Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold373
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: 3053563
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 20
Found at i:1687983 original size:32 final size:26
Alignment explanation
Indices: 1687913--1687980 Score: 127
Period size: 26 Copynumber: 2.6 Consensus size: 26
1687903 TTTTAACAAA
1687913 AAAAATTAAAATTAAACTCGAATTAT
1 AAAAATTAAAATTAAACTCGAATTAT
1687939 AAAAATTAAAATTAAACTCGAATTAT
1 AAAAATTAAAATTAAACTCGAATTAT
*
1687965 AAAAATAAAAATTAAA
1 AAAAATTAAAATTAAA
1687981 ATTTTAAATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.63, C:0.06, G:0.03, T:0.28
Consensus pattern (26 bp):
AAAAATTAAAATTAAACTCGAATTAT
Found at i:1689811 original size:21 final size:20
Alignment explanation
Indices: 1689787--1689838 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
1689777 TTTAGAAGAG
*
1689787 TTAGGAGAATAAAGTTTTTGT
1 TTAGGAGAATAAAGTGTTT-T
*
1689808 TTAGGAATGAA-ATAGTGTTTT
1 TTAGG-A-GAATAAAGTGTTTT
1689829 TTAGGAGAAT
1 TTAGGAGAAT
1689839 TTTTTGGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
19 3 0.12
20 1 0.04
21 11 0.42
22 8 0.31
23 3 0.12
ACGTcount: A:0.35, C:0.00, G:0.25, T:0.40
Consensus pattern (20 bp):
TTAGGAGAATAAAGTGTTTT
Found at i:1691516 original size:180 final size:176
Alignment explanation
Indices: 1691170--1691516 Score: 450
Period size: 180 Copynumber: 1.9 Consensus size: 176
1691160 CTTTTATAAC
* * *
1691170 AGTAGGAATATTTTCAGAGGCAAAGAAAAAGAATTAGGCAAGTTTTGGGCTTAAAGGATGCTAGT
1 AGTAGGAATA-TTTCAGAGGCAAAGAAAAAGAATTAGGCAAGTTTTAGGCTAAAAAGATGCTAGT
* * * * * *
1691235 AAGTGGCGACTGATAGTTACAGCAAGGGATGGCTTCAGACCAATTGGTTGATGCTGAAAATAGGG
65 AAATGGCGACTGATAGTTACAGCAAGAGATGGCTTCAGAACAATTGGTCGATGCTGAAAACAGAG
*
1691300 ATTTTGGTTGAATTAAAGAATTTAGAGAGAAAAAGTGAATATATTTT
130 ATTTTGGTTAAATTAAAGAATTTAGAGAGAAAAAGTGAATATATTTT
1691347 AGTAGGAATA-TTCAAGAGGCAAAGAAAAAGAATTAGGCAAGTTTTAGGCTCAAAAAGATGCTAG
1 AGTAGGAATATTTC-AGAGGCAAAGAAAAAGAATTAGGCAAGTTTTAGGCT-AAAAAGATGCTAG
* **
1691411 TAAATGGTGGTTGATAGATGT-CTATGACGAA-AGATGGCTTCAGAACAATTGGTCGATGCTGAA
64 TAAATGGCGACTGATAG-T-TAC-A-G-C-AAGAGATGGCTTCAGAACAATTGGTCGATGCTGAA
* *
1691474 AACA-AGATTTTGGTTAAATTGAAGAATTTTGAGAGAAAAAGTG
123 AACAGAGATTTTGGTTAAATTAAAGAATTTAGAGAGAAAAAGTG
1691517 GTGGAATAAG
Statistics
Matches: 147, Mismatches: 15, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
175 3 0.02
176 35 0.24
177 34 0.23
178 2 0.01
179 2 0.01
180 36 0.24
181 33 0.22
182 2 0.01
ACGTcount: A:0.38, C:0.08, G:0.27, T:0.27
Consensus pattern (176 bp):
AGTAGGAATATTTCAGAGGCAAAGAAAAAGAATTAGGCAAGTTTTAGGCTAAAAAGATGCTAGTA
AATGGCGACTGATAGTTACAGCAAGAGATGGCTTCAGAACAATTGGTCGATGCTGAAAACAGAGA
TTTTGGTTAAATTAAAGAATTTAGAGAGAAAAAGTGAATATATTTT
Found at i:1691682 original size:17 final size:17
Alignment explanation
Indices: 1691647--1691681 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1691637 GAAAATAAAT
1691647 AAGAAAGAGAAGAGAAA
1 AAGAAAGAGAAGAGAAA
1691664 AAGAAAGAGAA-AGAAA
1 AAGAAAGAGAAGAGAAA
1691680 AA
1 AA
1691682 ATACCAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (17 bp):
AAGAAAGAGAAGAGAAA
Found at i:1692975 original size:25 final size:25
Alignment explanation
Indices: 1692907--1692975 Score: 61
Period size: 25 Copynumber: 2.8 Consensus size: 25
1692897 GCCACTTCTC
* *
1692907 GTCTAACATGTTGGCACTACATTTG
1 GTCTAACGTGTTGGCGCTACATTTG
* * *
1692932 GTATAACGT-ATGAGTGCTACATCTT-
1 GTCTAACGTGTTG-GCGCTACAT-TTG
1692957 GTCTAACGTGTTGGCGCTA
1 GTCTAACGTGTTGGCGCTA
1692976 TGTCTGCTCC
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
24 2 0.06
25 27 0.82
26 4 0.12
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (25 bp):
GTCTAACGTGTTGGCGCTACATTTG
Found at i:1698059 original size:19 final size:20
Alignment explanation
Indices: 1698032--1698083 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
1698022 CGATACATTA
*
1698032 TATCGATACATGATT-ATAG
1 TATCAATACATGATTAATAG
* *
1698051 TATCAATACA-CATTGAATTG
1 TATCAATACATGATT-AATAG
1698071 TATCAATACATGA
1 TATCAATACATGA
1698084 AACTGGAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 3 0.12
19 9 0.35
20 13 0.50
21 1 0.04
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (20 bp):
TATCAATACATGATTAATAG
Found at i:1699104 original size:35 final size:34
Alignment explanation
Indices: 1698988--1699112 Score: 135
Period size: 34 Copynumber: 3.6 Consensus size: 34
1698978 TGTTACCTTT
* * *
1698988 AAGGCTAAGATATAACCT-TACAACTTTATCTTTTCA
1 AAGGCTTAGATAGAACCTCTAC-AC--TATCTTTTCG
* *
1699024 AAGGCTTAGATAGAACATCAACACTATCTTTTCG
1 AAGGCTTAGATAGAACCTCTACACTATCTTTTCG
* *
1699058 AAGGCTAAGATAGAACCTCTACACTATCTTTTTTG
1 AAGGCTTAGATAGAACCTCTACACTATC-TTTTCG
*
1699093 AAGGCTTAGATATAACCTCT
1 AAGGCTTAGATAGAACCTCT
1699113 TAATCACTTT
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
34 34 0.45
35 23 0.30
36 17 0.22
37 2 0.03
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (34 bp):
AAGGCTTAGATAGAACCTCTACACTATCTTTTCG
Found at i:1699598 original size:20 final size:20
Alignment explanation
Indices: 1699573--1699627 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
1699563 ATAAGGCCAA
1699573 ATGTATCGATACAATTCTTG
1 ATGTATCGATACAATTCTTG
*
1699593 ATGTATTGATACAATTCTTG
1 ATGTATCGATACAATTCTTG
1699613 ATGTATCGATACAAT
1 ATGTATCGATACAAT
1699628 CTAAACTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACAATTCTTG
Found at i:1699649 original size:41 final size:40
Alignment explanation
Indices: 1699573--1699649 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 40
1699563 ATAAGGCCAA
**
1699573 ATGTATCGATACAATTCTTGATGTATTGATACAATTCTTG
1 ATGTATCGATACAATTCTAAATGTATTGATACAATTCTTG
1699613 ATGTATCGATACAA-TCTAAACTTGTATTGATACAATT
1 ATGTATCGATACAATTCTAAA--TGTATTGATACAATT
1699650 GAAGGGCAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 4 0.12
40 14 0.42
41 15 0.45
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (40 bp):
ATGTATCGATACAATTCTAAATGTATTGATACAATTCTTG
Found at i:1700832 original size:78 final size:78
Alignment explanation
Indices: 1700727--1700927 Score: 224
Period size: 79 Copynumber: 2.6 Consensus size: 78
1700717 AATAACGGGG
* * * * * * *
1700727 TTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTAG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTAG
*
1700791 AAAAAAAATCGAGA
65 AAAAAAAACCGAGA
* *
1700805 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATA-TTTAG
* * * * *
1700870 GAATAAAGCCGGGG
65 AAAAAAAACCGAGA
* *
1700884 TTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
1700928 GAAATAACAA
Statistics
Matches: 103, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
77 1 0.01
78 50 0.49
79 52 0.50
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (78 bp):
TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGA
AAAAAAACCGAGA
Found at i:1700935 original size:28 final size:28
Alignment explanation
Indices: 1700879--1700950 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
1700869 GGAATAAAGC
** *
1700879 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1700907 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
**
1700935 CAAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
1700951 TCGACTGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:1701163 original size:263 final size:263
Alignment explanation
Indices: 1700828--1701328 Score: 767
Period size: 263 Copynumber: 1.9 Consensus size: 263
1700818 TCGAAAATAA
* * * * *
1700828 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTAT
1 CGGGGTTGGAATATCCCCAATTATGAAAAATCAATATTTTAGAAATAAAGCCGGGGTTGAAGTAT
* *
1700893 CCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAAT-AACAAGGTTGGAGTATCCTCGACT
66 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG--ATCAACAAGGTTGGAGTATCCCCGACT
1700957 GTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATT
129 GTGAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAA-GAAAATT
* *
1701020 GGTGTTTCGAAAATAAAACCGGGGTT-GAAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCA
193 AGTGTTTCGAAAATAAAACCGGAGTTGGAA-TATCCCCGATTGTGGAAAAATTAGTGTTTTAGCA
1701084 ATAAAAC
257 ATAAAAC
* * *
1701091 CGGGGTTGGAATATCCCCGATTATGAAAAATTAATATTTTAGAAATAAAGTCGGGGTTGAAGTAT
1 CGGGGTTGGAATATCCCCAATTATGAAAAATCAATATTTTAGAAATAAAGCCGGGGTTGAAGTAT
** *
1701156 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATCAACGGGGTTGGAGTATCCCCGATTGT
66 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATCAACAAGGTTGGAGTATCCCCGACTGT
* *
1701221 GAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTATAGAAAATTAGT
131 GAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAATTAGT
* *
1701286 GTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
196 GTTTCGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGA
1701329 GAATTGAAAA
Statistics
Matches: 215, Mismatches: 19, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
261 2 0.01
262 25 0.12
263 145 0.67
264 43 0.20
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.28
Consensus pattern (263 bp):
CGGGGTTGGAATATCCCCAATTATGAAAAATCAATATTTTAGAAATAAAGCCGGGGTTGAAGTAT
CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATCAACAAGGTTGGAGTATCCCCGACTGT
GAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAATTAGT
GTTTCGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAA
AAC
Found at i:1701305 original size:51 final size:52
Alignment explanation
Indices: 1700938--1701323 Score: 225
Period size: 52 Copynumber: 7.4 Consensus size: 52
1700928 GAAATAACAA
* * * * * *
1700938 GGTTGGAGTATCCTCGACTGT-GAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATAGAAAAATTAGT-GTTTTGAAAATAAAATCGG
* * * * * *
1700990 AGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTCGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGAAAATAAAATCGG
* * * * *
1701042 GGTTGAAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGA-AAATAAAATCGG
* * * *
1701094 GGTTGGAATATCCCCGATTAT-GAAAAATTAATATTTT-AGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGA-AAATAAAATCGG
* * **** * *** ** *
1701145 GGTTGAAGTATCCCCTCGGA-AATA-ACGGGGTTGGAGTATCCCCGATGAT-CAA-CGG
1 GGTTGGAGTAT-CCC-C-GATTATAGA-AAAATT--AGTGT-TTTGAAAATAAAATCGG
* * *
1701200 GGTTGGAGTATCCCCGATTGT-GAAGAAATTGGTGTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATAGAA-AAATTAGTG--TTTTGAAAATAAAATCGG
*
1701254 AGTTGGAGTATCCCCGATTATAG-AAAATTAGTGTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGAAAATAAAATCGG
* *
1701305 AGTTGGAATATCCCCGATT
1 GGTTGGAGTATCCCCGATT
1701324 GTGGAGAATT
Statistics
Matches: 252, Mismatches: 63, Indels: 39
0.71 0.18 0.11
Matches are distributed among these distances:
51 72 0.29
52 98 0.39
53 30 0.12
54 30 0.12
55 14 0.06
56 5 0.02
57 2 0.01
58 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.29
Consensus pattern (52 bp):
GGTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGAAAATAAAATCGG
