Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008003.1 Hibiscus syriacus cultivar Beakdansim tig00110462_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: 3297763
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 14
Found at i:1285148 original size:42 final size:42
Alignment explanation
Indices: 1285102--1285194 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 42
1285092 CCTCTTCAAC
* *
1285102 GATGACAGTGGCCTCTTGAACG-GTGGGGGGAGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGG-GACTCTTGAGG
* *
1285144 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
1285186 GATGACAGG
1 GATGACAGG
1285195 TGAGTCGGGC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
42 39 0.87
43 6 0.13
ACGTcount: A:0.22, C:0.15, G:0.42, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:1285159 original size:21 final size:21
Alignment explanation
Indices: 1285133--1285190 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
1285123 GGTGGGGGGA
*
1285133 GACTCTTGAGGGATGATAGGG
1 GACTCTTGAGGGATGAGAGGG
* **
1285154 GCCTCTTGAACGATTG-GAGGG
1 GACTCTTGAGGGA-TGAGAGGG
1285175 GACTCTTGAGGGATGA
1 GACTCTTGAGGGATGA
1285191 CAGGTGAGTC
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.22, C:0.14, G:0.40, T:0.24
Consensus pattern (21 bp):
GACTCTTGAGGGATGAGAGGG
Found at i:1285557 original size:20 final size:20
Alignment explanation
Indices: 1285532--1285569 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1285522 AATAATAGTT
1285532 TACTTTCGCAACACGAAACA
1 TACTTTCGCAACACGAAACA
*
1285552 TACTTTCGCAACGCGAAA
1 TACTTTCGCAACACGAAA
1285570 ATGACTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.29, G:0.13, T:0.21
Consensus pattern (20 bp):
TACTTTCGCAACACGAAACA
Found at i:1285584 original size:20 final size:20
Alignment explanation
Indices: 1285537--1285630 Score: 84
Period size: 20 Copynumber: 4.8 Consensus size: 20
1285527 TAGTTTACTT
* *
1285537 TCGCAACACGAAACAT-ACTT
1 TCGCAACGCGAAA-ATGACTA
1285557 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* * *
1285577 TCGTAACGCGGAAATGGCTA
1 TCGCAACGCGAAAATGACTA
* **
1285597 TCGCAATGCG-AAATGAAAA
1 TCGCAACGCGAAAATGACTA
*
1285616 TCGCAACGAGAAAAT
1 TCGCAACGCGAAAAT
1285631 CGCAATGCGA
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
19 16 0.27
20 44 0.73
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.17
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:1285618 original size:19 final size:19
Alignment explanation
Indices: 1285596--1285654 Score: 83
Period size: 19 Copynumber: 3.4 Consensus size: 19
1285586 GGAAATGGCT
1285596 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1285615 ATCGCAA--CG--A-GAAA
1 ATCGCAATGCGAAATGAAA
1285629 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1285648 ATCGCAA
1 ATCGCAA
1285655 CGACAAAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 11 0.31
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 18 0.51
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1285630 original size:14 final size:14
Alignment explanation
Indices: 1285611--1285668 Score: 62
Period size: 14 Copynumber: 3.8 Consensus size: 14
1285601 AATGCGAAAT
1285611 GAAAATCGCAACGA
1 GAAAATCGCAACGA
1285625 GAAAATCGCAATGCGAAA
1 GAAAATCGCAA--CG--A
1285643 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
*
1285658 CAAAATCGCAA
1 GAAAATCGCAA
1285669 TGCGAAACAC
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 21 0.55
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 11 0.29
ACGTcount: A:0.50, C:0.21, G:0.19, T:0.10
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:1285684 original size:19 final size:18
Alignment explanation
Indices: 1285596--1285692 Score: 75
Period size: 19 Copynumber: 5.7 Consensus size: 18
1285586 GGAAATGGCT
*
1285596 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAA-CAAA
*
1285615 ATCGCAA--CG--AGAAA
1 ATCGCAATGCGAAACAAA
*
1285629 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAA-CAAA
1285648 ATCGCAA--CG--ACAAA
1 ATCGCAATGCGAAACAAA
1285662 ATCGCAATGCGAAACACAA
1 ATCGCAATGCGAAACA-AA
*
1285681 ATCGCATTGCGA
1 ATCGCAATGCGA
1285693 TTTTCATTTC
Statistics
Matches: 66, Mismatches: 2, Indels: 20
0.75 0.02 0.23
Matches are distributed among these distances:
14 21 0.32
15 2 0.03
16 4 0.06
17 4 0.06
18 4 0.06
19 31 0.47
ACGTcount: A:0.45, C:0.22, G:0.20, T:0.13
Consensus pattern (18 bp):
ATCGCAATGCGAAACAAA
Found at i:1285686 original size:33 final size:33
Alignment explanation
Indices: 1285596--1285675 Score: 151
Period size: 33 Copynumber: 2.4 Consensus size: 33
1285586 GGAAATGGCT
*
1285596 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1285629 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1285662 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
1285676 CACAAATCGC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1285704 original size:19 final size:19
Alignment explanation
Indices: 1285682--1285811 Score: 110
Period size: 19 Copynumber: 7.6 Consensus size: 19
1285672 GAAACACAAA
1285682 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1285701 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
*
