Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008105.1 Hibiscus syriacus cultivar Beakdansim tig00110637_pilon, whole genome shotgun sequence
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: 5962497
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 30
Found at i:1573654 original size:10 final size:11
Alignment explanation
Indices: 1573630--1573703 Score: 85
Period size: 11 Copynumber: 6.1 Consensus size: 11
1573620 GAAAAATATA
1573630 ATTTATTTAAAT
1 ATTT-TTTAAAT
1573642 ATTTTTTAATATT
1 ATTTTTTAA-A-T
1573655 ATTATTTTAAAT
1 ATT-TTTTAAAT
1573667 ATTTTTTAATATT
1 ATTTTTTAA-A-T
1573680 ATTATTTTAAAT
1 ATT-TTTTAAAT
1573692 ATTTTTTAAAT
1 ATTTTTTAAAT
1573703 A
1 A
1573704 AGTATTATTT
Statistics
Matches: 56, Mismatches: 0, Indels: 13
0.81 0.00 0.19
Matches are distributed among these distances:
11 20 0.36
12 14 0.25
13 10 0.18
14 12 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
ATTTTTTAAAT
Found at i:1573662 original size:15 final size:15
Alignment explanation
Indices: 1573644--1573694 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
1573634 ATTTAAATAT
1573644 TTTTTAATATTATTA
1 TTTTTAATATTATTA
1573659 -TTTTAA-A-TA-T-
1 TTTTTAATATTATTA
1573669 TTTTTAATATTATTA
1 TTTTTAATATTATTA
*
1573684 TTTTAAATATT
1 TTTTTAATATT
1573695 TTTTAAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
11 7 0.23
12 3 0.10
13 3 0.10
14 7 0.23
15 10 0.33
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTTAATATTATTA
Found at i:1574664 original size:21 final size:21
Alignment explanation
Indices: 1574640--1574684 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1574630 ATAAAAAAAA
* *
1574640 TTACATAAAATATTATTATTT
1 TTACATAAAACATTAATATTT
*
1574661 TTACCTAAAACATTAATATTT
1 TTACATAAAACATTAATATTT
1574682 TTA
1 TTA
1574685 ATATTTCCGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (21 bp):
TTACATAAAACATTAATATTT
Found at i:1576224 original size:71 final size:71
Alignment explanation
Indices: 1576104--1576290 Score: 286
Period size: 71 Copynumber: 2.6 Consensus size: 71
1576094 TAAATATAAA
* * ** *
1576104 TGTGTCCAACTTCAACTGGA-TATGACTGCTAGCTGATTCATTAAATGTTTCTTTTATCATGGAG
1 TGTGTCCAACTTCAACTGGACT-TGACTGCTAGCTGATTTACTATTTGTTTCTTTTATCATGAAG
1576168 CATTAAC
65 CATTAAC
1576175 TGTGTCCAACTTCAACTGGACTTGACTGCTAGCTGATTTACTATTTGTTTCTTTTATCATGAAGC
1 TGTGTCCAACTTCAACTGGACTTGACTGCTAGCTGATTTACTATTTGTTTCTTTTATCATGAAGC
1576240 ATTAAC
66 ATTAAC
* * *
1576246 TATTTCTAACTTCAACTGGACTTGACTGCTAGCTGATTTACTATT
1 TGTGTCCAACTTCAACTGGACTTGACTGCTAGCTGATTTACTATT
1576291 CATCTTTATT
Statistics
Matches: 107, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
71 106 0.99
72 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (71 bp):
TGTGTCCAACTTCAACTGGACTTGACTGCTAGCTGATTTACTATTTGTTTCTTTTATCATGAAGC
ATTAAC
Found at i:1577230 original size:39 final size:40
Alignment explanation
Indices: 1577187--1577267 Score: 128
Period size: 40 Copynumber: 2.0 Consensus size: 40
1577177 GCATGATCAC
*
1577187 TTGAAAT-CCTTCTTTTACTCTTTATACTTTTGTAAGTGT
1 TTGAAATACCTTCTTTTACTCTTTAGACTTTTGTAAGTGT
* *
1577226 TTGAAATACTTTCTTTTACTCTTTAGACTTTTGTTAGTGT
1 TTGAAATACCTTCTTTTACTCTTTAGACTTTTGTAAGTGT
1577266 TT
1 TT
1577268 CTGAAAGGAC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 7 0.18
40 31 0.82
ACGTcount: A:0.20, C:0.14, G:0.11, T:0.56
Consensus pattern (40 bp):
TTGAAATACCTTCTTTTACTCTTTAGACTTTTGTAAGTGT
Found at i:1587103 original size:22 final size:22
Alignment explanation
Indices: 1587082--1587127 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1587072 ATAAAGAAAT
*
1587082 TATTTTTTAAA-ATTATAAAAA
1 TATTTTTAAAATATTATAAAAA
*
1587103 TATTTTTAAAATATTATAAATA
1 TATTTTTAAAATATTATAAAAA
1587125 TAT
1 TAT
1587128 ATTGTTGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TATTTTTAAAATATTATAAAAA
Found at i:1588191 original size:22 final size:23
Alignment explanation
Indices: 1588164--1588213 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
1588154 CATTAAGTCT
*
1588164 TCTTTATGACACGTTTT-ATCTG
1 TCTTTATGACACGTTTTCATATG
**
1588186 TCTTTATGGTACGTTTTCATATG
1 TCTTTATGACACGTTTTCATATG
1588209 TCTTT
1 TCTTT
1588214 TAGCATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.16, C:0.16, G:0.14, T:0.54
Consensus pattern (23 bp):
TCTTTATGACACGTTTTCATATG
Found at i:1589306 original size:20 final size:20
Alignment explanation
Indices: 1589218--1589333 Score: 71
Period size: 20 Copynumber: 5.8 Consensus size: 20
1589208 AATAACCAAT
*
1589218 GAATTCGCAACTCGAATTCG
1 GAATTCGCAACTCGAATTTG
*
1589238 G-ATTCGCAACTCGAAATCT-
1 GAATTCGCAACTCG-AATTTG
* * *
1589257 -AATTTCGCAAACAC-AGTTTTC
1 GAA-TTCGC-AACTCGA-ATTTG
*
1589278 GAATCCGCAACTCGAATTTG
1 GAATTCGCAACTCGAATTTG
* * *
1589298 GAATTCGCAACACAGAA-GTA
1 GAATTCGCAACTC-GAATTTG
1589318 GAATTCGCAACTCGAA
1 GAATTCGCAACTCGAA
1589334 CATGGAAATT
Statistics
Matches: 73, Mismatches: 14, Indels: 19
0.69 0.13 0.18
Matches are distributed among these distances:
19 17 0.23
20 42 0.58
21 12 0.16
22 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (20 bp):
GAATTCGCAACTCGAATTTG
Found at i:1589391 original size:22 final size:22
Alignment explanation
Indices: 1589363--1589421 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 22
1589353 CGAATTTCGT
1589363 TTTCGCAACTCGAATTCGCCAA
1 TTTCGCAACTCGAATTCGCCAA
*
1589385 TTTCGCAA-TAAGAATTCGCCAA
1 TTTCGCAACT-CGAATTCGCCAA
1589407 TTTCGCAACTC-AATT
1 TTTCGCAACTCGAATT
1589422 ACCGATATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
21 5 0.15
22 27 0.82
23 1 0.03
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.31
Consensus pattern (22 bp):
TTTCGCAACTCGAATTCGCCAA
Found at i:1590001 original size:20 final size:20
Alignment explanation
Indices: 1589956--1590067 Score: 70
Period size: 20 Copynumber: 5.7 Consensus size: 20
1589946 TTTCCATGTT
* *
1589956 GAGTTGCGAATT-CTACTTC
1 GAGTTGCGAATTCCAAATTC
*
1589975 TGTGTTGCGAATTCCAAATTC
1 -GAGTTGCGAATTCCAAATTC
* *
1589996 GAGTTGCGAATTCAGAAACT-
1 GAGTTGCGAATTC-CAAATTC
* ** *
1590016 GTGTTGCGAAATT-GGATTTC
1 GAGTTGCG-AATTCCAAATTC
*
1590036 GAGTTGCGAA-TCCGAATTC
1 GAGTTGCGAATTCCAAATTC
*
1590055 GAGTTACGAATTC
1 GAGTTGCGAATTC
1590068 ATTGGTTATT
Statistics
Matches: 72, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
18 1 0.01
19 19 0.26
20 39 0.54
21 13 0.18
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (20 bp):
GAGTTGCGAATTCCAAATTC
Found at i:1594168 original size:19 final size:19
Alignment explanation
Indices: 1594132--1594167 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1594122 GTTCCTATTT
1594132 TTTTAATTTATAAATTTTA
1 TTTTAATTTATAAATTTTA
*
1594151 TTTTCATTT-TAAATTTT
1 TTTTAATTTATAAATTTT
1594168 TTATAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTAATTTATAAATTTTA
Found at i:1598459 original size:77 final size:80
Alignment explanation
Indices: 1598307--1598576 Score: 252
Period size: 80 Copynumber: 3.4 Consensus size: 80
1598297 GAACCGATTC
* *
1598307 ACACCGCTAAATATTGTACTTTAGTGGCATTTTTTGAACAAACGCCGTAAATACTCGTCATTTAG
1 ACACCGCTAAATATTGTACTTTAGTGGCATTTTTT-AACAAACACCGTAAAGACTCGTCATTTAG
1598372 TGGCATTTTTATATAA
65 TGGCATTTTTATATAA
* *
1598388 ACACCGCT-AATATTTTACTTTAGTGG-GTTTTTT-ACAAACACCGCTAAAGACTCGT-ATTTAG
1 ACACCGCTAAATATTGTACTTTAGTGGCATTTTTTAACAAACACCG-TAAAGACTCGTCATTTAG
*
1598449 TGGC-GTTTT-TATAA
65 TGGCATTTTTATATAA
** * * * * * *
1598463 ATGCCGCGAAAGACTCGTACTTTAGTGGCGATTTTTTAAC-AACACCAATAAATACTC-TTATTT
1 ACACCGCTAAATA-TTGTACTTTAGTGGC-ATTTTTTAACAAACACC-GTAAAGACTCGTCA-TT
*
1598526 TAGTGGC-GTTTTATATAA
62 TAGTGGCATTTTTATATAA
* * * *
1598544 ACGCCTCTAAAGATTCGTACTTTAGTGACATTT
1 ACACCGCTAAATATT-GTACTTTAGTGGCATTT
1598577 GTAGACAAAA
Statistics
Matches: 159, Mismatches: 19, Indels: 23
0.79 0.09 0.11
Matches are distributed among these distances:
75 10 0.06
76 7 0.04
77 31 0.19
78 11 0.07
79 27 0.17
80 38 0.24
81 35 0.22
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.37
Consensus pattern (80 bp):
ACACCGCTAAATATTGTACTTTAGTGGCATTTTTTAACAAACACCGTAAAGACTCGTCATTTAGT
GGCATTTTTATATAA
Found at i:1604635 original size:30 final size:30
Alignment explanation
Indices: 1604601--1604674 Score: 112
Period size: 30 Copynumber: 2.4 Consensus size: 30
1604591 AATGTTCGAC
**
1604601 ACTTTATTTAATTGTTTGTTCATTTTGAAA
1 ACTTTATTTAATTGTTTGTTCATTTCAAAA
1604631 ACTTTATTTAATTGTTTGTTCATTTCAAAA
1 ACTTTATTTAATTGTTTGTTCATTTCAAAA
*
1604661 ACTTACATTTAATT
1 ACTT-TATTTAATT
1604675 ATTTCTTATA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 32 0.80
31 8 0.20
ACGTcount: A:0.30, C:0.09, G:0.07, T:0.54
Consensus pattern (30 bp):
ACTTTATTTAATTGTTTGTTCATTTCAAAA
Found at i:1606414 original size:85 final size:86
Alignment explanation
Indices: 1606304--1606499 Score: 247
Period size: 86 Copynumber: 2.3 Consensus size: 86
1606294 AAATACATGA
* * * *
1606304 TCAATACCGACGTTTTAC-AAAAAAATGCCACTAAAGTTTTAGATTATTTGTAG-CGTTTAT-AC
1 TCAATAGCGACGTTTTACTATAAAAATGCCACTAAAGTGTTAGATAATTTG-AGACGTTTATGAC
1606366 -AAAAAAGACCACTATAAAATTG
65 TAAAAAAG-CCACTATAAAATTG
* *
1606388 TCAATAGCGACATTTTACTATAAAAATGCCACTAAAGTGTTAGATAATTTGCGACGTTTATGACT
1 TCAATAGCGACGTTTTACTATAAAAATGCCACTAAAGTGTTAGATAATTTGAGACGTTTATGACT
* *
1606453 AAAAACGCCACTATAGAATTG
66 AAAAAAGCCACTATAAAATTG
* * *
1606474 TTAATAGTGGCGTTTTACTATAAAAA
1 TCAATAGCGACGTTTTACTATAAAAA
1606500 CGCAACTATA
Statistics
Matches: 96, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
84 17 0.18
85 36 0.38
86 37 0.39
87 6 0.06
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.32
Consensus pattern (86 bp):
TCAATAGCGACGTTTTACTATAAAAATGCCACTAAAGTGTTAGATAATTTGAGACGTTTATGACT
AAAAAAGCCACTATAAAATTG
Found at i:1612123 original size:2 final size:2
Alignment explanation
Indices: 1612118--1612142 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1612108 TTAATAATTA
1612118 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1612143 ATGATATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1615226 original size:21 final size:20