Found at i:1703686 original size:13 final size:13
Alignment explanation
Indices: 1703668--1703693 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1703658 ACAAAGATCC
1703668 ATGTATCGATACA
1 ATGTATCGATACA
1703681 ATGTATCGATACA
1 ATGTATCGATACA
1703694 CAAAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1703757 original size:19 final size:19
Alignment explanation
Indices: 1703733--1703787 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
1703723 CAGTAGCTAA
*
1703733 TTATGTATCGATACAATAC
1 TTATGTATCGATACAAAAC
1703752 TTATGTATCGATACAAAAC
1 TTATGTATCGATACAAAAC
1703771 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1703788 TCGTTGAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (19 bp):
TTATGTATCGATACAAAAC
Found at i:1706595 original size:13 final size:13
Alignment explanation
Indices: 1706577--1706601 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1706567 ATAGAAAAGA
1706577 TGTATCGATACAT
1 TGTATCGATACAT
1706590 TGTATCGATACA
1 TGTATCGATACA
1706602 ATTTGCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1706614 original size:20 final size:20
Alignment explanation
Indices: 1706589--1706626 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1706579 TATCGATACA
1706589 TTGTATCGATACAATTTGCT
1 TTGTATCGATACAATTTGCT
1706609 TTGTATCGATACAATTTG
1 TTGTATCGATACAATTTG
1706627 AAAAAATCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (20 bp):
TTGTATCGATACAATTTGCT
Found at i:1706785 original size:21 final size:18
Alignment explanation
Indices: 1706761--1706800 Score: 53
Period size: 21 Copynumber: 2.1 Consensus size: 18
1706751 ATTTAGGAAC
1706761 AATTAAGCACAAAACATCAAG
1 AATTAA-CAC-AAACA-CAAG
1706782 AATTAACACAAACACAAG
1 AATTAACACAAACACAAG
1706800 A
1 A
1706801 TCAATCAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 5 0.26
20 3 0.16
21 6 0.32
ACGTcount: A:0.60, C:0.20, G:0.07, T:0.12
Consensus pattern (18 bp):
AATTAACACAAACACAAG
Found at i:1706983 original size:17 final size:17
Alignment explanation
Indices: 1706961--1706994 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1706951 ACATTATCAC
* *
1706961 CAAAAATTTGATTAAAA
1 CAAAAATATGAATAAAA
1706978 CAAAAATATGAATAAAA
1 CAAAAATATGAATAAAA
1706995 TTTTATATGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (17 bp):
CAAAAATATGAATAAAA
Found at i:1711242 original size:51 final size:51
Alignment explanation
Indices: 1711183--1711282 Score: 146
Period size: 51 Copynumber: 2.0 Consensus size: 51
1711173 AGCTGCTGCC
*
1711183 AACAGATGTATTGATGCATTCATACAACGTATCGATACATTCAAAATAGTT
1 AACAGATGTATTGATACATTCATACAACGTATCGATACATTCAAAATAGTT
* * * * *
1711234 AACAGATGTATTGATACATTTATACAATGTATTGGTACATTCATAATAG
1 AACAGATGTATTGATACATTCATACAACGTATCGATACATTCAAAATAG
1711283 AACTTGTACA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (51 bp):
AACAGATGTATTGATACATTCATACAACGTATCGATACATTCAAAATAGTT
Found at i:1712343 original size:80 final size:80
Alignment explanation
Indices: 1712210--1712369 Score: 302
Period size: 80 Copynumber: 2.0 Consensus size: 80
1712200 TTTAAAGGCT
1712210 AAGTAAAAATCTCTTTCTTTTACAAAGATGAAATGTGTAAACAAAGAAAACTTCTAAAGTTAGGT
1 AAGTAAAAATCTCTTTCTTTTACAAAGATGAAATGTGTAAACAAAGAAAACTTCTAAAGTTAGGT
1712275 GTTTACAAGGTTAAG
66 GTTTACAAGGTTAAG
* *
1712290 AAGTAGAAATCTCTTTCTTTTACAAAGATGAAATGTGTAAATAAAGAAAACTTCTAAAGTTAGGT
1 AAGTAAAAATCTCTTTCTTTTACAAAGATGAAATGTGTAAACAAAGAAAACTTCTAAAGTTAGGT
1712355 GTTTACAAGGTTAAG
66 GTTTACAAGGTTAAG
1712370 CTTAAGGAAA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.32
Consensus pattern (80 bp):
AAGTAAAAATCTCTTTCTTTTACAAAGATGAAATGTGTAAACAAAGAAAACTTCTAAAGTTAGGT
GTTTACAAGGTTAAG
Found at i:1714902 original size:13 final size:13
Alignment explanation
Indices: 1714884--1714940 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
1714874 CATAAAGTGT
1714884 TGTATCGATACAA
1 TGTATCGATACAA
*
1714897 TGTATCAATACATAA
1 TGTATCGATAC--AA
1714912 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
1714929 TGTATCGATACA
1 TGTATCGATACA
1714941 TAAGTTTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 22 0.61
15 2 0.06
17 2 0.06
19 10 0.28
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1714919 original size:32 final size:32
Alignment explanation
Indices: 1714864--1714964 Score: 175
Period size: 32 Copynumber: 3.1 Consensus size: 32
1714854 TTCAACGATT
1714864 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
*
1714897 TGTATCAATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
1714929 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1714961 TGTA
1 TGTA
1714965 AGCTACTGCC
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 53 0.82
33 12 0.18
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1714953 original size:19 final size:18
Alignment explanation
Indices: 1714862--1714959 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
1714852 ATTTCAACGA
1714862 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
1714881 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
*
1714897 --TGTATCAATACATAAG
1 TTTGTATCGATACATAAG
1714913 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1714929 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1714945 TTTTGTATCGATACA
1 -TTTGTATCGATACA
1714960 ATGTAAGCTA
Statistics
Matches: 64, Mismatches: 2, Indels: 26
0.70 0.02 0.28
Matches are distributed among these distances:
13 21 0.33
15 4 0.06
17 4 0.06
19 23 0.36
20 12 0.19
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:1715018 original size:13 final size:13
Alignment explanation
Indices: 1715000--1715026 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1714990 ACATTACTCA
1715000 AATGTATCGATAC
1 AATGTATCGATAC
1715013 AATGTATCGATAC
1 AATGTATCGATAC
1715026 A
1 A
1715027 CTGATCTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1715070 original size:86 final size:84
Alignment explanation
Indices: 1714916--1715098 Score: 201
Period size: 86 Copynumber: 2.1 Consensus size: 84
1714906 ACATAAGTGT
* *
1714916 TGTATCGATACAATGTATCGATACATAAGTTTTGTATCGATACAATGTAAGCTACTGCCAAAAAA
1 TGTATCGATACAATGTATCGATACATAAGTTTTGTATCGATACAATGCAAGCAACTGCC-AAAAA
* *
1714981 TGTATCGATACATTACTCAAA
65 TGTATCGATACACTA-TAAAA
* * * *
1715002 TGTATCGATACAATGTATCGATACACTGA-TCTTTGTATCGATAC-ATGCAGGCAAATTTGCC-C
1 TGTATCGATACAATGTATCGATACA-TAAGT-TTTGTATCGATACAATGCAAGC-AA-CTGCCAA
* *
1715064 AGATGTATTGATACACTATAAAA
62 AAATGTATCGATACACTATAAAA
1715087 TGTATCGATACA
1 TGTATCGATACA
1715099 TGCAGGCAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
85 16 0.19
86 47 0.57
87 16 0.19
88 4 0.05
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (84 bp):
TGTATCGATACAATGTATCGATACATAAGTTTTGTATCGATACAATGCAAGCAACTGCCAAAAAT
GTATCGATACACTATAAAA
Found at i:1715160 original size:51 final size:51
Alignment explanation
Indices: 1715014--1715162 Score: 244
Period size: 52 Copynumber: 2.9 Consensus size: 51
1715004 TATCGATACA
***
1715014 ATGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAG
1 ATGTATCGATACACT-ATAAATGTATCGATACATGCAGGCAAATTTGCCCAG
*
1715066 ATGTATTGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAG
1 ATGTATCGATACACTAT-AAATGTATCGATACATGCAGGCAAATTTGCCCAG
1715118 ATGTATCGATACACTATAAATGTATCGATACATGCAGGCAAATTT
1 ATGTATCGATACACTATAAATGTATCGATACATGCAGGCAAATTT
1715163 TCATATTTCG
Statistics
Matches: 91, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
51 30 0.33
52 61 0.67
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (51 bp):
ATGTATCGATACACTATAAATGTATCGATACATGCAGGCAAATTTGCCCAG
Found at i:1718627 original size:20 final size:20
Alignment explanation
Indices: 1718598--1718642 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1718588 ATTATTATAT
1718598 ATGT-TGTATTTTGTTCATA
1 ATGTCTGTATTTTGTTCATA
1718617 ATGTCTGTATTTTGTTCATA
1 ATGTCTGTATTTTGTTCATA
1718637 ATGTCT
1 ATGTCT
1718643 AAGATGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.20, C:0.09, G:0.16, T:0.56
Consensus pattern (20 bp):
ATGTCTGTATTTTGTTCATA
Found at i:1719835 original size:17 final size:17
Alignment explanation
Indices: 1719801--1719839 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1719791 TTTTTTTAAA
*
1719801 AAATAAATAACAATAAT
1 AAATAAATAACAAAAAT
1719818 AAATAAATAA-ATAAAAT
1 AAATAAATAACA-AAAAT
1719835 AAATA
1 AAATA
1719840 TCCTTTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (17 bp):
AAATAAATAACAAAAAT
Found at i:1720267 original size:81 final size:80
Alignment explanation
Indices: 1720124--1720278 Score: 199
Period size: 81 Copynumber: 1.9 Consensus size: 80
1720114 GAACAATCTT
* *
1720124 GAATTTACATTCTTGGAGATACTACAAACCCATCTCTCCAAAAGAGGATATCCAACCTTATTTTT
1 GAATTTACATTCTAGGAGATACTACAAACCCATCTCTCCAAAAGAGGATATCCAACCCTATTTTT
*
1720189 CTTACAAAAAAAACTA
66 -GTACAAAAAAAACTA
* * *
1720205 GAATTTACATTCTCAGG-GATACTCCAAACCCATCTCTCCAAACG-GGATA-CTATAGCCCTATT
1 GAATTTACATTCT-AGGAGATACTACAAACCCATCTCTCCAAAAGAGGATATCCA-A-CCCTATT
1720267 TTTGTACAAAAA
63 TTTGTACAAAAA
1720279 GACTTGAACT
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
79 2 0.03
80 14 0.22
81 47 0.72
82 2 0.03
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.29
Consensus pattern (80 bp):
GAATTTACATTCTAGGAGATACTACAAACCCATCTCTCCAAAAGAGGATATCCAACCCTATTTTT
GTACAAAAAAAACTA
Found at i:1725328 original size:51 final size:52
Alignment explanation
Indices: 1725208--1725346 Score: 190
Period size: 51 Copynumber: 2.7 Consensus size: 52
1725198 AATTGCCTGC
* * * *
1725208 ATGTATCGATACACTGAAAAATGTATTGATAAATTTAGGTCAAAAAACTAGA
1 ATGTATCGATACAATGAAAAATGTATCGATACATTTAGGTCAAAAAACTAAA
* * * *
1725260 ATATATCGATACAATGAAGAATGTATCGATACATTTGGGTC-AAAACCTAAA
1 ATGTATCGATACAATGAAAAATGTATCGATACATTTAGGTCAAAAAACTAAA
*
1725311 ATGTATCGATACAATGAAAAATATATCGATACATTT
1 ATGTATCGATACAATGAAAAATGTATCGATACATTT
1725347 TTATTCTAGA
Statistics
Matches: 76, Mismatches: 11, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
51 41 0.54
52 35 0.46
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (52 bp):
ATGTATCGATACAATGAAAAATGTATCGATACATTTAGGTCAAAAAACTAAA
Found at i:1725442 original size:20 final size:20
Alignment explanation
Indices: 1725402--1725455 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
1725392 CATTTCAAAC
*
1725402 ATGTATTGATACATTCACTT
1 ATGTATCGATACATTCACTT
1725422 ATGTATCGATACATT-ACCTT
1 ATGTATCGATACATTCA-CTT
*
1725442 ATTGTATCAATACA
1 A-TGTATCGATACA
1725456 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 1 0.03
20 18 0.60
21 11 0.37
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTCACTT
Found at i:1726188 original size:61 final size:61
Alignment explanation
Indices: 1726035--1726167 Score: 248
Period size: 61 Copynumber: 2.2 Consensus size: 61
1726025 GCCATGTGCA
1726035 GATTCAAGGCCTACAACAATAGACTTAAAGATAATAAGGATGAGAAGAGTGTTAATATGAG