1285717 TCG--TTGCGGTTTTCATT
1 TCGCATTGCGATTTTCATT
* *
1285734 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
1285750 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1285767 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
1285783 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1285800 TCGCATTGCGAT
1 TCGCATTGCGAT
1285812 AGCCATTTCC
Statistics
Matches: 88, Mismatches: 8, Indels: 30
0.70 0.06 0.24
Matches are distributed among these distances:
14 17 0.19
15 9 0.10
16 12 0.14
17 12 0.14
18 9 0.10
19 29 0.33
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1285730 original size:33 final size:33
Alignment explanation
Indices: 1285687--1285811 Score: 232
Period size: 33 Copynumber: 3.8 Consensus size: 33
1285677 ACAAATCGCA
1285687 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
* *
1285720 TTGCGGTTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1285753 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1285786 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1285812 AGCCATTTCC
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.11, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:1285756 original size:14 final size:14
Alignment explanation
Indices: 1285737--1285795 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
1285727 TTTCATTTCG
1285737 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1285751 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
1285768 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
1285784 CGTTGCGATTTT
1 CGTTGCGATTTT
1285796 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1285830 original size:20 final size:19
Alignment explanation
Indices: 1285796--1285850 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1285786 TTGCGATTTT
*
1285796 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1285815 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1285835 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
1285851 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1286401 original size:18 final size:18
Alignment explanation
Indices: 1286376--1286417 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1286366 GTGGAGGTTT
1286376 ATAG-TCTGGGTGAGGTG
1 ATAGCTCTGGGTGAGGTG
1286393 ATAGCTCTGGGTGAGGTG
1 ATAGCTCTGGGTGAGGTG
*
1286411 ATGGCTC
1 ATAGCTC
1286418 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.17, C:0.12, G:0.43, T:0.29
Consensus pattern (18 bp):
ATAGCTCTGGGTGAGGTG
Found at i:1287784 original size:20 final size:20
Alignment explanation
Indices: 1287736--1287794 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1287726 AATAGTTTCT
* *
1287736 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
1287756 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
1287776 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
1287795 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:1288084 original size:22 final size:22
Alignment explanation
Indices: 1288057--1288100 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1288047 GATGGAGATA
1288057 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1288079 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1288101 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1288317 original size:20 final size:20
Alignment explanation
Indices: 1288267--1288361 Score: 77
Period size: 20 Copynumber: 4.7 Consensus size: 20
1288257 CGCTTTGAAA
*
1288267 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
1288288 ATCTCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* *
1288308 ATCGCATTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
1288329 ATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1288349 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1288362 TTACTTATTC
Statistics
Matches: 57, Mismatches: 13, Indels: 9
0.72 0.16 0.11
Matches are distributed among these distances:
19 5 0.09
20 27 0.47
21 23 0.40
22 2 0.04
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1288327 original size:41 final size:41
Alignment explanation
Indices: 1288267--1288363 Score: 167
Period size: 41 Copynumber: 2.4 Consensus size: 41
1288257 CGCTTTGAAA
* *
1288267 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
1288308 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
1288349 ATCGCATTGCGATTT
1 ATCGCATTGCGATTT
1288364 ACTTATTCGC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.38
Consensus pattern (41 bp):
ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:1288400 original size:21 final size:21
Alignment explanation
Indices: 1288370--1288443 Score: 114
Period size: 21 Copynumber: 3.5 Consensus size: 21
1288360 ATTTACTTAT
*
1288370 TCGCATTGCGAATTGAGAAAA
1 TCGCAATGCGAATTGAGAAAA
1288391 TCGCAATGCGAATTGAGAAAA
1 TCGCAATGCGAATTGAGAAAA
1288412 TCGCAATGCGAAATTG-GAAAA
1 TCGCAATGCG-AATTGAGAAAA
*
1288433 TCGCATTGCGA
1 TCGCAATGCGA
1288444 TAGTAATAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
20 1 0.02
21 44 0.88
22 5 0.10
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTGAGAAAA
Found at i:1288471 original size:41 final size:41
Alignment explanation
