Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 98 of 187
Found at i:28561534 original size:21 final size:22
Alignment explanation
Indices: 28561487--28561534 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
28561477 AAACTCCAAA
* * *
28561487 AAAGATTCAAGTACATGAAACT
1 AAAGATTAAAATACATGAAAAT
*
28561509 GAAGATTAAAATA-ATGAAAAT
1 AAAGATTAAAATACATGAAAAT
28561530 AAAGA
1 AAAGA
28561535 AATCTTGATC
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.58, C:0.06, G:0.15, T:0.21
Consensus pattern (22 bp):
AAAGATTAAAATACATGAAAAT
Found at i:28565968 original size:14 final size:14
Alignment explanation
Indices: 28565949--28565988 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
28565939 TTGATTGGCA
28565949 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
28565963 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
28565977 GGAAAATGTTTT
1 GTAAAATGTTTT
28565989 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:28565995 original size:34 final size:35
Alignment explanation
Indices: 28565957--28566023 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
28565947 CAGTAAAATG
* * *
28565957 TTTTCCGTAAAATGA-TTTCTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGACTTACAGGAAAATATTTTAC
*
28565991 TTTTCTGTAAAATGACTTACAGGAAAATATTTT
1 TTTTCCGTAAAATGACTTACAGGAAAATATTTT
28566024 CTGGTGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 14 0.50
35 14 0.50
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.43
Consensus pattern (35 bp):
TTTTCCGTAAAATGACTTACAGGAAAATATTTTAC
Found at i:28566010 original size:20 final size:20
Alignment explanation
Indices: 28565972--28566010 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
28565962 CGTAAAATGA
**
28565972 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGACTTACT
*
28565992 TTTCTGTAAAATGACTTAC
1 TTTCTGGAAAATGACTTAC
28566011 AGGAAAATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (20 bp):
TTTCTGGAAAATGACTTACT
Found at i:28569465 original size:8 final size:8
Alignment explanation
Indices: 28569452--28569476 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
28569442 CCATTACCAG
28569452 GAACAACA
1 GAACAACA
28569460 GAACAACA
1 GAACAACA
28569468 GAACAACA
1 GAACAACA
28569476 G
1 G
28569477 GAACGGCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.60, C:0.24, G:0.16, T:0.00
Consensus pattern (8 bp):
GAACAACA
Found at i:28570304 original size:24 final size:24
Alignment explanation
Indices: 28570277--28570349 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 24
28570267 TGCAATCGAT
*
28570277 AGGGTGAATAGAGGAGCTGTGGAA
1 AGGGTGAAGAGAGGAGCTGTGGAA
* *
28570301 AGGGTGAAGAGAGGAACAGTGGAA
1 AGGGTGAAGAGAGGAGCTGTGGAA
*
28570325 AAGGTGAAGAGAGGAGCTGTGGAA
1 AGGGTGAAGAGAGGAGCTGTGGAA
28570349 A
1 A
28570350 ATGTCTTACC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.38, C:0.04, G:0.45, T:0.12
Consensus pattern (24 bp):
AGGGTGAAGAGAGGAGCTGTGGAA
Found at i:28571684 original size:28 final size:28
Alignment explanation
Indices: 28571652--28571706 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
28571642 TATCACCACG
*
28571652 AGCAATAATATCACGAACAAACTGATAA
1 AGCAATAATATCACGAACAAAATGATAA
28571680 AGCAATAATATCACGAACAAAATGATA
1 AGCAATAATATCACGAACAAAATGATA
28571707 CCGAACATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.55, C:0.16, G:0.11, T:0.18
Consensus pattern (28 bp):
AGCAATAATATCACGAACAAAATGATAA
Found at i:28577057 original size:60 final size:61
Alignment explanation
Indices: 28576977--28577092 Score: 180
Period size: 60 Copynumber: 1.9 Consensus size: 61
28576967 ATTTGGTATC
* *
28576977 TGAACTTGACATTTTTTCCTAATTTGGTACCTAAACTTTTTTTT-GGTCCAATTTGATACT
1 TGAACTTGACACTTTCTCCTAATTTGGTACCTAAACTTTTTTTTAGGTCCAATTTGATACT
* * *
28577037 TGAACTTGGCACTTTCTCCTAATTTGGTACCTAAGCTTTTTTTTAGGTTCAATTTG
1 TGAACTTGACACTTTCTCCTAATTTGGTACCTAAACTTTTTTTTAGGTCCAATTTG
28577093 GTACCTAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
60 40 0.80
61 10 0.20
ACGTcount: A:0.22, C:0.17, G:0.14, T:0.47
Consensus pattern (61 bp):
TGAACTTGACACTTTCTCCTAATTTGGTACCTAAACTTTTTTTTAGGTCCAATTTGATACT
Found at i:28577571 original size:31 final size:31
Alignment explanation
Indices: 28577534--28577612 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
28577524 GGCCCTCAAA
*
28577534 AAGTTTAAGTACCAACTTAAGAAAAAATGTC
1 AAGTTTAAGTACCAAATTAAGAAAAAATGTC
* *
28577565 AAGTTTATGTACCAAATTAAGAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAAGAAAAAATGTC
* * *
28577596 AACTTCAAGTATCAAAT
1 AAGTTTAAGTACCAAAT
28577613 GTTATATTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.28
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAAGAAAAAATGTC
Found at i:28587224 original size:23 final size:23
Alignment explanation
Indices: 28587174--28587228 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
28587164 ATCAGGATCA
* * *
28587174 CACCATAGTGCTAGGAACAGGAG
1 CACCAAAGTGCAAGGAACAGAAG
*
28587197 CACCAAAGTGCAAGTAACAGAAG
1 CACCAAAGTGCAAGGAACAGAAG
*
28587220 TACCAAAGT
1 CACCAAAGT
28587229 ACAAATCAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.13
Consensus pattern (23 bp):
CACCAAAGTGCAAGGAACAGAAG
Found at i:28587534 original size:39 final size:40
Alignment explanation
Indices: 28587491--28587573 Score: 125
Period size: 39 Copynumber: 2.1 Consensus size: 40
28587481 GAAAGGAAAA
**
28587491 AAATTATTTCTAAGGTATTTATAT-TTTCTT-CATTTTGAT
1 AAATTATTTAAAAGGTATTTATATGTTT-TTACATTTTGAT
28587530 AAATTATTTAAAAGGTATTTATATGTTTTTACATTTTGAT
1 AAATTATTTAAAAGGTATTTATATGTTTTTACATTTTGAT
28587570 AAAT
1 AAAT
28587574 ATCTTTTAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
39 24 0.60
40 16 0.40
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (40 bp):
AAATTATTTAAAAGGTATTTATATGTTTTTACATTTTGAT
Found at i:28588110 original size:14 final size:15
Alignment explanation
Indices: 28588077--28588110 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
28588067 TTGATAAACA
*
28588077 TTAATATAAAATTGT
1 TTAATATAAAAATGT
28588092 TTAATATAAAAAT-T
1 TTAATATAAAAATGT
28588106 TTAAT
1 TTAAT
28588111 TTTGTTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
TTAATATAAAAATGT
Found at i:28591146 original size:6 final size:6
Alignment explanation
Indices: 28591135--28591182 Score: 96
Period size: 6 Copynumber: 8.0 Consensus size: 6
28591125 TAAGCTGAGT
28591135 CTATTA CTATTA CTATTA CTATTA CTATTA CTATTA CTATTA CTATTA
1 CTATTA CTATTA CTATTA CTATTA CTATTA CTATTA CTATTA CTATTA
28591183 TTTTGGTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (6 bp):
CTATTA
Found at i:28603957 original size:6 final size:6
Alignment explanation
Indices: 28603946--28603975 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
28603936 AAATAAAAGG
28603946 AATAAA AATAAA AATAAA AAT-AA AATAAA A
1 AATAAA AATAAA AATAAA AATAAA AATAAA A
28603976 TGTGTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AATAAA
Found at i:28603963 original size:12 final size:11
Alignment explanation
Indices: 28603946--28603975 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
28603936 AAATAAAAGG
28603946 AATAAAAATAAA
1 AATAAAAAT-AA
28603958 AATAAAAATAA
1 AATAAAAATAA
28603969 AATAAAA
1 AATAAAA
28603976 TGTGTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AATAAAAATAA
Found at i:28605625 original size:12 final size:13
Alignment explanation
Indices: 28605600--28605644 Score: 56
Period size: 12 Copynumber: 3.4 Consensus size: 13
28605590 TTTATTTGAG
28605600 TTATATATAAATA
1 TTATATATAAATA
28605613 TTATATA-AAATA
1 TTATATATAAATA
*
28605625 TTATACATATAATTA
1 TTAT--ATATAAATA
28605640 TTATA
1 TTATA
28605645 ATTATTAACC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 9 0.32
13 8 0.29
14 3 0.11
15 8 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (13 bp):
TTATATATAAATA
Found at i:28606143 original size:14 final size:14
Alignment explanation
Indices: 28606121--28606173 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
28606111 TTATATTATT
*
28606121 ATAACATAAAGTAA
1 ATAAAATAAAGTAA
*
28606135 ATAAAATAAAATGAA
1 ATAAAATAAAGT-AA
* *
28606150 ATAAAACAAAGCAA
1 ATAAAATAAAGTAA
*
28606164 ATGAAATAAA
1 ATAAAATAAA
28606174 AAGAAGGAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
14 20 0.65
15 11 0.35
ACGTcount: A:0.70, C:0.06, G:0.08, T:0.17
Consensus pattern (14 bp):
ATAAAATAAAGTAA
Found at i:28606464 original size:3 final size:3
Alignment explanation
Indices: 28606456--28606502 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
28606446 GTGAGGTAAG
28606456 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
28606503 AGATGAGTGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:28606812 original size:3 final size:3
Alignment explanation
Indices: 28606804--28606842 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
28606794 AGTTCAGGGN
28606804 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28606843 GAGTGGGAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:28606850 original size:336 final size:337
Alignment explanation
Indices: 28606468--28607142 Score: 1183
Period size: 336 Copynumber: 2.0 Consensus size: 337
28606458 TTATTATTAT
*
28606468 TATTATTATTATTATTATTATTATTATTATTATTAAGATGAGTGGGAATTAAATTGAATAGTTTA
1 TATTATTATTATTATTATTATTATTATTATTATTAAGATGAGTGGGAATTAAATTGAATAGTTGA
* * *
28606533 TATGAATTAAAATTTAAATTGTTTGTTGATTGAAAGCGGGAAGTGAATTTAAATCGAATAGTGAC
66 TATGAAATAAAATTTAAATTGTTTGTTGATTGAAAGCGGGAAATGAATTTAAATCGAATAGTGAA
28606598 TGATATTAAATTGAATGGAAATGTATTGAGTTGTGAAAATGTGTGAATTGTGGATTAATTATTGA
131 TGATATTAAATTGAATGGAAATGTATTGAGTTGTGAAAATGTGTGAATTGTGGATTAATTATTGA
*
28606663 TTGAAAGGTGG-AA-AAATGATTGAATTGAAAATGTGAGAAATTGTGATTGAATTGAGATTATAT
196 TTGAAAGGTGGAAAGAAAGGATTGAATTGAAAATGTGAGAAATTGTGATTGAATTGAGATTATAT