1 GATTCAAGGCCTACAACAATAGACTTAAAGATAATAAGGATGAGAAGAGTGTTAATATGAG
**
1726096 GATTCAAGGCCTACAACAATAGACTTAAAGATAATAAGGATGAGAAGAGTGTTAATATGCT
1 GATTCAAGGCCTACAACAATAGACTTAAAGATAATAAGGATGAGAAGAGTGTTAATATGAG
1726157 GATTCAAGGCC
1 GATTCAAGGCC
1726168 AGCAATATTG
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 70 1.00
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (61 bp):
GATTCAAGGCCTACAACAATAGACTTAAAGATAATAAGGATGAGAAGAGTGTTAATATGAG
Found at i:1726250 original size:47 final size:49
Alignment explanation
Indices: 1726197--1726302 Score: 126
Period size: 52 Copynumber: 2.1 Consensus size: 49
1726187 ATGAGAAGAA
* *
1726197 TGCCAATGTGCTAATTC-A-AGTGACATTGGACTTAAAAATGATAAGGG
1 TGCCAATGTGCTAATTCAACAGTGACATTAGACTTAAAAATGATAAAGG
* * *
1726244 TGCCAATGTGTTGATTCAAGGCCAGTGACATTAGATTTAAAAATGATAAAGG
1 TGCCAATGTGCTAATTCAA---CAGTGACATTAGACTTAAAAATGATAAAGG
1726296 TGCCAAT
1 TGCCAAT
1726303 ATGTTGATTC
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
47 15 0.31
48 1 0.02
52 33 0.67
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (49 bp):
TGCCAATGTGCTAATTCAACAGTGACATTAGACTTAAAAATGATAAAGG
Found at i:1726287 original size:52 final size:52
Alignment explanation
Indices: 1726215--1726367 Score: 175
Period size: 52 Copynumber: 2.9 Consensus size: 52
1726205 TGCTAATTCA
* * *
1726215 AGTGACATTGGACTTAAAAATGATAAGGGTGCCAATGTGTTGATTCAAGGCC
1 AGTGACATTAGACTTAAAAATGATAAAGGTGCCAATATGTTGATTCAAGGCC
*
1726267 AGTGACATTAGATTTAAAAATGATAAAGGTGCCAATATGTTGATTCAAGGCC
1 AGTGACATTAGACTTAAAAATGATAAAGGTGCCAATATGTTGATTCAAGGCC
*** * * * *
1726319 AACAACATTGGACTTAGAGAAA--ATGAAGGTGCAAATATGCTGATTCAAG
1 AGTGACATTAGACTTA-A-AAATGATAAAGGTGCCAATATGTTGATTCAAG
1726368 ACTAGCGATA
Statistics
Matches: 87, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
52 83 0.95
53 1 0.01
54 3 0.03
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (52 bp):
AGTGACATTAGACTTAAAAATGATAAAGGTGCCAATATGTTGATTCAAGGCC
Found at i:1726542 original size:32 final size:32
Alignment explanation
Indices: 1726504--1727334 Score: 298
Period size: 32 Copynumber: 27.2 Consensus size: 32
1726494 TAGACGAAGG
* *
1726504 TGCCACCAACTTATGTGGGCTTTTAAGAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTAAAAGGGT
* *
1726536 TGCCACCAACTTGTGTGGG-TTTTGAAAGGAAT
1 TGCCACCAACTTGTGTGGGCTTTTAAAAGG-GT
* * * *
1726568 TGCCACTAACTTATCTGGAC-TTTAGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTA-AAAGGGT
*** *
1726600 TGCCAATGACTTGTGTAGG-TTTTAAAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTT-AAAAGGGT
* * *
1726632 TGCCACCAACTTATGTGGGCTTTGAGAAA-AGT
1 TGCCACCAACTTGTGTGGGCTTTTA-AAAGGGT
* * *
1726664 TGCCACCAACTT-TTTAGG-TTTTAGAAAGGGC
1 TGCCACCAACTTGTGTGGGCTTTTA-AAAGGGT
* * * * * *
1726695 TACCACCGACTTGTGTAGGCTTTAAAAAGAGC
1 TGCCACCAACTTGTGTGGGCTTTTAAAAGGGT
* * *
1726727 TGCCACCAACTTGTATAGGCTTTAAAAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTT-TAAAAGGGT
* * * *
1726760 TGTCATCGACTTGTGTGGAC-TTTAAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTAAAAGGGT
* ** * *
1726791 TGTCACTGACTTATGTGGGC-TTTGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTAAAAGGGT
* * * * *
1726822 TACCATCGATTTGTGTGGGC-TTTGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTAAAAGGGT
* * * *
1726853 TACCATCGACTTGTGTGGGC-TTTGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTAAAAGGGT
* * * * * *
1726884 TACCA-TAGACTTGCGTGGGC-ATTGAAAGAGT
1 TGCCACCA-ACTTGTGTGGGCTTTTAAAAGGGT
* * * * * *
1726915 TACCATCGACTTGTGTGGACTTTGAAAA-AG-
1 TGCCACCAACTTGTGTGGGCTTTTAAAAGGGT
** **
1726945 TGCCACTGAC-T-TGTGGGCTTGGAAAA-GG-
1 TGCCACCAACTTGTGTGGGCTTTTAAAAGGGT
** * * *
1726973 TGCCACTGAC-T-TATGGGC-ATTGAAA--G-
1 TGCCACCAACTTGTGTGGGCTTTTAAAAGGGT
* * * * * * *
1726999 -G--ATCGATTTATGTGGGCTTTGAGAAGAGT
1 TGCCACCAACTTGTGTGGGCTTTTAAAAGGGT
* *
1727028 TGCCACCGACTTGTGTGGGC-TTTAAAAGAGT
1 TGCCACCAACTTGTGTGGGCTTTTAAAAGGGT
* * * * *
1727059 TGCCACCGACTT-TTTTGGCTTTGAAAA-AG-
1 TGCCACCAACTTGTGTGGGCTTTTAAAAGGGT
** * *
1727088 TGCCACTGAC-T-TGTGGACTTTGAAAA-GG-
1 TGCCACCAACTTGTGTGGGCTTTTAAAAGGGT
* * *
1727116 TGCCACTAAC-T-TGTGGGCTTTGAAAGGGGT
1 TGCCACCAACTTGTGTGGGCTTTTAAAAGGGT
* * * *
1727146 TGCCATCGATTTGTGTGGGC-ATTAAAAGGGGT
1 TGCCACCAACTTGTGTGGGCTTTTAAAA-GGGT
*** *
1727178 TGCCATTGATTTGTGTGGGC-TTTAAAAGGAGT
1 TGCCACCAACTTGTGTGGGCTTTTAAAAGG-GT
* * * **
1727210 TGCCACCAATTTGTGTGGGCTTTGAGAATAGT
1 TGCCACCAACTTGTGTGGGCTTTTAAAAGGGT
*
1727242 TGCCACCAACTTGTGTGGGC-TTTGAAAGGG-
1 TGCCACCAACTTGTGTGGGCTTTTAAAAGGGT
* *
1727272 TGCCACCAAC-T-TGTGGGCTTTGAAAA-GAT
1 TGCCACCAACTTGTGTGGGCTTTTAAAAGGGT
* * *
1727301 TGCCACTAA-TT-TATGGGC-TTTAAAAAGGT
1 TGCCACCAACTTGTGTGGGCTTTTAAAAGGGT
1727330 TGCCA
1 TGCCA
1727335 TGGAGTTATG
Statistics
Matches: 631, Mismatches: 133, Indels: 73
0.75 0.16 0.09
Matches are distributed among these distances:
23 3 0.00
24 1 0.00
25 7 0.01
26 4 0.01
27 3 0.00
28 83 0.13
29 40 0.06
30 39 0.06
31 193 0.31
32 216 0.34
33 42 0.07
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (32 bp):
TGCCACCAACTTGTGTGGGCTTTTAAAAGGGT
Found at i:1726734 original size:95 final size:95
Alignment explanation
Indices: 1726536--1726738 Score: 241
Period size: 95 Copynumber: 2.1 Consensus size: 95
1726526 TTAAGAGGGT
* * * *
1726536 TGCCACCAACTTGTGTGGGTTTTGAAAGGAATTGCCACTAACTTATCTGGACTTTAGAAAGGGTT
1 TGCCACCAACTTATGTGGGCTTTGAAA-GAATTGCCACCAACTTATCTGGACTTTAGAAAGGGCT
* * * * *
1726601 GCCAATGACTTGTGTAGGTTTTAAAAAGGGT
65 ACCAACGACTTGTGTAGGCTTTAAAAAGAGC
* *
1726632 TGCCACCAACTTATGTGGGCTTTGAGAA-AAGTTGCCACCAACTT-TTTAGG-TTTTAGAAAGGG
1 TGCCACCAACTTATGTGGGCTTTGA-AAGAA-TTGCCACCAACTTATCT-GGACTTTAGAAAGGG
*
1726694 CTACCACCGACTTGTGTAGGCTTTAAAAAGAGC
63 CTACCAACGACTTGTGTAGGCTTTAAAAAGAGC
1726727 TGCCACCAACTT
1 TGCCACCAACTT
1726739 GTATAGGCTT
Statistics
Matches: 92, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
95 53 0.58
96 37 0.40
97 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (95 bp):
TGCCACCAACTTATGTGGGCTTTGAAAGAATTGCCACCAACTTATCTGGACTTTAGAAAGGGCTA
CCAACGACTTGTGTAGGCTTTAAAAAGAGC
Found at i:1726772 original size:33 final size:32
Alignment explanation
Indices: 1726587--1726884 Score: 162
Period size: 31 Copynumber: 9.4 Consensus size: 32
1726577 CTTATCTGGA
* * **
1726587 CTTTAGAAAGGGTTGCCAATGACTTGTGTAGG
1 CTTTAAAAAGGGTTGTCACCGACTTGTGTAGG
* * * * *
1726619 TTTTAAAAAGGGTTGCCACCAACTTATGTGGG
1 CTTTAAAAAGGGTTGTCACCGACTTGTGTAGG
* * *
1726651 CTTTGAGAAAA--GTTGCCACCAACTT-TTTAGG
1 CTTT-A-AAAAGGGTTGTCACCGACTTGTGTAGG
* * * **
1726682 TTTTAGAAAGGGCTACCACCGACTTGTGTAGG
1 CTTTAAAAAGGGTTGTCACCGACTTGTGTAGG
* * * * *
1726714 CTTTAAAAAGAGCTGCCACCAACTTGTATAGG
1 CTTTAAAAAGGGTTGTCACCGACTTGTGTAGG
*
1726746 CTTTAAAAAAGGGTTGTCATCGACTTGTGT-GG
1 CTTT-AAAAAGGGTTGTCACCGACTTGTGTAGG
* * *
1726778 ACTTT-AAAAGGGTTGTCACTGACTTATGTGGG
1 -CTTTAAAAAGGGTTGTCACCGACTTGTGTAGG
* ** * * *
1726810 CTTT-GAAAGGGTTACCATCGATTTGTGTGGG
1 CTTTAAAAAGGGTTGTCACCGACTTGTGTAGG
* ** * *
1726841 CTTT-GAAAGGGTTACCATCGACTTGTGTGGG
1 CTTTAAAAAGGGTTGTCACCGACTTGTGTAGG
*
1726872 CTTT-GAAAGGGTT
1 CTTTAAAAAGGGTT
1726885 ACCATAGACT
Statistics
Matches: 219, Mismatches: 39, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
29 3 0.01
30 1 0.00
31 106 0.48
32 81 0.37
33 24 0.11
34 4 0.02
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (32 bp):
CTTTAAAAAGGGTTGTCACCGACTTGTGTAGG
Found at i:1726790 original size:31 final size:31
Alignment explanation
Indices: 1726753--1727296 Score: 278
Period size: 31 Copynumber: 18.1 Consensus size: 31
1726743 AGGCTTTAAA
** * *
1726753 AAAGGGTTGTCATCGACTTGTGTGGACTTTA
1 AAAGGGTTACCATCGACTTGTGTGGGCTTTG
** *
1726784 AAAGGGTTGTCA-CTGACTTATGTGGGCTTTG
1 AAAGGGTTACCATC-GACTTGTGTGGGCTTTG
*
1726815 AAAGGGTTACCATCGATTTGTGTGGGCTTTG
1 AAAGGGTTACCATCGACTTGTGTGGGCTTTG
1726846 AAAGGGTTACCATCGACTTGTGTGGGCTTTG
1 AAAGGGTTACCATCGACTTGTGTGGGCTTTG
* * *
1726877 AAAGGGTTACCATAGACTTGCGTGGGCATTG
1 AAAGGGTTACCATCGACTTGTGTGGGCTTTG
* *
1726908 AAAGAGTTACCATCGACTTGTGTGGACTTTG
1 AAAGGGTTACCATCGACTTGTGTGGGCTTTG
** * *
1726939 AAAAAG-TGCCA-CTGAC-T-TGTGGGCTTGG
1 AAAGGGTTACCATC-GACTTGTGTGGGCTTTG
* * * *
1726967 AAAAGG-TGCCA-CTGAC-T-TATGGGCATTG
1 AAAGGGTTACCATC-GACTTGTGTGGGCTTTG
* *
1726995 AAA-GG-----ATCGATTTATGTGGGCTTTG
1 AAAGGGTTACCATCGACTTGTGTGGGCTTTG
* * * *
1727020 AGAAGAGTTGCCACCGACTTGTGTGGGCTTTA
1 A-AAGGGTTACCATCGACTTGTGTGGGCTTTG
* * * * *
1727052 AAAGAGTTGCCACCGACTT-TTTTGGCTTTG
1 AAAGGGTTACCATCGACTTGTGTGGGCTTTG
** * *
1727082 AAAAAG-TGCCA-CTGAC-T-TGTGGACTTTG
1 AAAGGGTTACCATC-GACTTGTGTGGGCTTTG
* * *
1727110 AAAAGG-TGCCA-CTAAC-T-TGTGGGCTTTG
1 AAAGGGTTACCATC-GACTTGTGTGGGCTTTG
* * * *
1727138 AAAGGGGTTGCCATCGATTTGTGTGGGCATTA
1 AAA-GGGTTACCATCGACTTGTGTGGGCTTTG
* * * *
1727170 AAAGGGGTTGCCATTGATTTGTGTGGGCTTTA
1 AAA-GGGTTACCATCGACTTGTGTGGGCTTTG
* * * *
1727202 AAAGGAGTTGCCACCAATTTGTGTGGGCTTTG
1 AAAGG-GTTACCATCGACTTGTGTGGGCTTTG
** * * *
1727234 AGAATAGTTGCCACCAACTTGTGTGGGCTTTG
1 A-AAGGGTTACCATCGACTTGTGTGGGCTTTG
* * *
1727266 AAAGGG-TGCCACCAAC-T-TGTGGGCTTTG
1 AAAGGGTTACCATCGACTTGTGTGGGCTTTG
1727294 AAA
1 AAA
1727297 AGATTGCCAC
Statistics
Matches: 434, Mismatches: 58, Indels: 45
0.81 0.11 0.08
Matches are distributed among these distances:
23 3 0.01
24 2 0.00
25 10 0.02
26 2 0.00
27 3 0.01
28 88 0.20
29 13 0.03
30 37 0.09
31 165 0.38
32 109 0.25
33 2 0.00
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (31 bp):
AAAGGGTTACCATCGACTTGTGTGGGCTTTG
Found at i:1726864 original size:93 final size:93
Alignment explanation
Indices: 1726753--1727334 Score: 344
Period size: 93 Copynumber: 6.5 Consensus size: 93
1726743 AGGCTTTAAA
* * * * *
1726753 AAAGGGTTGTCATCGACTTGTGTGGACTTTAAAAGGGTTGTCACTGACTTATGTGGGCTTTGAAA
1 AAAGAGTTGCCATCGACTTGTGTGGGCTTTAAAAGGGTTGCCACTGACTTATGTGGGCATTGAAA
1726818 GGGTTACCATCGATTTGTGTGGGCTTTG
66 GGGTTACCATCGATTTGTGTGGGCTTTG
* * * * **
1726846 AAAGGGTTACCATCGACTTGTGTGGGCTTTGAAAGGGTTACCA-TAGACTTGCGTGGGCATTGAA
1 AAAGAGTTGCCATCGACTTGTGTGGGCTTTAAAAGGGTTGCCACT-GACTTATGTGGGCATTGAA
* * *
1726910 AGAGTTACCATCGACTTGTGTGGACTTTG
65 AGGGTTACCATCGATTTGTGTGGGCTTTG
* *
1726939 AAAAAG-TGCCA-CTGAC-T-TGTGGGCTTGGAAAA-GG-TGCCACTGACTTA--TGGGCATTGA
1 AAAGAGTTGCCATC-GACTTGTGTGGGCTT-TAAAAGGGTTGCCACTGACTTATGTGGGCATTGA
*
1726996 AA-GG-----ATCGATTTATGTGGGCTTTG
64 AAGGGTTACCATCGATTTGTGTGGGCTTTG
* * * * * *
1727020 AGAAGAGTTGCCACCGACTTGTGTGGGCTTTAAAAGAGTTGCCACCGACTT-TTTTGGCTTTGAA
1 A-AAGAGTTGCCATCGACTTGTGTGGGCTTTAAAAGGGTTGCCACTGACTTATGTGGGCATTGAA
** * * *
1727084 AAAG-TGCCA-CTGA-CT-TGTGGACTTTG
65 AGGGTTACCATC-GATTTGTGTGGGCTTTG
* * * * * *
1727110 AAA-AGGTGCCA-CTAAC-T-TGTGGGCTTTGAAAGGGGTTGCCA-TCGATTTGTGTGGGCATTA
1 AAAGAGTTGCCATC-GACTTGTGTGGGCTTT-AAAAGGGTTGCCACT-GACTTATGTGGGCATTG
* * *
1727170 AAAGGGGTTGCCATTGATTTGTGTGGGCTTTA
63 AAA-GGGTTACCATCGATTTGTGTGGGCTTTG
* * * * ** ** * *