Indices: 1288370--1288472 Score: 122
Period size: 42 Copynumber: 2.5 Consensus size: 41
1288360 ATTTACTTAT
1288370 TCGCATTGCGAATTGAGAAAATCGCAATGCGAATTGAGAAAA
1 TCGCATTGCGAATTG-GAAAATCGCAATGCGAATTGAGAAAA
* *
1288412 TCGCAATGCGAAATTGGAAAATCGCATTGCG-A-T-AGTAATAA
1 TCGCATTGCG-AATTGGAAAATCGCAATGCGAATTGAG-AA-AA
1288453 TCGCATTGCGAATCTGGAAA
1 TCGCATTGCGAAT-TGGAAA
1288473 CTGATTTGCG
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
39 2 0.04
40 6 0.11
41 18 0.33
42 23 0.43
43 5 0.09
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (41 bp):
TCGCATTGCGAATTGGAAAATCGCAATGCGAATTGAGAAAA
Found at i:1289558 original size:20 final size:20
Alignment explanation
Indices: 1289521--1289559 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1289511 ATAAACCCCC
*
1289521 AAAAAAACAAAGACAAAAAG
1 AAAAAAACAAAGAAAAAAAG
* *
1289541 AAAATAACAAGGAAAAAAA
1 AAAAAAACAAAGAAAAAAA
1289560 AGGAAGGAAG
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:0.79, C:0.08, G:0.10, T:0.03
Consensus pattern (20 bp):
AAAAAAACAAAGAAAAAAAG
Found at i:1292368 original size:14 final size:14
Alignment explanation
Indices: 1292332--1292378 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
1292322 AGGTTTCTAC
*
1292332 ATGAAGATG-ATAT
1 ATGAAGATGTTTAT
* *
1292345 GTGAAAATGTTTAT
1 ATGAAGATGTTTAT
1292359 ATGAAGATGTTTTAT
1 ATGAAGATG-TTTAT
1292374 ATGAA
1 ATGAA
1292379 AATAATCTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 7 0.26
14 10 0.37
15 10 0.37
ACGTcount: A:0.40, C:0.00, G:0.21, T:0.38
Consensus pattern (14 bp):
ATGAAGATGTTTAT
Found at i:1292587 original size:22 final size:22
Alignment explanation
Indices: 1292554--1292640 Score: 90
Period size: 22 Copynumber: 4.0 Consensus size: 22
1292544 TCGAGAGTTT
1292554 TATGTGGCACTTCGGTACAAACC
1 TATGTGGCACTTCGGTACAAA-C
*
1292577 TATGT-GCACTTCGGTGCAAATC
1 TATGTGGCACTTCGGTACAAA-C
* *
1292599 TATATGGTC-CTTCGGGACAAA-
1 TATGTGG-CACTTCGGTACAAAC
*
1292620 TATGTGGCACTTCGGTGCAAA
1 TATGTGGCACTTCGGTACAAA
1292641 TCATGTGAGC
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
20 1 0.02
21 16 0.30
22 19 0.36
23 16 0.30
24 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (22 bp):
TATGTGGCACTTCGGTACAAAC
Found at i:1292661 original size:43 final size:42
Alignment explanation
Indices: 1292558--1292642 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 42
1292548 GAGTTTTATG
*
1292558 TGGCACTTCGGTACAAACCTATGTGCACTTCGGTGCAAATCTATA
1 TGGC-CTTCGGGACAAA--TATGTGCACTTCGGTGCAAATCTATA
1292603 TGGTCCTTCGGGACAAATATGTGGCACTTCGGTGCAAATC
1 TGG-CCTTCGGGACAAATATGT-GCACTTCGGTGCAAATC
1292643 ATGTGAGCTG
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
43 5 0.14
44 17 0.46
45 14 0.38
46 1 0.03
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.28
Consensus pattern (42 bp):
TGGCCTTCGGGACAAATATGTGCACTTCGGTGCAAATCTATA
Found at i:1294571 original size:12 final size:12
Alignment explanation
Indices: 1294556--1294609 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
1294546 TTTCTCTAGT
1294556 TCTTTCCCTTGC
1 TCTTTCCCTTGC
*
1294568 TCTTGCCCTTGC
1 TCTTTCCCTTGC
1294580 -CTTTGCCCTTGC
1 TCTTT-CCCTTGC
* *
1294592 CCTTGCCCTTGAC
1 TCTTTCCCTTG-C
1294605 TCTTT
1 TCTTT
1294610 AAGAGGGGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
11 3 0.09
12 24 0.71
13 7 0.21
ACGTcount: A:0.02, C:0.41, G:0.13, T:0.44
Consensus pattern (12 bp):
TCTTTCCCTTGC
Found at i:1294578 original size:6 final size:6
Alignment explanation
Indices: 1294561--1294602 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
1294551 CTAGTTCTTT
* *
1294561 CCCTTG CTCTTG CCCTTG CCTTTG CCCTTG CCCTTG CCCTTG
1 CCCTTG CCCTTG CCCTTG CCCTTG CCCTTG CCCTTG CCCTTG
1294603 ACTCTTTAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.45, G:0.17, T:0.38
Consensus pattern (6 bp):
CCCTTG
Found at i:1294585 original size:18 final size:18
Alignment explanation
Indices: 1294561--1294608 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
1294551 CTAGTTCTTT
1294561 CCCTTGCTCTTGCCCTTG
1 CCCTTGCTCTTGCCCTTG
* *
1294579 CCTTTGCCCTTGCCCTTG
1 CCCTTGCTCTTGCCCTTG
1294597 CCCTTGACTCTT
1 CCCTTG-CTCTT
1294609 TAAGAGGGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.02, C:0.44, G:0.15, T:0.40
Consensus pattern (18 bp):
CCCTTGCTCTTGCCCTTG
Found at i:1295245 original size:3 final size:3
Alignment explanation
Indices: 1295237--1295273 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
1295227 AAGAATAAGA
*
1295237 AGG AGG AGG AGG AGG AGG TGG AGG AGG AGG AGG AGG A
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG A
1295274 AGGTGAGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.32, C:0.00, G:0.65, T:0.03
Consensus pattern (3 bp):
AGG
Found at i:1296304 original size:20 final size:20
Alignment explanation
Indices: 1296279--1296329 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
1296269 CACGAAATGT
1296279 AAGATTACCAATGGGAATAA
1 AAGATTACCAATGGGAATAA
1296299 AAGATTACCAATGGGAATAA
1 AAGATTACCAATGGGAATAA
1296319 AAGATTACCAA
1 AAGATTACCAA
1296330 CTAATAGGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.51, C:0.12, G:0.18, T:0.20
Consensus pattern (20 bp):
AAGATTACCAATGGGAATAA