Alignment explanation
Indices: 1615187--1615227 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1615177 GTGAACTGAT
* *
1615187 TGACAAAATTAAAACATTGA
1 TGACAAAAATAAAAAATTGA
1615207 TGACAAAAATAAAATAATTGA
1 TGACAAAAATAAAA-AATTGA
1615228 GTGGTAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.59, C:0.07, G:0.10, T:0.24
Consensus pattern (20 bp):
TGACAAAAATAAAAAATTGA
Found at i:1624942 original size:2 final size:2
Alignment explanation
Indices: 1624935--1625080 Score: 101
Period size: 2 Copynumber: 81.0 Consensus size: 2
1624925 CCGCCCCGAT
1624935 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
1624976 TT TA TA TA T- TT TA TA T- TA -A T- TA TA TA TA TA -A TA GTT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* *
1625014 TA TA T- TT TA TA T- TA -A T- TA TA TA TA TA -A TA T- TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1625050 TA T- TT TA TA TA T- TT TA TA T- TA -A T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1625081 AAATATTTTC
Statistics
Matches: 118, Mismatches: 8, Indels: 36
0.73 0.05 0.22
Matches are distributed among these distances:
1 17 0.14
2 100 0.85
3 1 0.01
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (2 bp):
TA
Found at i:1625068 original size:34 final size:34
Alignment explanation
Indices: 1624961--1625059 Score: 180
Period size: 34 Copynumber: 2.9 Consensus size: 34
1624951 TATATATATA
1624961 TATATATATATATATTTTATATATTTTATATTAAT
1 TATATATATA-ATATTTTATATATTTTATATTAAT
*
1624996 TATATATATAATAGTTTATATATTTTATATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
1625030 TATATATATAATATTTTATATATTTTATAT
1 TATATATATAATATTTTATATATTTTATAT
1625060 ATTTTATATT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
34 52 0.84
35 10 0.16
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (34 bp):
TATATATATAATATTTTATATATTTTATATTAAT
Found at i:1625086 original size:43 final size:43
Alignment explanation
Indices: 1624951--1625089 Score: 161
Period size: 43 Copynumber: 3.4 Consensus size: 43
1624941 TATATATATA
* *
1624951 TATATATATATATATATATATATATTTTATATATTTTATATTAA-
1 TATATATA-AAATAT-TTTATATATTTTATATATTTTATATTAAT
*
1624995 T-TATAT---ATA---TA-ATAGTTTATATATTTTATATTAAT
1 TATATATAAAATATTTTATATATTTTATATATTTTATATTAAT
*
1625030 TATATATATAATATTTTATATATTTTATATATTTTATATTAAT
1 TATATATAAAATATTTTATATATTTTATATATTTTATATTAAT
1625073 TATATATAAAATATTTT
1 TATATATAAAATATTTT
1625090 CGGGTTCGGG
Statistics
Matches: 83, Mismatches: 3, Indels: 19
0.79 0.03 0.18
Matches are distributed among these distances:
34 22 0.27
35 3 0.04
36 5 0.06
39 6 0.07
42 2 0.02
43 44 0.53
44 1 0.01
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.58
Consensus pattern (43 bp):
TATATATAAAATATTTTATATATTTTATATATTTTATATTAAT
Found at i:1626107 original size:60 final size:59
Alignment explanation
Indices: 1625964--1626110 Score: 181
Period size: 60 Copynumber: 2.4 Consensus size: 59
1625954 AGAATATGAT
1625964 AAAG-TACACAAATGGTCCCTCAACTATAAGGCATAGCTTTGTTAAGTCTCTCGACTATTA
1 AAAGTTACA-AAATGGTCCC-CAACTATAAGGCATAGCTTTGTTAAGTCTCTCGACTATTA
** ** * *
1626024 AAAGTTACAAAATTATCCTCCAACTATAAGGTGTTGCTTTGTTAAGTC-CATTGACTATTA
1 AAAGTTACAAAATGGTCC-CCAACTATAAGGCATAGCTTTGTTAAGTCTC-TCGACTATTA
1626084 AAAGTTACAAAATGGTCACCCAACTAT
1 AAAGTTACAAAATGGTC-CCCAACTAT
1626111 TCATAAGTCT
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
59 1 0.01
60 68 0.91
61 6 0.08
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (59 bp):
AAAGTTACAAAATGGTCCCCAACTATAAGGCATAGCTTTGTTAAGTCTCTCGACTATTA
Found at i:1629713 original size:37 final size:38
Alignment explanation
Indices: 1629668--1629830 Score: 183
Period size: 37 Copynumber: 4.4 Consensus size: 38
1629658 TCTATATTCC
1629668 AATCGAATATAAATTTAT-AATAATATA-TTCTTATTTT
1 AATCGAATATAAATTTATAAATAATATATTTC-TATTTT
* * *
1629705 AATTGAATATAAATTCATAAATAATATATTTGTA-TTT
1 AATCGAATATAAATTTATAAATAATATATTTCTATTTT
* * *
1629742 AATCAAATGTAAATTTATAAATAATATATTTCTATTTC
1 AATCGAATATAAATTTATAAATAATATATTTCTATTTT
* * *
1629780 AATCGAATATAAATTTGT-AATAGTATA-TTCGCATTTT
1 AATCGAATATAAATTTATAAATAATATATTTC-TATTTT
*
1629817 AATTGAATATAAAT
1 AATCGAATATAAAT
1629831 CATTAAGTAA
Statistics
Matches: 106, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
36 3 0.03
37 73 0.69
38 28 0.26
39 2 0.02
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.45
Consensus pattern (38 bp):
AATCGAATATAAATTTATAAATAATATATTTCTATTTT
Found at i:1629818 original size:75 final size:74
Alignment explanation
Indices: 1629668--1629830 Score: 186
Period size: 75 Copynumber: 2.2 Consensus size: 74
1629658 TCTATATTCC
* * *
1629668 AATCGAATATAAATTTATAATAATATATTCTTATTTTAATTGAATATAAATTCATAAATAATATA
1 AATCAAATATAAATTTATAATAATATATTCTTATTTCAATCGAATATAAATTCATAAATAATATA
* *
1629733 TTTGTATTT
66 TTCGCATTT
* ** *
1629742 AATCAAATGTAAATTTATAAATAATATATT-TCTATTTCAATCGAATATAAATTTGT-AATAGTA
1 AATCAAATATAAATTTAT-AATAATATATTCT-TATTTCAATCGAATATAAATTCATAAATAATA
1629805 TATTCGCATTTT
64 TATTCGCA-TTT
**
1629817 AATTGAATATAAAT
1 AATCAAATATAAAT
1629831 CATTAAGTAA
Statistics
Matches: 74, Mismatches: 12, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
74 29 0.39
75 45 0.61
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.45
Consensus pattern (74 bp):
AATCAAATATAAATTTATAATAATATATTCTTATTTCAATCGAATATAAATTCATAAATAATATA
TTCGCATTT
Found at i:1630261 original size:27 final size:25
Alignment explanation
Indices: 1630228--1630316 Score: 83
Period size: 25 Copynumber: 3.4 Consensus size: 25
1630218 TTAAATTCAT
1630228 AATATTTCATATATATTAACTTAAAAA
1 AATATTT--TATATATTAACTTAAAAA
* *
1630255 AATATTTT-TATATTAACCTATTAAA
1 AATATTTTATATATTAACTTA-AAAA
*
1630280 TATATTTTAT-TATTAACTTAATTTAAA
1 AATATTTTATATATTAACTTAA---AAA
1630307 AATATTTTAT
1 AATATTTTAT
1630317 TTTTAATATT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
24 11 0.22
25 20 0.39
26 1 0.02
27 19 0.37
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (25 bp):
AATATTTTATATATTAACTTAAAAA
Found at i:1630269 original size:24 final size:24
Alignment explanation
Indices: 1630239--1630314 Score: 73
Period size: 24 Copynumber: 3.0 Consensus size: 24
1630229 ATATTTCATA
1630239 TATATTAACTTAAAAAAATATTTT
1 TATATTAACTTAAAAAAATATTTT
* **
1630263 TATATTAACCT-ATTAAATATATTT
1 TATATTAACTTAAAAAAATAT-TTT
1630287 TATTATTAACTTAATTTAAAAATATTTT
1 TA-TATTAACTTAA---AAAAATATTTT
1630315 ATTTTTAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
23 7 0.17
24 15 0.38
25 8 0.20
26 1 0.03
28 3 0.08
29 6 0.15
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (24 bp):
TATATTAACTTAAAAAAATATTTT
Found at i:1630317 original size:27 final size:26
Alignment explanation
Indices: 1630241--1630322 Score: 91
Period size: 27 Copynumber: 3.2 Consensus size: 26
1630231 ATTTCATATA
1630241 TATTAACTTAA--AAAAATATTTT-T
1 TATTAACTTAATTAAAAATATTTTAT
* *
1630264 ATATTAACCT-ATTAAATATATTTTAT
1 -TATTAACTTAATTAAAAATATTTTAT
1630290 TATTAACTTAATTTAAAAATATTTTAT
1 TATTAACTTAA-TTAAAAATATTTTAT
*
1630317 TTTTAA
1 TATTAA
1630323 TATTTTATGT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
23 1 0.02
24 8 0.17
25 18 0.38
26 2 0.04
27 19 0.40
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (26 bp):
TATTAACTTAATTAAAAATATTTTAT
Found at i:1630497 original size:30 final size:31
Alignment explanation
Indices: 1630463--1630527 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
1630453 ATGACCACAT
*
1630463 CTTAATTAAAT-AAAACGAAAGTGATCATAC
1 CTTAATTAAATAAAAACGAAAGTGAACATAC
1630493 CTTAATTAAATAAAAACGAAAGTGAACATAC
1 CTTAATTAAATAAAAACGAAAGTGAACATAC
1630524 CTTA
1 CTTA
1630528 TGTTTTTCGA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 11 0.33
31 22 0.67
ACGTcount: A:0.51, C:0.14, G:0.09, T:0.26
Consensus pattern (31 bp):
CTTAATTAAATAAAAACGAAAGTGAACATAC
Found at i:1634214 original size:159 final size:160
Alignment explanation
Indices: 1633943--1634245 Score: 448
Period size: 159 Copynumber: 1.9 Consensus size: 160
1633933 GGGTGGAGTC
* *
1633943 GGGTTTAGGGTGAAAAATACTCGACCTGAAAAAAATAATTTTACCTTATATATTTAGGGATAATT
1 GGGTTTAGGGTGAAAAATACTCGACC-GAAAAAAAAAATTTTACCTTATATATTTAGGAATAATT
* * * * * *
1634008 ACAATATTATCCCTCTATATATTATTTTTTTCAATTAGATCCATATTTTTATTGATTGAAAATAA
65 ACAATAATATCACTCTATATATTATTTTTATCAATTAAATCCATATTTTTATTAAAT-AAAATAA
1634073 TATTTTTTATTATTTTGGGCTGGGTCGAGTTA
129 TATTTTTTATTATTTTGGGCTGGGTCGAGTTA
* * *
1634105 GGGTTTATGGTGAAAAATACTTGA-C-AAAAAAAAAATTTTATCTTATATATTTAGGAATAATTA
1 GGGTTTAGGGTGAAAAATACTCGACCGAAAAAAAAAATTTTACCTTATATATTTAGGAATAATTA
* * *
1634168 CAATAATATCATTCTATATATTATTTTTATCAATTAAATTCTTATTTTTATTAAATAAAATAATA
66 CAATAATATCACTCTATATATTATTTTTATCAATTAAATCCATATTTTTATTAAATAAAATAATA
1634233 TTTTTTATTATTT
131 TTTTTTATTATTT
1634246 CGAGTCGGAT
Statistics
Matches: 127, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
158 22 0.17
159 82 0.65
161 1 0.01
162 22 0.17
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.45
Consensus pattern (160 bp):
GGGTTTAGGGTGAAAAATACTCGACCGAAAAAAAAAATTTTACCTTATATATTTAGGAATAATTA
CAATAATATCACTCTATATATTATTTTTATCAATTAAATCCATATTTTTATTAAATAAAATAATA
TTTTTTATTATTTTGGGCTGGGTCGAGTTA
Found at i:1634228 original size:22 final size:21
Alignment explanation
Indices: 1634188--1634228 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1634178 ATTCTATATA
* *
1634188 TTATTTTTATCAATTAAATTC
1 TTATTTTTATAAATAAAATTC
1634209 TTATTTTTATTAAATAAAAT
1 TTATTTTTA-TAAATAAAAT
1634229 AATATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
TTATTTTTATAAATAAAATTC
Found at i:1644403 original size:12 final size:12
Alignment explanation
Indices: 1644383--1644429 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
1644373 CTGACTAGGC
*
1644383 GCCACATCACCT
1 GCCACATCAGCT
*
1644395 GCCATATCAGC-
1 GCCACATCAGCT
1644406 GACCACATCAGCT
1 G-CCACATCAGCT
*
1644419 GCCATATCAGC
1 GCCACATCAGC