28606726 GTGACTTAAATACCCTATTAACTAGTCGGGCTGAGTCAGATATAGTTGGCATGCCATAGGATTGG
261 GTGACTTAAATACCCTATTAACTAGTCGGGCTGAGTCAGATATAGTTGGCATGCCATAGGATTGG
28606791 AAGAGTTCAGGG
326 AAGAGTTCAGGG
**
28606803 NTATTATTATTATTATTATTATTATTATTATTATTATTATGAGTGGGAATTAAATTGAATAGTTG
1 -TATTATTATTATTATTATTATTATTATTATTATTAAGATGAGTGGGAATTAAATTGAATAGTTG
* * * *
28606868 ATATGAAATAATATTTGAATTGTTTGTTGATTGAAAGCGGGAAATGAATTTGAATCGAATTGTGA
65 ATATGAAATAAAATTTAAATTGTTTGTTGATTGAAAGCGGGAAATGAATTTAAATCGAATAGTGA
* *
28606933 ATGGTATTAAATTGTATGGAAATGTATTGAGTTGTGAAAATGTGTGAATTGTGGATTAATTATTG
130 ATGATATTAAATTGAATGGAAATGTATTGAGTTGTGAAAATGTGTGAATTGTGGATTAATTATTG
*
28606998 ATTGAAAGGTGGAAAAGGAAAGGATTGAATTGAAAATGTGAGAAATTGTGATTGAATTGGGATTA
195 ATTGAAAGGTGG-AAA-GAAAGGATTGAATTGAAAATGTGAGAAATTGTGATTGAATTGAGATTA
28607063 TATGTGACTTAAATACCCTATTAACTAGTCGGGCTGAGTCAGATATAGTTGGCATGCCATAGGAT
258 TATGTGACTTAAATACCCTATTAACTAGTCGGGCTGAGTCAGATATAGTTGGCATGCCATAGGAT
28607128 TGGAAGAGTTCAGGG
323 TGGAAGAGTTCAGGG
28607143 ATACTTCGAC
Statistics
Matches: 321, Mismatches: 14, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
336 194 0.60
338 2 0.01
340 125 0.39
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.37
Consensus pattern (337 bp):
TATTATTATTATTATTATTATTATTATTATTATTAAGATGAGTGGGAATTAAATTGAATAGTTGA
TATGAAATAAAATTTAAATTGTTTGTTGATTGAAAGCGGGAAATGAATTTAAATCGAATAGTGAA
TGATATTAAATTGAATGGAAATGTATTGAGTTGTGAAAATGTGTGAATTGTGGATTAATTATTGA
TTGAAAGGTGGAAAGAAAGGATTGAATTGAAAATGTGAGAAATTGTGATTGAATTGAGATTATAT
GTGACTTAAATACCCTATTAACTAGTCGGGCTGAGTCAGATATAGTTGGCATGCCATAGGATTGG
AAGAGTTCAGGG
Found at i:28611671 original size:26 final size:26
Alignment explanation
Indices: 28611641--28611694 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
28611631 TATTCAAGAA
**
28611641 ATGAAAAATGCTTGATTGAAA-ACTTG
1 ATGAAAAACACTTGA-TGAAAGACTTG
28611667 ATGAAAAACACTTGATGAAAGACTTG
1 ATGAAAAACACTTGATGAAAGACTTG
28611693 AT
1 AT
28611695 TAATGAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (26 bp):
ATGAAAAACACTTGATGAAAGACTTG
Found at i:28613748 original size:27 final size:27
Alignment explanation
Indices: 28613704--28613760 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
28613694 TTTCCTCCGT
* *
28613704 ATTTTTAACTCTAGAAGC-GAGATTAAG
1 ATTTTTAACTCCACAAGCAGA-ATTAAG
28613731 ATTTTTAACTCCACAAGCAGAATTAAG
1 ATTTTTAACTCCACAAGCAGAATTAAG
28613758 ATT
1 ATT
28613761 ATTTTTTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 25 0.93
28 2 0.07
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (27 bp):
ATTTTTAACTCCACAAGCAGAATTAAG
Found at i:28636655 original size:37 final size:36
Alignment explanation
Indices: 28636609--28636684 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 36
28636599 ATTCCAAAAA
28636609 TAATATTATTTTAATAGT-TTAATATTAAATTTAAT-T
1 TAATATTATTTTAATAGTGTT-ATATT-AATTTAATAT
*
28636645 TAATACTTATTTTAATAGTGTTTTATTAATTTAATAT
1 TAATA-TTATTTTAATAGTGTTATATTAATTTAATAT
28636682 TAA
1 TAA
28636685 AGTGACTATC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
36 13 0.36
37 21 0.58
38 2 0.06
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.55
Consensus pattern (36 bp):
TAATATTATTTTAATAGTGTTATATTAATTTAATAT
Found at i:28636869 original size:23 final size:25
Alignment explanation
Indices: 28636821--28636868 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
28636811 AGTTGTAGAA
28636821 AGAAAATTCTTTGAAGAGATTATTTT
1 AGAAAATTCTTT-AAGAGATTATTTT
28636847 AGAAAATT-TTT-AGAGA-TATTTT
1 AGAAAATTCTTTAAGAGATTATTTT
28636869 TCTGATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 6 0.27
23 5 0.23
25 3 0.14
26 8 0.36
ACGTcount: A:0.40, C:0.02, G:0.15, T:0.44
Consensus pattern (25 bp):
AGAAAATTCTTTAAGAGATTATTTT
Found at i:28637032 original size:18 final size:18
Alignment explanation
Indices: 28637009--28637050 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
28636999 ATTACTCGGT
28637009 CGAAGCGCTCATCCTAGA
1 CGAAGCGCTCATCCTAGA
28637027 CGAAGCGCTCATCCTAGA
1 CGAAGCGCTCATCCTAGA
28637045 CGAAGC
1 CGAAGC
28637051 AAAAAGATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.29, C:0.33, G:0.24, T:0.14
Consensus pattern (18 bp):
CGAAGCGCTCATCCTAGA
Found at i:28638263 original size:27 final size:28
Alignment explanation
Indices: 28638230--28638299 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 28
28638220 GACAAAATCC
*
28638230 AAACTTTTCAATGGA-T-TGAATTGAGT
1 AAACTTTTCAATGAATTGTGAATTGAGT
**
28638256 AAATCTTTTTTATGAATTGTGAATTGAGT
1 AAA-CTTTTCAATGAATTGTGAATTGAGT
28638285 AAACTTTTCAATGAA
1 AAACTTTTCAATGAA
28638300 GTAAGGTGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 3 0.08
27 9 0.25
28 11 0.31
29 13 0.36
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (28 bp):
AAACTTTTCAATGAATTGTGAATTGAGT
Found at i:28639729 original size:21 final size:21
Alignment explanation
Indices: 28639713--28639764 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
28639703 TCTGGTTTCT
*
28639713 GGTTTTGGGTGAATGGTTTAG
1 GGTTTTGGGTAAATGGTTTAG
*
28639734 GGTTTTGGGTAAATGGTTTAA
1 GGTTTTGGGTAAATGGTTTAG
*
28639755 GGTTTAGGGT
1 GGTTTTGGGT
28639765 TTAGAGTTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.17, C:0.00, G:0.40, T:0.42
Consensus pattern (21 bp):
GGTTTTGGGTAAATGGTTTAG
Found at i:28639743 original size:7 final size:7
Alignment explanation
Indices: 28639727--28639795 Score: 50
Period size: 7 Copynumber: 9.7 Consensus size: 7
28639717 TTGGGTGAAT
28639727 GGTTTAG
1 GGTTTAG
*
28639734 GGTTTTG
1 GGTTTAG
** *
28639741 GGTAAAT
1 GGTTTAG
*
28639748 GGTTTAA
1 GGTTTAG
28639755 GGTTTAG
1 GGTTTAG
28639762 GGTTTAG
1 GGTTTAG
*
28639769 AG-TTAG
1 GGTTTAG
*
28639775 AGTTTTTAG
1 -G-GTTTAG
28639784 GGTTTAG
1 GGTTTAG
28639791 GGTTT
1 GGTTT
28639796 TAAAGAAAAA
Statistics
Matches: 46, Mismatches: 13, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
6 4 0.09
7 37 0.80
8 1 0.02
9 4 0.09
ACGTcount: A:0.19, C:0.00, G:0.36, T:0.45
Consensus pattern (7 bp):
GGTTTAG
Found at i:28640279 original size:126 final size:125
Alignment explanation
Indices: 28640054--28640597 Score: 772
Period size: 126 Copynumber: 4.3 Consensus size: 125
28640044 TTGTTAATTT
*
28640054 AAAGAAGCTCCCATGTGGAC-GCATTTTTGCTACAGTAGCTCTTGAAAAAATAATTTCAAGTTGA
1 AAAGAAGCTCCCACGTGGACAGC--TTTTGCTACAGTAGCTCTTGAAAAAATAATTTCAAGTTGA
* * *
28640118 CGTTTCTGAGCAAATAGTGTCAAAAACGCTTT-AGTTAGGATGATTTGTTAGCAAAAGTACTG
64 CGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAG-CAGGATGCTTTGTCAGCAAAAGTACTG
* * ** *
28640180 AAAGAAGCTCCCACGTGGACATGCTTTTCCTACAGTAGCTCCTGAAAAAATAATTTTGAGTTGAT
1 AAAGAAGCTCCCACGTGGACA-GCTTTTGCTACAGTAGCTCTTGAAAAAATAATTTCAAGTTGAC
* * * *
28640245 GTTTCTGAACAAATAGTGTCAAAAACGCTTT-AGTTAGGATGCTTTGTTAGCAAAAGTATTG
65 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAG-CAGGATGCTTTGTCAGCAAAAGTACTG
* * *
28640306 AAAGAAGCTCCCACGTGGACGAGCTTTTGCTACAGTAGCTCTTGAAAAAATAATTTCGAGTAGAT
1 AAAGAAGCTCCCACGTGGAC-AGCTTTTGCTACAGTAGCTCTTGAAAAAATAATTTCAAGTTGAC
* * * *
28640371 ATTTTTGAGCAAATAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAAAAGTATTG
65 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTG
*
28640432 AAAGAAGCTTCCACGTGGACGAGCTTTTGCTACAGTAGCTCTTGAAAAAATAATTTCAAGTAT-A
1 AAAGAAGCTCCCACGTGGAC-AGCTTTTGCTACAGTAGCTCTTGAAAAAATAATTTCAAGT-TGA
28640496 CGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTG
64 CGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTG
* *
28640558 AAAGAAGCTCCCACGTGGACGTGTTTTTGCTACAGTAGCT
1 AAAGAAGCTCCCACGTGGAC-AGCTTTTGCTACAGTAGCT
28640598 TCTGTTAGGC
Statistics
Matches: 383, Mismatches: 30, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
126 378 0.99
127 3 0.01
128 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.30
Consensus pattern (125 bp):
AAAGAAGCTCCCACGTGGACAGCTTTTGCTACAGTAGCTCTTGAAAAAATAATTTCAAGTTGACG
TTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTG
Found at i:28643718 original size:33 final size:32
Alignment explanation
Indices: 28643679--28643777 Score: 107
Period size: 28 Copynumber: 3.2 Consensus size: 32
28643669 TATAATCTAT
* *
28643679 TAAAAATATTAAAGTAAATTACAATTGGTACA
1 TAAAAATGTAAAAGTAAATTACAATTGGTACA
* * * *
28643711 TAGAAAATGTAAAAG--AATTTCTATT-ATA-T
1 TA-AAAATGTAAAAGTAAATTACAATTGGTACA
28643740 TAAAAATGTAAAAGTAAATTACAATTGGTACA
1 TAAAAATGTAAAAGTAAATTACAATTGGTACA
28643772 TAAAAA
1 TAAAAA
28643778 ATCTAATCTA
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
28 12 0.23
29 2 0.04
30 10 0.19
31 10 0.19
32 8 0.15
33 10 0.19
ACGTcount: A:0.54, C:0.05, G:0.10, T:0.31
Consensus pattern (32 bp):
TAAAAATGTAAAAGTAAATTACAATTGGTACA
Found at i:28643718 original size:49 final size:50
Alignment explanation
Indices: 28643663--28643798 Score: 121
Period size: 61 Copynumber: 2.5 Consensus size: 50
28643653 CTTATTTAAA
28643663 AGAAAATATAATCTATTAAAAATATT-AAAGTAAATTACAATTGGTACAT
1 AGAAAATATAATCTATTAAAAATATTAAAAGTAAATTACAATTGGTACAT
* *
28643712 AGAAAATGTAAAAGAATTTCTATTATATTAAAAATGTAAAAGTAAATTACAATTGGTACAT
1 AGAAAA--T---ATAA--TCTATTA-A--AAATAT-TAAAAGTAAATTACAATTGGTACAT
* * *
28643773 AAAAAATCTAATCTATTAAACATATT
1 AGAAAATATAATCTATTAAAAATATT
28643799 GCCTTATTTA
Statistics
Matches: 68, Mismatches: 7, Indels: 23
0.69 0.07 0.23
Matches are distributed among these distances:
49 6 0.09
50 1 0.01
51 5 0.07
53 1 0.01
54 10 0.15
56 9 0.13
57 1 0.01
59 6 0.09
60 1 0.01
61 28 0.41
ACGTcount: A:0.52, C:0.07, G:0.08, T:0.33
Consensus pattern (50 bp):
AGAAAATATAATCTATTAAAAATATTAAAAGTAAATTACAATTGGTACAT
Found at i:28643725 original size:61 final size:61
Alignment explanation
Indices: 28643659--28643779 Score: 170
Period size: 61 Copynumber: 2.0 Consensus size: 61
28643649 TTGACTTATT
* * *
28643659 TAAAAGAAAATATAATCTATTAAAAATATTAAAGTAAATTACAATTGGTACATAGAAAATG