Found at i:1297090 original size:2 final size:2
Alignment explanation
Indices: 1297083--1297158 Score: 83
Period size: 2 Copynumber: 41.0 Consensus size: 2
1297073 TTGTTCGGAT
* * *
1297083 TA TA TA TA -A T- TA -A TA TA -A AA TA TA TA -A AA TA T- TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1297119 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1297159 ATCGGGGCGG
Statistics
Matches: 64, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
1 6 0.09
2 58 0.91
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1297100 original size:9 final size:10
Alignment explanation
Indices: 1297081--1297160 Score: 55
Period size: 9 Copynumber: 8.2 Consensus size: 10
1297071 TTTTGTTCGG
1297081 ATTATATATA
1 ATTATATATA
1297091 ATTA-ATATA
1 ATTATATATA
*
1297100 A-AATATATA
1 ATTATATATA
*
1297109 A-AATAT-TA
1 ATTATATATA
*
1297117 TTTATATAT-
1 ATTATATATA
1297126 A-TATATATA
1 ATTATATATA
1297135 TATATATATATA
1 -AT-TATATATA
1297147 TATATATATATA
1 -AT-TATATATA
1297159 AT
1 AT
1297161 CGGGGCGGGG
Statistics
Matches: 59, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
8 10 0.17
9 21 0.36
10 6 0.10
11 2 0.03
12 20 0.34
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
ATTATATATA
Found at i:1302808 original size:12 final size:12
Alignment explanation
Indices: 1302787--1302853 Score: 57
Period size: 12 Copynumber: 5.6 Consensus size: 12
1302777 ATTACCTAAA
*
1302787 TTCTGTTTTGAT
1 TTCTGATTTGAT
1302799 TTCTGATTTGGA-
1 TTCTGATTT-GAT
1302811 TTCT-ATTCTGAT
1 TTCTGATT-TGAT
* * *
1302823 ATCTAATTTGAA
1 TTCTGATTTGAT
*
1302835 TTCTGTTTTGAT
1 TTCTGATTTGAT
1302847 TTCTGAT
1 TTCTGAT
1302854 ATCTCCGTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
11 5 0.12
12 33 0.77
13 5 0.12
ACGTcount: A:0.18, C:0.10, G:0.15, T:0.57
Consensus pattern (12 bp):
TTCTGATTTGAT
Found at i:1302813 original size:24 final size:24
Alignment explanation
Indices: 1302785--1302853 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 24
1302775 ACATTACCTA
1302785 AATTCTGTTTTGATTTCTGATTTG
1 AATTCTGTTTTGATTTCTGATTTG
* * * * *
1302809 GATTCTATTCTGATATCTAATTTG
1 AATTCTGTTTTGATTTCTGATTTG
1302833 AATTCTGTTTTGATTTCTGAT
1 AATTCTGTTTTGATTTCTGAT
1302854 ATCTCCGTTT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.20, C:0.10, G:0.14, T:0.55
Consensus pattern (24 bp):
AATTCTGTTTTGATTTCTGATTTG
Found at i:1315102 original size:21 final size:20
Alignment explanation
Indices: 1315058--1315103 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
1315048 TGTTGCATAT
*
1315058 ATAAAATAAAAACAATTATT
1 ATAAAATAAAAACAATTATA
1315078 ATAAAATAAATAACAAATTA-A
1 ATAAAATAAA-AAC-AATTATA
1315099 ATAAA
1 ATAAA
1315104 TATTATCTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 10 0.43
21 8 0.35
22 5 0.22
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (20 bp):
ATAAAATAAAAACAATTATA
Found at i:1318506 original size:30 final size:31
Alignment explanation
Indices: 1318472--1318554 Score: 91
Period size: 29 Copynumber: 2.7 Consensus size: 31
1318462 TAAGATCAAA
*
1318472 ATCAAAATTAAAATTTAATAATATAATCG-T
1 ATCAAAATTAAAATTTAATAATAAAATCGTT
* * *
1318502 ATC-AATTTAAAATTTAATTATAAAATTGTT
1 ATCAAAATTAAAATTTAATAATAAAATCGTT
*
1318532 AT-AAAATCTAAAATTAAATAATA
1 ATCAAAAT-TAAAATTTAATAATA
1318555 GATAATGCAG
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
29 21 0.49
30 9 0.21
31 13 0.30
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (31 bp):
ATCAAAATTAAAATTTAATAATAAAATCGTT
Found at i:1325334 original size:2 final size:2
Alignment explanation
Indices: 1325329--1325357 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1325319 TTTTATCGGG
1325329 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1325358 GTTTCCTTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1333048 original size:4 final size:4
Alignment explanation
Indices: 1333039--1333174 Score: 272
Period size: 4 Copynumber: 34.0 Consensus size: 4
1333029 CTCAGCAAAC
1333039 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1333087 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1333135 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1333175 GAGTAGAAAA
Statistics
Matches: 132, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 132 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:1340843 original size:35 final size:34
Alignment explanation
Indices: 1340758--1340844 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
1340748 ATTTGATATT
*
1340758 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
1340792 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
1340830 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
1340845 ACTAAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:1341096 original size:9 final size:9
Alignment explanation
Indices: 1341059--1341103 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
1341049 ACTCCTCGCT
1341059 GTCATCGTC
1 GTCATCGTC
* *
1341068 ATCGTCGTC
1 GTCATCGTC
* *
1341077 GTCACCATC
1 GTCATCGTC
1341086 GTCATCGTC
1 GTCATCGTC
1341095 GTCATCGTC
1 GTCATCGTC
1341104 ATTGTCGTCG
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.13, C:0.36, G:0.20, T:0.31
Consensus pattern (9 bp):