1727202 AAAGGAGTTGCCACCAATTTGTGTGGGCTTTGAGAATAGTTGCCACCAACTTGTGTGGGCTTTGA
1 AAA-GAGTTGCCATCGACTTGTGTGGGCTTT-AAAAGGGTTGCCACTGACTTATGTGGGCATTGA
* * **
1727267 AAGGG-TGCCA-CCAACT-TGTGGGCTTTG
64 AAGGGTTACCATCGATTTGTGTGGGCTTTG
* * * *
1727294 AAA-AGATTGCCA-CTAATT-TATGGGCTTTAAAAAGGTTGCCA
1 AAAGAG-TTGCCATCGACTTGTGTGGGCTTTAAAAGGGTTGCCA
1727335 TGGAGTTATG
Statistics
Matches: 384, Mismatches: 70, Indels: 75
0.73 0.13 0.14
Matches are distributed among these distances:
81 18 0.05
82 4 0.01
83 8 0.02
84 6 0.02
85 10 0.03
86 22 0.06
87 39 0.10
88 30 0.08
89 21 0.05
90 36 0.09
91 14 0.04
92 36 0.09
93 85 0.22
94 14 0.04
95 5 0.01
96 36 0.09
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.31
Consensus pattern (93 bp):
AAAGAGTTGCCATCGACTTGTGTGGGCTTTAAAAGGGTTGCCACTGACTTATGTGGGCATTGAAA
GGGTTACCATCGATTTGTGTGGGCTTTG
Found at i:1726969 original size:28 final size:28
Alignment explanation
Indices: 1726922--1727140 Score: 169
Period size: 28 Copynumber: 7.6 Consensus size: 28
1726912 AGTTACCATC
1726922 GACTTGTGTGGACTTTGAAAAAGTGCCACT
1 GACTTGTG-GG-CTTTGAAAAAGTGCCACT
* *
1726952 GACTTGTGGGCTTGGAAAAGGTGCCACT
1 GACTTGTGGGCTTTGAAAAAGTGCCACT
* * * * *
1726980 GACTTATGGGCATTG-AAAGGAT-CGATT
1 GACTTGTGGGCTTTGAAAAAG-TGCCACT
* * *
1727007 TA--TGTGGGCTTTGAGAAGAGTTGCCACC
1 GACTTGTGGGCTTTGA-AAAAG-TGCCACT
*
1727035 GACTTGTGTGGGCTTT-AAAAGAGTTGCCACC
1 GAC-T-TGTGGGCTTTGAAAA-AG-TGCCACT
* *
1727066 GACTTTTTTGGCTTTGAAAAAGTGCCACT
1 GAC-TTGTGGGCTTTGAAAAAGTGCCACT
* *
1727095 GACTTGTGGACTTTGAAAAGGTGCCACT
1 GACTTGTGGGCTTTGAAAAAGTGCCACT
*
1727123 AACTTGTGGGCTTTGAAA
1 GACTTGTGGGCTTTGAAA
1727141 GGGGTTGCCA
Statistics
Matches: 152, Mismatches: 27, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
25 9 0.06
27 13 0.09
28 69 0.45
29 11 0.07
30 20 0.13
31 20 0.13
32 10 0.07
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (28 bp):
GACTTGTGGGCTTTGAAAAAGTGCCACT
Found at i:1727115 original size:143 final size:143
Alignment explanation
Indices: 1726857--1727142 Score: 394
Period size: 143 Copynumber: 2.0 Consensus size: 143
1726847 AAGGGTTACC
* * * * *
1726857 ATCGACTTGTGTGGGCTTTGAAAGGGTTACCATAGACTTGCGTGGGCATTGAAAGAGTTACCATC
1 ATCGACTTATGTGGGCTTTGAAAGAGTTACCACAGACTTGCGTGGGCATTAAAAGAGTTACCACC
* *
1726922 GACTTGTGTGGACTTTGAAAAAGTGCCACTGACTTGTGGGCTTGGAAAAGGTGCCACTGACTTAT
66 GACTTGTGTGGACTTTGAAAAAGTGCCACTGACTTGTGGACTTGGAAAAGGTGCCACTAACTTAT
1726987 GGGCATTGAAAGG
131 GGGCATTGAAAGG
* * * * * *
1727000 ATCGATTTATGTGGGCTTTGAGAAGAGTTGCCACCGACTTGTGTGGGCTTTAAAAGAGTTGCCAC
1 ATCGACTTATGTGGGCTTTGA-AAGAGTTACCACAGACTTGCGTGGGCATTAAAAGAGTTACCAC
* * * *
1727065 CGACTTTTTTGG-CTTTGAAAAAGTGCCACTGACTTGTGGACTTTGAAAAGGTGCCACTAACTTG
65 CGACTTGTGTGGACTTTGAAAAAGTGCCACTGACTTGTGGACTTGGAAAAGGTGCCACTAACTTA
*
1727129 TGGGCTTTGAAAGG
130 TGGGCATTGAAAGG
1727143 GGTTGCCATC
Statistics
Matches: 124, Mismatches: 18, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
143 80 0.65
144 44 0.35
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.30
Consensus pattern (143 bp):
ATCGACTTATGTGGGCTTTGAAAGAGTTACCACAGACTTGCGTGGGCATTAAAAGAGTTACCACC
GACTTGTGTGGACTTTGAAAAAGTGCCACTGACTTGTGGACTTGGAAAAGGTGCCACTAACTTAT
GGGCATTGAAAGG
Found at i:1727333 original size:184 final size:182
Alignment explanation
Indices: 1727003--1727335 Score: 445
Period size: 184 Copynumber: 1.8 Consensus size: 182
1726993 TGAAAGGATC
* * *
1727003 GATTTATGTGGGCTTTGAGAAGAGTTGCCACCGACTTGTGTGGGCTTTAAAAGAGTTGCCACCGA
1 GATTTATGTGGGCTTTGAAAAGAGTTGCCACCAACTTGTGTGGGCTTTAAAAGAGTTGCCACCAA
* * ** *
1727068 CTTTTTTGGCTTTGAAAAAGTGCCACTGACTTGTGGACTTTGAAAAGGTGCCACTAACTTGTGGG
66 CTTTGTGGGCTTTGAAAAAGTGCCACCAACTTGTGGACTTTGAAAAGGTGCCACTAACTTATGGG
**
1727133 CTTTGAAAGGGGTTGCCATCGATTTGTGTGGGCATTAAAAGGGGTTGCCATT
131 CTTTGAAAAAGGTTGCCATCGATTTGTGTGGGCATTAAAAGGGGTTGCCATT
* * * *
1727185 GATTTGTGTGGGCTTT-AAAAGGAGTTGCCACCAATTTGTGTGGGCTTTGAGAATAGTTGCCACC
1 GATTTATGTGGGCTTTGAAAA-GAGTTGCCACCAACTTGTGTGGGCTTT-AAAAGAGTTGCCACC
** * * *
1727249 AACTTGTGTGGGCTTTGAAAGGGTGCCACCAACTTGTGGGCTTTGAAAAGATTGCCACTAATTTA
64 AACTT-TGTGGGCTTTGAAAAAGTGCCACCAACTTGTGGACTTTGAAAAG-GTGCCACTAACTTA
1727314 TGGGCTTT-AAAAAGGTTGCCAT
127 TGGGCTTTGAAAAAGGTTGCCAT
1727336 GGAGTTATGG
Statistics
Matches: 128, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
181 3 0.02
182 40 0.31
183 17 0.13
184 49 0.38
185 19 0.15
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (182 bp):
GATTTATGTGGGCTTTGAAAAGAGTTGCCACCAACTTGTGTGGGCTTTAAAAGAGTTGCCACCAA
CTTTGTGGGCTTTGAAAAAGTGCCACCAACTTGTGGACTTTGAAAAGGTGCCACTAACTTATGGG
CTTTGAAAAAGGTTGCCATCGATTTGTGTGGGCATTAAAAGGGGTTGCCATT
Found at i:1727431 original size:91 final size:90
Alignment explanation
Indices: 1727318--1727650 Score: 287
Period size: 91 Copynumber: 3.7 Consensus size: 90
1727308 AATTTATGGG
* * *
1727318 CTTT-AAAAAGGTTGCCATGGAGTTATGGACTTTGAAAATGGTGCCACGGAGTTGTGGAATTTAA
1 CTTTAAAAAAGGTTGCCATGGAGTTATGGACTTTGAAAAGGGTGCCACAGAGTTGTGGACTTTAA
** * * *
1727382 AAAAATTATGCCATAAAGTTGTGGA
66 AAAAAAGATGCAACAAAGTTGTAGA
* * * *
1727407 CTTTAAAAAAAAGTTACCATGGAGTTATGGACTTTTAAAAAGGGTGCCATAGAGTTGTGGACTTT
1 CTTT-AAAAAAGGTTGCCATGGAGTTATGGAC-TTTGAAAAGGGTGCCACAGAGTTGTGGACTTT
* *
1727472 AAACAAAAAGGTGCAACAGAGTTGTAGA
64 AAA-AAAAAGATGCAACAAAGTTGTAGA
* * * * * *
1727500 CTTTTAAAAAGGGTGCAACGGAGTTATAGACTTTGAAAAGGGTGCCACAAAGTTGTGGACTTTAG
1 CTTTAAAAAAGGTTGCCATGGAGTTATGGACTTTGAAAAGGGTGCCACAGAGTTGTGGACTTTA-
* * * * ** **
1727565 AAAAGAGGGTGCTACGGAGTTGGGGA
65 AAAAAAAGATGCAACAAAGTTGTAGA
* * * * * **
1727591 CTTT-AAAGAGG-TGCCA-CGAGTTATGGACTTTGAGAAGGATGACATGGAGTTGTGGACTTT
1 CTTTAAAAAAGGTTGCCATGGAGTTATGGACTTTGAAAAGGGTGCCACAGAGTTGTGGACTTT
1727651 TGAAAAGGGT
Statistics
Matches: 199, Mismatches: 40, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
88 36 0.18
89 8 0.04
90 6 0.03
91 76 0.38
92 52 0.26
93 21 0.11
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.28
Consensus pattern (90 bp):
CTTTAAAAAAGGTTGCCATGGAGTTATGGACTTTGAAAAGGGTGCCACAGAGTTGTGGACTTTAA
AAAAAAGATGCAACAAAGTTGTAGA
Found at i:1727456 original size:61 final size:62
Alignment explanation
Indices: 1727390--1727515 Score: 173
Period size: 62 Copynumber: 2.0 Consensus size: 62
1727380 AAAAAAATTA
* * ** *
1727390 TGCCATAAAGTTGTGGACTTTAAA-AAAAAGTTACCATGGAGTTATGGACTTTTAAAAAGGG
1 TGCCATAAAGTTGTGGACTTTAAACAAAAAGGTACAACAGAGTTATAGACTTTTAAAAAGGG
* * *
1727451 TGCCATAGAGTTGTGGACTTTAAACAAAAAGGTGCAACAGAGTTGTAGACTTTTAAAAAGGG
1 TGCCATAAAGTTGTGGACTTTAAACAAAAAGGTACAACAGAGTTATAGACTTTTAAAAAGGG
1727513 TGC
1 TGC
1727516 AACGGAGTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
61 23 0.41
62 33 0.59
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.28
Consensus pattern (62 bp):
TGCCATAAAGTTGTGGACTTTAAACAAAAAGGTACAACAGAGTTATAGACTTTTAAAAAGGG
Found at i:1727462 original size:30 final size:30
Alignment explanation
Indices: 1727319--1727884 Score: 269
Period size: 30 Copynumber: 19.0 Consensus size: 30
1727309 ATTTATGGGC
* * *
1727319 TTTAAAAAGGTTGCCATGGAGTTATGGAC-
1 TTTAAAAAGGGTGCCACGGAGTTGTGGACT
* * *
1727348 TTTGAAAATGGTGCCACGGAGTTGTGGAAT
1 TTTAAAAAGGGTGCCACGGAGTTGTGGACT
* *** ***
1727378 TTAAAAAAATTATGCCATAAAGTTGTGGACT
1 TT-TAAAAAGGGTGCCACGGAGTTGTGGACT
* * * * * *
1727409 TTAAAAAAAAGTTACCATGGAGTTATGGACT
1 TT-TAAAAAGGGTGCCACGGAGTTGTGGACT
**
1727440 TTTAAAAAGGGTGCCATAGAGTTGTGGACT
1 TTTAAAAAGGGTGCCACGGAGTTGTGGACT
* * * * *
1727470 TTAAACAAAAAGGTGCAACAGAGTTGTAGACT
1 TT-TA-AAAAGGGTGCCACGGAGTTGTGGACT
* * *
1727502 TTTAAAAAGGGTGCAACGGAGTTATAGAC-
1 TTTAAAAAGGGTGCCACGGAGTTGTGGACT
* **
1727531 TTTGAAAAGGGTGCCACAAAGTTGTGGACT
1 TTTAAAAAGGGTGCCACGGAGTTGTGGACT
* * *
1727561 TTAGAAAAGAGGGTGCTACGGAGTTGGGGAC-
1 TT-TAAAA-AGGGTGCCACGGAGTTGTGGACT
* *
1727592 TTTAAAGA-GGTGCCAC-GAGTTATGGAC-
1 TTTAAAAAGGGTGCCACGGAGTTGTGGACT
* * * * *
1727619 TTTGAGAAGGATGACATGGAGTTGTGGACT
1 TTTAAAAAGGGTGCCACGGAGTTGTGGACT
* *
1727649 TTTGAAAAGGGTGCCACAGAGTTGTGGAC-
1 TTTAAAAAGGGTGCCACGGAGTTGTGGACT
* * * * *
1727678 TTTAAGAGGGTGTGACACAGAGTCGTGGAC-
1 TTTAAAAAGG-GTGCCACGGAGTTGTGGACT
* * **
1727708 ATT-AAAAGGATGCCACGGAGTCATGGAC-
1 TTTAAAAAGGGTGCCACGGAGTTGTGGACT
* * * **
1727736 TTTGAGAAGAGTTGCCATTGAGTTGTGGACT
1 TTTAAAAAG-GGTGCCACGGAGTTGTGGACT
* * * * *
1727767 TTTGAGAAGGGTGCCACTGAGTCGTTGAC-
1 TTTAAAAAGGGTGCCACGGAGTTGTGGACT
* * * * *
1727796 TTGAGAAAGGATGCCAC-AAGTCGTGGACT
1 TTTAAAAAGGGTGCCACGGAGTTGTGGACT
* * * *
1727825 TTGAAAAAAAGG-GCCACTGAGTCGTGGAC-
1 TT-TAAAAAGGGTGCCACGGAGTTGTGGACT
* * **
1727854 TTTGATAAGGGTGCCATTGAGTTGTGGACT
1 TTTAAAAAGGGTGCCACGGAGTTGTGGACT
1727884 T
1 T
1727885 GAGAAGGGAT
Statistics
Matches: 412, Mismatches: 106, Indels: 37
0.74 0.19 0.07
Matches are distributed among these distances:
27 14 0.03
28 43 0.10
29 108 0.26
30 143 0.35
31 62 0.15
32 42 0.10
ACGTcount: A:0.31, C:0.12, G:0.30, T:0.27
Consensus pattern (30 bp):
TTTAAAAAGGGTGCCACGGAGTTGTGGACT
Found at i:1727660 original size:118 final size:118
Alignment explanation
Indices: 1727531--1727783 Score: 327
Period size: 118 Copynumber: 2.1 Consensus size: 118
1727521 AGTTATAGAC
* * *
1727531 TTTGAAAAGGGTGCCACAAAGTTGTGGACTTTAGAAAAGAGG-GTG-CTACGGAGTTGGGGACTT
1 TTTGAAAAGGGTGCCACAAAGTTGTGGACTTT--AAAAG-GGTGTGAC-ACAGAGTCGGGGACAT
*
1727594 TAAAGAGG-TGCCAC-GAGTTATGGACTTTGAGAAG-GATGACATGGAGTTGTGGACT
62 TAAA-AGGATGCCACGGAGTCATGGACTTTGAGAAGAGATGACATGGAGTTGTGGACT
* * *
1727649 TTTGAAAAGGGTGCCACAGAGTTGTGGACTTTAAGAGGGTGTGACACAGAGTCGTGGACATTAAA
1 TTTGAAAAGGGTGCCACAAAGTTGTGGACTTTAAAAGGGTGTGACACAGAGTCGGGGACATTAAA
* * *
1727714 AGGATGCCACGGAGTCATGGACTTTGAGAAGAGTTGCCATTGAGTTGTGGACT
66 AGGATGCCACGGAGTCATGGACTTTGAGAAGAGATGACATGGAGTTGTGGACT
*
1727767 TTTGAGAAGGGTGCCAC
1 TTTGAAAAGGGTGCCAC
1727784 TGAGTCGTTG
Statistics
Matches: 119, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
115 5 0.04
116 29 0.24
117 20 0.17
118 65 0.55
ACGTcount: A:0.28, C:0.13, G:0.34, T:0.25
Consensus pattern (118 bp):
TTTGAAAAGGGTGCCACAAAGTTGTGGACTTTAAAAGGGTGTGACACAGAGTCGGGGACATTAAA
AGGATGCCACGGAGTCATGGACTTTGAGAAGAGATGACATGGAGTTGTGGACT
Found at i:1727810 original size:29 final size:30
Alignment explanation
Indices: 1727528--1728004 Score: 255
Period size: 29 Copynumber: 16.3 Consensus size: 30
1727518 CGGAGTTATA
* ** *
1727528 GACTTTGA-AAAGGGTGCCACAAAGTTGTG
1 GACTTTGAGAAAGGATGCCACTGAGTCGTG
* * * * * *
1727557 GACTTTAGAAAAGAGGGTGCTACGGAGTTGGG
1 GACTTT-GAGAA-AGGATGCCACTGAGTCGTG
**
1727589 GACTTT-A-AAGAGG-TGCCAC-GAGTTATG
1 GACTTTGAGAA-AGGATGCCACTGAGTCGTG
* *
1727616 GACTTTGAG-AAGGATGACA-TGGAGTTGTG
1 GACTTTGAGAAAGGATGCCACT-GAGTCGTG
* * *
1727645 GACTTTTGA-AAAGGGTGCCACAGAGTTGTG
1 GAC-TTTGAGAAAGGATGCCACTGAGTCGTG
* * * * *
1727675 GACTTTAAG-AGGGTGTGACACAGAGTCGTG
1 GACTTTGAGAAAGG-ATGCCACTGAGTCGTG
* * *
1727705 GACATT-A-AAAGGATGCCACGGAGTCATG
1 GACTTTGAGAAAGGATGCCACTGAGTCGTG
* * *
1727733 GACTTTGAG-AAGAGTTGCCATTGAGTTGTG