1 TAAAAGAAAATATAATATATTAAAAATATAAAAGTAAATTACAATTGGTACATAAAAAATG
** * * *
28643720 TAAAAGAATTTCTATTATATTAAAAATGTAAAAGTAAATTACAATTGGTACATAAAAAAT
1 TAAAAGAAAATATAATATATTAAAAATATAAAAGTAAATTACAATTGGTACATAAAAAAT
28643780 CTAATCTATT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 52 1.00
ACGTcount: A:0.55, C:0.05, G:0.09, T:0.31
Consensus pattern (61 bp):
TAAAAGAAAATATAATATATTAAAAATATAAAAGTAAATTACAATTGGTACATAAAAAATG
Found at i:28643779 original size:33 final size:33
Alignment explanation
Indices: 28643680--28643779 Score: 102
Period size: 33 Copynumber: 3.2 Consensus size: 33
28643670 ATAATCTATT
* *
28643680 AAAAATATTAAAGTAAATTACAATTGGTACATA
1 AAAAATGTAAAAGTAAATTACAATTGGTACATA
* * * * *
28643713 GAAAATGTAAAAG--AATTTCTA-T--TATATT
1 AAAAATGTAAAAGTAAATTACAATTGGTACATA
28643741 AAAAATGTAAAAGTAAATTACAATTGGTACATA
1 AAAAATGTAAAAGTAAATTACAATTGGTACATA
28643774 AAAAAT
1 AAAAAT
28643780 CTAATCTATT
Statistics
Matches: 50, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
28 16 0.32
30 7 0.14
31 7 0.14
33 20 0.40
ACGTcount: A:0.54, C:0.05, G:0.10, T:0.31
Consensus pattern (33 bp):
AAAAATGTAAAAGTAAATTACAATTGGTACATA
Found at i:28644359 original size:18 final size:18
Alignment explanation
Indices: 28644333--28644375 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
28644323 ACTAGAAAAA
*
28644333 AGGAAACATATAAA-GGCT
1 AGGATACATA-AAAGGGCT
*
28644351 AGGATACATAAAAGGGTT
1 AGGATACATAAAAGGGCT
28644369 AGGATAC
1 AGGATAC
28644376 GTACCTGGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.47, C:0.09, G:0.26, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:28645029 original size:7 final size:7
Alignment explanation
Indices: 28645017--28645055 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
28645007 TTAATTATAT
28645017 ATACTAA
1 ATACTAA
28645024 ATACTAA
1 ATACTAA
28645031 ATACTAA
1 ATACTAA
28645038 ATACTAA
1 ATACTAA
28645045 ATACTAA
1 ATACTAA
28645052 ATAC
1 ATAC
28645056 CAATCGACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.28
Consensus pattern (7 bp):
ATACTAA
Found at i:28646590 original size:43 final size:43
Alignment explanation
Indices: 28646542--28646782 Score: 246
Period size: 43 Copynumber: 5.7 Consensus size: 43
28646532 CTTTGAATGT
*
28646542 AAGG-GGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTG
1 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATG
* *
28646584 AAAGG-GGTTGCTATGTGCTGATTCC-CCGTATCATTGATTAT-
1 -AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATG
* * * * *
28646625 AAGGTGGTTGTTAAGTGTTGATTCTACCGTATCCTTAATTGTG
1 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATG
* * *
28646668 AAAGG-GGTTGCTATGTGTTGATTCC-CCGTATCATTGATTAT-
1 -AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATG
* * * **
28646709 AAGGTGGTTGCTAAGTGTTGATTCTACCGGGATCCTTTGAACATG
1 AAGGTGGTTGCTAAGTGCTGATTCCACC-GTATCC-TTGATTATG
28646754 -AGGTGGTTGCTAAGTGCTGATTCCACCGT
1 AAGGTGGTTGCTAAGTGCTGATTCCACCGT
28646783 GTAACGGTTA
Statistics
Matches: 164, Mismatches: 25, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
40 8 0.05
41 34 0.21
42 42 0.26
43 45 0.27
44 35 0.21
ACGTcount: A:0.21, C:0.16, G:0.27, T:0.36
Consensus pattern (43 bp):
AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATG
Found at i:28646647 original size:41 final size:40
Alignment explanation
Indices: 28646541--28646732 Score: 213
Period size: 42 Copynumber: 4.6 Consensus size: 40
28646531 TCTTTGAATG
* * *
28646541 TAAGGGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTG
1 TAAGGGGTTGCTAAGTGTTGATTCC-CCGTATCATTGATTA
* *
28646582 TGAAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTA
1 T--AAGGGGTTGCTAAGTGTTGATTCCCCGTATCATTGATTA
* * * * *
28646624 TAAGGTGGTTGTTAAGTGTTGATTCTACCGTATCCTTAATTG
1 TAAGG-GGTTGCTAAGTGTTGATTC-CCCGTATCATTGATTA
*
28646666 TGAAAGGGGTTGCTATGTGTTGATTCCCCGTATCATTGATTA
1 T--AAGGGGTTGCTAAGTGTTGATTCCCCGTATCATTGATTA
28646708 TAAGGTGGTTGCTAAGTGTTGATTC
1 TAAGG-GGTTGCTAAGTGTTGATTC
28646733 TACCGGGATC
Statistics
Matches: 127, Mismatches: 17, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
40 8 0.06
41 35 0.28
42 40 0.31
43 40 0.31
44 4 0.03
ACGTcount: A:0.21, C:0.15, G:0.27, T:0.38
Consensus pattern (40 bp):
TAAGGGGTTGCTAAGTGTTGATTCCCCGTATCATTGATTA
Found at i:28646690 original size:84 final size:84
Alignment explanation
Indices: 28646541--28646737 Score: 342
Period size: 84 Copynumber: 2.4 Consensus size: 84
28646531 TCTTTGAATG
* * *
28646541 TAAGG-GGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGAAAGGGGTTGCTATGTGCTGA
1 TAAGGTGGTTGCTAAGTGTTGATTCTACCGTATCCTTAATTGTGAAAGGGGTTGCTATGTGCTGA
28646605 TTCCCCGTATCATTGATTA
66 TTCCCCGTATCATTGATTA
* *
28646624 TAAGGTGGTTGTTAAGTGTTGATTCTACCGTATCCTTAATTGTGAAAGGGGTTGCTATGTGTTGA
1 TAAGGTGGTTGCTAAGTGTTGATTCTACCGTATCCTTAATTGTGAAAGGGGTTGCTATGTGCTGA
28646689 TTCCCCGTATCATTGATTA
66 TTCCCCGTATCATTGATTA
28646708 TAAGGTGGTTGCTAAGTGTTGATTCTACCG
1 TAAGGTGGTTGCTAAGTGTTGATTCTACCG
28646738 GGATCCTTTG
Statistics
Matches: 107, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
83 5 0.05
84 102 0.95
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (84 bp):
TAAGGTGGTTGCTAAGTGTTGATTCTACCGTATCCTTAATTGTGAAAGGGGTTGCTATGTGCTGA
TTCCCCGTATCATTGATTA
Found at i:28649243 original size:11 final size:11
Alignment explanation
Indices: 28649227--28649251 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28649217 TTTACGATTT
28649227 AAAAAAAATTA
1 AAAAAAAATTA
28649238 AAAAAAAATTA
1 AAAAAAAATTA
28649249 AAA
1 AAA
28649252 CTATTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAAAAATTA
Found at i:28651758 original size:10 final size:10
Alignment explanation
Indices: 28651717--28651761 Score: 63
Period size: 11 Copynumber: 4.2 Consensus size: 10
28651707 TTTTAAAAAT
28651717 AATTTGAGAGG
1 AATTTGAGA-G
28651728 AATTTGAGAG
1 AATTTGAGAG
28651738 AATATTAGAGAG
1 AAT-TT-GAGAG
28651750 AATTTGAGAG
1 AATTTGAGAG
28651760 AA
1 AA
28651762 ATGATTAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 11 0.34
11 13 0.41
12 8 0.25
ACGTcount: A:0.44, C:0.00, G:0.29, T:0.27
Consensus pattern (10 bp):
AATTTGAGAG
Found at i:28653480 original size:15 final size:15
Alignment explanation
Indices: 28653462--28653493 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
28653452 AAATGTCGCG
28653462 ATAACAAATACAACA
1 ATAACAAATACAACA
*
28653477 ATAATAAATACAACA
1 ATAACAAATACAACA
28653492 AT
1 AT
28653494 GACATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.16, G:0.00, T:0.19
Consensus pattern (15 bp):
ATAACAAATACAACA
Found at i:28653519 original size:13 final size:14
Alignment explanation
Indices: 28653501--28653537 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
28653491 AATGACATAA
28653501 AAATAATATAAAC-
1 AAATAATATAAACG
28653514 AAATAA-ATAAACG
1 AAATAATATAAACG
28653527 AAACTAATATA
1 AAA-TAATATA
28653538 CATAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 9 0.43
14 3 0.14
15 3 0.14
ACGTcount: A:0.68, C:0.08, G:0.03, T:0.22
Consensus pattern (14 bp):
AAATAATATAAACG
Found at i:28654076 original size:21 final size:22
Alignment explanation
Indices: 28654020--28654077 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
28654010 AATAAAAACA
28654020 AAAACATATGTATAAAATATAT
1 AAAACATATGTATAAAATATAT
* * **
28654042 ATAAGCATACGTATACTATATAT
1 A-AAACATATGTATAAAATATAT
28654065 AAAACA-ATGTATA
1 AAAACATATGTATA
28654078 TATTACATAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 6 0.21
22 5 0.17
23 18 0.62
ACGTcount: A:0.53, C:0.09, G:0.07, T:0.31
Consensus pattern (22 bp):
AAAACATATGTATAAAATATAT
Found at i:28654598 original size:21 final size:23
Alignment explanation
Indices: 28654572--28654629 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 23
28654562 AAAAGGTATC
*
28654572 TACAAATTCA-ATC-TCTAAGAT
1 TACAAAATCATATCTTCTAAGAT
*
28654593 TACAAAATCATATCTTTTAAGAT
1 TACAAAATCATATCTTCTAAGAT
* *
28654616 TGC-ATATCATATCT
1 TACAAAATCATATCT
28654630 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 9 0.29
22 13 0.42
23 9 0.29
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (23 bp):
TACAAAATCATATCTTCTAAGAT
Found at i:28654623 original size:17 final size:17
Alignment explanation
Indices: 28654601--28654652 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
28654591 ATTACAAAAT
28654601 CATATCTTTTAAGATTG
1 CATATCTTTTAAGATTG
*
28654618 CATATCATATCTAAGATTG
1 CATATC-T-TTTAAGATTG
* *
28654637 CATATCCTTGAAGATT
1 CATATCTTTTAAGATT
28654653 ATGTTTCCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 13 0.45
18 1 0.03
19 15 0.52
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATATCTTTTAAGATTG
Found at i:28655116 original size:17 final size:18
Alignment explanation
Indices: 28655094--28655128 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
28655084 CCTTTATAAA
*
28655094 AAATAATTTAAT-TTTTT
1 AAATAAATTAATATTTTT
28655111 AAATAAATTAATATTTTT
1 AAATAAATTAATATTTTT
28655129 TAGTGTTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AAATAAATTAATATTTTT
Found at i:28660129 original size:108 final size:108
Alignment explanation
Indices: 28659934--28660135 Score: 246
Period size: 108 Copynumber: 1.9 Consensus size: 108
28659924 TCATATGGAA
* * * * *
28659934 ATCCCATGTTTGTTGCAGTTCCATTCACATGGAAATTCTGTTGCTGCTGAAATTGAGTAGTCCAA
1 ATCCCACGTTTGCTGCAGTTCCATTCACATGGAAATTCTGCTGCTGCTGAAATTGAGGAGTCAAA
* *
28659999 GGATCGGTTTGTCCAGTCAAACCATGTGTGTCATATCCAGGTG
66 GGATCGGTTTGACCAGCCAAACCATGTGTGTCATATCCAGGTG
* * * * *
28660042 ATCCCACGTTTGCTGCATTTCCATTCGCGT-GAAAGTTCTGCTGGTGCTGAATTTGAGGAGTCAA
1 ATCCCACGTTTGCTGCAGTTCCATTCACATGGAAA-TTCTGCTGCTGCTGAAATTGAGGAGTCAA
* *
28660106 AGGATTGGTTTGACCA-CCAAAACCTTGTGT
65 AGGATCGGTTTGACCAGCC-AAACCATGTGT