1644430 CGTTAACTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 1 0.03
12 27 0.93
13 1 0.03
ACGTcount: A:0.28, C:0.40, G:0.15, T:0.17
Consensus pattern (12 bp):
GCCACATCAGCT
Found at i:1644420 original size:24 final size:24
Alignment explanation
Indices: 1644384--1644429 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1644374 TGACTAGGCG
1644384 CCACATCACCTGCCATATCAGCGA
1 CCACATCACCTGCCATATCAGCGA
*
1644408 CCACATCAGCTGCCATATCAGC
1 CCACATCACCTGCCATATCAGC
1644430 CGTTAACTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.41, G:0.13, T:0.17
Consensus pattern (24 bp):
CCACATCACCTGCCATATCAGCGA
Found at i:1645719 original size:59 final size:59
Alignment explanation
Indices: 1645591--1645726 Score: 148
Period size: 60 Copynumber: 2.3 Consensus size: 59
1645581 ATAGTCGGGT
* *** * * * * *
1645591 GACCATTTTGTAACTTTTAATAGTTGGGGGACTAAAAAAGTAATATCCTATAGTCGGGG
1 GACCATTTTGTAACTTTTAATAGTCGAAAGACTAAAAAAGCAACATCCTAAAGTCAGGA
* *
1645650 GATCATTTTGTAACTTTTAATAGTCGAAAGACTTAACAAAGCAACATCCTAAAGTCAGGA
1 GACCATTTTGTAACTTTTAATAGTCGAAAGAC-TAAAAAAGCAACATCCTAAAGTCAGGA
1645710 GACCATTTGTGT-ACTTT
1 GACCATTT-TGTAACTTT
1645727 ACCCTTATAT
Statistics
Matches: 63, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
59 27 0.43
60 33 0.52
61 3 0.05
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (59 bp):
GACCATTTTGTAACTTTTAATAGTCGAAAGACTAAAAAAGCAACATCCTAAAGTCAGGA
Found at i:1646792 original size:17 final size:18
Alignment explanation
Indices: 1646761--1646796 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1646751 ATTTAACTTT
1646761 TTTTTAAAATAAAAATTA
1 TTTTTAAAATAAAAATTA
*
1646779 TTTTTAATAT-AAAATTA
1 TTTTTAAAATAAAAATTA
1646796 T
1 T
1646797 AATTTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTTAAAATAAAAATTA
Found at i:1646824 original size:20 final size:22
Alignment explanation
Indices: 1646801--1646842 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
1646791 AATTATAATT
1646801 TAAAAATTAAA-TA-TAAAAAA
1 TAAAAATTAAATTACTAAAAAA
1646821 TAAAAATTAAATTACTAAAAAA
1 TAAAAATTAAATTACTAAAAAA
1646843 ATTGAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 11 0.55
21 2 0.10
22 7 0.35
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (22 bp):
TAAAAATTAAATTACTAAAAAA
Found at i:1648973 original size:20 final size:20
Alignment explanation
Indices: 1648935--1648973 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1648925 ACTAATGAAC
* *
1648935 CGGAAAAAATCGAGAAAAAT
1 CGGAAAAAACCGAAAAAAAT
1648955 CGGAAAAAACCGAAAAAAA
1 CGGAAAAAACCGAAAAAAA
1648974 CCGCCAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.64, C:0.13, G:0.18, T:0.05
Consensus pattern (20 bp):
CGGAAAAAACCGAAAAAAAT
Found at i:1649668 original size:22 final size:21
Alignment explanation
Indices: 1649643--1649683 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1649633 TATAAAAAAT
1649643 TATTTTTATTAAATATTTTTGG
1 TATTTTTATTAAAT-TTTTTGG
*
1649665 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
1649684 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGG
Found at i:1650532 original size:12 final size:12
Alignment explanation
Indices: 1650515--1650539 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1650505 ATGATACGTA
1650515 GGCTTGTTAGAG
1 GGCTTGTTAGAG
1650527 GGCTTGTTAGAG
1 GGCTTGTTAGAG
1650539 G
1 G
1650540 TCACGTTGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.44, T:0.32
Consensus pattern (12 bp):
GGCTTGTTAGAG
Found at i:1655285 original size:70 final size:71
Alignment explanation
Indices: 1655202--1655378 Score: 239
Period size: 70 Copynumber: 2.5 Consensus size: 71
1655192 AAGGATCGAT
*
1655202 CCCAAACTTTATGTTGTGTAAAGGATCGATCCCTTTCCAAAATGATCGAT-ACTCAACCAAAAAG
1 CCCAAACTTTATGTTGTGTAAAGGATCGATCCCTTTCCAAAATGATCAATCACTCAACCAAAAAG
1655266 ATCAAG
66 ATCAAG
* * * * *
1655272 CCCAAACTTTATGTTGTGCAAAGAATCGATCCCTTTCCAAAATGATCAATCTCTCGACCAAAAGG
1 CCCAAACTTTATGTTGTGTAAAGGATCGATCCCTTTCCAAAATGATCAATCACTCAACCAAAAAG
*
1655337 ATCAAT
66 ATCAAG
* * *
1655343 CCCAAAATTTCTGTTGTGTCAAAATGATCGATCCCT
1 CCCAAACTTTATGTTGTGT--AAAGGATCGATCCCT
1655379 CAAGGAAAAT
Statistics
Matches: 92, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
70 47 0.51
71 32 0.35
73 13 0.14
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (71 bp):
CCCAAACTTTATGTTGTGTAAAGGATCGATCCCTTTCCAAAATGATCAATCACTCAACCAAAAAG
ATCAAG
Found at i:1655389 original size:21 final size:22
Alignment explanation
Indices: 1655363--1655420 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
1655353 CTGTTGTGTC
*
1655363 AAAATGATCGATCCCTC-AAGG
1 AAAATGATCGATCCCTCGAAAG
*
1655384 AAAATGATCGATCTCTCGAAAG
1 AAAATGATCGATCCCTCGAAAG
*
1655406 -AAATGATCAATCCCT
1 AAAATGATCGATCCCT
1655421 TAGCTATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 29 0.91
22 3 0.09
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (22 bp):
AAAATGATCGATCCCTCGAAAG
Found at i:1657641 original size:28 final size:28
Alignment explanation
Indices: 1657610--1657686 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
1657600 GGCTTTGTTT
*
1657610 CCTGATTGATATATGGTCGGTTATACCA
1 CCTGATTGATATATGGTCGGTCATACCA
* * *
1657638 CCTGATTGATATATGGTCGGCCCTACCG
1 CCTGATTGATATATGGTCGGTCATACCA
* *
1657666 CATGAATGATATATGGTCGGT
1 CCTGATTGATATATGGTCGGT
1657687 ACTACCGCCT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.32
Consensus pattern (28 bp):
CCTGATTGATATATGGTCGGTCATACCA
Found at i:1657691 original size:28 final size:28
Alignment explanation
Indices: 1657616--1657694 Score: 97
Period size: 28 Copynumber: 2.8 Consensus size: 28
1657606 GTTTCCTGAT
* * *
1657616 TGATATATGGTCGGTTA-TACCACCTGAT
1 TGATATATGGTCGG-TACTACCGCATGAA
**
1657644 TGATATATGGTCGGCCCTACCGCATGAA
1 TGATATATGGTCGGTACTACCGCATGAA
1657672 TGATATATGGTCGGTACTACCGC
1 TGATATATGGTCGGTACTACCGC
1657695 CTAAGTATTA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (28 bp):
TGATATATGGTCGGTACTACCGCATGAA
Found at i:1662501 original size:26 final size:26
Alignment explanation
Indices: 1662465--1662518 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
1662455 TATAAGAATC
*
1662465 ATCTTCTAATACTATCTACAAAATTT
1 ATCTTCTAATAATATCTACAAAATTT
1662491 ATCTTCTAATAATATCTACAAAATTT
1 ATCTTCTAATAATATCTACAAAATTT
1662517 AT
1 AT
1662519 GGTGATTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.43
Consensus pattern (26 bp):
ATCTTCTAATAATATCTACAAAATTT
Found at i:1667291 original size:51 final size:51
Alignment explanation
Indices: 1667236--1667429 Score: 230
Period size: 51 Copynumber: 3.8 Consensus size: 51
1667226 AGATGTACAT
* * * * *
1667236 ACTTACATCGGTGTAAGTATGTGTTAAATGATATACTTTTTTATTTTATTT
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTC
* * *
1667287 ACTTACACCGTTGTAAGTATGTGTTGAGTGCTACATTTTTTTTATTTTATTC
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACA-CTTTTTTATTTTATTC
* * * * *
1667339 ATTTACACTGATGT-AGTATGTGCTAAGTGCTACACTTGTTTATTTTATTC
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTC
* *
1667389 ACTTACACCGGTGTAAATATGTGTTAAGCGCTACA-TTTTTT
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTT
1667430 CATAGTATGA
Statistics
Matches: 119, Mismatches: 22, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
50 30 0.25
51 64 0.54
52 25 0.21
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.47
Consensus pattern (51 bp):
ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTC
Found at i:1667614 original size:17 final size:18
Alignment explanation
Indices: 1667582--1667617 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1667572 ACCGTTTAGG
1667582 CTAAAAGGTACGGTTAAC
1 CTAAAAGGTACGGTTAAC
*
1667600 CTAAATGGT-CGGTTAAC
1 CTAAAAGGTACGGTTAAC
1667617 C
1 C
1667618 GTCCATGTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (18 bp):
CTAAAAGGTACGGTTAAC
Found at i:1670062 original size:24 final size:24
Alignment explanation
Indices: 1670017--1670063 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1670007 ATCATTTACG
* **
1670017 TTCGTTTATATTCATTTGTTTGTA
1 TTCGTTTACATTCATTCATTTGTA
*
1670041 TTCGTTTACATTCGTTCATTTGT
1 TTCGTTTACATTCATTCATTTGT
1670064 TAGTTTATCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.15, C:0.13, G:0.13, T:0.60
Consensus pattern (24 bp):
TTCGTTTACATTCATTCATTTGTA
Found at i:1671008 original size:3 final size:3
Alignment explanation
Indices: 1671000--1671058 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
1670990 TTTGTTTTAT
** *
1671000 TTA TTA TTA TCG TTA TT- TTA TTA TTA TTA TGA TTA TTA TTA TCT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
*
1671044 TGA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
1671059 ATTACATATT
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
2 2 0.04
3 42 0.93
4 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1671037 original size:15 final size:15
Alignment explanation
Indices: 1671017--1671058 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
1671007 TATCGTTATT
1671017 TTATTATTATTATGA
1 TTATTATTATTATGA
1671032 TTATTATTATCT-TGA
1 TTATTATTAT-TATGA
1671047 TTATTATTATTA
1 TTATTATTATTA
1671059 ATTACATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 1 0.04
15 23 0.92
16 1 0.04
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (15 bp):
TTATTATTATTATGA
Found at i:1673617 original size:28 final size:28
Alignment explanation
Indices: 1673585--1673647 Score: 126
Period size: 28 Copynumber: 2.2 Consensus size: 28
1673575 TTAAATATCT
1673585 TTGATCTATTAGGTACCCTTTTGATTGG
1 TTGATCTATTAGGTACCCTTTTGATTGG
1673613 TTGATCTATTAGGTACCCTTTTGATTGG
1 TTGATCTATTAGGTACCCTTTTGATTGG
1673641 TTGATCT
1 TTGATCT
1673648 GATGCCTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (28 bp):
TTGATCTATTAGGTACCCTTTTGATTGG
Found at i:1674164 original size:70 final size:72
Alignment explanation
Indices: 1673973--1674164 Score: 262
Period size: 70 Copynumber: 2.7 Consensus size: 72
1673963 GGGTAAAGTA
* * * *