1 GACTTTGAGAAAG-GATGCCACTGAGTCGTG
* *
1727763 GACTTTTGAG-AAGGGTGCCACTGAGTCGTT
1 GAC-TTTGAGAAAGGATGCCACTGAGTCGTG
*
1727793 GAC-TTGAGAAAGGATGCCAC-AAGTCGTG
1 GACTTTGAGAAAGGATGCCACTGAGTCGTG
*
1727821 GACTTTGAAAAAAAGG--GCCACTGAGTCGTG
1 GACTTTG--AGAAAGGATGCCACTGAGTCGTG
* * * *
1727851 GACTTTGA-TAAGGGTGCCATTGAGTTGTG
1 GACTTTGAGAAAGGATGCCACTGAGTCGTG
* * *
1727880 GAC-TTGAGAAGGGATGTCACTAAGTCGTG
1 GACTTTGAGAAAGGATGCCACTGAGTCGTG
* **
1727909 GACTTTGA-AAAGAGATGCCACAGAGTTAT-
1 GACTTTGAGAAAG-GATGCCACTGAGTCGTG
* *
1727938 GACTTT-AAAAAGGGATGCCACTGAG-CATG
1 GACTTTGAGAAA-GGATGCCACTGAGTCGTG
* *
1727967 GACTTTGA-AAATGGATGCCACTAAGTCATG
1 GACTTTGAGAAA-GGATGCCACTGAGTCGTG
1727997 GACTTTGA
1 GACTTTGA
1728005 ATGGGTTACT
Statistics
Matches: 358, Mismatches: 57, Indels: 65
0.75 0.12 0.14
Matches are distributed among these distances:
27 19 0.05
28 50 0.14
29 131 0.37
30 120 0.34
31 17 0.05
32 21 0.06
ACGTcount: A:0.29, C:0.14, G:0.32, T:0.25
Consensus pattern (30 bp):
GACTTTGAGAAAGGATGCCACTGAGTCGTG
Found at i:1727906 original size:58 final size:58
Alignment explanation
Indices: 1727528--1728004 Score: 283
Period size: 58 Copynumber: 8.1 Consensus size: 58
1727518 CGGAGTTATA
* ** * * * ** *
1727528 GACTTTGAAAAGGGTGCCACAAAGTTGTGGACTTTAGAAAAGAGGGTGCTACGGAGTTGGG
1 GACTTTGAGAAGGGTGCCACTGAGTCGTGGACTTT-G-AAA-AGGATGCCATTGAGTTGTG
** * * *
1727589 GACTTT-A-AAGAGGTGCCAC-GAGTTATGGACTTTGAGAAGGATGACATGGAGTTGTG
1 GACTTTGAGAAG-GGTGCCACTGAGTCGTGGACTTTGAAAAGGATGCCATTGAGTTGTG
* * * * * * ** *
1727645 GACTTTTGAAAAGGGTGCCACAGAGTTGTGGACTTT-AAGAGGGTGTGACACAGAGTCGTG
1 GAC-TTTGAGAAGGGTGCCACTGAGTCGTGGACTTTGAA-AAGG-ATGCCATTGAGTTGTG
* * * * * * *
1727705 GACATT-AAAAGGATGCCACGGAGTCATGGACTTTGAGAAGAGTTGCCATTGAGTTGTG
1 GACTTTGAGAAGGGTGCCACTGAGTCGTGGACTTTGAAAAG-GATGCCATTGAGTTGTG
* ** *
1727763 GACTTTTGAGAAGGGTGCCACTGAGTCGTTGAC-TTGAGAAAGGATGCCA-CAAGTCGTG
1 GAC-TTTGAGAAGGGTGCCACTGAGTCGTGGACTTTGA-AAAGGATGCCATTGAGTTGTG
* * * *
1727821 GACTTTGAAAAAAAGG-GCCACTGAGTCGTGGACTTTGATAAGGGTGCCATTGAGTTGTG
1 GACTTTG--AGAAGGGTGCCACTGAGTCGTGGACTTTGAAAAGGATGCCATTGAGTTGTG
* * ** *
1727880 GAC-TTGAGAAGGGATGTCACTAAGTCGTGGACTTTGAAAAGAGATGCCACAGAGTTAT-
1 GACTTTGAGAAGGG-TGCCACTGAGTCGTGGACTTTGAAAAG-GATGCCATTGAGTTGTG
* * * * * **
1727938 GACTTTAAAAAGGGATGCCACTGAG-CATGGACTTTGAAAATGGATGCCACTAAGTCATG
1 GACTTTGAGAAGGG-TGCCACTGAGTCGTGGACTTTGAAAA-GGATGCCATTGAGTTGTG
1727997 GACTTTGA
1 GACTTTGA
1728005 ATGGGTTACT
Statistics
Matches: 330, Mismatches: 64, Indels: 46
0.75 0.15 0.10
Matches are distributed among these distances:
56 22 0.07
57 9 0.03
58 141 0.43
59 105 0.32
60 47 0.14
61 6 0.02
ACGTcount: A:0.29, C:0.14, G:0.32, T:0.25
Consensus pattern (58 bp):
GACTTTGAGAAGGGTGCCACTGAGTCGTGGACTTTGAAAAGGATGCCATTGAGTTGTG
Found at i:1727989 original size:88 final size:88
Alignment explanation
Indices: 1727261--1728005 Score: 455
Period size: 88 Copynumber: 8.4 Consensus size: 88
1727251 CTTGTGTGGG
* * * * * * * * *
1727261 CTTTG-AAAGGGTGCCACCAACTTGTGGGCTTTGAAAAGA-TTGCCACTA-ATTTATGGGCTTTA
1 CTTTGAAAAGGATGCCACTAAGTCGTGGACTTTGAAAAGAGGTGCCAC-AGAGTTGTGGACTTTA
* *
1727323 AAAAGGTTGCCA-TGGAGTTATGGA
65 AAAAGGGTGCCACT-GAGTCATGGA
** * * * * ** * *
1727347 CTTTGAAAATGG-TGCCACGGAGTTGTGGAATTTAAAAAAATTATGCCATAAAGTTGTGGACTTT
1 CTTTGAAAA-GGATGCCACTAAGTCGTGGACTTTGAAAAGA-GGTGCCACAGAGTTGTGGACTTT
* * * *
1727411 AAAAAAAAGTTACCA-TGGAGTTATGGA
64 --AAAAAGGGTGCCACT-GAGTCATGGA
* * * * * * *
1727438 CTTTTAAAAAGGGTGCCA-TAGAGTTGTGGACTTTAAACAAAAAGGTGCAACAGAGTTGTAGACT
1 C-TTTGAAAAGGATGCCACTA-AGTCGTGGACTTT-GA-AAAGAGGTGCCACAGAGTTGTGGAC-
* * * *
1727502 TTTAAAAAGGGTGCAACGGAGTTATAGA
61 TTTAAAAAGGGTGCCACTGAGTCATGGA
* * * * * *
1727530 CTTTGAAAAGGGTGCCACAAAGTTGTGGACTTTAGAAAAGAGGGTGCTACGGAGTTGGGGACTTT
1 CTTTGAAAAGGATGCCACTAAGTCGTGGACTTT-GAAAAGA-GGTGCCACAGAGTTGTGGACTTT
* *
1727595 AAAGA-GGTGCCAC-GAGTTATGGA
64 AAAAAGGGTGCCACTGAGTCATGGA
* * * *
1727618 CTTTGAGAAGGATGACA-TGGAGTTGTGGACTTTTGAAAAG-GGTGCCACAGAGTTGTGGACTTT
1 CTTTGAAAAGGATGCCACT-AAGTCGTGGAC-TTTGAAAAGAGGTGCCACAGAGTTGTGGACTTT
* * * * *
1727681 AAGAGGGTGTGACACAGAGTCGTGGA
64 AAAAAGG-GTGCCACTGAGTCATGGA
* ** * * * ** *
1727707 CATT-AAAAGGATGCCACGGAGTCATGGACTTTGAGAAGAGTTGCCATTGAGTTGTGGACTTTTG
1 CTTTGAAAAGGATGCCACTAAGTCGTGGACTTTGAAAAGAGGTGCCACAGAGTTGTGGAC-TTTA
* * *
1727771 AGAAGGGTGCCACTGAGTCGTTGA
65 AAAAGGGTGCCACTGAGTCATGGA
* * *
1727795 C-TTGAGAAAGGATGCCAC-AAGTCGTGGACTTTGAAAAAAAGG-GCCACTGAGTCGTGGACTTT
1 CTTTGA-AAAGGATGCCACTAAGTCGTGGACTTTG-AAAAGAGGTGCCACAGAGTTGTGGACTTT
* * * **
1727857 GATAAGGGTGCCATTGAGTTGTGGA
64 AAAAAGGGTGCCACTGAGTCATGGA
* * * *
1727882 C-TTGAGAAGGGATGTCACTAAGTCGTGGACTTTGAAAAGAGATGCCACAGAGTTAT-GACTTTA
1 CTTTGA-AAAGGATGCCACTAAGTCGTGGACTTTGAAAAGAGGTGCCACAGAGTTGTGGACTTTA
1727945 AAAAGGGATGCCACTGAG-CATGGA
65 AAAAGGG-TGCCACTGAGTCATGGA
*
1727969 CTTTGAAAATGGATGCCACTAAGTCATGGACTTTGAA
1 CTTTGAAAA-GGATGCCACTAAGTCGTGGACTTTGAA
1728006 TGGGTTACTT
Statistics
Matches: 531, Mismatches: 96, Indels: 62
0.77 0.14 0.09
Matches are distributed among these distances:
86 27 0.05
87 100 0.19
88 192 0.36
89 61 0.11
90 11 0.02
91 72 0.14
92 44 0.08
93 16 0.03
94 8 0.02
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.26
Consensus pattern (88 bp):
CTTTGAAAAGGATGCCACTAAGTCGTGGACTTTGAAAAGAGGTGCCACAGAGTTGTGGACTTTAA
AAAGGGTGCCACTGAGTCATGGA
Found at i:1732803 original size:20 final size:20
Alignment explanation
Indices: 1732780--1732855 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
1732770 AAAGTACCCA
1732780 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
* * * *
1732800 AATGTAACGATACATGTATG
1 AATGTATCGATACATTTTTC
* *
1732820 AATGTATCGATATATTCTTC
1 AATGTATCGATACATTTTTC
1732840 AATGTATCGATACATT
1 AATGTATCGATACATT
1732856 CTATTTTTTT
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:1736937 original size:13 final size:13
Alignment explanation
Indices: 1736919--1736943 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1736909 CAATTCATCA
1736919 TGTATCGATACAT
1 TGTATCGATACAT
1736932 TGTATCGATACA
1 TGTATCGATACA
1736944 ATGTGCCATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1736954 original size:33 final size:32
Alignment explanation
Indices: 1736899--1736963 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
1736889 TTTGAAGTAA
1736899 TGTATCGATACAATTCATCATGTATCGATACAT
1 TGTATCGATACAATTCA-CATGTATCGATACAT
*
1736932 TGTATCGATACAATGTGC-CATGTATTGATACA
1 TGTATCGATACAAT-T-CACATGTATCGATACA
1736964 AACAGTGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAATTCACATGTATCGATACAT
Found at i:1739397 original size:22 final size:21
Alignment explanation
Indices: 1739362--1739411 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1739352 TTTGTTGATG
*
1739362 ATTTTG-A-TGAAAAATGAAGT
1 ATTTTGAAGTGAAAAAT-AAGA
1739382 ATTTTGAAGTGAAAAATAAGA
1 ATTTTGAAGTGAAAAATAAGA
*
1739403 AATTTGAAG
1 ATTTTGAAG
1739412 AATATTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 12 0.46
22 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAATAAGA
Found at i:1739408 original size:21 final size:22
Alignment explanation
Indices: 1739369--1739411 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1739359 ATGATTTTGA
* *
1739369 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
1739391 TGAAAAAT-AAGAAATTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
1739412 AATATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:1741545 original size:113 final size:113
Alignment explanation
Indices: 1741347--1741570 Score: 439
Period size: 113 Copynumber: 2.0 Consensus size: 113
1741337 TTCTTATAGT
1741347 TGGATGATCACCTGGTCTTTTTACTAAAGACCAAACTTTGCTTCTCTCAAATTGATTTAGTTCTT
1 TGGATGATCACCTGGTCTTTTTACTAAAGACCAAACTTTGCTTCTCTCAAATTGATTTAGTTCTT
1741412 CTTACATAGCCATAATCCAATTTTCATTTTGTATAGCCTCATCTATGC
66 CTTACATAGCCATAATCCAATTTTCATTTTGTATAGCCTCATCTATGC
*
1741460 TGGATGATCACCTGGTCTTTTTACTAAAGACCAAACTTTGCTTCTCTCATATTGATTTAGTTCTT
1 TGGATGATCACCTGGTCTTTTTACTAAAGACCAAACTTTGCTTCTCTCAAATTGATTTAGTTCTT
1741525 CTTACATAGCCATAATCCAATTTTCATTTTGTATAGCCTCATCTAT
66 CTTACATAGCCATAATCCAATTTTCATTTTGTATAGCCTCATCTAT
1741571 TCTTTTAGGT
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
113 110 1.00
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.42
Consensus pattern (113 bp):
TGGATGATCACCTGGTCTTTTTACTAAAGACCAAACTTTGCTTCTCTCAAATTGATTTAGTTCTT
CTTACATAGCCATAATCCAATTTTCATTTTGTATAGCCTCATCTATGC
Found at i:1745871 original size:20 final size:19
Alignment explanation
Indices: 1745827--1745880 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
1745817 GTTTGAAGCA
1745827 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCA-C
*
1745847 TTGTATCGATACAATGTGC-C
1 ATGTATCGATACAAT-T-CAC
1745867 ATGTATCGATACAA
1 ATGTATCGATACAA
1745881 ACAGTGGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 28 0.93
21 1 0.03
22 1 0.03
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (19 bp):
ATGTATCGATACAATTCAC
Found at i:1746295 original size:19 final size:20
Alignment explanation
Indices: 1746268--1746320 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
1746258 ACACCCAAAA
* *
1746268 GTATTGATACATGATC-ATT
1 GTATCGATACATGAGCAATT
*
1746287 GTATCGATACATGGGCAATT
1 GTATCGATACATGAGCAATT
*
1746307 GTATCGAAACATGA
1 GTATCGATACATGA
1746321 AACTGGCAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGAGCAATT
Found at i:1747233 original size:20 final size:20
Alignment explanation
Indices: 1747210--1747260 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1747200 CCTTTAAATA
1747210 TATCGATACAAATTGCACAG
1 TATCGATACAAATTGCACAG
*
1747230 TATCGATACAAATTGCATAG
1 TATCGATACAAATTGCACAG
1747250 TATCGATACAA
1 TATCGATACAA
1747261 TGTATCGATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (20 bp):
TATCGATACAAATTGCACAG
Found at i:1747311 original size:21 final size:20
Alignment explanation
Indices: 1747259--1747313 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
1747249 GTATCGATAC
**
1747259 AATGTATCGATACATGACCA
1 AATGTATCGATACATGAAAA
* *
1747279 AATGCATTGATACATGAAAA
1 AATGTATCGATACATGAAAA
1747299 GAATGTATCGATACA
1 -AATGTATCGATACA
1747314 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACATGAAAA
Found at i:1747383 original size:13 final size:13
Alignment explanation
Indices: 1747365--1747390 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1747355 ACTCACAATA
1747365 TGTATCGATACAT
1 TGTATCGATACAT
1747378 TGTATCGATACAT
1 TGTATCGATACAT
1747391 CCCAAAATGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1747406 original size:33 final size:32
Alignment explanation
Indices: 1747345--1747412 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
1747335 GTAGCCAAAT
*
1747345 TTGTATCGATACTCACAATATGTATCGATACA
1 TTGTATCGATACTCACAAAATGTATCGATACA
*
1747377 TTGTATCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATAC-TCACAAAATGTATCGATACA