28660136 TCTTGAAGAA
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
107 5 0.06
108 73 0.94
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.33
Consensus pattern (108 bp):
ATCCCACGTTTGCTGCAGTTCCATTCACATGGAAATTCTGCTGCTGCTGAAATTGAGGAGTCAAA
GGATCGGTTTGACCAGCCAAACCATGTGTGTCATATCCAGGTG
Found at i:28669111 original size:100 final size:100
Alignment explanation
Indices: 28668936--28669137 Score: 386
Period size: 100 Copynumber: 2.0 Consensus size: 100
28668926 ATACATGAGT
28668936 ATCTCATATTATTTATATATATGGTTTTAATGTAAAACACATGAAAGTTTTATTCAACATATATC
1 ATCTCATATTATTTATATATATGGTTTTAATGTAAAACACATGAAAGTTTTATTCAACATATATC
* *
28669001 TTCTTGATCTGAAAAACAATATTATATTTTACGAA
66 TTATTAATCTGAAAAACAATATTATATTTTACGAA
28669036 ATCTCATATTATTTATATATATGGTTTTAATGTAAAACACATGAAAGTTTTATTCAACATATATC
1 ATCTCATATTATTTATATATATGGTTTTAATGTAAAACACATGAAAGTTTTATTCAACATATATC
28669101 TTATTAATCTGAAAAACAATATTATATTTTACGAA
66 TTATTAATCTGAAAAACAATATTATATTTTACGAA
28669136 AT
1 AT
28669138 TTTGCATCAC
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 100 1.00
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.42
Consensus pattern (100 bp):
ATCTCATATTATTTATATATATGGTTTTAATGTAAAACACATGAAAGTTTTATTCAACATATATC
TTATTAATCTGAAAAACAATATTATATTTTACGAA
Found at i:28670464 original size:16 final size:16
Alignment explanation
Indices: 28670407--28670480 Score: 62
Period size: 16 Copynumber: 4.8 Consensus size: 16
28670397 ATTTTTCGGA
28670407 TTAAATTATTTT-AA-
1 TTAAATTATTTTGAAT
*
28670421 TTGAATTATTTTGAAT
1 TTAAATTATTTTGAAT
* * **
28670437 TTAGATTTTTTTGGGT
1 TTAAATTATTTTGAAT
* *
28670453 TTAAATTATTTTAAAC
1 TTAAATTATTTTGAAT
*
28670469 TCAAATTATTTT
1 TTAAATTATTTT
28670481 TAAATTTGAA
Statistics
Matches: 45, Mismatches: 13, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
14 11 0.24
15 2 0.04
16 32 0.71
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.57
Consensus pattern (16 bp):
TTAAATTATTTTGAAT
Found at i:28670819 original size:16 final size:16
Alignment explanation
Indices: 28670798--28670840 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
28670788 CAAATGACTC
28670798 AAACCCAAAACAATTA
1 AAACCCAAAACAATTA
* * *
28670814 AAACCCGAAATAATTT
1 AAACCCAAAACAATTA
*
28670830 AAACTCAAAAC
1 AAACCCAAAAC
28670841 CACCTTAACA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.58, C:0.23, G:0.02, T:0.16
Consensus pattern (16 bp):
AAACCCAAAACAATTA
Found at i:28671019 original size:10 final size:9
Alignment explanation
Indices: 28670995--28671024 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
28670985 TCTATCTTCC
28670995 AAAAAATAA
1 AAAAAATAA
28671004 AAAAAATAA
1 AAAAAATAA
28671013 AATAAAATAA
1 AA-AAAATAA
28671023 AA
1 AA
28671025 CACAGGTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (9 bp):
AAAAAATAA
Found at i:28675764 original size:12 final size:11
Alignment explanation
Indices: 28675738--28675766 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
28675728 TATATTTTAA
28675738 TTTTTATGAAC
1 TTTTTATGAAC
28675749 TTTTTATGAAC
1 TTTTTATGAAC
28675760 TTTTTAT
1 TTTTTAT
28675767 ATAATTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (11 bp):
TTTTTATGAAC
Found at i:28685795 original size:31 final size:32
Alignment explanation
Indices: 28685750--28685812 Score: 110
Period size: 31 Copynumber: 2.0 Consensus size: 32
28685740 AGATAATTTT
28685750 AAAGAGTTTTTATTAAGATTCAATTACTCTTG
1 AAAGAGTTTTTATTAAGATTCAATTACTCTTG
*
28685782 AAAGAG-TTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTTATTAAGATTCAATTACTCTTG
28685813 TAATTTGCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 24 0.80
32 6 0.20
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (32 bp):
AAAGAGTTTTTATTAAGATTCAATTACTCTTG
Found at i:28691285 original size:31 final size:31
Alignment explanation
Indices: 28691236--28691298 Score: 110
Period size: 31 Copynumber: 2.0 Consensus size: 31
28691226 TATTAGATAA
28691236 TTTTAAAGAGTTTTTATTAGGATTCAATTAC
1 TTTTAAAGAGTTTTTATTAGGATTCAATTAC
28691267 TTTTGAAAGAG-TTTTATTAGGATTCAATTAC
1 TTTT-AAAGAGTTTTTATTAGGATTCAATTAC
28691298 T
1 T
28691299 CTTGTAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 25 0.81
32 6 0.19
ACGTcount: A:0.32, C:0.06, G:0.14, T:0.48
Consensus pattern (31 bp):
TTTTAAAGAGTTTTTATTAGGATTCAATTAC
Found at i:28694338 original size:24 final size:24
Alignment explanation
Indices: 28694293--28694346 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
28694283 AGAATCAAAT
*
28694293 TCAGAACATGTCTCAATATCAGAA
1 TCAGAACATATCTCAATATCAGAA
*
28694317 TCAGAACATATGTC-ATAGTCAGAA
1 TCAGAACATATCTCAATA-TCAGAA
28694341 TCAGAA
1 TCAGAA
28694347 TTAAAACATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 3 0.11
24 24 0.89
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.24
Consensus pattern (24 bp):
TCAGAACATATCTCAATATCAGAA
Found at i:28697675 original size:42 final size:40
Alignment explanation
Indices: 28697603--28697720 Score: 141
Period size: 40 Copynumber: 2.9 Consensus size: 40
28697593 CCGGGATTCT
* *
28697603 TTAAATGTAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCC
1 TTAATTGTAAGGTGGTTGCTAAGTGCTGATTCCA-C-TATCA
*
28697645 TTAATTGTGAAGG-GGTTGCTATGTGCTGATTCCTA-TATCA
1 TTAATTGT-AAGGTGGTTGCTAAGTGCTGATTCC-ACTATCA
* *
28697685 TTGATTATAAGGTGGTTGCTAAGTGCTGATTCCACT
1 TTAATTGTAAGGTGGTTGCTAAGTGCTGATTCCACT
28697721 GGGATCCTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
39 5 0.08
40 30 0.45
42 26 0.39
43 5 0.08
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.37
Consensus pattern (40 bp):
TTAATTGTAAGGTGGTTGCTAAGTGCTGATTCCACTATCA
Found at i:28704959 original size:27 final size:27
Alignment explanation
Indices: 28704929--28704982 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
28704919 ATAATTGGGG
*
28704929 GAGTCGGTAATATACATATATATATAT
1 GAGTCGGTAATATACATATACATATAT
* ** *
28704956 GAGTGGGTTGTATATATATACATATAT
1 GAGTCGGTAATATACATATACATATAT
28704983 ATACGTGGGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.39
Consensus pattern (27 bp):
GAGTCGGTAATATACATATACATATAT
Found at i:28704970 original size:29 final size:27
Alignment explanation
Indices: 28704938--28705014 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 27
28704928 GGAGTCGGTA
28704938 ATATACATATATATATATGA-GTGGGTTG
1 ATATACATATATATATAT-ACGTGGG-TG
* *
28704966 TATATATATACATATATATACGTGGGTG
1 -ATATACATATATATATATACGTGGGTG
*
28704994 ATTATGCATATATAATATATA
1 A-TATACATATAT-ATATATA
28705015 TGCATGGATT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
27 1 0.03
28 11 0.28
29 28 0.70
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.40
Consensus pattern (27 bp):
ATATACATATATATATATACGTGGGTG
Found at i:28705034 original size:28 final size:28
Alignment explanation
Indices: 28705002--28705103 Score: 107
Period size: 28 Copynumber: 3.5 Consensus size: 28
28704992 TGATTATGCA
28705002 TATATAATATATATGCATGGATTTATTT
1 TATATAATATATATGCATGGATTTATTT
** *
28705030 TATATAATATATATTAATGGATTTTGATGT
1 TATATAATATATATGCATGGA-TTT-ATTT
*
28705060 TATATATATAATATATGCATGG-TTCTATTG
1 TATATA-AT-ATATATGCATGGATT-TATTT
*
28705090 TATACAATATATAT
1 TATATAATATATAT
28705104 AATTATGGGT
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
28 25 0.41
29 5 0.08
30 18 0.30
31 3 0.05
32 10 0.16
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (28 bp):
TATATAATATATATGCATGGATTTATTT
Found at i:28710624 original size:28 final size:22
Alignment explanation
Indices: 28710566--28710610 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
28710556 AGTGTCCACA
28710566 AGTATACAAATCAAATTGTAAT
1 AGTATACAAATCAAATTGTAAT
28710588 AGTATACAAATCAAATTGTAAT
1 AGTATACAAATCAAATTGTAAT
28710610 A
1 A
28710611 TAGTATGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (22 bp):
AGTATACAAATCAAATTGTAAT
Found at i:28719465 original size:28 final size:28
Alignment explanation
Indices: 28719397--28719465 Score: 66
Period size: 28 Copynumber: 2.5 Consensus size: 28
28719387 CCAGAAAAGT
* *
28719397 GGAAGGTCTGCCAAGGGCTATCTTAAGA
1 GGAAAGTCTGCCAAGGACTATCTTAAGA
* * * * *
28719425 AGAAAGTCCGCCAAGGATTATCTTAGGC
1 GGAAAGTCTGCCAAGGACTATCTTAAGA
*
28719453 GGAATGTCTGCCA
1 GGAAAGTCTGCCA
28719466 GGGGCTGACT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (28 bp):
GGAAAGTCTGCCAAGGACTATCTTAAGA
Found at i:28726031 original size:12 final size:13
Alignment explanation
Indices: 28726008--28726037 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
28725998 ACTTAGTTAT
28726008 TTTTAGGGTTTTA
1 TTTTAGGGTTTTA
28726021 TTTTA-GGTTTTA
1 TTTTAGGGTTTTA
28726033 TTTTA
1 TTTTA
28726038 TTTCAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.67
Consensus pattern (13 bp):
TTTTAGGGTTTTA
Found at i:28728519 original size:4 final size:4
Alignment explanation
Indices: 28728510--28728539 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
28728500 TCCAAATAGG
28728510 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA
28728540 AATTTTCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:28730146 original size:19 final size:19
Alignment explanation
Indices: 28730122--28730166 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
28730112 TGTTTCCTTA
*
28730122 AAGTATTTGTAC-TTCGCTT
1 AAGTATCTGTACATT-GCTT
28730141 AAGTATCTGTACATTGCTT
1 AAGTATCTGTACATTGCTT
28730160 AAGTATC
1 AAGTATC
28730167 GATACTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 22 0.92
20 2 0.08
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.42
Consensus pattern (19 bp):
AAGTATCTGTACATTGCTT
Found at i:28731006 original size:15 final size:17
Alignment explanation
Indices: 28730976--28731023 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 17
28730966 GTAATTTAGA
28730976 ATTTTATCTCATTCACT