1673973 TAGGAAGTGTGGATTTCTATGCATGGTGCTGCCTTTTGTTCGGTTTAAGTTAAATCAATGTACTT
1 TAGGAAGTATGGATTTCTATGCATGGTGTTGGCTTTTGTTCGGTTTAAATT-AA-CAATGTACTT
1674038 ATTTTAGGG
64 ATTTTAGGG
* * * * **
1674047 TAGAAAGTACGGATTTCTATTCATGGTGTTTGCTTTTGTTCAATTTAAATT-A-AATGTACTTAT
1 TAGGAAGTATGGATTTCTATGCATGGTGTTGGCTTTTGTTCGGTTTAAATTAACAATGTACTTAT
1674110 TTTAGGG
66 TTTAGGG
1674117 TAGGAAGTATGGATTTCTATGCATGGTGTTGGCTTTTGTTCGGTTTAA
1 TAGGAAGTATGGATTTCTATGCATGGTGTTGGCTTTTGTTCGGTTTAA
1674165 GCTCTTTAAC
Statistics
Matches: 102, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
70 60 0.59
72 1 0.01
74 41 0.40
ACGTcount: A:0.23, C:0.09, G:0.24, T:0.44
Consensus pattern (72 bp):
TAGGAAGTATGGATTTCTATGCATGGTGTTGGCTTTTGTTCGGTTTAAATTAACAATGTACTTAT
TTTAGGG
Found at i:1675173 original size:8 final size:8
Alignment explanation
Indices: 1675160--1675184 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1675150 CTCGCATTGC
1675160 ATGGATGT
1 ATGGATGT
1675168 ATGGATGT
1 ATGGATGT
1675176 ATGGATGT
1 ATGGATGT
1675184 A
1 A
1675185 ATCTTACCCT
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:0.28, C:0.00, G:0.36, T:0.36
Consensus pattern (8 bp):
ATGGATGT
Found at i:1675567 original size:13 final size:13
Alignment explanation
Indices: 1675549--1675573 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1675539 ATCGGATTTT
1675549 TTTTAACCGGTTA
1 TTTTAACCGGTTA
1675562 TTTTAACCGGTT
1 TTTTAACCGGTT
1675574 TGGAGAAAAA
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:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (13 bp):
TTTTAACCGGTTA
Found at i:1677975 original size:21 final size:21
Alignment explanation
Indices: 1677951--1677990 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1677941 TTTATTTTAT
1677951 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
1677972 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
1677991 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:1678038 original size:33 final size:33
Alignment explanation
Indices: 1677985--1678083 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
1677975 TTTGTTTCAA
1677985 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1678017 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
1678050 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1678083 T
1 T
1678084 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:1678112 original size:13 final size:13
Alignment explanation
Indices: 1678069--1678123 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
1678059 TTGGAAGTAT
1678069 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
1678082 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
1678096 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
1678109 TTAAGTATTTGAA
1 TTAAGTATTTCAA
1678122 TT
1 TT
1678124 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:1678345 original size:21 final size:21
Alignment explanation
Indices: 1678319--1678375 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
1678309 TGGAGCGTGG
*
1678319 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
1678340 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
1678361 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
1678376 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:1678567 original size:15 final size:15
Alignment explanation
Indices: 1678542--1678597 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
1678532 ATCTGGAATA
*
1678542 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
1678557 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
1678572 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
1678589 TTAAAACCG
1 TTAAAACCG
1678598 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:1678606 original size:21 final size:18
Alignment explanation
Indices: 1678561--1678594 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1678551 GTTTTTTTAT
1678561 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
1678578 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
1678595 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:1678737 original size:16 final size:17
Alignment explanation
Indices: 1678689--1678734 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 17
1678679 TTCTATGGGA
1678689 AAAAACCGGATCGGAAC
1 AAAAACCGGATCGGAAC
1678706 AAAACCGATCCGGATCGGAAC
1 AAAA---A-CCGGATCGGAAC
1678727 AAAAACCG
1 AAAAACCG
1678735 ATCCGGATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
17 7 0.28
18 1 0.04
20 1 0.04
21 16 0.64
ACGTcount: A:0.46, C:0.26, G:0.22, T:0.07
Consensus pattern (17 bp):
AAAAACCGGATCGGAAC
Found at i:1678757 original size:22 final size:22
Alignment explanation
Indices: 1678694--1678746 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
1678684 TGGGAAAAAA
1678694 CCGGATCGGAAC-AAAACCGAT
1 CCGGATCGGAACAAAAACCGAT
1678715 CCGGATCGGAACAAAAACCGAT
1 CCGGATCGGAACAAAAACCGAT
1678737 CCGGATCGGA
1 CCGGATCGGA
1678747 TTGAAATCCG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 12 0.39
22 19 0.61
ACGTcount: A:0.36, C:0.28, G:0.26, T:0.09
Consensus pattern (22 bp):
CCGGATCGGAACAAAAACCGAT
Found at i:1678966 original size:42 final size:42
Alignment explanation
Indices: 1678902--1678984 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
1678892 AGTCAACATA
* * *
1678902 ATCATCTGGCGTCTTTTGGAAGACGTTCGGAATATATGCATT
1 ATCATCTGGCGTCTTTTAGAAGACGTTAGGAAGATATGCATT
1678944 ATCATCTGGCGTCTTTTAGAAGACGTTAGGAAGATATGCAT
1 ATCATCTGGCGTCTTTTAGAAGACGTTAGGAAGATATGCAT
1678985 CTCCTCCATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.34
Consensus pattern (42 bp):
ATCATCTGGCGTCTTTTAGAAGACGTTAGGAAGATATGCATT
Found at i:1679757 original size:11 final size:10
Alignment explanation
Indices: 1679730--1679755 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1679720 AAGGGAAAAT
1679730 AAAAAATATA
1 AAAAAATATA
1679740 AAAAAATATA
1 AAAAAATATA
1679750 AAAAAA
1 AAAAAA
1679756 ATGAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAATATA
Found at i:1680976 original size:20 final size:18
Alignment explanation
Indices: 1680947--1680999 Score: 65
Period size: 17 Copynumber: 2.9 Consensus size: 18
1680937 GGCCTACAAA
*
1680947 AATAAAAAAT-AATAAAT
1 AATAAATAATAAATAAAT
1680964 AAT-AATAATAAATAAAT
1 AATAAATAATAAATAAAT
1680981 AAATAAATAAATAAATAAA
1 -AATAAAT-AATAAATAAA
1681000 CAACAATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
16 5 0.16
17 10 0.32
18 3 0.10
19 3 0.10
20 10 0.32
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (18 bp):
AATAAATAATAAATAAAT
Found at i:1680977 original size:4 final size:4
Alignment explanation
Indices: 1680946--1680999 Score: 73
Period size: 4 Copynumber: 14.8 Consensus size: 4
1680936 GGGCCTACAA
1680946 AAAT AAA- AAAT -AAT AAAT -AAT -AAT -AAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1680989 AAAT AAAT AAA
1 AAAT AAAT AAA
1681000 CAACAATATA
Statistics
Matches: 47, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
3 15 0.32
4 32 0.68
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1682202 original size:106 final size:106
Alignment explanation
Indices: 1681926--1682773 Score: 1337
Period size: 106 Copynumber: 8.0 Consensus size: 106
1681916 TTGTTCCGAA
* * **
1681926 TCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGAGAAATTGTTTATTGACAACC
1 TCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACC
* * * *
1681990 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAG
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
* * *
1682032 TCCAA-ATCTTTTGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCA
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCA
*
1682096 GCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
* * *
1682137 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCA
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCA
*
1682202 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
* *
1682243 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGATATTGGGAAATTGTTTATTGACAACCA
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCA
1682308 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
* * * *
1682349 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAACCA
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCA
*
1682414 GCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
*
1682455 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG-GAAAGTTATTTATTGACAACC
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TTGTTTATTGACAACC
1682519 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
* * *
1682561 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCA
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCA
*
1682626 GCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
* * * * *
1682667 TCCACTATCATTCACTGTGAAGTTGAAATTGGCTCTAGAAGTGGA-AAATTG-TTATTGACAACC
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAATTGAGAAATTGTTTATTGACAACC
1682730 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
1682772 TC
1 TC
1682774 TAATTTTCTT
Statistics
Matches: 688, Mismatches: 49, Indels: 11
0.92 0.07 0.01
Matches are distributed among these distances:
105 150 0.22
106 529 0.77
107 9 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCA
GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
Found at i:1686567 original size:10 final size:9
Alignment explanation
Indices: 1686547--1686595 Score: 62
Period size: 9 Copynumber: 5.2 Consensus size: 9
1686537 AATTAAAGGG
1686547 AAAATAAAA
1 AAAATAAAA
1686556 AAAATAAAA
1 AAAATAAAA
1686565 AAATATTAAAA
1 AAA-A-TAAAA
* *
1686576 AATATTAAA
1 AAAATAAAA
1686585 AAAATAAAA
1 AAAATAAAA
1686594 AA
1 AA
1686596 TGAATAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
9 25 0.74
10 2 0.06
11 7 0.21
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (9 bp):
AAAATAAAA
Found at i:1686584 original size:21 final size:20
