATGTGATAC
*
28251676 TTTCCATTTTATTT
1 TTTGCATTTTATTT
28251690 TTTTATATAT
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
24 5 0.09
25 20 0.37
26 24 0.44
27 5 0.09
ACGTcount: A:0.22, C:0.08, G:0.09, T:0.61
Consensus pattern (26 bp):
TTTGCATTTTATTTAATATGTGATAC
Found at i:28251690 original size:26 final size:26
Alignment explanation
Indices: 28251619--28251690 Score: 101
Period size: 26 Copynumber: 2.8 Consensus size: 26
28251609 ATTTAATTTG
*
28251619 TGATTCTTTGCATTTTA-TTTATATA
1 TGATACTTTGCATTTTATTTTATATA
*
28251644 TGTTACTTTGCATTTTATTTTATATA
1 TGATACTTTGCATTTTATTTTATATA
* *
28251670 TGATGCTTTCCATTTTATTTT
1 TGATACTTTGCATTTTATTTT
28251691 TTTATATATG
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
25 15 0.37
26 26 0.63
ACGTcount: A:0.21, C:0.10, G:0.08, T:0.61
Consensus pattern (26 bp):
TGATACTTTGCATTTTATTTTATATA
Found at i:28262068 original size:49 final size:49
Alignment explanation
Indices: 28262001--28262558 Score: 275
Period size: 49 Copynumber: 11.5 Consensus size: 49
28261991 ACCCTAGAGT
28262001 TGAAGAGGGAAAGATTAAAGCCGTAACGATGGATCTTACACCCTAAAAC
1 TGAAGAGGGAAAGATTAAAGCCGTAACGATGGATCTTACACCCTAAAAC
* * * * * * * * * *
28262050 TGAATAGGGATAGGTTAAAGCCGTAATGGTAGACCTAACACTCTAAAAT
1 TGAAGAGGGAAAGATTAAAGCCGTAACGATGGATCTTACACCCTAAAAC
* * * *
28262099 TAAAGAGGGAAAGATTAAAGCC-T--CAATAGCAGATTTTACACCCTAAAAT
1 TGAAGAGGGAAAGATTAAAGCCGTAACGAT-G--GATCTTACACCCTAAAAC
* * * ** *** * *
28262148 TAAAGA-CGAATAGGTTAAAGCCACAACGACAAACCTAACACCCTAAAA-
1 TGAAGAGGGAA-AGATTAAAGCCGTAACGATGGATCTTACACCCTAAAAC
* * * ** *
28262196 TCAAAGCGGGAAAGAATAAAGCCACAAC-AGTAGATCTTACACCCTAAAAC
1 T-GAAGAGGGAAAGATTAAAGCCGTAACGA-TGGATCTTACACCCTAAAAC
* ** * * *** * * * *
28262246 TAAAGAATGATAGGTTAAAGCCGTAACGACAAACCTAATACCTTAAAAC
1 TGAAGAGGGAAAGATTAAAGCCGTAACGATGGATCTTACACCCTAAAAC
* * * *
28262295 CGAAGAGGGAAAGATTAAAGTCGTAAC-AGTGAATATTACACCCTAAAA-
1 TGAAGAGGGAAAGATTAAAGCCGTAACGA-TGGATCTTACACCCTAAAAC
*** * * *
28262343 TCGAA-AGGGGAAAGATTAAAGTAATAACGGTAGATCTTACAACCTAAAA-
1 T-GAAGA-GGGAAAGATTAAAGCCGTAACGATGGATCTTACACCCTAAAAC
** * *
28262392 TCGAAGAGGGAAAGATTAAAGCCACAACGGTGGATCTTATACCCTAAAAC
1 T-GAAGAGGGAAAGATTAAAGCCGTAACGATGGATCTTACACCCTAAAAC
* ** * * * *
28262442 T-AA-A--GAGAGATTAAAATCGTAATGACGGATCTAACACCCTAAAAT
1 TGAAGAGGGAAAGATTAAAGCCGTAACGATGGATCTTACACCCTAAAAC
* * * * *
28262487 TGAAAAGGGACAGATTAAAGCTGTAAC-AGTGAATCTTACACCCTAAAAA
1 TGAAGAGGGAAAGATTAAAGCCGTAACGA-TGGATCTTACACCCTAAAAC
*
28262536 TGAAAAGGGATAA-ATTAAAGCCG
1 TGAAGAGGGA-AAGATTAAAGCCG
28262559 CAATGGCGAA
Statistics
Matches: 381, Mismatches: 104, Indels: 48
0.71 0.20 0.09
Matches are distributed among these distances:
45 31 0.08
46 3 0.01
47 2 0.01
48 11 0.03
49 324 0.85