1747410 TTG
1 TTG
1747413 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 12 0.36
33 21 0.64
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACTCACAAAATGTATCGATACA
Found at i:1749476 original size:13 final size:13
Alignment explanation
Indices: 1749458--1749482 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1749448 ACATTCCTTG
1749458 TATCGATACATTA
1 TATCGATACATTA
1749471 TATCGATACATT
1 TATCGATACATT
1749483 GTGTCAATAC
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:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (13 bp):
TATCGATACATTA
Found at i:1751406 original size:24 final size:22
Alignment explanation
Indices: 1751379--1751425 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
1751369 GAAAATAAAT
1751379 ATTTGTTTTGATAAAGGGGGAGAA
1 ATTT-TTTT-ATAAAGGGGGAGAA
**
1751403 ATTTTTTTATCTAGGGGGAGAA
1 ATTTTTTTATAAAGGGGGAGAA
1751425 A
1 A
1751426 ATCTCGTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 13 0.62
23 4 0.19
24 4 0.19
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (22 bp):
ATTTTTTTATAAAGGGGGAGAA
Found at i:1752035 original size:19 final size:18
Alignment explanation
Indices: 1752010--1752067 Score: 80
Period size: 19 Copynumber: 3.1 Consensus size: 18
1752000 TTGTATCGAT
*
1752010 ACATTGTATCAATACATG
1 ACATTGTATCGATACATG
1752028 ATCATTGTATCGATACATGG
1 A-CATTGTATCGATACAT-G
1752048 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
1752067 A
1 A
1752068 AACTGGCAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 1 0.03
19 18 0.50
20 17 0.47
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (18 bp):
ACATTGTATCGATACATG
Found at i:1752056 original size:20 final size:20
Alignment explanation
Indices: 1752011--1752066 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
1752001 TGTATCGATA
*
1752011 CATTGTATCAATACAT-GAT
1 CATTGTATCGATACATGGAT
1752030 CATTGTATCGATACATGGA-
1 CATTGTATCGATACATGGAT
1752049 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
1752067 AAACTGGCAG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (20 bp):
CATTGTATCGATACATGGAT
Found at i:1752129 original size:13 final size:13
Alignment explanation
Indices: 1752111--1752141 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1752101 CGATACATGG
*
1752111 TACATTGTATCGA
1 TACATTGTATCAA
1752124 TACATTGTATCAA
1 TACATTGTATCAA
1752137 TACAT
1 TACAT
1752142 GATGAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (13 bp):
TACATTGTATCAA
Found at i:1752140 original size:33 final size:33
Alignment explanation
Indices: 1752095--1752161 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
1752085 CTACCATTGT
* *
1752095 TTGTATCGATACATGGT-ACATTGTATCGATACA
1 TTGTATCAATACATGATGA-ATTGTATCGATACA
1752128 TTGTATCAATACATGATGAATTGTATCGATACA
1 TTGTATCAATACATGATGAATTGTATCGATACA
1752161 T
1 T
1752162 GGCTTGTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.37
Consensus pattern (33 bp):
TTGTATCAATACATGATGAATTGTATCGATACA
Found at i:1758137 original size:19 final size:19
Alignment explanation
Indices: 1758113--1758175 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
1758103 TAGCCAAACT
1758113 TGTATCGATACACAAAGTA
1 TGTATCGATACACAAAGTA
1758132 TGTATCGAT--AC--A--A
1 TGTATCGATACACAAAGTA
1758145 TGTATCGATACACAAAGTA
1 TGTATCGATACACAAAGTA
1758164 TGTATCGATACA
1 TGTATCGATACA
1758176 ATGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 10 0.26
15 3 0.08
17 3 0.08
19 22 0.58
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (19 bp):
TGTATCGATACACAAAGTA
Found at i:1758149 original size:13 final size:13
Alignment explanation
Indices: 1758131--1758188 Score: 62
Period size: 13 Copynumber: 4.0 Consensus size: 13
1758121 TACACAAAGT
1758131 ATGTATCGATACA
1 ATGTATCGATACA
1758144 ATGTATCGATACACAAA
1 ATGTATCGAT--AC--A
1758161 GTATGTATCGATACA
1 --ATGTATCGATACA
1758176 ATGTATCGATACA
1 ATGTATCGATACA
1758189 CCAAAAATTG
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.59
15 3 0.08
17 3 0.08
19 10 0.26
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1758154 original size:32 final size:32
Alignment explanation
Indices: 1758113--1758208 Score: 158
Period size: 32 Copynumber: 3.0 Consensus size: 32
1758103 TAGCCAAACT
1758113 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAGTATGTATCGATACAA
1758145 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAGTATGTATCGATACAA
*
1758177 TGTATCGATACACCAAA-AATTGTATCGATACA
1 TGTATCGATACA-CAAAGTA-TGTATCGATACA
1758209 TTGGCTTGTA
Statistics
Matches: 61, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
32 45 0.74
33 16 0.26
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAAGTATGTATCGATACAA
Found at i:1758273 original size:20 final size:22
Alignment explanation
Indices: 1758242--1758285 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
1758232 GCTACATTTT
1758242 CAAATATGTATCGATACA-TCA
1 CAAATATGTATCGATACATTCA
1758263 CAAAT-TGTATCGATACATTCA
1 CAAATATGTATCGATACATTCA
1758284 CA
1 CA
1758286 CGGGAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (22 bp):
CAAATATGTATCGATACATTCA
Found at i:1760444 original size:22 final size:21
Alignment explanation
Indices: 1760416--1760468 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1760406 ATTGCAAGTT
1760416 AAAATAAAAAATTTAGCTAATG-
1 AAAATAAAAAA-TTAGCTAA-GA
**
1760438 AAAATAATGAATTAGCTAAGA
1 AAAATAAAAAATTAGCTAAGA
1760459 AAAATAAAAA
1 AAAATAAAAA
1760469 CTTGCATGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 16 0.62
22 9 0.35
ACGTcount: A:0.64, C:0.04, G:0.09, T:0.23
Consensus pattern (21 bp):
AAAATAAAAAATTAGCTAAGA
Found at i:1760454 original size:21 final size:21
Alignment explanation
Indices: 1760394--1760461 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
1760384 ACTTTGAAAA
1760394 GAAAATAAATGAATT-GC-AAGT
1 GAAAAT-AATGAATTAGCTAA-T
* **
1760415 TAAAATAAAAAATTTAGCTAAT
1 GAAAATAATGAA-TTAGCTAAT
1760437 GAAAATAATGAATTAGCTAA-
1 GAAAATAATGAATTAGCTAAT
1760457 GAAAA
1 GAAAA
1760462 ATAAAAACTT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
20 9 0.24
21 15 0.39
22 12 0.32
23 2 0.05
ACGTcount: A:0.57, C:0.04, G:0.13, T:0.25
Consensus pattern (21 bp):
GAAAATAATGAATTAGCTAAT
Found at i:1764391 original size:13 final size:13
Alignment explanation
Indices: 1764373--1764411 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1764363 ACATTTTTCT
1764373 TTGTATCGATACA
1 TTGTATCGATACA
1764386 TTGTATCGATACA
1 TTGTATCGATACA
*
1764399 CTGTATCGATACA
1 TTGTATCGATACA
1764412 GGGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1764878 original size:20 final size:21
Alignment explanation
Indices: 1764853--1764895 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
1764843 GCAGCACCCA
*
1764853 CCAGGTCGCGACC-GGCACTC
1 CCAGGTCGCAACCGGGCACTC
1764873 CCAGGTCGCAACCGGGCACTC
1 CCAGGTCGCAACCGGGCACTC
1764894 CC
1 CC
1764896 CACACTAGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.16, C:0.47, G:0.28, T:0.09
Consensus pattern (21 bp):
CCAGGTCGCAACCGGGCACTC
Found at i:1766075 original size:22 final size:20
Alignment explanation
Indices: 1766033--1766075 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
1766023 GTGTTTAATG
*
1766033 TATTTGCTTGACTTTGTTTT
1 TATTTGCTTGACTTTGATTT
1766053 TATTTGCATTGTACTTTGATTT
1 TATTTGC-TTG-ACTTTGATTT
1766075 T
1 T
1766076 TTAATCTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 3 0.15
22 10 0.50
ACGTcount: A:0.14, C:0.09, G:0.14, T:0.63
Consensus pattern (20 bp):
TATTTGCTTGACTTTGATTT
Found at i:1767007 original size:13 final size:13
Alignment explanation
Indices: 1766989--1767014 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1766979 TACACAAAGT
1766989 ATGTATCGATACA
1 ATGTATCGATACA
1767002 ATGTATCGATACA
1 ATGTATCGATACA
1767015 CCAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1767012 original size:32 final size:33
Alignment explanation
Indices: 1766971--1767034 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1766961 TAGCCAAACT
*
1766971 TGTATCGATACA-C-AAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAAT-TGTATCGATACAA
1767003 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
1767035 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 12 0.41
33 13 0.45
34 4 0.14
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:1767099 original size:20 final size:22
Alignment explanation
Indices: 1767068--1767111 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
1767058 GCTACATTTT
1767068 CAAATATGTATCGATACA-TCA
1 CAAATATGTATCGATACATTCA
1767089 CAAAT-TGTATCGATACATTCA
1 CAAATATGTATCGATACATTCA
1767110 CA
1 CA
1767112 CGGGAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (22 bp):
CAAATATGTATCGATACATTCA
Found at i:1768256 original size:51 final size:52
Alignment explanation
Indices: 1768143--1768278 Score: 193
Period size: 51 Copynumber: 2.6 Consensus size: 52
1768133 TACCTACAAC
* * * *
1768143 TATCAATACATTGAAGAATGTATCGATACATTTAGGTTAAAAACCCAAAATG
1 TATCGATACAATGAAGAATGTATAGATACATTTAGGGTAAAAACCCAAAATG
* *
1768195 TATCGATACAATGAAGAATGTATTGATACATTT-GGGTCAAAACCCAAAATG
1 TATCGATACAATGAAGAATGTATAGATACATTTAGGGTAAAAACCCAAAATG
* *
1768246 TATTGATACAATGAAAAATGTATAGATACATTT
1 TATCGATACAATGAAGAATGTATAGATACATTT
1768279 TCATTCCAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
51 46 0.61
52 30 0.39
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (52 bp):
TATCGATACAATGAAGAATGTATAGATACATTTAGGGTAAAAACCCAAAATG
Found at i:1771032 original size:20 final size:20
Alignment explanation
Indices: 1770980--1771061 Score: 112
Period size: 21 Copynumber: 4.0 Consensus size: 20
1770970 AAAAAAAAAA
1770980 ATTC-CAAATGTATCGATAC
1 ATTCACAAATGTATCGATAC
***
1770999 ATTTGTAGAATGTATCGATAC
1 ATTCACA-AATGTATCGATAC
1771020 ATTCACAAATGTATCGATAC
1 ATTCACAAATGTATCGATAC
1771040 ATTCTACAAATGTATCGATAC
1 ATTC-ACAAATGTATCGATAC
1771061 A
1 A
1771062 GGGTCCCAAC
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
19 3 0.05
20 18 0.33
21 34 0.62
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (20 bp):
ATTCACAAATGTATCGATAC
Found at i:1771041 original size:41 final size:40
Alignment explanation
Indices: 1770980--1771061 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 40
1770970 AAAAAAAAAA
* *
1770980 ATTCCAAATGTATCGATACATTTGTA-GAATGTATCGATAC
1 ATTCCAAATGTATCGATACA-TTCTACAAATGTATCGATAC
1771020 ATTCACAAATGTATCGATACATTCTACAAATGTATCGATAC
1 ATTC-CAAATGTATCGATACATTCTACAAATGTATCGATAC
1771061 A
1 A
1771062 GGGTCCCAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 8 0.21
41 30 0.79
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (40 bp):
ATTCCAAATGTATCGATACATTCTACAAATGTATCGATAC
Found at i:1771121 original size:19 final size:19
Alignment explanation
Indices: 1771097--1771164 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1771087 AATTCAACGA