Alignment explanation
Indices: 1686551--1686590 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
1686541 AAAGGGAAAA
1686551 TAAAAAAAATAAAAAAATAT
1 TAAAAAAAATAAAAAAATAT
*
1686571 TAAAAAATATTAAAAAAATA
1 TAAAAAA-AATAAAAAAATA
1686591 AAAAATGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (20 bp):
TAAAAAAAATAAAAAAATAT
Found at i:1697154 original size:25 final size:23
Alignment explanation
Indices: 1697109--1697154 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
1697099 GAATGATTTA
* *
1697109 TTTATTTAATTTTTTAGTATTAG
1 TTTATTTAATTTTATAATATTAG
1697132 TTTATATTAATTTGTATAATATT
1 TTTAT-TTAATTT-TATAATATT
1697155 TATTAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 7 0.37
25 7 0.37
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (23 bp):
TTTATTTAATTTTATAATATTAG
Found at i:1700337 original size:16 final size:17
Alignment explanation
Indices: 1700309--1700341 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1700299 TAAGTTTTCA
1700309 TAAAAAATGAAAATTAT
1 TAAAAAATGAAAATTAT
1700326 TAAAAAAT-AAAATTAT
1 TAAAAAATGAAAATTAT
1700342 ACATTTTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (17 bp):
TAAAAAATGAAAATTAT
Found at i:1715763 original size:22 final size:22
Alignment explanation
Indices: 1715737--1715790 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
1715727 TAAATACAAG
1715737 AGTAATTGAGCGTTCATTATCA
1 AGTAATTGAGCGTTCATTATCA
* *
1715759 AGTAATTAAACGTTCATTATCA
1 AGTAATTGAGCGTTCATTATCA
*
1715781 AATAATTGAG
1 AGTAATTGAG
1715791 AATACATAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (22 bp):
AGTAATTGAGCGTTCATTATCA
Found at i:1716278 original size:24 final size:21
Alignment explanation
Indices: 1716233--1716280 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
1716223 ATCACTATTT
*
1716233 TTATTGAATAAAAATATTTTA
1 TTATTAAATAAAAATATTTTA
*
1716254 TTATTAAATAAAAATATTTTG
1 TTATTAAATAAAAATATTTTA
1716275 TTATTA
1 TTATTA
1716281 TTTCGGGTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (21 bp):
TTATTAAATAAAAATATTTTA
Found at i:1722849 original size:20 final size:20
Alignment explanation
Indices: 1722824--1722869 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1722814 CATATTTTTT
*
1722824 ATGATTGATGTTGAAATTTG
1 ATGATTGATGCTGAAATTTG
1722844 ATGATTGATGCTGAAATTTG
1 ATGATTGATGCTGAAATTTG
1722864 ATGATT
1 ATGATT
1722870 TTAAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.30, C:0.02, G:0.24, T:0.43
Consensus pattern (20 bp):
ATGATTGATGCTGAAATTTG
Found at i:1731955 original size:29 final size:28
Alignment explanation
Indices: 1731912--1731999 Score: 113
Period size: 29 Copynumber: 3.0 Consensus size: 28
1731902 CATTTTACAG
* **
1731912 AAATAGCACCCTTTTTAATTAAATTCCTG
1 AAATAGCACCCTTTTGAATT-AATTCCCA
*
1731941 GAATAGCACCCTTTTCGAATTAATTCCCA
1 AAATAGCACCCTTTT-GAATTAATTCCCA
1731970 AAATAGCACCCATTTTGAATTAATTCCCA
1 AAATAGCACCC-TTTTGAATTAATTCCCA
1731999 A
1 A
1732000 CATGTCACTC
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
29 44 0.85
30 8 0.15
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (28 bp):
AAATAGCACCCTTTTGAATTAATTCCCA
Found at i:1732063 original size:23 final size:18
Alignment explanation
Indices: 1732017--1732053 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1732007 CTCGGTCAAA
1732017 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
1732035 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
1732053 G
1 G
1732054 AACCGGTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.22, G:0.51, T:0.16
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:1739248 original size:29 final size:29
Alignment explanation
Indices: 1739122--1739235 Score: 149
Period size: 29 Copynumber: 3.9 Consensus size: 29
1739112 CATTTTACAT
** *
1739122 AAATAGCA-CCATTTTTAATTAAATTCCCA
1 AAATAGCACCCATTTCGAATT-AATTCTCA
* *
1739151 AAATAGCACCCTTTTTGAATTAATTCTCA
1 AAATAGCACCCATTTCGAATTAATTCTCA
* *
1739180 AAATAGCACCCATTTCGATTTAATTCCCA
1 AAATAGCACCCATTTCGAATTAATTCTCA
1739209 AAATAGCACCCATTTCGAATTAATTCT
1 AAATAGCACCCATTTCGAATTAATTCT
1739236 TAACATGTCA
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
29 65 0.87
30 10 0.13
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (29 bp):
AAATAGCACCCATTTCGAATTAATTCTCA
Found at i:1746115 original size:158 final size:159
Alignment explanation
Indices: 1745800--1746100 Score: 595
Period size: 159 Copynumber: 1.9 Consensus size: 159
1745790 TTTGGATCTC
1745800 AAAAATTATAATTTTTTTATTTTTATAAATGCAAATATAATTAAATAAATAAGTAATTACAAAAT
1 AAAAATTATAATTTTTTTATTTTTATAAATGCAAATATAATTAAATAAATAAGTAATTACAAAAT
1745865 AATTTGAATAATTAAAAAATTCAAAAAATATTTTTTTTAAATTTTAAAAATATATTATTTTTCAT
66 AATTTGAATAATTAAAAAATTCAAAAAATATTTTTTTTAAATTTTAAAAATATATTATTTTTCAT
1745930 ATACTTTTTTAAATGCAAATATAATTTTA
131 ATACTTTTTTAAATGCAAATATAATTTTA
1745959 AAAAATTATAATTTTTTTATTTTTATAAATGCAAATATAATTAAATAAATAAGTAATTACAAAAT
1 AAAAATTATAATTTTTTTATTTTTATAAATGCAAATATAATTAAATAAATAAGTAATTACAAAAT
1746024 AATTTGAATAATTAAAAAATTCAAAAAATA-TTTTTTTAAATTTTAAAAATATATTATTTTTCAT
66 AATTTGAATAATTAAAAAATTCAAAAAATATTTTTTTTAAATTTTAAAAATATATTATTTTTCAT
1746088 ATACTTTTTTAAA
131 ATACTTTTTTAAA
1746101 AATGAAATTT
Statistics
Matches: 142, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
158 47 0.33
159 95 0.67
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (159 bp):
AAAAATTATAATTTTTTTATTTTTATAAATGCAAATATAATTAAATAAATAAGTAATTACAAAAT
AATTTGAATAATTAAAAAATTCAAAAAATATTTTTTTTAAATTTTAAAAATATATTATTTTTCAT
ATACTTTTTTAAATGCAAATATAATTTTA
Found at i:1750954 original size:31 final size:31
Alignment explanation
Indices: 1750919--1750977 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1750909 ATTGTAAGAT
*
1750919 ATTGATAAATTTAATGAGTATTTTATAACAA
1 ATTGATAAATGTAATGAGTATTTTATAACAA
*
1750950 ATTGATAAATGTATTGAGTATTTTATAA
1 ATTGATAAATGTAATGAGTATTTTATAA
1750978 GTTTTGAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.44
Consensus pattern (31 bp):
ATTGATAAATGTAATGAGTATTTTATAACAA
Found at i:1751551 original size:31 final size:31
Alignment explanation
Indices: 1751481--1751551 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
1751471 ACTAGTTAGA
1751481 CCTTGAACTTTGATAAAATATCAATTTGATC
1 CCTTGAACTTTGATAAAATATCAATTTGATC
* *
1751512 CC-TAAACTTTAGATAAAATATTAATTTGA-C
1 CCTTGAACTTT-GATAAAATATCAATTTGATC
1751542 CCTTGAACTT
1 CCTTGAACTT
1751552 GATCAAAGTC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 10 0.29
31 25 0.71
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (31 bp):
CCTTGAACTTTGATAAAATATCAATTTGATC
Found at i:1759756 original size:20 final size:20
Alignment explanation
Indices: 1759731--1759768 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1759721 TATAAATTAG
* *
1759731 TTAAAAATTAAAGGTAAAAT
1 TTAAAAATAAAAGATAAAAT
1759751 TTAAAAATAAAAGATAAA
1 TTAAAAATAAAAGATAAA
1759769 TTATACCAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (20 bp):
TTAAAAATAAAAGATAAAAT
Found at i:1761384 original size:31 final size:32
Alignment explanation
Indices: 1761323--1761384 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
1761313 CTTTACGTAA
* * *
1761323 ATATATATTTTGGTGTTTAAACTTGGTTTTAAG
1 ATATATAATTTGGTGTCTAAACAT-GTTTTAAG
1761356 ATATATAATTTGGTGTCTAAACAT-TTTTA
1 ATATATAATTTGGTGTCTAAACATGTTTTA
1761385 TTTCAATTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 5 0.19
33 21 0.81
ACGTcount: A:0.31, C:0.05, G:0.15, T:0.50
Consensus pattern (32 bp):
ATATATAATTTGGTGTCTAAACATGTTTTAAG
Found at i:1766300 original size:316 final size:316
Alignment explanation
Indices: 1765727--1766364 Score: 1008
Period size: 316 Copynumber: 2.0 Consensus size: 316
1765717 ATCTTTAATT
* * * *
1765727 TTACTTGTAGCTTATATACCAGCTTTATTCTACACCACTCTACTACAATTTGCTTAGTTGCCGAC
1 TTACTTGTAGCTTATATACCAGCGTTATTCTACACCACTCTACCACAATTTGCGTAATTGCCGAC
* * * *
1765792 TTGTTTCTCTCCTGCGCATAAGGCTCTTTTGTATGATTGATACATCGTTTTATCTGAATTAACTA
66 TTGTTTCTCTCCAGAGCATAAGACTCTTTTGTATGACTGATACATCGTTTTATCTGAATTAACTA
*
1765857 TATGCATTGGATTGAAGTATCAAAATATACTGAAATTTAAAAGGTTTTTGAAATTCCATGCTAAT
131 TATGCATTGGACTGAAGTATCAAAATATACTGAAATTTAAAAGGTTTTTGAAATTCCATGCTAAT
* *
1765922 ATAATCAAGTCGGTGACTGCAATGTGATGGATGGCATTCAATTCTTTTAGTAGTGGTGTTTATGG
196 ATAATCAAGTCAGTGACTGCAATGTGATGGATGGAATTCAATTCTTTTAGTAGTGGTGTTTATGG
*
1765987 AATACGGATGGTATAAAGTAACCTGTTAATGTCGGTGTCGTTTGAACATTCTGTCA
261 AATACGGATGGTATAAAGTAACCTGTTAATGTCGGTGTCGTTAGAACATTCTGTCA
* * * *
1766043 TTACTTGTAGCTTATCTACTAGGGTTATTCTACATCACTCTACCACAATTTGCGTAATTGCC-AG
1 TTACTTGTAGCTTATATACCAGCGTTATTCTACACCACTCTACCACAATTTGCGTAATTGCCGA-
* * *
1766107 CTTGTTTCTCTCCAGAGCATGAGATTCTTTTGTATGACTGATACATTGTTTTATCTGAATTAACT
65 CTTGTTTCTCTCCAGAGCATAAGACTCTTTTGTATGACTGATACATCGTTTTATCTGAATTAACT
* * *
1766172 ATTTGCATTGGACTGAAGTATCAAAATATACTGAAATTTTAAAGGTTTTTGAAATTCCATGCTAT
130 ATATGCATTGGACTGAAGTATCAAAATATACTGAAATTTAAAAGGTTTTTGAAATTCCATGCTAA
* * * * *
1766237 TATATTCAAGTCAGTGATTGTAATGTGATGTATGGAATTCACTTCTTTTAGTAGTGGTGTTTATG
195 TATAATCAAGTCAGTGACTGCAATGTGATGGATGGAATTCAATTCTTTTAGTAGTGGTGTTTATG
*
1766302 GAATACGGATGGTATAAAGTAGCCTGTTAATGTCGGTGTCGTTAGAACATTCTGTCA
260 GAATACGGATGGTATAAAGTAACCTGTTAATGTCGGTGTCGTTAGAACATTCTGTCA
1766359 TTACTT
1 TTACTT
1766365 AATCTATTTG
Statistics
Matches: 293, Mismatches: 28, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
315 1 0.00
316 292 1.00
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.39
Consensus pattern (316 bp):
TTACTTGTAGCTTATATACCAGCGTTATTCTACACCACTCTACCACAATTTGCGTAATTGCCGAC
TTGTTTCTCTCCAGAGCATAAGACTCTTTTGTATGACTGATACATCGTTTTATCTGAATTAACTA
TATGCATTGGACTGAAGTATCAAAATATACTGAAATTTAAAAGGTTTTTGAAATTCCATGCTAAT
ATAATCAAGTCAGTGACTGCAATGTGATGGATGGAATTCAATTCTTTTAGTAGTGGTGTTTATGG
AATACGGATGGTATAAAGTAACCTGTTAATGTCGGTGTCGTTAGAACATTCTGTCA
Found at i:1768542 original size:2 final size:2
Alignment explanation
Indices: 1768535--1768564 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1768525 GTGGCCCTGT