GTCATCGTC
Found at i:1341100 original size:15 final size:15
Alignment explanation
Indices: 1341063--1341112 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
1341053 CTCGCTGTCA
*
1341063 TCGTCATCGTCGTCG
1 TCGTCATCGTCATCG
**
1341078 TCACCATCGTCATCG
1 TCGTCATCGTCATCG
*
1341093 TCGTCATCGTCATTG
1 TCGTCATCGTCATCG
1341108 TCGTC
1 TCGTC
1341113 GTCCTGAGCA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.12, C:0.34, G:0.20, T:0.34
Consensus pattern (15 bp):
TCGTCATCGTCATCG
Found at i:1343147 original size:111 final size:110
Alignment explanation
Indices: 1343014--1343226 Score: 372
Period size: 111 Copynumber: 1.9 Consensus size: 110
1343004 ATTACAAAAA
* * *
1343014 TTAATTTTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
1343079 AATTAAAACGTTAAAATGTTATCGTATCAACAAAGTGTCGATATAT
66 AATT-AAACGTTAAAATGTTACCGTATCAACAAAGTGTCGATATAT
1343125 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
1343190 AATTAAACGTTAAAATGTTACCGTATCAGCAAAGTGT
66 AATTAAACGTTAAAATGTTACCGTATCAACAAAGTGT
1343227 AGAGATATAT
Statistics
Matches: 97, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
110 31 0.32
111 66 0.68
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.38
Consensus pattern (110 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAACGTTAAAATGTTACCGTATCAACAAAGTGTCGATATAT
Found at i:1348295 original size:127 final size:127
Alignment explanation
Indices: 1348065--1348344 Score: 479
Period size: 127 Copynumber: 2.2 Consensus size: 127
1348055 ATACTATTCA
* * *
1348065 CGTGAAGGCGCATTCCCGGGGGCGCGTCTTCCATTATTTTATCAGAGAATATGTTATCATTGCCC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTATCAGAGAATATATTATCATTGCCC
* *
1348130 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACATATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCCAGAAACTATTCATGTCAATACATATTATTCCTTAGGGGAC
*
1348192 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATATTATCATTGCCC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTATCAGAGAATATATTATCATTGCCC
* *
1348257 TATTATGTCACTTATGTCCCCCAGAAACTATTCGTGTCAATACCTATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCCAGAAACTATTCATGTCAATACATATTATTCCTTAGGGGAC
*
1348319 CGTGAAGGGGCGTTCCCGGGGGCGCG
1 CGTGAAGGCGCGTTCCCGGGGGCGCG
1348345 TGTTGAAAAC
Statistics
Matches: 144, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
127 144 1.00
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.31
Consensus pattern (127 bp):
CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTATCAGAGAATATATTATCATTGCCC
TATTATGTCACTTATGTCCCCCAGAAACTATTCATGTCAATACATATTATTCCTTAGGGGAC
Found at i:1356451 original size:24 final size:23
Alignment explanation
Indices: 1356401--1356474 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
1356391 GCTTCAACTT
* *
1356401 TTTGGATTGTTTGATTTTGTGAC
1 TTTGGATTGTTTGATGTTGTGAA
1356424 TTTGGATTTGTTTGGATGTT-TGAA
1 TTTGGA-TTGTTT-GATGTTGTGAA
*
1356448 TTTGTGGATTGATTGAT-TT-TGAA
1 -TT-TGGATTGTTTGATGTTGTGAA
1356471 TTTG
1 TTTG
1356475 TTTGGATTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
21 2 0.05
22 2 0.05
23 12 0.27
24 12 0.27
25 12 0.27
26 4 0.09
ACGTcount: A:0.16, C:0.01, G:0.27, T:0.55
Consensus pattern (23 bp):
TTTGGATTGTTTGATGTTGTGAA
Found at i:1358084 original size:127 final size:127
Alignment explanation
Indices: 1357909--1358141 Score: 396
Period size: 127 Copynumber: 1.8 Consensus size: 127
1357899 TAACTCAACA
1357909 GCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGTCACTTATGTCCCC
1 GCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGTCACTTATGTCCCC
*
1357974 C-GAGAACTATTTATGTCAATACATATTATTCCTTAAGGGACCGTGAAGGCGCGTTCCCGGGG
66 CGGA-AACTATTCATGTCAATACATATTATTCCTTAAGGGACCGTGAAGGCGCGTTCCCGGGG
* * * *
1358036 GCGCGCCTTTCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCATTTATGTCTCC
1 GCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGTCACTTATGTCCCC
*
1358101 CGGAAACTATTCATGTCAATACATATTATTCCTTAGGGGAC
66 CGGAAACTATTCATGTCAATACATATTATTCCTTAAGGGAC
1358142 TTTAAAGCGC
Statistics
Matches: 99, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
127 97 0.98
128 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (127 bp):
GCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGTCACTTATGTCCCC
CGGAAACTATTCATGTCAATACATATTATTCCTTAAGGGACCGTGAAGGCGCGTTCCCGGGG
Found at i:1358446 original size:14 final size:14
Alignment explanation
Indices: 1358427--1358456 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1358417 GATAAGTTGA
*
1358427 TTTTAATGTATATG
1 TTTTAATATATATG
1358441 TTTTAATATATATG
1 TTTTAATATATATG
1358455 TT
1 TT
1358457 AATGATAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (14 bp):
TTTTAATATATATG
Found at i:1358609 original size:34 final size:33
Alignment explanation
Indices: 1358571--1358665 Score: 101
Period size: 28 Copynumber: 3.0 Consensus size: 33
1358561 GAATTTAATG
1358571 TTAAATTTTGAATACTATAATTTATATTTTAAAT
1 TTAAATTTTGAATACTATAATTT-TATTTTAAAT
* * *
1358605 TTAAA-TTT-CA-A--ATAATATTATTTTAATT
1 TTAAATTTTGAATACTATAATTTTATTTTAAAT
*
1358633 TTAAATTTCGAATACTATAATTTGTATTTTAAA
1 TTAAATTTTGAATACTATAATTT-TATTTTAAA
1358666 AACATTTATT