50 8 0.02
52 2 0.01
ACGTcount: A:0.45, C:0.17, G:0.19, T:0.19
Consensus pattern (49 bp):
TGAAGAGGGAAAGATTAAAGCCGTAACGATGGATCTTACACCCTAAAAC
Found at i:28262184 original size:98 final size:97
Alignment explanation
Indices: 28262003--28262447 Score: 333
Period size: 98 Copynumber: 4.5 Consensus size: 97
28261993 CCTAGAGTTG
** * * **
28262003 AAGAGGGAAAGATTAAAGCCGTAAC-G-ATGGATCTTACACCCTAAAACTGAATAGGGATAGGTT
1 AAGAGGGAAAGATTAAAGCCACAACAGCA--GATCTTACACCCTAAAACTAAAGAACGATAGGTT
** * ** * *
28262066 AAAGCCGTAATGGTAGACCTAACACTCTAAAATTA
64 AAAGCCACAACGACAAACCTAACAC-CTAAAATCA
* * * *
28262101 AAGAGGGAAAGATTAAAGCCTCAATAGCAGATTTTACACCCTAAAATTAAAG-ACGAATAGGTTA
1 AAGAGGGAAAGATTAAAGCCACAACAGCAGATCTTACACCCTAAAACTAAAGAACG-ATAGGTTA
28262165 AAGCCACAACGACAAACCTAACACCCTAAAATCA
65 AAGCCACAACGACAAACCTAACA-CCTAAAATCA
* * * *
28262199 AAGCGGGAAAGAATAAAGCCACAACAGTAGATCTTACACCCTAAAACTAAAGAATGATAGGTTAA
1 AAGAGGGAAAGATTAAAGCCACAACAGCAGATCTTACACCCTAAAACTAAAGAACGATAGGTTAA
** * * *
28262264 AGCCGTAACGACAAACCTAATACCTTAAAACCG
66 AGCCACAACGACAAACCTAACACC-TAAAATCA
* ** * * * ** * *
28262297 AAGAGGGAAAGATTAAAGTCGTAACAG-TGAATATTACACCCTAAAATCGAAAG-GGGAAAGATT
1 AAGAGGGAAAGATTAAAGCCACAACAGCAG-ATCTTACACCCTAAAA-CTAAAGAACGATAGGTT
** * ** * * * *
28262360 AAAGTAATAACGGTAGATCTTACAACCTAAAATCG
64 AAAGCCACAACGACAAACCTAAC-ACCTAAAATCA
* ** *
28262395 AAGAGGGAAAGATTAAAGCCACAACGGTGGATCTTATACCCTAAAACTAAAGA
1 AAGAGGGAAAGATTAAAGCCACAACAGCAGATCTTACACCCTAAAACTAAAGA
28262448 GAGATTAAAA
Statistics
Matches: 277, Mismatches: 59, Indels: 22
0.77 0.16 0.06
Matches are distributed among these distances:
97 9 0.03
98 254 0.92
99 13 0.05
100 1 0.00
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.19
Consensus pattern (97 bp):
AAGAGGGAAAGATTAAAGCCACAACAGCAGATCTTACACCCTAAAACTAAAGAACGATAGGTTAA
AGCCACAACGACAAACCTAACACCTAAAATCA
Found at i:28262341 original size:196 final size:194
Alignment explanation
Indices: 28262003--28262534 Score: 513
Period size: 196 Copynumber: 2.7 Consensus size: 194
28261993 CCTAGAGTTG
* ** * *
28262003 AAGAGGGAAAGATTAAAGCCGTAAC-GATGGATCTTACACCCTAAAACTGAATAG-GGATAGGTT
1 AAGAGGGAAAGAATAAAGCCACAACAG-TAGATCTTACACCCTAAAACT-AA-AGAAGATAGGTT
** * * * *
28262066 AAAGCCGTAATGGTAGACCTAACA-CTCTAAAATTAAAGAGGGAAAGATTAAAGCCTCAATAG-C
63 AAAGCCGTAATGACAGACCTAACACCT-TAAAATTGAAGAGGGAAAGATTAAAGCGT-AACAGTG
* * * * *
28262129 AGATTTTACACCCTAAAAT-TAAAGACGAATAGGTTAAAGCCACAACGACAAACCTAACACCCTA
126 A-ATATTACACCCTAAAATCGAAAGACGAA-AGATTAAAGCAACAACGACAAACCTAACAACCTA
28262193 AAATCA
189 AAATCA
*
28262199 AAGCGGGAAAGAATAAAGCCACAACAGTAGATCTTACACCCTAAAACTAAAGAATGATAGGTTAA
1 AAGAGGGAAAGAATAAAGCCACAACAGTAGATCTTACACCCTAAAACTAAAGAA-GATAGGTTAA
* * * **