1768535 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1768565 CCTATATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1771852 original size:37 final size:37
Alignment explanation
Indices: 1771778--1771853 Score: 91
Period size: 37 Copynumber: 2.1 Consensus size: 37
1771768 TTTAGATAAT
* * * *
1771778 GTCAGATCAGGTGGATGATATATATTTTTTAGGTCGG
1 GTCAGACCAGGTGGAGGATATATATTTTCTAGATCGG
*
1771815 GTCAGACCGGGTGGAGGATATATAATTTTCT-GATCGG
1 GTCAGACCAGGTGGAGGATATAT-ATTTTCTAGATCGG
1771852 GT
1 GT
1771854 TCGAATGGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
37 27 0.82
38 6 0.18
ACGTcount: A:0.24, C:0.11, G:0.32, T:0.34
Consensus pattern (37 bp):
GTCAGACCAGGTGGAGGATATATATTTTCTAGATCGG
Found at i:1772786 original size:21 final size:21
Alignment explanation
Indices: 1772760--1772801 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1772750 GATTAGGGAT
1772760 GGCAACTCAACCCGAATCCGA
1 GGCAACTCAACCCGAATCCGA
1772781 GGCAACTCAACCCGAATCCGA
1 GGCAACTCAACCCGAATCCGA
1772802 CGGGTTCCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.38, G:0.19, T:0.10
Consensus pattern (21 bp):
GGCAACTCAACCCGAATCCGA
Found at i:1779585 original size:39 final size:39
Alignment explanation
Indices: 1779542--1779639 Score: 117
Period size: 39 Copynumber: 2.5 Consensus size: 39
1779532 AACTAAAACC
* *
1779542 ATCACCCTATACCCATTGATAAAATACGAAGGCCAAAAG
1 ATCACCCTATACTCATTGAGAAAATACGAAGGCCAAAAG
* ** *
1779581 ATCACCCCATACTCATTGAGGTAATACGAGGGCCAAAAG
1 ATCACCCTATACTCATTGAGAAAATACGAAGGCCAAAAG
*
1779620 ATTA-CCTCATACTCATTGAG
1 ATCACCCT-ATACTCATTGAG
1779640 GCAATATGAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
38 2 0.04
39 48 0.96
ACGTcount: A:0.38, C:0.26, G:0.15, T:0.21
Consensus pattern (39 bp):
ATCACCCTATACTCATTGAGAAAATACGAAGGCCAAAAG
Found at i:1779640 original size:39 final size:39
Alignment explanation
Indices: 1779564--1779652 Score: 133
Period size: 39 Copynumber: 2.3 Consensus size: 39
1779554 CCATTGATAA
*
1779564 AATACGAAGGCCAAAAGATCACCCCATACTCATTGAGGT
1 AATACGAAGGCCAAAAGATCACCCCATACTCATTGAGGC
* * *
1779603 AATACGAGGGCCAAAAGATTACCTCATACTCATTGAGGC
1 AATACGAAGGCCAAAAGATCACCCCATACTCATTGAGGC
*
1779642 AATATGAAGGC
1 AATACGAAGGC
1779653 TACTCATTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.19
Consensus pattern (39 bp):
AATACGAAGGCCAAAAGATCACCCCATACTCATTGAGGC
Found at i:1780751 original size:30 final size:29
Alignment explanation
Indices: 1780717--1780822 Score: 104
Period size: 30 Copynumber: 3.6 Consensus size: 29
1780707 TTAAAACAAT
* *
1780717 AAAAACAGAAACTTAAGAGTCAAAATAGCA
1 AAAAACAAAAACTTAAGGGTCAAAATAG-A
* * *
1780747 AAAAACAAAAACTTTAGGGGCTAAAATATA
1 AAAAACAAAAACTTAAGGGTC-AAAATAGA
* *
1780777 TAAAACAAAAACTTTAGGGATCAAAATAGA
1 AAAAACAAAAACTTAAGGG-TCAAAATAGA
* *
1780807 TAAAACAGAAACTTAA
1 AAAAACAAAAACTTAA
1780823 AGGACTGAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
30 57 0.89
31 7 0.11
ACGTcount: A:0.58, C:0.11, G:0.12, T:0.18
Consensus pattern (29 bp):
AAAAACAAAAACTTAAGGGTCAAAATAGA
Found at i:1780834 original size:60 final size:60
Alignment explanation
Indices: 1780687--1780834 Score: 147
Period size: 60 Copynumber: 2.5 Consensus size: 60
1780677 CAAAAATGGT
* * * * *
1780687 AAAAACATAAACTTAAATGATTAAAACA-ATAAAAACAGAAACTTAAGAGTCAAAATAGCA
1 AAAAACAAAAACTTAAAGGACTAAAATATAT-AAAACAAAAACTTAAGAGTCAAAATAGCA
* * * * *
1780747 AAAAACAAAAACTTTAGGGGCTAAAATATATAAAACAAAAACTTTAGGGATCAAAATAG-A
1 AAAAACAAAAACTTAAAGGACTAAAATATATAAAACAAAAACTTAAGAG-TCAAAATAGCA
* * *
1780807 TAAAACAGAAACTTAAAGGACTGAAATA
1 AAAAACAAAAACTTAAAGGACTAAAATA
1780835 GCATAAACAT
Statistics
Matches: 70, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
60 59 0.84
61 11 0.16
ACGTcount: A:0.59, C:0.11, G:0.11, T:0.19
Consensus pattern (60 bp):
AAAAACAAAAACTTAAAGGACTAAAATATATAAAACAAAAACTTAAGAGTCAAAATAGCA
Found at i:1782279 original size:3 final size:3
Alignment explanation
Indices: 1782260--1782302 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
1782250 AATGTAAATG
* *
1782260 TAA TAT TAA TAA T-A TAA TAA TAA TAA TAA TAA T-A TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1782303 CTATTACTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1782289 original size:20 final size:20
Alignment explanation
Indices: 1782260--1782302 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1782250 AATGTAAATG
* *
1782260 TAATATTAATAATATAATAA
1 TAATAATAATAATATAAAAA
1782280 TAATAATAATAATATAAAAA
1 TAATAATAATAATATAAAAA
1782300 TAA
1 TAA
1782303 CTATTACTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TAATAATAATAATATAAAAA
Found at i:1782418 original size:39 final size:39
Alignment explanation
Indices: 1782351--1782519 Score: 232
Period size: 39 Copynumber: 4.4 Consensus size: 39
1782341 ACAAAGGTTA
* *
1782351 AAAAG-TCACCCCATACTCATTGATGCAATACGAAGGCC
1 AAAAGATCACCCTATACTCATTGATGCAATACAAAGGCC
* * * * **
1782389 CAAAGATCATCCTATACTCATTGACGCAATACGAAGGTT
1 AAAAGATCACCCTATACTCATTGATGCAATACAAAGGCC
* *
1782428 AAAAGATCACCCTATACTCATTGATGCGATAAAAAGGCC
1 AAAAGATCACCCTATACTCATTGATGCAATACAAAGGCC
*
1782467 AAAAGATCACCCTATACTCATTGATGCGATACAAAGGCC
1 AAAAGATCACCCTATACTCATTGATGCAATACAAAGGCC
1782506 AAAAGATCACCCTA
1 AAAAGATCACCCTA
1782520 GGCCAAAAGA
Statistics
Matches: 115, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
38 4 0.03
39 111 0.97
ACGTcount: A:0.39, C:0.25, G:0.15, T:0.21
Consensus pattern (39 bp):
AAAAGATCACCCTATACTCATTGATGCAATACAAAGGCC
Found at i:1782524 original size:18 final size:18
Alignment explanation
Indices: 1782501--1782537 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1782491 TGCGATACAA
1782501 AGGCCAAAAGATCACCCT
1 AGGCCAAAAGATCACCCT
*
1782519 AGGCCAAAAGATCATCCT
1 AGGCCAAAAGATCACCCT
1782537 A
1 A
1782538 TACGCATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.30, G:0.16, T:0.14
Consensus pattern (18 bp):
AGGCCAAAAGATCACCCT
Found at i:1782555 original size:57 final size:57
Alignment explanation
Indices: 1782462--1782576 Score: 185
Period size: 57 Copynumber: 2.0 Consensus size: 57
1782452 TGCGATAAAA
* *
1782462 AGGCCAAAAGATCACCCTATACTCATTGATGCGATACAAAGGCCAAAAGATCACCCT
1 AGGCCAAAAGATCACCCTATACGCATTGATGAGATACAAAGGCCAAAAGATCACCCT
* * *
1782519 AGGCCAAAAGATCATCCTATACGCATTGATGAGATACAAAGGCCCAAAGATCATCCT
1 AGGCCAAAAGATCACCCTATACGCATTGATGAGATACAAAGGCCAAAAGATCACCCT
1782576 A
1 A
1782577 TACTCATTGA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.39, C:0.26, G:0.17, T:0.18
Consensus pattern (57 bp):
AGGCCAAAAGATCACCCTATACGCATTGATGAGATACAAAGGCCAAAAGATCACCCT
Found at i:1782573 original size:39 final size:39
Alignment explanation
Indices: 1782519--1782654 Score: 175
Period size: 39 Copynumber: 3.5 Consensus size: 39
1782509 AGATCACCCT
* *
1782519 AGGCCAAAAGATCATCCTATACGCATTGATGAGATACAA
1 AGGCCAAAAGATCACCCTATACTCATTGATGAGATACAA
* * * *
1782558 AGGCCCAAAGATCATCCTATACTCATTGACGCA-ATACGA
1 AGGCCAAAAGATCACCCTATACTCATTGATG-AGATACAA
** *
1782597 AGGTTAAAAGATCACCCTATACTCATTGATGCGATACAA
1 AGGCCAAAAGATCACCCTATACTCATTGATGAGATACAA
1782636 AGGCCAAAAGATCACCCTA
1 AGGCCAAAAGATCACCCTA
1782655 GGCCAAAAGA
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 81 0.99
40 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.21
Consensus pattern (39 bp):
AGGCCAAAAGATCACCCTATACTCATTGATGAGATACAA
Found at i:1782606 original size:96 final size:96
Alignment explanation
Indices: 1782428--1782615 Score: 277
Period size: 96 Copynumber: 2.0 Consensus size: 96
1782418 TACGAAGGTT
* * *
1782428 AAAAGATCACCCTATACTCATTGATGCGATAAAAAGGCCAAAAGATCACCCTATACTCATTGATG
1 AAAAGATCACCCTATACGCATTGATGAGATAAAAAGGCCAAAAGATCACCCTATACTCATTGACG
*
1782493 CGATACAAAGGCCAAAAGATCACCCTAGGCC
66 CAATACAAAGGCCAAAAGATCACCCTAGGCC
* * * *
1782524 AAAAGATCATCCTATACGCATTGATGAGATACAAAGGCCCAAAGATCATCCTATACTCATTGACG
1 AAAAGATCACCCTATACGCATTGATGAGATAAAAAGGCCAAAAGATCACCCTATACTCATTGACG
* **
1782589 CAATACGAAGGTTAAAAGATCACCCTA
66 CAATACAAAGGCCAAAAGATCACCCTA
1782616 TACTCATTGA
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
96 81 1.00
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.20
Consensus pattern (96 bp):
AAAAGATCACCCTATACGCATTGATGAGATAAAAAGGCCAAAAGATCACCCTATACTCATTGACG
CAATACAAAGGCCAAAAGATCACCCTAGGCC
Found at i:1782626 original size:135 final size:135
Alignment explanation
Indices: 1782384--1782917 Score: 892
Period size: 135 Copynumber: 4.0 Consensus size: 135
1782374 TGCAATACGA
* * * * *** *
1782384 AGGCCCAAAGATCATCCTATACTCATTGACGCA-ATACGAAGGTTAAAAGATCACCCTATACTCA
1 AGGCCAAAAGATCATCCTATACGCATTGATG-AGATACAAAGGCCCAAAGATCATCCTATACTCA
* * ** **
1782448 TTGATGCGATAAAAAGGCCAAAAGATCACCCTATACTCATTGATGCGATACAAAGGCCAAAAGAT
65 TTGACGCAATACGAAGGTTAAAAGATCACCCTATACTCATTGATGCGATACAAAGGCCAAAAGAT
1782513 CACCCT
130 CACCCT
1782519 AGGCCAAAAGATCATCCTATACGCATTGATGAGATACAAAGGCCCAAAGATCATCCTATACTCAT
1 AGGCCAAAAGATCATCCTATACGCATTGATGAGATACAAAGGCCCAAAGATCATCCTATACTCAT
1782584 TGACGCAATACGAAGGTTAAAAGATCACCCTATACTCATTGATGCGATACAAAGGCCAAAAGATC
66 TGACGCAATACGAAGGTTAAAAGATCACCCTATACTCATTGATGCGATACAAAGGCCAAAAGATC
1782649 ACCCT
131 ACCCT
*
1782654 AGGCCAAAAGATCATCCTATATGCATTGATGAGATACAAAGGCCCAAAGATCATCCTATACTCAT
1 AGGCCAAAAGATCATCCTATACGCATTGATGAGATACAAAGGCCCAAAGATCATCCTATACTCAT
1782719 TGACGCAATACGAAGGTTAAAAGATCACCCTATACTCATTGATGCGATACAAAGGCCAAAAGATC
66 TGACGCAATACGAAGGTTAAAAGATCACCCTATACTCATTGATGCGATACAAAGGCCAAAAGATC
1782784 ACCCT
131 ACCCT
1782789 AGGCCAAAAGATCATCCTATACGCATTGATGAGATACAAAGGCCCAAAGATCATCCTATACTCAT
1 AGGCCAAAAGATCATCCTATACGCATTGATGAGATACAAAGGCCCAAAGATCATCCTATACTCAT
*
1782854 TGACGCAATACGAAGGTTAAAAGATCATCCC-ATACTCATTGATGCGATAAAAAGGCCAAAAGAT
66 TGACGCAATACGAAGGTTAAAAGATCA-CCCTATACTCATTGATGCGATACAAAGGCCAAAAGAT
1782918 AGCCAATACT
Statistics
Matches: 380, Mismatches: 17, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
134 1 0.00
135 376 0.99
136 3 0.01
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.21