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
28 14 0.29
29 8 0.17
30 1 0.02
31 2 0.04
32 1 0.02
33 9 0.19
34 13 0.27
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (33 bp):
TTAAATTTTGAATACTATAATTTTATTTTAAAT
Found at i:1359217 original size:21 final size:20
Alignment explanation
Indices: 1359189--1359237 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
1359179 GGTATAAAAC
**
1359189 CCTGCGGGCTAGGCCTGTAA
1 CCTGCGGGCTAGGAATGTAA
1359209 CCTGACGGGCTAGGAATGTAA
1 CCTG-CGGGCTAGGAATGTAA
1359230 CCTTGCGG
1 CC-TGCGG
1359238 AGATGACATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 4 0.16
21 19 0.76
22 2 0.08
ACGTcount: A:0.18, C:0.27, G:0.35, T:0.20
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:1359276 original size:42 final size:42
Alignment explanation
Indices: 1359230--1359314 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
1359220 AGGAATGTAA
* * *
1359230 CCTTGCGGAGATGACATATGAACTGGTGGGCTTGGCATATAC
1 CCTTGAGGAGATGACATATGAACTGGAGGGCTGGGCATATAC
* * * *
1359272 CCTTGAGGAGATGGCATCTGAAGTGGAGGGCTGGGCATGTAC
1 CCTTGAGGAGATGACATATGAACTGGAGGGCTGGGCATATAC
1359314 C
1 C
1359315 ATTGTGGCAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.24
Consensus pattern (42 bp):
CCTTGAGGAGATGACATATGAACTGGAGGGCTGGGCATATAC
Found at i:1361957 original size:35 final size:35
Alignment explanation
Indices: 1361910--1361995 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
1361900 AAAACAGTCA
* * *
1361910 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * *
1361945 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
*
1361980 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
1361996 ATACTTCAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:1361989 original size:21 final size:21
Alignment explanation
Indices: 1361964--1362006 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1361954 TTCTAAACCC
1361964 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
1361985 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
1362006 T
1 T
1362007 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:1362161 original size:16 final size:18
Alignment explanation
Indices: 1362129--1362162 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1362119 TATTAATGTA
1362129 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
1362147 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
1362163 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:1362831 original size:130 final size:129
Alignment explanation
Indices: 1362628--1362874 Score: 404
Period size: 130 Copynumber: 1.9 Consensus size: 129
1362618 AATTTTCTTC
* * *
1362628 TAATTAGGAGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
*
1362693 CATGATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CATAATTAAATGATTAATTTATTAAA-TTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
1362758 TAATTAGGTGGTAACACGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
*
1362823 CCTAATTAAATGATTAATTTATTAAATTTATTTAATTTAGGACCAAATTGAT
66 CATAATTAAATGATTAATTTATTAAATTTATTTAATTTAGGACCAAATTGAT
1362875 TATATAAATA
Statistics
Matches: 108, Mismatches: 9, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
129 26 0.24
130 82 0.76
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (129 bp):
TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CATAATTAAATGATTAATTTATTAAATTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:1363529 original size:29 final size:30
Alignment explanation
Indices: 1363477--1363544 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
1363467 GCAAACAGAA
* *
1363477 TAAATGTTGGGGGACTGTATTGCAAG-TTT
1 TAAATGTTGGGGGACTGAAATGCAAGCTTT
1363506 TAAATGTTGGGGGACCT-AAATGCAAGCTTT
1 TAAATGTTGGGGGA-CTGAAATGCAAGCTTT
1363536 TGAAATGTT
1 T-AAATGTT
1363545 CAGTGACCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 21 0.62
30 6 0.18
31 7 0.21
ACGTcount: A:0.28, C:0.09, G:0.28, T:0.35
Consensus pattern (30 bp):
TAAATGTTGGGGGACTGAAATGCAAGCTTT
Found at i:1364061 original size:2 final size:2
Alignment explanation
Indices: 1364054--1364128 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
1364044 TTTCAAAAAG
1364054 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1364096 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1364129 CAGAGAGAGA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1368421 original size:2 final size:2
Alignment explanation
Indices: 1368414--1368473 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
1368404 GACATTTCAA
1368414 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1368456 AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT A
1368474 GGATAAATAT
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 56 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1377273 original size:15 final size:15
Alignment explanation
Indices: 1377230--1377278 Score: 57
Period size: 14 Copynumber: 3.2 Consensus size: 15
1377220 TTTAATTTTT
1377230 TAAATTTAATTACT-
1 TAAATTTAATTACTC
1377244 TAAATTTCAAATTACTCC
1 TAAATTT--AATTACT-C
1377262 T-AATTTAATTACTC
1 TAAATTTAATTACTC
1377276 TAA
1 TAA
1377279 CTTTCAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