1771097 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1771116 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1771131 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1771148 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1771165 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1771135 original size:32 final size:32
Alignment explanation
Indices: 1771099--1771161 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1771089 TTCAACGATT
*
1771099 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1771131 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
1771162 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1771136 original size:13 final size:13
Alignment explanation
Indices: 1771118--1771142 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1771108 ACATAAGTTT
1771118 TGTATCGATACAA
1 TGTATCGATACAA
1771131 TGTATCGATACA
1 TGTATCGATACA
1771143 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1771222 original size:13 final size:13
Alignment explanation
Indices: 1771204--1771229 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1771194 CATTTTTCTG
1771204 TGTATCGATACAT
1 TGTATCGATACAT
1771217 TGTATCGATACAT
1 TGTATCGATACAT
1771230 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1771226 original size:33 final size:33
Alignment explanation
Indices: 1771184--1771250 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1771174 GCCAAGGAAA
***
1771184 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1771217 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1771250 T
1 T
1771251 TGGAATTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1773762 original size:28 final size:27
Alignment explanation
Indices: 1773695--1773767 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
1773685 CTTCACAATC
* *
1773695 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
1773722 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
1773750 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
1773768 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:1773812 original size:51 final size:51
Alignment explanation
Indices: 1773750--1773920 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
1773740 TTATTTCTGA
* * *
1773750 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
1773801 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
1773854 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
1773906 GAGGATACTCCAACC
1 GGGGATACTCCAACC
1773921 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:1773939 original size:28 final size:28
Alignment explanation
Indices: 1773903--1773984 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
1773893 ATTTTTCACA
*
1773903 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
1773931 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
1773959 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
1773985 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 41 0.89
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:1786393 original size:13 final size:13
Alignment explanation
Indices: 1786375--1786454 Score: 65
Period size: 13 Copynumber: 5.9 Consensus size: 13
1786365 ACCTTCTCTT
1786375 CAAAAAAAAAGAG
1 CAAAAAAAAAGAG
*
1786388 CAAAAAAAAAAAAG
1 C-AAAAAAAAAGAG
* *
1786402 CAAAAAAAAAAAA
1 CAAAAAAAAAGAG
*
1786415 CAAAAAAACAA-AA
1 CAAAAAAA-AAGAG
1786428 CAAAGAAAAAGAGAG
1 CAAA-AAAAA-AGAG
1786443 -AAAAGAAAAAGA
1 CAAAA-AAAAAGA
1786455 ACCTGCTTAA
Statistics
Matches: 58, Mismatches: 3, Indels: 12
0.79 0.04 0.16
Matches are distributed among these distances:
13 31 0.53
14 26 0.45
15 1 0.02
ACGTcount: A:0.81, C:0.07, G:0.11, T:0.00
Consensus pattern (13 bp):
CAAAAAAAAAGAG
Found at i:1786395 original size:14 final size:14
Alignment explanation
Indices: 1786376--1786454 Score: 76
Period size: 14 Copynumber: 5.8 Consensus size: 14
1786366 CCTTCTCTTC
1786376 AAAAAAAAAGAGCA
1 AAAAAAAAAGAGCA
*
1786390 AAAAAAAAAAAGCA
1 AAAAAAAAAGAGCA
*
1786404 AAAAAAAAA-AACA
1 AAAAAAAAAGAGCA
1786417 AAAAAACAAA-A-CA
1 AAAAAA-AAAGAGCA
*
1786430 AAGAAAAAGAGAG-A
1 AA-AAAAAAAGAGCA
*
1786444 AAAGAAAAAGA
1 AAAAAAAAAGA
1786455 ACCTGCTTAA
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
13 22 0.39
14 34 0.61
ACGTcount: A:0.82, C:0.06, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAGAGCA
Found at i:1786397 original size:16 final size:14
Alignment explanation
Indices: 1786376--1786437 Score: 83
Period size: 14 Copynumber: 4.6 Consensus size: 14
1786366 CCTTCTCTTC
*
1786376 AAAAAAAAAGAGCA
1 AAAAAAAAAAAGCA
1786390 AAAAAAAAAAAGCA
1 AAAAAAAAAAAGCA
1786404 AAAAAAAAAAA-CA
1 AAAAAAAAAAAGCA
*
1786417 AAAAAACAAAA-CA
1 AAAAAAAAAAAGCA
*
1786430 AAGAAAAA
1 AAAAAAAA
1786438 GAGAGAAAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
13 20 0.45
14 24 0.55
ACGTcount: A:0.85, C:0.08, G:0.06, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGCA
Found at i:1786446 original size:27 final size:26
Alignment explanation
Indices: 1786375--1786453 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 26
1786365 ACCTTCTCTT
1786375 CAAAAAAAAAGAGCAAAAAAAAAAAAG
1 CAAAAAAAAAGAG-AAAAAAAAAAAAG
*
1786402 CAAAAAAAAA-A-AACAAAAAAACAAAA
1 CAAAAAAAAAGAGAA-AAAAAAA-AAAG
* * *
1786428 CAAAGAAAAAGAGAGAAAAGAAAAAG
1 CAAAAAAAAAGAGAAAAAAAAAAAAG
1786454 AACCTGCTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
24 2 0.05
25 7 0.16
26 16 0.37
27 17 0.40
28 1 0.02
ACGTcount: A:0.81, C:0.08, G:0.11, T:0.00
Consensus pattern (26 bp):
CAAAAAAAAAGAGAAAAAAAAAAAAG
Found at i:1787504 original size:55 final size:55
Alignment explanation
Indices: 1787420--1788997 Score: 2076
Period size: 55 Copynumber: 28.3 Consensus size: 55
1787410 TCCGCTTTTT
1787420 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* ** *
1787475 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAGGTTGGTGGCATTTTTT
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
** *
1787530 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGA--C---ACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1787591 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
1787646 AGTCCTCGAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
1787701 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * ** *
1787756 AATCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTT
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
** * ** *
1787811 AGTCCTCAAAGAGCAGGATGCTTTGTCTTTTCAAAGCCCACACAAGTTGGTGGCGTCTTCC
1 AGTCCTCAAAGAGCAGGA--C---ACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* *
1787872 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
1787927 AGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCGACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
*
1787983 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
*
1788038 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
* *
1788093 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACCCAAGTTGGTGGCA-TTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1788147 TAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 -AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
1788203 AGTCCCCAAAGAGCAGGACACCT-TTCAAAGCCCACCCAAGTTGGTGGCA-TTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1788257 TAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 -AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
1788313 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
1788367 TAGTCCTCAAAGAACAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGCC-TTC
1 -AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
1788422 TAGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 -AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * **
1788478 AGTCCCCGAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1788533 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
* * *
1788589 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACTAGTTGGTGGCGCCTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
1788644 AGTTCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
1788699 AGTCCCCGAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
* **
1788754 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAGGTTGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
*** * *
1788809 AGTCCTCAAAGAGCAGGATGCTTTTTATTTTCAAAGCCTACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGA--C---ACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
*
1788870 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * * * *
1788925 AGTCCTCAAAGAGCAAGACGCCT-TTCAAAGCCCATACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
1788980 ACTCCTCAATGAGAAGGA
1 AGTCCTCAAAGAGCAGGA
1788998 TACACTTTAT
Statistics
Matches: 1373, Mismatches: 108, Indels: 84
0.88 0.07 0.05
Matches are distributed among these distances:
54 23 0.02
55 1073 0.78
56 129 0.09
57 5 0.00
59 3 0.00
60 10 0.01
61 130 0.09
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:1787613 original size:26 final size:26
Alignment explanation
Indices: 1787583--1787670 Score: 79
Period size: 26 Copynumber: 3.3 Consensus size: 26
1787573 AAGTTGGTGG
1787583 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCTCAAAGAGCAGGA
* * * **
1787609 CACCTTTCAAAGCCCACACAAGTTGGTGG-
1 CACCTTTC--AGTCCTCA-AAG-AGCAGGA
*
1787638 CACCTTTCAGTCCTCGAAGAGCAGGA
1 CACCTTTCAGTCCTCAAAGAGCAGGA
1787664 CACCTTT
1 CACCTTT
1787671 TAAAGCCCAC
Statistics
Matches: 46, Mismatches: 11, Indels: 10
0.69 0.16 0.15
Matches are distributed among these distances:
25 3 0.07
26 18 0.39
27 5 0.11
28 6 0.13
29 11 0.24
30 3 0.07
ACGTcount: A:0.27, C:0.32, G:0.19, T:0.22
Consensus pattern (26 bp):
CACCTTTCAGTCCTCAAAGAGCAGGA
Found at i:1789711 original size:21 final size:20
Alignment explanation
Indices: 1789684--1789760 Score: 91
Period size: 21 Copynumber: 3.8 Consensus size: 20
1789674 AAAAAATTCC
*
1789684 AAATGTATCGATACATTTGT
1 AAATGTATCGATACATTTAT
* * *
1789704 AGAATGTATTGATACATTCAC
1 A-AATGTATCGATACATTTAT
*
1789725 AAATGTATCGATACATTCTAC
1 AAATGTATCGATACATT-TAT
1789746 AAATGTATCGATACA
1 AAATGTATCGATACA
1789761 GGGTCCCAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
20 16 0.33
21 33 0.67
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (20 bp):
AAATGTATCGATACATTTAT
Found at i:1789751 original size:41 final size:40
Alignment explanation
Indices: 1789679--1789760 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 40
1789669 AAAAAAAAAA
* * *
1789679 ATTCCAAATGTATCGATACATTTGTAGAATGTATTGATAC
1 ATTCCAAATGTATCGATACATTTCTAAAATGTATCGATAC
1789719 ATTCACAAATGTATCGATACA-TTCTACAAATGTATCGATAC
1 ATTC-CAAATGTATCGATACATTTCTA-AAATGTATCGATAC
1789760 A
1 A
1789761 GGGTCCCAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 8 0.22
41 29 0.78
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (40 bp):