1 ATTTTATCTCATTCACT
28730993 -TTTTATCTCA-TCACT
1 ATTTTATCTCATTCACT
*
28731008 ATTTCATCTCACTTCA
1 ATTTTATCTCA-TTCA
28731024 TTTATATTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 5 0.19
16 19 0.70
18 3 0.11
ACGTcount: A:0.23, C:0.27, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTTATCTCATTCACT
Found at i:28737365 original size:16 final size:16
Alignment explanation
Indices: 28737346--28737382 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
28737336 TTGGTTCGTT
28737346 GTAATGGAATAAAGGC
1 GTAATGGAATAAAGGC
*
28737362 GTAATGGAATAGAGGC
1 GTAATGGAATAAAGGC
28737378 GTAAT
1 GTAAT
28737383 AATAATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.32, T:0.22
Consensus pattern (16 bp):
GTAATGGAATAAAGGC
Found at i:28737659 original size:24 final size:23
Alignment explanation
Indices: 28737632--28737687 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
28737622 ATTTAATAAA
*
28737632 AATATATAATTTAATAAAATTCTT
1 AATATATAATTTAATAAAA-TCAT
* *
28737656 AATAT-TAAATTACTAAAATCAT
1 AATATATAATTTAATAAAATCAT
28737678 AATATATAAT
1 AATATATAAT
28737688 ACTATAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 8 0.30
23 14 0.52
24 5 0.19
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (23 bp):
AATATATAATTTAATAAAATCAT
Found at i:28737743 original size:18 final size:18
Alignment explanation
Indices: 28737720--28737755 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
28737710 AATTATTATT
28737720 AAATATAATTTAATAAAA
1 AAATATAATTTAATAAAA
28737738 AAATATAATTTAATAAAA
1 AAATATAATTTAATAAAA
28737756 TTCCTAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATATAATTTAATAAAA
Found at i:28737796 original size:120 final size:123
Alignment explanation
Indices: 28737615--28737857 Score: 397
Period size: 120 Copynumber: 2.0 Consensus size: 123
28737605 AATTATTATT
* *
28737615 AAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATTACTAAAATCATAA
1 AAATATAATTTAATAAAAATATATAATTTAATAAAATCCTTAATATGAAATTACTAAAATCATAA
28737680 TATATAATACTATAAAATATAATTTAACATAATTATTATTAAATATAATTTAATAAAA
66 TATATAATACTATAAAATATAATTTAACATAATTATTATTAAATATAATTTAATAAAA
* *
28737738 AAATATAATTTAAT-AAAAT-TCCTAATATT-A-AAAATCCTT-ATATGAATTTACTAAAATCAT
1 AAATATAATTTAATAAAAATAT-ATAAT-TTAATAAAATCCTTAATATGAAATTACTAAAATCAT
28737798 AATATATAATACTATAAAATATAATTTAACATAATTATTATTAAATATAATTTAATAAAA
64 AATATATAATACTATAAAATATAATTTAACATAATTATTATTAAATATAATTTAATAAAA
28737858 TTCTTAATAT
Statistics
Matches: 114, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
120 79 0.69
121 9 0.08
122 10 0.09
123 16 0.14
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (123 bp):
AAATATAATTTAATAAAAATATATAATTTAATAAAATCCTTAATATGAAATTACTAAAATCATAA
TATATAATACTATAAAATATAATTTAACATAATTATTATTAAATATAATTTAATAAAA
Found at i:28737844 original size:26 final size:26
Alignment explanation
Indices: 28737801--28737956 Score: 94
Period size: 26 Copynumber: 6.1 Consensus size: 26
28737791 AAATCATAAT
* *
28737801 ATATAA-TACTATAAAATATAATTTA
1 ATATAATTATTATTAAATATAATTTA
*
28737826 ACATAATTATTATTAAATATAATTTA
1 ATATAATTATTATTAAATATAATTTA
* * * *
28737852 ATAAAATTCTTAATATTAAATAT--TCTG
1 ATATAA---TTATTATTAAATATAATTTA
* *
28737879 ATATAAAT-TTACTAAAATCATAA--T-
1 ATATAATTATTA-TTAAAT-ATAATTTA
** *
28737903 ATATAA-TGCTATAAAATATAATTTA
1 ATATAATTATTATTAAATATAATTTA
*
28737928 ACATAATTATTATTAAATATAATTTA
1 ATATAATTATTATTAAATATAATTTA
28737954 ATA
1 ATA
28737957 AAAATATATA
Statistics
Matches: 100, Mismatches: 18, Indels: 25
0.70 0.13 0.17
Matches are distributed among these distances:
22 4 0.04
23 9 0.09
24 15 0.15
25 13 0.13
26 39 0.39
27 7 0.07
29 13 0.13
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.42
Consensus pattern (26 bp):
ATATAATTATTATTAAATATAATTTA
Found at i:28737866 original size:102 final size:102
Alignment explanation
Indices: 28737738--28737959 Score: 390
Period size: 102 Copynumber: 2.2 Consensus size: 102
28737728 TTTAATAAAA
* *
28737738 AAATATAATTTAATAAAATTCCTAATATTAAAAATCCTTATATGAATTTACTAAAATCATAATAT
1 AAATATAATTTAATAAAATTCCTAATATTAAAAATCCTGATATAAATTTACTAAAATCATAATAT
28737803 ATAATACTATAAAATATAATTTAACATAATTATTATT
66 ATAATACTATAAAATATAATTTAACATAATTATTATT
* * *
28737840 AAATATAATTTAATAAAATTCTTAATATTAAATATTCTGATATAAATTTACTAAAATCATAATAT
1 AAATATAATTTAATAAAATTCCTAATATTAAAAATCCTGATATAAATTTACTAAAATCATAATAT
*
28737905 ATAATGCTATAAAATATAATTTAACATAATTATTATT
66 ATAATACTATAAAATATAATTTAACATAATTATTATT
28737942 AAATATAATTTAATAAAA
1 AAATATAATTTAATAAAA
28737960 ATATATAATT
Statistics
Matches: 114, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 114 1.00
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (102 bp):
AAATATAATTTAATAAAATTCCTAATATTAAAAATCCTGATATAAATTTACTAAAATCATAATAT
ATAATACTATAAAATATAATTTAACATAATTATTATT
Found at i:28737917 original size:61 final size:61
Alignment explanation
Indices: 28737852--28738038 Score: 204
Period size: 61 Copynumber: 3.1 Consensus size: 61
28737842 ATATAATTTA
*
28737852 ATAAAATTCTTAATATTAAATATTCTGATATAAATTTACTAAAATCATAATATATAATGCT
1 ATAAAATTCTTAATATTAAATATTCTTATATAAATTTACTAAAATCATAATATATAATGCT
* * * * ** * * *
28737913 ATAAAA-T-ATAAT-TTAACATAATTATTAT-TAAATATAATTTAATAAAAATATATAAT-TT
1 ATAAAATTCTTAATATTAA-AT-ATTCTTATATAAATTTACTAAAATCATAATATATAATGCT
* *
28737971 AATGAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATGCT
1 -ATAAAATTCTTAATATTAAATATTCTTATATAAATTTACTAAAATCATAATATATAATGCT
28738033 ATAAAA
1 ATAAAA
28738039 ATATTGTATA
Statistics
Matches: 96, Mismatches: 22, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
58 5 0.05
59 33 0.34
60 15 0.16
61 38 0.40
62 5 0.05
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (61 bp):
ATAAAATTCTTAATATTAAATATTCTTATATAAATTTACTAAAATCATAATATATAATGCT
Found at i:28737988 original size:222 final size:225
Alignment explanation
Indices: 28737597--28738038 Score: 732
Period size: 222 Copynumber: 2.0 Consensus size: 225
28737587 TTAATCATAT
28737597 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
28737662 AAATTACTAAAATCATAATATATAATACTATAAAATATAATTTAACATAATTATTATTAAATATA
66 AAATTACTAAAATCATAATATATAATACTATAAAATATAATTTAACATAATTATTATTAAATATA
28737727 ATTTAATAAAAAAATATAATTTAATAAAATTCCTAATATTAAAAATCCTTATATGAATTTACTAA
131 ATTTAATAAAAAAATATAATTTAATAAAATTCCTAATATTAAAAATCCTTATATGAATTTACTAA
28737792 AATCATAATATATAATACTATAAAATATAA
196 AATCATAATATATAATACTATAAAATATAA
* * * *
28737822 TTTAACATAATTATTATTAAATATAATTTAATAAAATTCT-TAATATT-A-AATATTC-TGATA-
1 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAAT-TTAATAAAATTCTTAATAT
*
28737882 TAAATTTACTAAAATCATAATATATAATGCTATAAAATATAATTTAACATAATTATTATTAAATA
65 TAAA-TTACTAAAATCATAATATATAATACTATAAAATATAATTTAACATAATTATTATTAAATA
* * * * *
28737947 TAATTTAATAAAAATATATAATTTAATGAAATTCTTAATATTAAATATTCTTATATGAATTTACT
129 TAATTTAATAAAAAAATATAATTTAATAAAATTCCTAATATTAAAAATCCTTATATGAATTTACT
*
28738012 AAAATCATAATATATAATGCTATAAAA
194 AAAATCATAATATATAATACTATAAAA
28738039 ATATTGTATA
Statistics
Matches: 204, Mismatches: 11, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
221 4 0.02
222 149 0.73
223 6 0.03
224 5 0.02
225 40 0.20
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (225 bp):
TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
AAATTACTAAAATCATAATATATAATACTATAAAATATAATTTAACATAATTATTATTAAATATA
ATTTAATAAAAAAATATAATTTAATAAAATTCCTAATATTAAAAATCCTTATATGAATTTACTAA
AATCATAATATATAATACTATAAAATATAA
Found at i:28738025 original size:59 final size:58
Alignment explanation
Indices: 28737841--28738025 Score: 173
Period size: 59 Copynumber: 3.1 Consensus size: 58
28737831 ATTATTATTA
*
28737841 AATATAATTTAATAAAATTCTTAATATTAAATATTCTGATATAAATTTACTAAAATCAT
1 AATATAATTTAATAAAATTCTTAATATTAAATATTCTTATAT-AATTTACTAAAATCAT
* * * * * *
28737900 AATATATAATGCT-ATAAAATATAATTTAACA-TAATTATTATTAAATATAATTTAATAAAA--A
1 -A-ATATAAT-TTAATAAAAT-T--CTTAATATTAAATATTCTT--ATATAATTTACTAAAATCA
28737961 T
58 T
*
28737962 -ATATAATTTAATGAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
1 AATATAATTTAATAAAATTCTTAATATTAAATATTCTTATAT-AATTTACTAAAATCAT
28738020 AATATA
1 AATATA
28738026 TAATGCTATA
Statistics
Matches: 98, Mismatches: 14, Indels: 27
0.71 0.10 0.19
Matches are distributed among these distances:
55 4 0.04
56 16 0.16
57 9 0.09
58 4 0.04
59 18 0.18
60 1 0.01
61 14 0.14
62 4 0.04
63 8 0.08
64 16 0.16
65 4 0.04
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.42
Consensus pattern (58 bp):
AATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATAATTTACTAAAATCAT
Found at i:28740365 original size:13 final size:13
Alignment explanation
Indices: 28740347--28740376 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
28740337 CCAAGGGGTT
*
28740347 AACAAGGAAATCA
1 AACAAGAAAATCA
28740360 AACAAGAAAATCA
1 AACAAGAAAATCA
28740373 AACA
1 AACA
28740377 TGCAATACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.17, G:0.10, T:0.07
Consensus pattern (13 bp):
AACAAGAAAATCA
Found at i:28744431 original size:30 final size:31
Alignment explanation
Indices: 28744395--28744454 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
28744385 AAACCTTTTA
*
28744395 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
** *
28744425 TTTTCCCTTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
28744455 TCCCACCTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:28744578 original size:21 final size:21
Alignment explanation
Indices: 28744549--28744588 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
28744539 TCCCTCAAAC
28744549 TTTTGCTCCCCAAAACTTTTTA
1 TTTTGCT-CCCAAAACTTTTTA
*
28744571 TTTT-CTCCCTAAACTTTT
1 TTTTGCTCCCAAAACTTTT
28744589 ACTTCTCACC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.20, C:0.28, G:0.03, T:0.50
Consensus pattern (21 bp):