Consensus pattern (135 bp):
AGGCCAAAAGATCATCCTATACGCATTGATGAGATACAAAGGCCCAAAGATCATCCTATACTCAT
TGACGCAATACGAAGGTTAAAAGATCACCCTATACTCATTGATGCGATACAAAGGCCAAAAGATC
ACCCT
Found at i:1782658 original size:96 final size:96
Alignment explanation
Indices: 1782558--1782750 Score: 246
Period size: 96 Copynumber: 2.0 Consensus size: 96
1782548 TGAGATACAA
* * **
1782558 AGGCCCAAAGATCATCCTATACT-CATTGACGCA-ATACGAAGGTTAAAAGATCACCCTATACTC
1 AGGCCAAAAGATCATCCTATA-TGCATTGACG-AGATACAAAGGCCAAAAGATCACCCTATACTC
* *
1782621 ATTGATGCGATACAAAGGCCAAAAGATCACCCT
64 ATTGACGCAATACAAAGGCCAAAAGATCACCCT
* * *
1782654 AGGCCAAAAGATCATCCTATATGCATTGATGAGATACAAAGGCCCAAAGATCATCCTATACTCAT
1 AGGCCAAAAGATCATCCTATATGCATTGACGAGATACAAAGGCCAAAAGATCACCCTATACTCAT
* **
1782719 TGACGCAATACGAAGGTTAAAAGATCACCCT
66 TGACGCAATACAAAGGCCAAAAGATCACCCT
1782750 A
1 A
1782751 TACTCATTGA
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
95 2 0.02
96 81 0.98
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.21
Consensus pattern (96 bp):
AGGCCAAAAGATCATCCTATATGCATTGACGAGATACAAAGGCCAAAAGATCACCCTATACTCAT
TGACGCAATACAAAGGCCAAAAGATCACCCT
Found at i:1782659 original size:18 final size:18
Alignment explanation
Indices: 1782636--1782672 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1782626 TGCGATACAA
1782636 AGGCCAAAAGATCACCCT
1 AGGCCAAAAGATCACCCT
*
1782654 AGGCCAAAAGATCATCCT
1 AGGCCAAAAGATCACCCT
1782672 A
1 A
1782673 TATGCATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.30, G:0.16, T:0.14
Consensus pattern (18 bp):
AGGCCAAAAGATCACCCT
Found at i:1782690 original size:57 final size:57
Alignment explanation
Indices: 1782602--1782711 Score: 168
Period size: 57 Copynumber: 1.9 Consensus size: 57
1782592 TACGAAGGTT
*
1782602 AAAAGATCACCCTATACTCATTGATGCGATACAAAGGCCAAAAGATCACCCTAGGCC
1 AAAAGATCACCCTATACTCATTGATGAGATACAAAGGCCAAAAGATCACCCTAGGCC
* * *
1782659 AAAAGATCATCCTATA-TGCATTGATGAGATACAAAGGCCCAAAGATCATCCTA
1 AAAAGATCACCCTATACT-CATTGATGAGATACAAAGGCCAAAAGATCACCCTA
1782712 TACTCATTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
56 1 0.02
57 47 0.98
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.20
Consensus pattern (57 bp):
AAAAGATCACCCTATACTCATTGATGAGATACAAAGGCCAAAAGATCACCCTAGGCC
Found at i:1782705 original size:174 final size:174
Alignment explanation
Indices: 1782363--1782789 Score: 526
Period size: 174 Copynumber: 2.5 Consensus size: 174
1782353 AAGTCACCCC
1782363 ATACTCATTGATGCAATACGAAGGCCCAAAGATCATCCTATACTCATTGACGCAATACGAAGGTT
1 ATACTCATTGATGCAATACGAAGGCCCAAAGATCATCCTATACTCATTGACGCAATACGAAGGTT
* **
1782428 AAAAGATCACCCTATACTCATTGATGCGATAAAAAGGCCAAAAGATCACCCTATACTCATTGATG
66 AAAAGATCACCCTATACTCATTGATGCGATAAAAAGGCCAAAAGATCACCCTAGACTCAAAGATG
**
1782493 CGATACAAAGGCCAAAAGATCACCCTAGGCCAAAAGATCATCCT
131 CGATACAAAGGCCAAAAGATCACCAAAGGCCAAAAGATCATCCT
* *
1782537 ATACGCATTGATG-AGATACAAAGGCCCAAAGATCATCCTATACTCATTGACGCAATACGAAGGT
1 ATACTCATTGATGCA-ATACGAAGGCCCAAAGATCATCCTATACTCATTGACGCAATACGAAGGT
* *
1782601 TAAAAGATCACCCTATACTCATTGATGCGATACAAAGGCCAAAAGATCACCCTAGGC-CAAAAGA
65 TAAAAGATCACCCTATACTCATTGATGCGATAAAAAGGCCAAAAGATCACCCTAGACTC-AAAGA
* * * * *
1782665 T-C-ATCCTATATG-CATTGATGAGAT-A-CAAAGGCCCAAAGATCATCCT
129 TGCGATAC-AAAGGCCA---A-AAGATCACCAAAGGCCAAAAGATCATCCT
* *** * * * * **
1782711 ATACTCATTGACGCAATACGAAGGTTAAAAGATCACCCTATACTCATTGATGCGATACAAAGGCC
1 ATACTCATTGATGCAATACGAAGGCCCAAAGATCATCCTATACTCATTGACGCAATACGAAGGTT
1782776 AAAAGATCACCCTA
66 AAAAGATCACCCTA
1782790 GGCCAAAAGA
Statistics
Matches: 219, Mismatches: 26, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
172 5 0.02
173 6 0.03
174 201 0.92
175 3 0.01
176 4 0.02
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.21
Consensus pattern (174 bp):
ATACTCATTGATGCAATACGAAGGCCCAAAGATCATCCTATACTCATTGACGCAATACGAAGGTT
AAAAGATCACCCTATACTCATTGATGCGATAAAAAGGCCAAAAGATCACCCTAGACTCAAAGATG
CGATACAAAGGCCAAAAGATCACCAAAGGCCAAAAGATCATCCT
Found at i:1782708 original size:39 final size:39
Alignment explanation
Indices: 1782654--1782789 Score: 168
Period size: 39 Copynumber: 3.5 Consensus size: 39
1782644 AGATCACCCT
*
1782654 AGGCCAAAAGATCATCCTATA-TGCATTGATGAGATACAA
1 AGGCCAAAAGATCACCCTATACT-CATTGATGAGATACAA
* * * *
1782693 AGGCCCAAAGATCATCCTATACTCATTGACGCA-ATACGA
1 AGGCCAAAAGATCACCCTATACTCATTGATG-AGATACAA
** *
1782732 AGGTTAAAAGATCACCCTATACTCATTGATGCGATACAA
1 AGGCCAAAAGATCACCCTATACTCATTGATGAGATACAA
1782771 AGGCCAAAAGATCACCCTA
1 AGGCCAAAAGATCACCCTA
1782790 GGCCAAAAGA
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
39 80 0.98
40 2 0.02
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.21
Consensus pattern (39 bp):
AGGCCAAAAGATCACCCTATACTCATTGATGAGATACAA
Found at i:1782793 original size:96 final size:96
Alignment explanation
Indices: 1782693--1782880 Score: 243
Period size: 96 Copynumber: 2.0 Consensus size: 96
1782683 TGAGATACAA
* * * **
1782693 AGGCCCAAAGATCATCCTATACTCATTGACGCA-ATACGAAGGTTAAAAGATCACCCTATACTCA
1 AGGCCAAAAGATCATCCTATACGCATTGACG-AGATACAAAGGCCAAAAGATCACCCTATACTCA
* *
1782757 TTGATGCGATACAAAGGCCAAAAGATCACCCT
65 TTGACGCAATACAAAGGCCAAAAGATCACCCT
* * *
1782789 AGGCCAAAAGATCATCCTATACGCATTGATGAGATACAAAGGCCCAAAGATCATCCTATACTCAT
1 AGGCCAAAAGATCATCCTATACGCATTGACGAGATACAAAGGCCAAAAGATCACCCTATACTCAT
* **
1782854 TGACGCAATACGAAGGTTAAAAGATCA
66 TGACGCAATACAAAGGCCAAAAGATCA
1782881 TCCCATACTC
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
95 1 0.01
96 77 0.99
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.21
Consensus pattern (96 bp):
AGGCCAAAAGATCATCCTATACGCATTGACGAGATACAAAGGCCAAAAGATCACCCTATACTCAT
TGACGCAATACAAAGGCCAAAAGATCACCCT
Found at i:1782794 original size:18 final size:18
Alignment explanation
Indices: 1782771--1782807 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1782761 TGCGATACAA
1782771 AGGCCAAAAGATCACCCT
1 AGGCCAAAAGATCACCCT
*
1782789 AGGCCAAAAGATCATCCT
1 AGGCCAAAAGATCACCCT
1782807 A
1 A
1782808 TACGCATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.30, G:0.16, T:0.14
Consensus pattern (18 bp):
AGGCCAAAAGATCACCCT
Found at i:1782825 original size:57 final size:57
Alignment explanation
Indices: 1782737--1782846 Score: 175
Period size: 57 Copynumber: 1.9 Consensus size: 57
1782727 TACGAAGGTT
* *
1782737 AAAAGATCACCCTATACTCATTGATGCGATACAAAGGCCAAAAGATCACCCTAGGCC
1 AAAAGATCACCCTATACGCATTGATGAGATACAAAGGCCAAAAGATCACCCTAGGCC
* * *
1782794 AAAAGATCATCCTATACGCATTGATGAGATACAAAGGCCCAAAGATCATCCTA
1 AAAAGATCACCCTATACGCATTGATGAGATACAAAGGCCAAAAGATCACCCTA
1782847 TACTCATTGA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.19
Consensus pattern (57 bp):
AAAAGATCACCCTATACGCATTGATGAGATACAAAGGCCAAAAGATCACCCTAGGCC
Found at i:1782843 original size:39 final size:39
Alignment explanation
Indices: 1782789--1783033 Score: 266
Period size: 39 Copynumber: 6.4 Consensus size: 39
1782779 AGATCACCCT
*
1782789 AGGCCAAAAGATCATCCTATACGCATTGATGAGATACAA
1 AGGCCAAAAGATCATCCTATACTCATTGATGAGATACAA
* * *
1782828 AGGCCCAAAGATCATCCTATACTCATTGACGCA-ATACGA
1 AGGCCAAAAGATCATCCTATACTCATTGATG-AGATACAA
** * * *
1782867 AGGTTAAAAGATCATCCCATACTCATTGATGCGATAAAA
1 AGGCCAAAAGATCATCCTATACTCATTGATGAGATACAA
* * *
1782906 AGGCCAAAAGAT-AGCCAATACTCACTGAT-ATGATACAA
1 AGGCCAAAAGATCATCCTATACTCATTGATGA-GATACAA
* ** *
1782944 AGGCCAAAAGATCACCCTATACTCGCTGATGGGATACAA
1 AGGCCAAAAGATCATCCTATACTCATTGATGAGATACAA
* * *
1782983 A-GCCAAAAGATCACCCTATACT-ATTGATGCGATATAA
1 AGGCCAAAAGATCATCCTATACTCATTGATGAGATACAA
1783020 AGGCCAAAAGATCA
1 AGGCCAAAAGATCA
1783034 CACCCTATAT
Statistics
Matches: 173, Mismatches: 27, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
37 12 0.07
38 65 0.38
39 95 0.55
40 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.20
Consensus pattern (39 bp):
AGGCCAAAAGATCATCCTATACTCATTGATGAGATACAA
Found at i:1782946 original size:38 final size:39
Alignment explanation
Indices: 1782789--1783061 Score: 257
Period size: 39 Copynumber: 7.0 Consensus size: 39
1782779 AGATCACCCT
* * * *
1782789 AGGCCAAAAGATCATCCTATACGCATTGATGAGATACAA
1 AGGCCAAAAGATCACCCTATACTCACTGATGCGATACAA
* * * * * *
1782828 AGGCCCAAAGATCATCCTATACTCATTGACGCAATACGA
1 AGGCCAAAAGATCACCCTATACTCACTGATGCGATACAA
** * *
1782867 AGGTTAAAAGATCATCCC-ATACTCATTGATGCGATAAAA
1 AGGCCAAAAGATCA-CCCTATACTCACTGATGCGATACAA
* * **
1782906 AGGCCAAAAGAT-AGCCAATACTCACTGATATGATACAA
1 AGGCCAAAAGATCACCCTATACTCACTGATGCGATACAA
* *
1782944 AGGCCAAAAGATCACCCTATACTCGCTGATGGGATACAA
1 AGGCCAAAAGATCACCCTATACTCACTGATGCGATACAA
* *
1782983 A-GCCAAAAGATCACCCTATACT-ATTGATGCGATATAA
1 AGGCCAAAAGATCACCCTATACTCACTGATGCGATACAA
* *
1783020 AGGCCAAAAGATCACACCCTATATGCTCATTGATGCAATACA
1 AGGCCAAAAGAT--CACCCTATA--CTCACTGATGCGATACA
1783062 GATGATAAAA
Statistics
Matches: 193, Mismatches: 32, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
37 14 0.07
38 61 0.32
39 93 0.48
40 11 0.06
42 2 0.01
43 12 0.06
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (39 bp):
AGGCCAAAAGATCACCCTATACTCACTGATGCGATACAA
Found at i:1782966 original size:77 final size:78
Alignment explanation
Indices: 1782789--1783061 Score: 284
Period size: 77 Copynumber: 3.5 Consensus size: 78
1782779 AGATCACCCT
* * * * *
1782789 AGGCCAAAAGATCATCCTATACGCATTGATGAGATACAAAGGCCCAAAGATCATCCTATACTCAT
1 AGGCCAAAAGATCACCCTATACTCATTGATGCGATACAAAGGCCAAAAGATCACCCTATACTCAT
* * *
1782854 TGACGCAATACGA
66 TGATGCGATACAA
** * * *
1782867 AGGTTAAAAGATCATCCC-ATACTCATTGATGCGATAAAAAGGCCAAAAGAT-AGCCAATACTCA
1 AGGCCAAAAGATCA-CCCTATACTCATTGATGCGATACAAAGGCCAAAAGATCACCCTATACTCA
* **
1782930 CTGATATGATACAA
65 TTGATGCGATACAA
** *
1782944 AGGCCAAAAGATCACCCTATACTCGCTGATGGGATACAAA-GCCAAAAGATCACCCTATACT-AT
1 AGGCCAAAAGATCACCCTATACTCATTGATGCGATACAAAGGCCAAAAGATCACCCTATACTCAT
*
1783007 TGATGCGATATAA
66 TGATGCGATACAA
*
1783020 AGGCCAAAAGATCACACCCTATATGCTCATTGATGCAATACA
1 AGGCCAAAAGAT--CACCCTATA--CTCATTGATGCGATACA
1783062 GATGATAAAA