ATTCCAAATGTATCGATACATTTCTAAAATGTATCGATAC
Found at i:1789820 original size:19 final size:19
Alignment explanation
Indices: 1789796--1789863 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1789786 AATTCAACGA
1789796 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1789815 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1789830 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1789847 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1789864 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1789834 original size:32 final size:32
Alignment explanation
Indices: 1789798--1789860 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1789788 TTCAACGATT
*
1789798 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1789830 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
1789861 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1789835 original size:13 final size:13
Alignment explanation
Indices: 1789817--1789841 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1789807 ACATAAGTTT
1789817 TGTATCGATACAA
1 TGTATCGATACAA
1789830 TGTATCGATACA
1 TGTATCGATACA
1789842 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1789921 original size:13 final size:13
Alignment explanation
Indices: 1789903--1789928 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1789893 CATTTTTCTG
1789903 TGTATCGATACAT
1 TGTATCGATACAT
1789916 TGTATCGATACAT
1 TGTATCGATACAT
1789929 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1789925 original size:33 final size:33
Alignment explanation
Indices: 1789883--1789949 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1789873 GCCAAGGAAA
***
1789883 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1789916 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1789949 T
1 T
1789950 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1792460 original size:28 final size:27
Alignment explanation
Indices: 1792393--1792465 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
1792383 CTTCACAATC
* *
1792393 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
1792420 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
1792448 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
1792466 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:1792510 original size:51 final size:51
Alignment explanation
Indices: 1792448--1792618 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
1792438 TTATTTCTGA
* * *
1792448 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
1792499 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
1792552 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
1792604 GAGGATACTCCAACC
1 GGGGATACTCCAACC
1792619 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:1792637 original size:28 final size:28
Alignment explanation
Indices: 1792601--1792682 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
1792591 ATTTTTCACA
*
1792601 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
1792629 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
1792657 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
1792683 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 41 0.89
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:1794557 original size:51 final size:54
Alignment explanation
Indices: 1794501--1794611 Score: 138
Period size: 59 Copynumber: 2.0 Consensus size: 54
1794491 CAAGAAACCC
*
1794501 AAGCTCATGC-T-TAAGTATAAAACTATTTAATTAAATATGCATATC-GAAATA
1 AAGCTCATGCATATAAGTATAAAAATATTTAATTAAATATGCATATCGGAAATA
1794552 AAGCTCATGCATATCGAAATAAGTATAAAAATATTTAATTAAATATGCATATCGGAAATA
1 AAGCTCATGC--AT----ATAAGTATAAAAATATTTAATTAAATATGCATATCGGAAATA
1794612 TAAATAAAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
51 10 0.20
54 1 0.02
59 33 0.66
60 6 0.12
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (54 bp):
AAGCTCATGCATATAAGTATAAAAATATTTAATTAAATATGCATATCGGAAATA
Found at i:1796026 original size:28 final size:29
Alignment explanation
Indices: 1795986--1796044 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
1795976 AGTTTAGACA
* *
1795986 TTGTCTTCTTAAGATGA-CCTTATTT-GAT
1 TTGTCTTATTAAGA-CATCCTTATTTGGAT
1796014 TTGTCTTATTAAGACATCCTTATTTGGAT
1 TTGTCTTATTAAGACATCCTTATTTGGAT
1796043 TT
1 TT
1796045 CTCAAATCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 1 0.04
28 21 0.78
29 5 0.19
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.51
Consensus pattern (29 bp):
TTGTCTTATTAAGACATCCTTATTTGGAT
Found at i:1805660 original size:79 final size:79
Alignment explanation
Indices: 1805570--1805729 Score: 250
Period size: 80 Copynumber: 2.0 Consensus size: 79
1805560 TTCATTATAA
* *
1805570 TACAAAAACTTTCAATAAGAAATTACTTTCTCTAAAATTTACAC-AACCTAAATAACACTATTGG
1 TACAAAAACTTTCAATAAGAAAATACTTTCT-TAAAATTTACACAAACCAAAATAACACTATTGG
*
1805634 TTCAATTATAATCCT
65 TTAAATTATAATCCT
* *
1805649 TACAAAGACTTTCAATAAGAAAATACTTTCTTAAAATTTACACAAAACCAAAATTACACTATTGG
1 TACAAAAACTTTCAATAAGAAAATACTTTCTTAAAATTTACAC-AAACCAAAATAACACTATTGG
1805714 TTAAATTATAATCCT
65 TTAAATTATAATCCT
1805729 T
1 T
1805730 GTTTTTTGGT
Statistics
Matches: 74, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
78 12 0.16
79 29 0.39
80 33 0.45
ACGTcount: A:0.44, C:0.17, G:0.04, T:0.34
Consensus pattern (79 bp):
TACAAAAACTTTCAATAAGAAAATACTTTCTTAAAATTTACACAAACCAAAATAACACTATTGGT
TAAATTATAATCCT
Found at i:1808357 original size:22 final size:21
Alignment explanation
Indices: 1808332--1808382 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
1808322 TATGATAAAA
1808332 TATATTTATTTTTAAA-ATTT
1 TATATTTATTTTTAAATATTT
* *
1808352 TTTATATATATTTTAAATATTT
1 TATATTTAT-TTTTAAATATTT
*
1808374 TATTTTTAT
1 TATATTTAT
1808383 ACAAATATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 7 0.29
21 7 0.29
22 10 0.42
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TATATTTATTTTTAAATATTT
Found at i:1810925 original size:16 final size:16
Alignment explanation
Indices: 1810904--1810938 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1810894 TTTAATTTAA
1810904 AAAATAATTTAAATAT
1 AAAATAATTTAAATAT
*
1810920 AAAATAATTTAAATTT
1 AAAATAATTTAAATAT
1810936 AAA
1 AAA
1810939 TTTAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAATAATTTAAATAT
Found at i:1815444 original size:20 final size:20
Alignment explanation
Indices: 1815419--1815487 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 20
1815409 AAATAAAATT
1815419 ATATAATAAAAATAATATAA
1 ATATAATAAAAATAATATAA
* *
1815439 ATATAATTAGAAT-ATATGAA
1 ATATAATAAAAATAATAT-AA
* *
1815459 ATA-AA-AAATAAAAACATAA
1 ATATAATAAA-AATAATATAA
1815478 A-ATAATAAAA
1 ATATAATAAAA
1815488 CAAAAATTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 11
0.69 0.11 0.20
Matches are distributed among these distances:
18 2 0.05
19 14 0.37
20 22 0.58
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.26
Consensus pattern (20 bp):
ATATAATAAAAATAATATAA
Found at i:1815846 original size:17 final size:17
Alignment explanation
Indices: 1815826--1815862 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1815816 ATTTAGCATG
1815826 ATAACTAATTTAATATT
1 ATAACTAATTTAATATT
* *
1815843 ATAATTAATTTATTATT
1 ATAACTAATTTAATATT
1815860 ATA
1 ATA
1815863 TTTTTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
ATAACTAATTTAATATT
Found at i:1816225 original size:21 final size:21
Alignment explanation
Indices: 1816193--1816232 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1816183 TTTGATTTTA
1816193 AAAATTAATAAA-TTGAATCT
1 AAAATTAATAAATTTGAATCT
*
1816213 AAAATTACCTAAATTTGAAT
1 AAAATTA-ATAAATTTGAAT
1816233 AATTTGATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 4 0.24
22 6 0.35
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAATTAATAAATTTGAATCT
Found at i:1821956 original size:24 final size:23
Alignment explanation
Indices: 1821917--1821962 Score: 83
Period size: 24 Copynumber: 2.0 Consensus size: 23
1821907 AAATAATAAG
1821917 AAAAGATAGAAAAATGAAGAAAA
1 AAAAGATAGAAAAATGAAGAAAA
1821940 AAAAGATGAGAAAAATGAAGAAA
1 AAAAGAT-AGAAAAATGAAGAAA
1821963 TGTGGTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.72, C:0.00, G:0.20, T:0.09
Consensus pattern (23 bp):
AAAAGATAGAAAAATGAAGAAAA
Found at i:1822832 original size:48 final size:48
Alignment explanation
Indices: 1822761--1822859 Score: 162
Period size: 48 Copynumber: 2.1 Consensus size: 48
1822751 TCACATATTT
* * * *
1822761 TTAACCTAGAGGTTTACATAAAACAAAATACATTTTTTAATAAAGCAA
1 TTAACCTAGAGGCTTACAAAAAACAAAATACATATTTTAATAAAACAA
1822809 TTAACCTAGAGGCTTACAAAAAACAAAATACATATTTTAATAAAACAA
1 TTAACCTAGAGGCTTACAAAAAACAAAATACATATTTTAATAAAACAA
1822857 TTA
1 TTA
1822860 TTTAAAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.51, C:0.13, G:0.07, T:0.29
Consensus pattern (48 bp):
TTAACCTAGAGGCTTACAAAAAACAAAATACATATTTTAATAAAACAA
Found at i:1823036 original size:46 final size:47
Alignment explanation
Indices: 1822975--1823069 Score: 149
Period size: 46 Copynumber: 2.0 Consensus size: 47
1822965 ATGAAATTTG
* *
1822975 ATGGGAATTTGAAAATCATCC-AGGTAAGATAATGA-AAAAAATTGGA
1 ATGGGAATTTAAAAATCATCCGA-GTAAGATAATGATAAAAAATTAGA
1823021 ATGGGAATTTAAAAATCATCCGAGTAAGATAATGATAAAAAATTAGA
1 ATGGGAATTTAAAAATCATCCGAGTAAGATAATGATAAAAAATTAGA
1823068 AT
1 AT
1823070 AAGGAATGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
46 32 0.71
47 13 0.29
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.25
Consensus pattern (47 bp):
ATGGGAATTTAAAAATCATCCGAGTAAGATAATGATAAAAAATTAGA
Found at i:1823851 original size:29 final size:30
Alignment explanation
Indices: 1823819--1823889 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
1823809 TTCCGTCTAG
* *
1823819 GCCATTTCTTTGATTTTTGCTT-TTTCCAA
1 GCCATTTCTTTGATTTCTGCTTCTGTCCAA
* * *
1823848 GCCATTTC-TCGATTTCTGGTTCTGTCTAA
1 GCCATTTCTTTGATTTCTGCTTCTGTCCAA
1823877 GCCATTTCTTTGA
1 GCCATTTCTTTGA
1823890 GTCTTGTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
28 10 0.29
29 21 0.62
30 3 0.09
ACGTcount: A:0.14, C:0.23, G:0.14, T:0.49
Consensus pattern (30 bp):
GCCATTTCTTTGATTTCTGCTTCTGTCCAA
Found at i:1823950 original size:46 final size:47
Alignment explanation
Indices: 1823879--1823992 Score: 131
Period size: 46 Copynumber: 2.4 Consensus size: 47
1823869 CTGTCTAAGC
* * * * *
1823879 CATTTCTTTGAGTCTTGTTTTCATTCAAGTCATTGGTTTCATCCAAGA
1 CATTTCATT-AGTCTTGGTTCCATTCAACTCATTAGTTTCATCCAAGA
* * *
1823927 CATTTCATT-GTCTTGGTTCCATTCAACTCATTAGTTTTATCCAGGC
1 CATTTCATTAGTCTTGGTTCCATTCAACTCATTAGTTTCATCCAAGA
1823973 CATTTCATTAAGTCTTGGTT
1 CATTTCATT-AGTCTTGGTT
1823993 TTGCCTAAGT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
46 39 0.70
48 17 0.30
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.46
Consensus pattern (47 bp):
CATTTCATTAGTCTTGGTTCCATTCAACTCATTAGTTTCATCCAAGA
Done.