14 9 0.30
15 8 0.27
16 7 0.23
17 5 0.17
18 1 0.03
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (15 bp):
TAAATTTAATTACTC
Found at i:1377930 original size:31 final size:34
Alignment explanation
Indices: 1377890--1377956 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 34
1377880 TTAGTTAAGT
*
1377890 AAAGATTAAATTGA-TAAATT-TTTTTAAATATA
1 AAAGATTAAATTGATTAAATTATTTTGAAATATA
* *
1377922 AAAG-TTAAATTTATTAAATTATTTTGAATTATA
1 AAAGATTAAATTGATTAAATTATTTTGAAATATA
1377955 AA
1 AA
1377957 CAAACTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
31 8 0.27
32 10 0.33
33 12 0.40
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (34 bp):
AAAGATTAAATTGATTAAATTATTTTGAAATATA
Found at i:1379420 original size:22 final size:22
Alignment explanation
Indices: 1379392--1379470 Score: 83
Period size: 22 Copynumber: 3.7 Consensus size: 22
1379382 GAATTTACGT
*
1379392 TTCGCAACACGAATTTGTCAAA
1 TTCGCAACTCGAATTTGTCAAA
* *
1379414 TTCGCAATTC-AGTTT-TCAAA
1 TTCGCAACTCGAATTTGTCAAA
* * *
1379434 TTCGCAACTCGAATTCGCCAAT
1 TTCGCAACTCGAATTTGTCAAA
1379456 TTCGCAACTC-AATTT
1 TTCGCAACTCGAATTT
1379471 TGACCCAGAG
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
20 14 0.30
21 11 0.24
22 21 0.46
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.33
Consensus pattern (22 bp):
TTCGCAACTCGAATTTGTCAAA
Found at i:1379438 original size:42 final size:42
Alignment explanation
Indices: 1379392--1379471 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
1379382 GAATTTACGT
* * * *
1379392 TTCGCAACACGAATTTGTCAAATTCGCAATTCAGTTTTCAAA
1 TTCGCAACACGAATTCGCCAAATTCGCAACTCAATTTTCAAA
* *
1379434 TTCGCAACTCGAATTCGCCAATTTCGCAACTCAATTTT
1 TTCGCAACACGAATTCGCCAAATTCGCAACTCAATTTT
1379472 GACCCAGAGA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (42 bp):
TTCGCAACACGAATTCGCCAAATTCGCAACTCAATTTTCAAA
Found at i:1380198 original size:413 final size:405
Alignment explanation
Indices: 1379434--1380268 Score: 1402
Period size: 413 Copynumber: 2.0 Consensus size: 405
1379424 AGTTTTCAAA
* *
1379434 TTCGCAACTCGAATTCGCCAATTTCGCAACTCAATTTTGACCCAGAGATCACTCCAGGCAAGACC
1 TTCGCAACTCGAATTCGCCAATTTCGCAACTCAATTTTGACCCAGAGATCACTCCAGGAAAGACA
1379499 TGTTTTCCAGGTCCGTGCTTCGGACGCCGACGACGAATGAGGCCCAGACAAGGAGGAGCCGGTTG
66 TGTTTTCCAGGTCCGTGCTTCGGACGCCGACGACGAATGAGGCCCAGACAAGGAGGAGCCGGTTG
* *
1379564 TGATAGAAAGTCCTGGAGTGGTCGTGGCAGAAGAAGCCTGACCCAGAGGTGGAAATCCAGAGCTT
131 TGATAGAAAGTCCTGGAGTGGTCGAGGCAGAAGAAGCCTGACCAAGAGGTGGAAATCCAGAGCTT
1379629 GAAGAAAGCTTTGGGGGATTCGTTTTATGGGACTGATCGTGGATTGAAAGCTAGTAGTGAGACCA
196 GAAGAAAGCTTTGGGGGATTCGTTTTATGGGACTGATCGTGGATTGAAAGCTAGTAGTGAGACCA
*
1379694 GGGCTGAGATTGTTGAGCTTATAACTCAGCTCGAGGCGAAGAACCCTACTCCAGCACCCACCGAG
261 GGGCTGAGATTGTTGAGCTTATAACTCAGCTCGAGGCGAAGAACCCCACTCCAGCACCCACCGAG
* * *
1379759 GCGTTGCCTCTACTCAACGGCAAATGGATTCTCGCGTAAGTTCGTTGCCTCTGCCCATCGATCTA
326 GCGTTGCCTCTACTCAACGACAAATGGATTCTCGCGTAAGTTCGTTACCTCTGCCCACCGATCTA
1379824 AACAAGAATTTACAT
391 AACAAGAATTTACAT
*
1379839 TTCGCAACTCGAATTCGCTAATTTCGCAACTCAATTTTGACCCAGAGATCACTCCAGGAAAGACA
1 TTCGCAACTCGAATTCGCCAATTTCGCAACTCAATTTTGACCCAGAGATCACTCCAGGAAAGACA
* * *
1379904 TGTTTTCCAGGTCTGTGCTTCGGACGCCGACGATGAATGGGGCCCAGACAAGGAGGAGCCGGTTG
66 TGTTTTCCAGGTCCGTGCTTCGGACGCCGACGACGAATGAGGCCCAGACAAGGAGGAGCCGGTTG
* *
1379969 TGATAGAGAGTCCTGGAGTGGCTATGGCAGAAGAAG-AGAAGAAGCCTGACCAAGTGGTGGAAAT
131 TGATAGAAAGTCCTGGAGTGG---T--C-G-AG--GCAGAAGAAGCCTGACCAAGAGGTGGAAAT
*
1380033 CCAGAGCTTGAAGAAAGCTTTGGTGGATTCGTTTTATGGGACTGATCGTGGATTGAAAGCTAGTA
187 CCAGAGCTTGAAGAAAGCTTTGGGGGATTCGTTTTATGGGACTGATCGTGGATTGAAAGCTAGTA
* *
1380098 GTGAGACCAGGGTTGAGATTGTTGAGCTTATAACTCAGCTCGAGGCGAAGAACCCCACTTCAGCA
252 GTGAGACCAGGGCTGAGATTGTTGAGCTTATAACTCAGCTCGAGGCGAAGAACCCCACTCCAGCA
* *
1380163 CCCACCGAGGCGTTGCCTCTGCTCAACGACAAATGGATTCTCGCGTAAGTTCGTTACCTCTGCCT
317 CCCACCGAGGCGTTGCCTCTACTCAACGACAAATGGATTCTCGCGTAAGTTCGTTACCTCTGCCC
*
1380228 ACCGGTCTAAACAAGAATTTACAT
382 ACCGATCTAAACAAGAATTTACAT
1380252 TTCGCAACTCGAATTCG
1 TTCGCAACTCGAATTCG
1380269 AAAATTGAGT
Statistics
Matches: 401, Mismatches: 20, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
405 144 0.36
408 1 0.00
410 1 0.00
411 1 0.00
412 1 0.00
413 252 0.63
414 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (405 bp):
TTCGCAACTCGAATTCGCCAATTTCGCAACTCAATTTTGACCCAGAGATCACTCCAGGAAAGACA
TGTTTTCCAGGTCCGTGCTTCGGACGCCGACGACGAATGAGGCCCAGACAAGGAGGAGCCGGTTG
TGATAGAAAGTCCTGGAGTGGTCGAGGCAGAAGAAGCCTGACCAAGAGGTGGAAATCCAGAGCTT
GAAGAAAGCTTTGGGGGATTCGTTTTATGGGACTGATCGTGGATTGAAAGCTAGTAGTGAGACCA
GGGCTGAGATTGTTGAGCTTATAACTCAGCTCGAGGCGAAGAACCCCACTCCAGCACCCACCGAG
GCGTTGCCTCTACTCAACGACAAATGGATTCTCGCGTAAGTTCGTTACCTCTGCCCACCGATCTA
AACAAGAATTTACAT
Found at i:1380785 original size:11 final size:11
Alignment explanation
Indices: 1380769--1380795 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1380759 GAATTTATCC
1380769 AAAAAGAAAAG
1 AAAAAGAAAAG
1380780 AAAAAGAAAAG
1 AAAAAGAAAAG
1380791 AAAAA
1 AAAAA
1380796 CACACATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:1391417 original size:20 final size:20
Alignment explanation
Indices: 1391389--1391437 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1391379 GCGAATTTGT