TTTTGCTCCCAAAACTTTTTA
Found at i:28745215 original size:5 final size:5
Alignment explanation
Indices: 28745205--28745245 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
28745195 CTCGAAAATT
** *
28745205 TTCGA TTCGA TTTAA TTCGA TTCGA TTTGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
28745246 CGAATGCTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.46
Consensus pattern (5 bp):
TTCGA
Found at i:28745223 original size:15 final size:15
Alignment explanation
Indices: 28745205--28745245 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
28745195 CTCGAAAATT
28745205 TTCGATTCGATTTAA
1 TTCGATTCGATTTAA
*
28745220 TTCGATTCGATTTGA
1 TTCGATTCGATTTAA
28745235 TTCGATTCGAT
1 TTCGATTCGAT
28745246 CGAATGCTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.46
Consensus pattern (15 bp):
TTCGATTCGATTTAA
Found at i:28751295 original size:23 final size:24
Alignment explanation
Indices: 28751258--28751302 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
28751248 AGTTAGACCT
28751258 GAAATTTAAAATTTAAAAAATAGA
1 GAAATTTAAAATTTAAAAAATAGA
* *
28751282 GAAA-TTAAATTTTATAAAATA
1 GAAATTTAAAATTTAAAAAATA
28751303 AAAATATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (24 bp):
GAAATTTAAAATTTAAAAAATAGA
Found at i:28754476 original size:22 final size:22
Alignment explanation
Indices: 28754451--28754496 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
28754441 GTATATAGAG
28754451 AATATAAAATA-ATAAATAAATA
1 AATATAAAATATA-AAATAAATA
* *
28754473 AATATAACATATAAAATACATA
1 AATATAAAATATAAAATAAATA
28754495 AA
1 AA
28754497 GGGTTGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (22 bp):
AATATAAAATATAAAATAAATA
Found at i:28755999 original size:19 final size:19
Alignment explanation
Indices: 28755949--28756000 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 19
28755939 TTTCTGATTT
* *
28755949 TTATTTTTAATATTTAAAA
1 TTATTATTAATTTTTAAAA
* * *
28755968 ATATTCATGAATTTTTTAAA
1 TTATT-ATTAATTTTTAAAA
28755988 TTATTATTAATTT
1 TTATTATTAATTT
28756001 ATTCTTTTAA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (19 bp):
TTATTATTAATTTTTAAAA
Found at i:28756556 original size:4 final size:4
Alignment explanation
Indices: 28756547--28756848 Score: 338
Period size: 4 Copynumber: 75.2 Consensus size: 4
28756537 TATGTTATCT
*
28756547 TATG TATG TATG TATG TATG TATG TATG TATG TATA TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
28756595 TATG TATG TAATG TATG TATG TATG TATG TATG CATG TATG TATG TATG
1 TATG TATG T-ATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * *
28756644 TATG TATG TATG TATG TATG CATG CATG CATG TATAG -ATG CATG GATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT-G TATG TATG TATG
* * * * * * * *
28756692 TATA TATG GATG TATG TATG CATG GATG TATG GATG CATG CATG CATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * * * * * * *
28756740 TATG CT-TC CATA CATG CATA TATG CATG CATG CATG GATG TATG TATG
1 TATG -TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
28756788 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
28756836 TATG TATG TATG T
1 TATG TATG TATG T
28756849 TTTTTGTGAA
Statistics
Matches: 265, Mismatches: 28, Indels: 10
0.87 0.09 0.03
Matches are distributed among these distances:
3 1 0.00
4 258 0.97
5 6 0.02
ACGTcount: A:0.26, C:0.06, G:0.25, T:0.43
Consensus pattern (4 bp):
TATG
Found at i:28758728 original size:25 final size:25
Alignment explanation
Indices: 28758693--28758906 Score: 125
Period size: 25 Copynumber: 8.6 Consensus size: 25
28758683 CCTAGCATTG
*
28758693 GTGGCGGGTTATCTATAAAGCCTTT
1 GTGGCGAGTTATCTATAAAGCCTTT
*
28758718 GTGGCGAGTTATCTGTAAAGCCTTT
1 GTGGCGAGTTATCTATAAAGCCTTT
* * * *
28758743 AT-GAGAGTTAAT-TGTAAAGTCTTT
1 GTGGCGAGTT-ATCTATAAAGCCTTT
* * *
28758767 GTGGTGAGTTAAT-TGTAAGGCCTTT
1 GTGGCGAGTT-ATCTATAAAGCCTTT
* * **
28758792 ATGGCGAGTTATCTGTAAAGAATTT
1 GTGGCGAGTTATCTATAAAGCCTTT
* ** *
28758817 TTGGAAAATTATCTATAAAG-CTCTT
1 GTGGCGAGTTATCTATAAAGCCT-TT
* * * *
28758842 GTGGTGAATTATCTAAAAAGCCTAT
1 GTGGCGAGTTATCTATAAAGCCTTT
* *
28758867 GTGACGTA-TTAT-TCATAAAGCCTTA
1 GTGGCG-AGTTATCT-ATAAAGCCTTT
28758892 GTGGCGAAGTTATCT
1 GTGGCG-AGTTATCT
28758907 GGGAAGCCCT
Statistics
Matches: 148, Mismatches: 32, Indels: 16
0.76 0.16 0.08
Matches are distributed among these distances:
24 22 0.15
25 118 0.80
26 7 0.05
27 1 0.01
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (25 bp):
GTGGCGAGTTATCTATAAAGCCTTT
Found at i:28758767 original size:49 final size:50
Alignment explanation
Indices: 28758700--28758811 Score: 140
Period size: 49 Copynumber: 2.3 Consensus size: 50
28758690 TTGGTGGCGG
*
28758700 GTTATCTATAAAGCCTTTGTGGCGAGTT-ATCTGTAAAGCCTTTAT-GAGA
1 GTTATCTGTAAAGCCTTTGTGGCGAGTTAAT-TGTAAAGCCTTTATGGAGA
* * * *
28758749 GTTAAT-TGTAAAGTCTTTGTGGTGAGTTAATTGTAAGGCCTTTATGGCGA
1 GTT-ATCTGTAAAGCCTTTGTGGCGAGTTAATTGTAAAGCCTTTATGGAGA
28758799 GTTATCTGTAAAG
1 GTTATCTGTAAAG
28758812 AATTTTTGGA
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
49 37 0.69
50 17 0.31
ACGTcount: A:0.26, C:0.11, G:0.25, T:0.38
Consensus pattern (50 bp):
GTTATCTGTAAAGCCTTTGTGGCGAGTTAATTGTAAAGCCTTTATGGAGA
Found at i:28760425 original size:32 final size:32
Alignment explanation
Indices: 28760380--28760457 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 32
28760370 CAATAATTTT
* * *
28760380 TAAAGGTTGATTAATACAAATGCC-TGAAGAAA
1 TAAAGATTGATTAATACAAA-CCCTTAAAGAAA
* *
28760412 TTAGGATTGATTAATACAAACCCTTAAAGAAA
1 TAAAGATTGATTAATACAAACCCTTAAAGAAA
28760444 TAAAGATTGATTAA
1 TAAAGATTGATTAA
28760458 AAATTTACCA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 2 0.05
32 36 0.95
ACGTcount: A:0.47, C:0.09, G:0.15, T:0.28
Consensus pattern (32 bp):
TAAAGATTGATTAATACAAACCCTTAAAGAAA
Found at i:28772453 original size:6 final size:6
Alignment explanation
Indices: 28772442--28772470 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
28772432 ATCCTTAATC
28772442 TCTGCG TCTGCG TCTGCG TCTGCG TCTGC
1 TCTGCG TCTGCG TCTGCG TCTGCG TCTGC
28772471 TTCTTTCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.34, G:0.31, T:0.34
Consensus pattern (6 bp):
TCTGCG
Found at i:28792114 original size:20 final size:20
Alignment explanation
Indices: 28792089--28792130 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
28792079 TAGAGCTAAG
28792089 CAATCGAGCATG-AATGTGTT
1 CAATCGA-CATGAAATGTGTT
*
28792109 CAATCGACTTGAAATGTGTT
1 CAATCGACATGAAATGTGTT
28792129 CA
1 CA
28792131 GTAAGAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (20 bp):
CAATCGACATGAAATGTGTT
Found at i:28795001 original size:6 final size:6
Alignment explanation
Indices: 28794990--28795031 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
28794980 TTATGGAATG
*
28794990 AATGAA AATGAA AATGAA AATGAA AATAAA AATGAA AA-GAA A
1 AATGAA AATGAA AATGAA AATGAA AATGAA AATGAA AATGAA A
28795032 TATATTGCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
5 4 0.12
6 30 0.88
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (6 bp):
AATGAA
Found at i:28798646 original size:23 final size:23
Alignment explanation
Indices: 28798591--28798647 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
28798581 GACGTCATTT
* *
28798591 ATCGCGTCATCAGGATGTGAAAA
1 ATCGCGTCATCAGGACGAGAAAA
* *
28798614 TTCACGTCATCAGGACGAGAAAA
1 ATCGCGTCATCAGGACGAGAAAA
*
28798637 ATCGCATCATC
1 ATCGCGTCATC
28798648 TCGACATGGC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (23 bp):
ATCGCGTCATCAGGACGAGAAAA
Found at i:28814954 original size:12 final size:12
Alignment explanation
Indices: 28814937--28814964 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
28814927 ATGTCATCAT
28814937 ATTAATTTTTGA
1 ATTAATTTTTGA
28814949 ATTAATTTTTGA
1 ATTAATTTTTGA
28814961 ATTA
1 ATTA
28814965 CACTATCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (12 bp):
ATTAATTTTTGA
Found at i:28822187 original size:9 final size:9
Alignment explanation
Indices: 28822147--28822189 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 9
28822137 CACTTAGTTA
28822147 ATTTTTTTT
1 ATTTTTTTT
28822156 ATGTTTTTTT
1 AT-TTTTTTT
**
28822166 AGTTGCTTTT
1 A-TTTTTTTT
28822176 ATTTTTTTT
1 ATTTTTTTT
28822185 ATTTT
1 ATTTT
28822190 GTGTTGTAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
9 13 0.46
10 14 0.50
11 1 0.04
ACGTcount: A:0.12, C:0.02, G:0.07, T:0.79
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:28825236 original size:7 final size:7
Alignment explanation
Indices: 28825226--28825258 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
28825216 GTACATTATA
28825226 TATTAAT
1 TATTAAT
28825233 TATTAAT
1 TATTAAT
28825240 TATTAAT
1 TATTAAT
28825247 TATTATAT
1 TATTA-AT
28825255 TATT
1 TATT
28825259 TGAAATATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
TATTAAT
Found at i:28825243 original size:14 final size:15
Alignment explanation
Indices: 28825220--28825258 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
28825210 ATAGAAGTAC
28825220 ATTATA-TATTAATT
1 ATTATATTATTAATT
28825234 ATTA-ATTATTAATT
1 ATTATATTATTAATT
28825248 ATTATATTATT
1 ATTATATTATT
28825259 TGAAATATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.04
14 16 0.70
15 6 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTATATTATTAATT
Found at i:28825404 original size:16 final size:17
Alignment explanation
Indices: 28825383--28825415 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28825373 TATACTATAG
28825383 ATTTTA-ATAATTATTA
1 ATTTTATATAATTATTA
*
28825399 ATTTTATATATTTATTA
1 ATTTTATATAATTATTA
28825416 TACATATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTTATATAATTATTA
Found at i:28833274 original size:9 final size:9
Alignment explanation
Indices: 28833260--28833288 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