28262264 AGCCGTAACGACAAACCTAATACCTTAAAACCGAAGAGGGAAAGATTAAAGTCGTAACAGTGAAT
65 AGCCGTAATGACAGACCTAACACCTTAAAATTGAAGAGGGAAAGATTAAAG-CGTAACAGTGAAT
** * * ** * * *
28262329 ATTACACCCTAAAATCGAAAGGGGAAAGATTAAAGTAATAACGGTAGATCTTACAACCTAAAATC
129 ATTACACCCTAAAATCGAAAGACGAAAGATTAAAGCAACAACGACAAACCTAACAACCTAAAATC
*
28262394 G
194 A
* * * * *
28262395 AAGAGGGAAAGATTAAAGCCACAACGGTGGATCTTATACCCTAAAACTAAAG-AG--AGATTAAA
1 AAGAGGGAAAGAATAAAGCCACAACAGTAGATCTTACACCCTAAAACTAAAGAAGATAGGTTAAA
** * * * * * *
28262457 ATCGTAATGACGGATCTAACACCCTAAAATTGAAAAGGGACAGATTAAAGCTGTAACAGTGAATC
66 GCCGTAATGACAGACCTAACACCTTAAAATTGAAGAGGGAAAGATTAAAGC-GTAACAGTGAATA
28262522 TTACACCCTAAAA
130 TTACACCCTAAAA
28262535 ATGAAAAGGG
Statistics
Matches: 277, Mismatches: 51, Indels: 20
0.80 0.15 0.06
Matches are distributed among these distances:
191 1 0.00
192 70 0.25
194 3 0.01
195 3 0.01
196 187 0.68
197 13 0.05
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.19
Consensus pattern (194 bp):
AAGAGGGAAAGAATAAAGCCACAACAGTAGATCTTACACCCTAAAACTAAAGAAGATAGGTTAAA
GCCGTAATGACAGACCTAACACCTTAAAATTGAAGAGGGAAAGATTAAAGCGTAACAGTGAATAT
TACACCCTAAAATCGAAAGACGAAAGATTAAAGCAACAACGACAAACCTAACAACCTAAAATCA
Found at i:28262570 original size:49 final size:49
Alignment explanation
Indices: 28262470--28262583 Score: 129
Period size: 49 Copynumber: 2.3 Consensus size: 49
28262460 GTAATGACGG
* * * * * *
28262470 ATCTAACACCCTAAAATTGAAAAGGGACAGATTAAAGCTGTAACAGTGA
1 ATCTTACACCCTAAAAATGAAAAGGGACAAATTAAAGCCGCAACAGCGA
* **
28262519 ATCTTACACCCTAAAAATGAAAAGGGATAAATTAAAGCCGCAATGGCGA
1 ATCTTACACCCTAAAAATGAAAAGGGACAAATTAAAGCCGCAACAGCGA
*
28262568 ATCTTGCACCCCTAAA
1 ATCTTACA-CCCTAAA
28262584 CCCGAAGAGA
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
49 47 0.87
50 7 0.13
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (49 bp):
ATCTTACACCCTAAAAATGAAAAGGGACAAATTAAAGCCGCAACAGCGA
Found at i:28262980 original size:13 final size:13
Alignment explanation
Indices: 28262962--28262987 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28262952 TATTATGAAT
28262962 CAGAAAAAGAAAA
1 CAGAAAAAGAAAA
28262975 CAGAAAAAGAAAA
1 CAGAAAAAGAAAA
28262988 AGTAAAGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.08, G:0.15, T:0.00
Consensus pattern (13 bp):
CAGAAAAAGAAAA
Found at i:28264794 original size:17 final size:17
Alignment explanation
Indices: 28264772--28264805 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28264762 GAAAAAATCC
*
28264772 ATTTAAATGTTATTTAA
1 ATTTAAATATTATTTAA
28264789 ATTTAAATATTATTTAA
1 ATTTAAATATTATTTAA
28264806 TCATGTAAAA
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:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATATTATTTAA
Done.