Statistics
Matches: 157, Mismatches: 31, Indels: 12
0.79 0.16 0.06
Matches are distributed among these distances:
76 36 0.23
77 56 0.36
78 50 0.32
79 2 0.01
80 13 0.08
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (78 bp):
AGGCCAAAAGATCACCCTATACTCATTGATGCGATACAAAGGCCAAAAGATCACCCTATACTCAT
TGATGCGATACAA
Found at i:1788372 original size:3 final size:3
Alignment explanation
Indices: 1788364--1788414 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
1788354 CGGGCTTTAA
1788364 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1788412 AAT
1 AAT
1788415 GGATTATTAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1793400 original size:64 final size:65
Alignment explanation
Indices: 1793173--1793385 Score: 245
Period size: 65 Copynumber: 3.3 Consensus size: 65
1793163 TATTCAAAGG
* * * *
1793173 CATGCACCGATGCATCAGTCCATGCATCGATGCA-TCGATGAAT-TAATT-GAAACATCGAATGC
1 CATGCATCGATGCA-CACTCCATGCATCGATGCACTC-A-GAATAT-TTTCAAAACATCGAATGC
*
1793235 ATTC
62 ATTT
* ** *
1793239 CATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAAAACATCGAATGCATTT
* * **
1793304 GATGCATCGATGCACAATCCATGCATCGATGCACTCAGGCTATTTTC-AAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAAAACATCGAATGCATTT
1793368 CATGCATCGATGCACACT
1 CATGCATCGATGCACACT
1793386 TGGTGCACCG
Statistics
Matches: 127, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
64 39 0.31
65 72 0.57
66 16 0.13
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (65 bp):
CATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAAAACATCGAATGCATTT
Found at i:1799894 original size:21 final size:21
Alignment explanation
Indices: 1799870--1799929 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
1799860 CCGTCCTCCT
1799870 GTTCCTCAACATCCTAATCCC
1 GTTCCTCAACATCCTAATCCC
** * *
1799891 GTTCCTCCTCAACCTAATCCT
1 GTTCCTCAACATCCTAATCCC
*
1799912 GATCCTCAAGC-TCCTAAT
1 GTTCCTCAA-CATCCTAAT
1799930 GGCTTATTGA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
21 29 0.97
22 1 0.03
ACGTcount: A:0.23, C:0.40, G:0.07, T:0.30
Consensus pattern (21 bp):
GTTCCTCAACATCCTAATCCC
Found at i:1800755 original size:21 final size:21
Alignment explanation
Indices: 1800729--1800772 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1800719 ACTCCGGGAG
*
1800729 CTAGTTCTTCTCGAGCTGCTC
1 CTAGTTCTTCTCGAGCTCCTC
*
1800750 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCTCGAGCTCCTC
1800771 CT
1 CT
1800773 CCTCCTCCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.07, C:0.36, G:0.16, T:0.41
Consensus pattern (21 bp):
CTAGTTCTTCTCGAGCTCCTC
Found at i:1807357 original size:16 final size:16
Alignment explanation
Indices: 1807333--1807368 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1807323 ACATATTTCT
* *
1807333 TTTTTAATTTTTTTAA
1 TTTTAAATTATTTTAA
1807349 TTTTAAATTATTTTAA
1 TTTTAAATTATTTTAA
1807365 TTTT
1 TTTT
1807369 TTAGAAAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTAAATTATTTTAA
Found at i:1808582 original size:112 final size:112
Alignment explanation
Indices: 1808276--1808761 Score: 671
Period size: 112 Copynumber: 4.4 Consensus size: 112
1808266 TCAAATCTTT
* * *
1808276 AGAGGGATCTGTTCCGCTTCTTCT--AAGGGAATATCATATATGGGAAAATTGATCTATTGAATC
1 AGAGGGATCTGTTCCGCTTCTT-TGAAAGGGAATATCAGATCTGGGAAAATTGATCCATTGAATC
*
1808339 GGGGTAGACTTGTTCTGCTGTCACTCAAGG-AATATCAAATCTTGGAAG
65 GAGGTAGACTTGTTCTGCTGTCACTC-AGGAAATATCAAATCTTGGAAG
* * * * *
1808387 ATATGGATTTGTTCCGCTTCTTCT--AAGGGGATATCAGATCTGGGAAAGTTGATCCATTGAATC
1 AGAGGGATCTGTTCCGCTTCTT-TGAAAGGGAATATCAGATCTGGGAAAATTGATCCATTGAATC
* *
1808450 -AGGGTAAACTTGTTCTGCTGTCACTCAGGAAATATCAAATATTGGAAG
65 GA-GGTAGACTTGTTCTGCTGTCACTCAGGAAATATCAAATCTTGGAAG
* * *
1808498 AGGGGGATCTGTTTCGCTTCTTTGAAAGGGAATATCAGATCTGAGAAAATTGATCCATTGAATCG
1 AGAGGGATCTGTTCCGCTTCTTTGAAAGGGAATATCAGATCTGGGAAAATTGATCCATTGAATCG
* *
1808563 AGGTAGACTTGTTCTGCTGTCACACAGGAAATATCAAATCTTGGAAT
66 AGGTAGACTTGTTCTGCTGTCACTCAGGAAATATCAAATCTTGGAAG
**
1808610 AGATAGATCTGTTCCGCTTCTTTGAAAGGGAATATCAGATCTGGGAAAATTGATCCATTGAATCG
1 AGAGGGATCTGTTCCGCTTCTTTGAAAGGGAATATCAGATCTGGGAAAATTGATCCATTGAATCG
* *
1808675 AGGTAGACTTGTTAC-GTTGTCACTCAGGGAATATCAAATCTTGGAAG
66 AGGTAGACTTGTT-CTGCTGTCACTCAGGAAATATCAAATCTTGGAAG
* **
1808722 AAAGAAATCTGTTCCGCTTCTTTGAAAGGGAATATCAGAT
1 AGAGGGATCTGTTCCGCTTCTTTGAAAGGGAATATCAGAT
1808762 TTGAGGGAGT
Statistics
Matches: 334, Mismatches: 35, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
110 4 0.01
111 112 0.34
112 216 0.65
113 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (112 bp):
AGAGGGATCTGTTCCGCTTCTTTGAAAGGGAATATCAGATCTGGGAAAATTGATCCATTGAATCG
AGGTAGACTTGTTCTGCTGTCACTCAGGAAATATCAAATCTTGGAAG
Found at i:1809961 original size:5 final size:5
Alignment explanation
Indices: 1809951--1810024 Score: 71
Period size: 5 Copynumber: 14.4 Consensus size: 5
1809941 TTTTTGTTTA
* * *
1809951 TTCTT TTCTT TTCTT TTATT TTCTT TTCTT TT-TT ATCTT TT-TT AATCTTT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT -TTC-TT
1810001 TTCATT TTCTT TCTCTT TTCTT TT
1 TTC-TT TTCTT T-TCTT TTCTT TT
1810025 TTGTTTTAAG
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
4 5 0.09
5 38 0.67
6 12 0.21
7 2 0.04
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (5 bp):
TTCTT
Found at i:1814693 original size:2 final size:2
Alignment explanation
Indices: 1814686--1814711 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1814676 TAAAATGTTC
1814686 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1814712 TTATGTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1820296 original size:26 final size:26
Alignment explanation
Indices: 1820267--1820333 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
1820257 AATTTATCTT
1820267 TTTAATTTTGTAAAAAAAAT-TATGAA
1 TTTAATTTTGTAAAAAAAATATAT-AA
* *
1820293 TTTAAATTTTTTAAAGAAAATATATAA
1 TTT-AATTTTGTAAAAAAAATATATAA
*
1820320 ATTAATTATTGTAA
1 TTTAATT-TTGTAA
1820334 TATTATAGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
26 7 0.21
27 24 0.71
28 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (26 bp):
TTTAATTTTGTAAAAAAAATATATAA
Found at i:1820515 original size:18 final size:19
Alignment explanation
Indices: 1820492--1820535 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1820482 TCATTAATCC
1820492 TATTCCA-TAGTAATCTTT
1 TATTCCACTAGTAATCTTT
*
1820510 TATTCCCACTGGTAATCTTT
1 TATT-CCACTAGTAATCTTT
*
1820530 CATTCC
1 TATTCC
1820536 GTGAATCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 4 0.18
19 5 0.23
20 13 0.59
ACGTcount: A:0.23, C:0.25, G:0.07, T:0.45
Consensus pattern (19 bp):
TATTCCACTAGTAATCTTT
Found at i:1830873 original size:20 final size:20
Alignment explanation
Indices: 1830833--1830878 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1830823 CTAAATCTTG
** *
1830833 TTCTTCTCTTCTTTGTTTAT
1 TTCTTCTCTTCTTCATCTAT
1830853 TTCTTCTCTTCTTCATCTAT
1 TTCTTCTCTTCTTCATCTAT
1830873 TT-TTCT
1 TTCTTCT
1830879 TCTCTAATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.07, C:0.24, G:0.02, T:0.67
Consensus pattern (20 bp):
TTCTTCTCTTCTTCATCTAT
Found at i:1835186 original size:18 final size:18
Alignment explanation
Indices: 1835152--1835186 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1835142 CAGGACGGTC
*
1835152 GGATCAGGCAGGTGGGTT
1 GGATCAGGCAGGCGGGTT
*
1835170 GGATCAGGTAGGCGGGT
1 GGATCAGGCAGGCGGGT
1835187 CGGGTAGCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.11, G:0.51, T:0.20
Consensus pattern (18 bp):
GGATCAGGCAGGCGGGTT
Found at i:1841712 original size:20 final size:20
Alignment explanation
Indices: 1841687--1841739 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1841677 ACCATGACCC
* *
1841687 CGATATCGATACCCCTAACT
1 CGATATCAACACCCCTAACT
1841707 CGATATCAACACCCCTAACT
1 CGATATCAACACCCCTAACT
1841727 CGATATCAACACC
1 CGATATCAACACC
1841740 ATTGTCCAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.34, C:0.38, G:0.08, T:0.21
Consensus pattern (20 bp):
CGATATCAACACCCCTAACT
Found at i:1849474 original size:3 final size:3
Alignment explanation
Indices: 1849449--1849517 Score: 95
Period size: 3 Copynumber: 23.0 Consensus size: 3
1849439 TTTCGACCTC
* * *
1849449 CTT CTT TTT CTT GTT CTT C-T CTT CTT TTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1849496 CTT CTT CTT CTT CTT CCTT CTT
1 CTT CTT CTT CTT CTT -CTT CTT
1849518 TCTTTGGAGC
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
2 2 0.03
3 53 0.91
4 3 0.05
ACGTcount: A:0.00, C:0.30, G:0.01, T:0.68
Consensus pattern (3 bp):
CTT
Found at i:1858114 original size:183 final size:183
Alignment explanation
Indices: 1857800--1858165 Score: 723
Period size: 183 Copynumber: 2.0 Consensus size: 183
1857790 AATGAAAAAT
1857800 TTTCACCACCTTGTTATAGCTAGTAGCATAGGTGTAAAGTGAAACTAATTCTTCCTTTCTTTTAC
1 TTTCACCACCTTGTTATAGCTAGTAGCATAGGTGTAAAGTGAAACTAATTCTTCCTTTCTTTTAC
1857865 AATGATCGATAATCTGGGAAGCTCCAATTAAAATTAGTTTAACAATAAAATCTCAGAAGGACAAT
66 AATGATCGATAATCTGGGAAGCTCCAATTAAAATTAGTTTAACAATAAAATCTCAGAAGGACAAT
1857930 ATTCAACTGCAATTTATGAATATTTTTGTTCTTTAGTTTCCCCTCTCTAACAA
131 ATTCAACTGCAATTTATGAATATTTTTGTTCTTTAGTTTCCCCTCTCTAACAA
1857983 TTTCACCACCTTGTTATAGCTAGTAGCATAGGTGTAAAGTGAAACTAATTCTTCCTTTCTTTTAC
1 TTTCACCACCTTGTTATAGCTAGTAGCATAGGTGTAAAGTGAAACTAATTCTTCCTTTCTTTTAC
*
1858048 AATGATCGATAATCTGGGAAGCTCCAATTAAAATTAGTTTAACAATAAAATCTCAGAAGTACAAT
66 AATGATCGATAATCTGGGAAGCTCCAATTAAAATTAGTTTAACAATAAAATCTCAGAAGGACAAT
1858113 ATTCAACTGCAATTTATGAATATTTTTGTTCTTTAGTTTCCCCTCTCTAACAA
131 ATTCAACTGCAATTTATGAATATTTTTGTTCTTTAGTTTCCCCTCTCTAACAA
1858166 GGGAAAAAAA
Statistics
Matches: 182, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
183 182 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (183 bp):
TTTCACCACCTTGTTATAGCTAGTAGCATAGGTGTAAAGTGAAACTAATTCTTCCTTTCTTTTAC
AATGATCGATAATCTGGGAAGCTCCAATTAAAATTAGTTTAACAATAAAATCTCAGAAGGACAAT
ATTCAACTGCAATTTATGAATATTTTTGTTCTTTAGTTTCCCCTCTCTAACAA
Done.