28833250 TTAGATGATT
28833260 TTATATTAA
1 TTATATTAA
28833269 TTATATTAA
1 TTATATTAA
28833278 TTATATTAA
1 TTATATTAA
28833287 TT
1 TT
28833289 TGGTTTTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTATATTAA
Found at i:28836254 original size:17 final size:17
Alignment explanation
Indices: 28836232--28836267 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
28836222 ACAAGATGAT
28836232 ATAGAGATTAATGAAAG
1 ATAGAGATTAATGAAAG
28836249 ATAGAGATTAATGAAAG
1 ATAGAGATTAATGAAAG
28836266 AT
1 AT
28836268 TTATTGACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.25
Consensus pattern (17 bp):
ATAGAGATTAATGAAAG
Found at i:28849106 original size:13 final size:13
Alignment explanation
Indices: 28849088--28849151 Score: 92
Period size: 13 Copynumber: 4.9 Consensus size: 13
28849078 ACACTCAAAT
*
28849088 TTCTCAAAAACAC
1 TTCTCAAAAGCAC
28849101 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
* * *
28849114 TTTTGAAAAGCAT
1 TTCTCAAAAGCAC
28849127 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
28849140 TTCTCAAAAGCA
1 TTCTCAAAAGCA
28849152 ATAAAGAACT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 44 1.00
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.27
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:28854100 original size:24 final size:24
Alignment explanation
Indices: 28854060--28854105 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
28854050 TCCTTTTGTT
*
28854060 TTCTTAAATTTCATCTTTCCTTTC
1 TTCTTAAATTTCATCTTACCTTTC
*
28854084 TTCTT-AATTTGCTTCTTACCTT
1 TTCTTAAATTT-CATCTTACCTT
28854106 GCTGCCATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.15, C:0.24, G:0.02, T:0.59
Consensus pattern (24 bp):
TTCTTAAATTTCATCTTACCTTTC
Found at i:28857109 original size:20 final size:19
Alignment explanation
Indices: 28857076--28857114 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
28857066 GTAGATCATA
28857076 ATTCTTAGAAAATAGAATTT
1 ATTCTTAGAAAATA-AATTT
**
28857096 ATTCTTAGTTAATAAATTT
1 ATTCTTAGAAAATAAATTT
28857115 CTACTACTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (19 bp):
ATTCTTAGAAAATAAATTT
Found at i:28860196 original size:31 final size:30
Alignment explanation
Indices: 28860161--28860222 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 30
28860151 AACCATTAAC
* *
28860161 TTTTATTT-TTATTTTGTTGTTTGTTTTTCTT
1 TTTTATTTATTAGTTTG-TGTTTG-GTTTCTT
28860192 TTTTATTTATTAGTTTGTGTTTGGTTTCTT
1 TTTTATTTATTAGTTTGTGTTTGGTTTCTT
28860222 T
1 T
28860223 AGCGGGCCGG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 7 0.25
31 14 0.50
32 7 0.25
ACGTcount: A:0.08, C:0.03, G:0.13, T:0.76
Consensus pattern (30 bp):
TTTTATTTATTAGTTTGTGTTTGGTTTCTT
Found at i:28860512 original size:44 final size:44
Alignment explanation
Indices: 28860415--28860940 Score: 434
Period size: 44 Copynumber: 12.1 Consensus size: 44
28860405 ACTGGATGCG
* * * ** *
28860415 ATCTGCTCAACTGCCACTTTAGAAAGATAAGATCTGTGCTT-TT-A
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TG-GTTTCTTCA
* * *
28860459 ATCTACTCCACTGCAACTTCAGGGACATAGGATTGGTTTCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCA
* *
28860503 ATCTGCTCCACT-CAACTTCAGAGAGATAAGATTGGTTTCTTCT
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCA
* * * *
28860546 GTCTGCTCCATTGCAACTTCAGGGAGATAAGACTAGATTT-TTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGGTTTCTTCA
* * * *
28860590 ATCTGCTCCATTGCAACTTCAAGGAGATAAGACTGGATTCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCA
* * * ** *
28860634 ATCTGCTCCATTGTAACTTCAGGGAGATAAGACTGAATCCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCA
* * *
28860678 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGG--GCAT-G
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCA
* * * *
28860719 ATCTGCTCTACTGCAACTTTAGAGAGATAAGATCTGTGGTT-TT-A
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TG-GTTTCTTCA
* ** * * *
28860763 TTCCACTCCGA-TGCAACTTCAGGGAGATATGATTAGTTTTTTCA
1 ATCTGCTCC-ACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCA
* ** * * *
28860807 ATCTGATTTACTGCAACTTCAGGGAGATAAGATTGG---ATGCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCA
* * *
28860848 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCT-GTTAT-TTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TGGTT-TCTTCA
* *
28860892 ATCTGCTCCGCTGCAACTTCAGGGAGATAGGATTGGTTTCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCA
28860936 ATCTG
1 ATCTG
28860941 TTCTCTGAGG
Statistics
Matches: 388, Mismatches: 74, Indels: 40
0.77 0.15 0.08
Matches are distributed among these distances:
41 63 0.16
42 11 0.03
43 51 0.13
44 257 0.66
45 6 0.02
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCA
Found at i:28860936 original size:129 final size:129
Alignment explanation
Indices: 28860459--28860940 Score: 478
Period size: 129 Copynumber: 3.7 Consensus size: 129
28860449 TGTGCTTTTA
* * * * *
28860459 ATCTACTCCACTGCAACTTCAGGGACATAGGAT-TG-GTTTCTTCAATCTGCTCCACT-CAACTT
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGATT-TT-AATCTGCTCCACTGCAACTT
* ** * * *
28860521 CAGAGAGATAAGATTGGTTTCTTCTGTCTGCTCCATTGCAACTTCAGGGAGATAAGACTAGATTT
64 CAGGGAGATAAGATTGGTTTCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGA---
* *
28860586 TTCA
126 TGCG
* * *
28860590 ATCTGCTCCATTGCAACTTCA-AGGAGATAAGA-CTG-GATTCTTCAATCTGCTCCATTGTAACT
1 ATCTGCTCCACTGCAACTTCAGA-GAGATAAGATCTGTGATT-TT-AATCTGCTCCACTGCAACT
* ** *
28860652 TCAGGGAGATAAGACTGAATCCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGG--G
63 TCAGGGAGATAAGATTGGTTTCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGATG
28860715 CATG
128 C--G
* * * * **
28860719 ATCTGCTCTACTGCAACTTTAGAGAGATAAGATCTGTGGTTTTATTCCACTCCGA-TGCAACTTC
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCTGCTCC-ACTGCAACTTC
* * * * **
28860783 AGGGAGATATGATTAGTTTTTTCAATCTGATTTACTGCAACTTCAGGGAGATAAGATTGGATGCG
65 AGGGAGATAAGATTGGTTTCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGATGCG
* * *
28860848 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTTATTTTAATCTGCTCCGCTGCAACTTCA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCTGCTCCACTGCAACTTCA
*
28860913 GGGAGATAGGATTGGTTTCTTCAATCTG
66 GGGAGATAAGATTGGTTTCTTCAATCTG
28860941 TTCTCTGAGG
Statistics
Matches: 291, Mismatches: 48, Indels: 26
0.80 0.13 0.07
Matches are distributed among these distances:
127 1 0.00
129 175 0.60
130 7 0.02
131 52 0.18
132 56 0.19
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (129 bp):
ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCTGCTCCACTGCAACTTCA
GGGAGATAAGATTGGTTTCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGATGCG
Found at i:28861830 original size:26 final size:26
Alignment explanation
Indices: 28861771--28861824 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
28861761 AGTATCTTGA
* *
28861771 AAAGATTAAAGTATTCCAAGAACAGC
1 AAAGAATAAAGTATTCCAAGAACAAC
* *
28861797 AAAGAATAAAGTATTCTAAGAATAAC
1 AAAGAATAAAGTATTCCAAGAACAAC
28861823 AA
1 AA
28861825 GTAATATGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.56, C:0.11, G:0.13, T:0.20
Consensus pattern (26 bp):
AAAGAATAAAGTATTCCAAGAACAAC
Found at i:28862162 original size:45 final size:44
Alignment explanation
Indices: 28862100--28862184 Score: 134
Period size: 45 Copynumber: 1.9 Consensus size: 44
28862090 CTCTCCCTTT
28862100 TTTTTTTAGACTCAAAGCACCCTTTGCGGGTTTTCACCTTAGTC
1 TTTTTTTAGACTCAAAGCACCCTTTGCGGGTTTTCACCTTAGTC
* * *
28862144 TTTTTTTAGGATTCAAAGCGCTCTTTGCGGGTTTTCACCTT
1 TTTTTTTA-GACTCAAAGCACCCTTTGCGGGTTTTCACCTT
28862185 GATCCATCCT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
44 8 0.22
45 29 0.78
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.44
Consensus pattern (44 bp):
TTTTTTTAGACTCAAAGCACCCTTTGCGGGTTTTCACCTTAGTC
Found at i:28874388 original size:30 final size:30
Alignment explanation
Indices: 28874337--28874397 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 30
28874327 AACCATTAAC
**
28874337 TTTTATTTTTGTTTTGTTGTTTTTTTTCTT
1 TTTTATTTTTGTTTTGTTGTTTGGTTTCTT
28874367 TTTTATTTATTAG-TTTG-TGTTTGGTTTCTT
1 TTTTATTT-TT-GTTTTGTTGTTTGGTTTCTT
28874397 T
1 T
28874398 AGCGGGCTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 20 0.74
31 6 0.22
32 1 0.04
ACGTcount: A:0.07, C:0.03, G:0.13, T:0.77
Consensus pattern (30 bp):
TTTTATTTTTGTTTTGTTGTTTGGTTTCTT
Found at i:28880521 original size:19 final size:19
Alignment explanation
Indices: 28880497--28880550 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
28880487 AATCTTCAAG
28880497 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
28880516 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
28880535 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
28880551 AGATATGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:28880526 original size:36 final size:36
Alignment explanation
Indices: 28880486--28880557 Score: 94
Period size: 38 Copynumber: 2.0 Consensus size: 36
28880476 TATGGAAACA
28880486 TAATCTT-CA-AGGATATGCAATCTTAGATATGATATG
1 TAATCTTACATAGGATATGCAATCTTAGA-A-GATATG
* *
28880522 TAATCTTAGATATGATATGCAATCTTAGAAGATATG
1 TAATCTTACATAGGATATGCAATCTTAGAAGATATG
28880558 ATTTTGTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 13 0.41
37 2 0.06
38 17 0.53
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (36 bp):
TAATCTTACATAGGATATGCAATCTTAGAAGATATG
Found at i:28880541 original size:38 final size:40
Alignment explanation
Indices: 28880497--28880573 Score: 113
Period size: 38 Copynumber: 1.9 Consensus size: 40
28880487 AATCTTCAAG
28880497 GATATGCAATCTT-AGATATGA-TATGTAATCTTAGATAT
1 GATATGCAATCTTAAGATATGATTATGTAATCTTAGATAT
*
28880535 GATATGCAATCTTAGAAGATATGATTTTGTAATCTTAGA
1 GATATGCAATCTT--AAGATATGATTATGTAATCTTAGA
28880574 GATTTAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
38 13 0.38
41 8 0.24
42 13 0.38
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (40 bp):
GATATGCAATCTTAAGATATGATTATGTAATCTTAGATAT
Found at i:28880800 original size:23 final size:23
Alignment explanation
Indices: 28880756--28880800 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
28880746 TCTTATTTTG
* *
28880756 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
28880779 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
28880801 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:28881029 original size:3 final size:3
Alignment explanation
Indices: 28881021--28881056 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
28881011 ATTAATCTTG
*
28881021 TAT TAT TAT TAT TATT TAT TAT TAT TAA TAT TAT TA
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TA
28881057 CCACGTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:28884251 original size:20 final size:20
Alignment explanation
Indices: 28884226--28884268 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
28884216 CTTCCGCATC
28884226 ATTCTTTCATTCATAATTAT
1 ATTCTTTCATTCATAATTAT
28884246 ATTCTTTCATTCATAATTAT
1 ATTCTTTCATTCATAATTAT
28884266 ATT
1 ATT
28884269 GTACAAATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.14, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTCTTTCATTCATAATTAT
Found at i:28886553 original size:88 final size:88
Alignment explanation
Indices: 28886404--28887062 Score: 925
Period size: 88 Copynumber: 7.5 Consensus size: 88
28886394 ATCAGTGAAG
* * * *
28886404 ATAGCAGATCTTGCCTTCCTACATCGACAGCGAAGCAGATCGAAGACACTAGCCTTGCCTCCTTG
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
*
28886469 GATTGCAGCGAAGCAGGTTAAAA
66 GGTTGCAGCGAAGCAGGTTAAAA
* * * *
28886492 ATAGCAGATCTTGTCTTCCTACACTGACAGCAAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
28886557 GGTTGCAGC-AGAGCAGGTTAAAA
66 GGTTGCAGCGA-AGCAGGTTAAAA
**
28886580 ATTA-CAGATCTTATCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCT
1 A-TAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCT
28886644 GGGTTGCAGC-AGAGCAGGTTAAAA
65 GGGTTGCAGCGA-AGCAGGTTAAAA
** *
28886668 ATTA-CAGATCTTATCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCT
1 A-TAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCT
* * *
28886732 GGGTTGTAACGGAGCAGGTTAAAA
65 GGGTTGCAGCGAAGCAGGTTAAAA
* * * * *
28886756 ATAACAGATCTTGCCTTCCTGC-CTCGACAACGAAGCTGATCAAAGACACTAGCCTTGCCTCCCT
1 ATAGCAGATCTTGCCTTCCTGCAC-CGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCT
*
28886820 GGGTTGCAGCGGAGCAGGTTAAAA
65 GGGTTGCAGCGAAGCAGGTTAAAA
* * * * *
28886844 ATAACAGATCTTGCCTTCCTGTACCAACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTA
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
28886909 GGTTGCAGC-AGAGCAGGTTAAAA
66 GGTTGCAGCGA-AGCAGGTTAAAA
*
28886932 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTA
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
*
28886997 GGTTGCAGCGAAGTAGGTTAAAA
66 GGTTGCAGCGAAGCAGGTTAAAA
* * *
28887020 ATAGGAGATCTTGCCTTCCTGCATCGACAACGAAGCAGATCGA
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGA
28887063 TGACCCCAAA
Statistics
Matches: 522, Mismatches: 41, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
87 4 0.01
88 514 0.98
89 4 0.01
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (88 bp):
ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
GGTTGCAGCGAAGCAGGTTAAAA
Found at i:28886572 original size:43 final size:43
Alignment explanation
Indices: 28886519--28886660 Score: 108
Period size: 43 Copynumber: 3.3 Consensus size: 43
28886509 CCTACACTGA
*
28886519 CAGCAAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTG
1 CAGCAGAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTG
* ** * * * ** * ****
28886562 CAGCAGAGCAGGTTAAAAATTA-CAGATCTTATCTTCCTGCACCG
1 CAGCAGAGCAGATCGAAGA-CACCAG-CCTTGCCTCCCTGGGTTG
28886606 ACAGC-GAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTG
1 -CAGCAG-AGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTG
28886650 CAGCAGAGCAG
1 CAGCAGAGCAG
28886661 GTTAAAAATT
Statistics
Matches: 66, Mismatches: 27, Indels: 12
0.63 0.26 0.11
Matches are distributed among these distances:
43 26 0.39
44 24 0.36
45 16 0.24
ACGTcount: A:0.28, C:0.30, G:0.25, T:0.18
Consensus pattern (43 bp):
CAGCAGAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTG
Found at i:28886771 original size:44 final size:44
Alignment explanation
Indices: 28886721--28886864 Score: 130
Period size: 44 Copynumber: 3.3 Consensus size: 44
28886711 AGACACCAAC
*
28886721 CTTGCCTCCCTGGGTTGTAACGGAGCAGGTTAAAAATAACAGAT
1 CTTGCCTCCCTGGGTTGCAACGGAGCAGGTTAAAAATAACAGAT
* ** * * * * * * * *
28886765 CTTGCCTTCCTGCCTCGACAACGAAGCTGATCAAAGA-CACTAG-C
1 CTTGCCTCCCTGGGTTG-CAACGGAGCAGGTTAAAAATAAC-AGAT
*
28886809 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAACAGAT
1 CTTGCCTCCCTGGGTTGCAACGGAGCAGGTTAAAAATAACAGAT
*
28886853 CTTGCCTTCCTG
1 CTTGCCTCCCTG
28886865 TACCAACAGC
Statistics
Matches: 71, Mismatches: 25, Indels: 8
0.68 0.24 0.08
Matches are distributed among these distances:
43 15 0.21
44 41 0.58
45 15 0.21
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (44 bp):
CTTGCCTCCCTGGGTTGCAACGGAGCAGGTTAAAAATAACAGAT
Found at i:28886881 original size:45 final size:45
Alignment explanation
Indices: 28886826--28886969 Score: 116
Period size: 44 Copynumber: 3.2 Consensus size: 45
28886816 CCCTGGGTTG
*
28886826 CAGCGGAGCAGGTTAAAAATAACAGATCTTGCCTTCCTGTACCAA
1 CAGCGAAGCAGGTTAAAAATAACAGATCTTGCCTTCCTGTACCAA
* ** * * * * ** *
28886871 CAGCGAAGCAGATCGAAGACACCAG-CCTTGCCTTCCTAGGTTGCAG
1 CAGCGAAGCAGGTTAAAAATAACAGATCTTGCCTTCCT--GTACCAA
* * *
28886917 CA--G-AGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCACCGA
1 CAGCGAAGCAGGTTAAAAATAACAGATCTTGCCTTCCTGTACCAA
28886959 CAGCGAAGCAG
1 CAGCGAAGCAG
28886970 ATCGAAGACA
Statistics
Matches: 70, Mismatches: 23, Indels: 12
0.67 0.22 0.11
Matches are distributed among these distances:
42 4 0.06
43 13 0.19
44 24 0.34
45 23 0.33
46 6 0.09
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.19
Consensus pattern (45 bp):
CAGCGAAGCAGGTTAAAAATAACAGATCTTGCCTTCCTGTACCAA
Found at i:28886901 original size:44 final size:44
Alignment explanation
Indices: 28886853--28886991 Score: 122
Period size: 44 Copynumber: 3.2 Consensus size: 44
28886843 AATAACAGAT
28886853 CTTGCCTTCCTGTACCAACAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCCTGTACCAACAGCGAAGCAGATCGAAGACACCAGC
** * * ** * * * *
28886897 CTTGCCTTCCTAGGTTGCAGCA--G-AGCAGGTTAAAAATAGCAGAT
1 CTTGCCTTCCT--GTACCAACAGCGAAGCAGATCGAAGACACCAG-C
* *
28886941 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCCTGTACCAACAGCGAAGCAGATCGAAGACACCAGC
28886985 CTTGCCT
1 CTTGCCT
28886992 CCCTAGGTTG
Statistics
Matches: 67, Mismatches: 22, Indels: 12
0.66 0.22 0.12
Matches are distributed among these distances:
42 4 0.06
43 13 0.19
44 31 0.46
45 13 0.19
46 6 0.09
ACGTcount: A:0.27, C:0.31, G:0.22, T:0.19
Consensus pattern (44 bp):
CTTGCCTTCCTGTACCAACAGCGAAGCAGATCGAAGACACCAGC
Found at i:28887008 original size:43 final size:43
Alignment explanation
Indices: 28886871--28887009 Score: 129
Period size: 43 Copynumber: 3.2 Consensus size: 43
28886861 CCTGTACCAA
28886871 CAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTAGGTTG
1 CAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTAGGTTG
* ** * * * * ***
28886914 CAGC-AGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCT-GCACCG
1 CAGCGA-AGCAGATCGAAGACACCAG-CCTTGCCTTCCTAG-GTTG
*
28886958 ACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTTG
1 -CAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTAGGTTG
28887002 CAGCGAAG
1 CAGCGAAG
28887010 TAGGTTAAAA
Statistics
Matches: 69, Mismatches: 21, Indels: 12
0.68 0.21 0.12
Matches are distributed among these distances:
42 1 0.01
43 26 0.38
44 23 0.33
45 18 0.26
46 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.25, T:0.17
Consensus pattern (43 bp):
CAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTAGGTTG
Found at i:28887136 original size:44 final size:43
Alignment explanation
Indices: 28887073--28887191 Score: 150
Period size: 44 Copynumber: 2.7 Consensus size: 43
28887063 TGACCCCAAA
*
28887073 CCTATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGT-AAGT
1 CCTATCTCCCTGG-CAGCAGTGGAATAGGTTAAAGATTGTGAA-T
*
28887117 CCTATCTCCCTGGTCAGCAGTGAAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGG-CAGCAGTGGAATAGGTTAAAGATTGTGAAT
* * *
28887161 CCTATCTTCCTGAGCAACAGTGGAGTAGGTT
1 CCTATCTCCCTG-GCAGCAGTGGAATAGGTT
28887192 CAAAATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
44 63 0.95
45 3 0.05
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (43 bp):
CCTATCTCCCTGGCAGCAGTGGAATAGGTTAAAGATTGTGAAT
Found at i:28887654 original size:45 final size:44
Alignment explanation
Indices: 28887603--28887720 Score: 130
Period size: 45 Copynumber: 2.7 Consensus size: 44
28887593 GAAGATGGCG
*
28887603 AGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTCAAGAAATCA
1 AGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAAGAAA-CA
* * * *
28887648 AGTCTTATCCCCCTGAAA-TTACAGTGGGGCAGACTAAATAAACA
1 AGTCTTATCTCCCT-AAAGTTGCAGTGGAGCAGACTAAAGAAACA
* ** *
28887692 AATCACATCTCCCTAAAGTTGTAGTGGAG
1 AGTCTTATCTCCCTAAAGTTGCAGTGGAG
28887721 TGGATTAGAA
Statistics
Matches: 59, Mismatches: 12, Indels: 5
0.78 0.16 0.07
Matches are distributed among these distances:
43 3 0.05
44 20 0.34
45 33 0.56
46 3 0.05
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (44 bp):
AGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAAGAAACA
Done.