1391389 AAATT-GCAACACAAAAGTC
1 AAATTCGCAACACAAAAGTC
* *
1391408 AAATTCGCAACACATAAGTT
1 AAATTCGCAACACAAAAGTC
1391428 AAATTCGCAA
1 AAATTCGCAA
1391438 AGCGCGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 5 0.19
20 22 0.81
ACGTcount: A:0.49, C:0.20, G:0.10, T:0.20
Consensus pattern (20 bp):
AAATTCGCAACACAAAAGTC
Found at i:1391610 original size:22 final size:22
Alignment explanation
Indices: 1391585--1391638 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
1391575 TCACTCTCTA
* *
1391585 CGACGACATCAGTTCCCATCTC
1 CGACGAAATCAGTCCCCATCTC
*
1391607 CGACGAAATCCGTCCCCATCTC
1 CGACGAAATCAGTCCCCATCTC
*
1391629 CGACAAAATC
1 CGACGAAATC
1391639 CGTCTATCTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.28, C:0.41, G:0.13, T:0.19
Consensus pattern (22 bp):
CGACGAAATCAGTCCCCATCTC
Found at i:1391639 original size:22 final size:22
Alignment explanation
Indices: 1391599--1391642 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1391589 GACATCAGTT
*
1391599 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
1391621 CCCATCTCCGACAAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
1391643 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.45, G:0.11, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACAAAATCCGTC
Found at i:1393741 original size:42 final size:41
Alignment explanation
Indices: 1393694--1393793 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 41
1393684 GTTAGGGGAG
* *
1393694 TTACGTGATGAGGTCGGTGCTTTGCGTCATGAGGT-CGGTACT
1 TTACGTGATGAGGT-GGTGCATGGCGTCATGAGGTACGGT-CT
* ** *
1393736 TTACGTGAAGACAATGGTGCATGGCGTGATGAGGTACGGTCT
1 TTACGTGATGA-GGTGGTGCATGGCGTCATGAGGTACGGTCT
*
1393778 TTACGTGGTGAGGTGG
1 TTACGTGATGAGGTGG
1393794 ATGTTTTACG
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
41 3 0.07
42 38 0.83
43 5 0.11
ACGTcount: A:0.18, C:0.14, G:0.38, T:0.30
Consensus pattern (41 bp):
TTACGTGATGAGGTGGTGCATGGCGTCATGAGGTACGGTCT
Found at i:1394198 original size:42 final size:42
Alignment explanation
Indices: 1394151--1394269 Score: 132
Period size: 42 Copynumber: 2.8 Consensus size: 42
1394141 AATTCACATG
* * * * *
1394151 TCATCGTTCAAGAGGCATCTCCTATCGTTCAAGAGGCCATTC
1 TCATCGTTCAAGAGGCACCTCCCACCATTCAAGAGGCCACTC
* * *
1394193 TCATCGTTCAAGAGGCCCCTCCCACCATTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCACCTCCCACCATTCAAGAGGCCACTC
* *
1394235 TCATCGTTCAAGAGGTC-CATCCCACCGTTCAAGAG
1 TCATCGTTCAAGAGG-CACCTCCCACCATTCAAGAG
1394270 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
42 65 0.98
43 1 0.02
ACGTcount: A:0.24, C:0.34, G:0.19, T:0.24
Consensus pattern (42 bp):
TCATCGTTCAAGAGGCACCTCCCACCATTCAAGAGGCCACTC
Found at i:1394209 original size:21 final size:20
Alignment explanation
Indices: 1394151--1394269 Score: 105
Period size: 21 Copynumber: 5.7 Consensus size: 20
1394141 AATTCACATG
1394151 TCATCGTTCAAGAGG-CATC
1 TCATCGTTCAAGAGGCCATC
1394170 TCCTATCGTTCAAGAGGCCATTC
1 T-C-ATCGTTCAAGAGGCCA-TC
*
1394193 TCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGG-CCATC
* * * * *
1394214 CCACCATTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGG-CCATC
1394235 TCATCGTTCAAGAGGTCCATC
1 TCATCGTTCAAGAGG-CCATC
* *
1394256 CCACCGTTCAAGAG
1 TCATCGTTCAAGAG
1394270 CCCGATTCAC
Statistics
Matches: 82, Mismatches: 13, Indels: 8
0.80 0.13 0.08
Matches are distributed among these distances:
19 1 0.01
20 1 0.01
21 72 0.88
22 5 0.06
23 3 0.04
ACGTcount: A:0.24, C:0.34, G:0.19, T:0.24
Consensus pattern (20 bp):
TCATCGTTCAAGAGGCCATC
Found at i:1395722 original size:64 final size:64
Alignment explanation
Indices: 1395612--1395769 Score: 264
Period size: 64 Copynumber: 2.5 Consensus size: 64
1395602 TTAATTGAAT
* *
1395612 TTTACATTGATTTGTAAAAGTTGATTTGTTTAATTGATTAGGAAATAATAATTATTTTTTTCTTG
1 TTTA-ATTGATTTGTAAAAGTTGATTTGTTTAATTGATTAGGAAATAAGAATTATTTTTTGCTTG
*
1395677 TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGT-GTAAATAAGAATTATTTTTTGCTTG
1 TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGAT-TAGGAAATAAGAATTATTTTTTGCTTG
1395741 TTTAATTGATTTGTAAAAGTTGATTTGTT
1 TTTAATTGATTTGTAAAAGTTGATTTGTT
1395770 GTTTTAAATT
Statistics
Matches: 89, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
64 84 0.94
65 5 0.06
ACGTcount: A:0.30, C:0.02, G:0.16, T:0.53
Consensus pattern (64 bp):
TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATTAGGAAATAAGAATTATTTTTTGCTTG
Found at i:1398460 original size:24 final size:24
Alignment explanation
Indices: 1398393--1398446 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
1398383 CTGAAACATC
*
1398393 ATCAAAATCC-GAGTATTGACCAAG
1 ATCAAAGTCCAGA-TATTGACCAAG
* *
1398417 ATCAAAGTCCAGGTACTGACCAAG
1 ATCAAAGTCCAGATATTGACCAAG
1398441 ATCAAA
1 ATCAAA
1398447 TTTCGAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.43, C:0.22, G:0.17, T:0.19
Consensus pattern (24 bp):
ATCAAAGTCCAGATATTGACCAAG
Found at i:1399416 original size:20 final size:20
Alignment explanation
Indices: 1399380--1399462 Score: 96
Period size: 20 Copynumber: 4.2 Consensus size: 20
1399370 CCTGTTGCAA
* * *
1399380 AATT-AAAATTCGTGTTGTG
1 AATTCAAAAATCGAGTTGCG
1399399 AATTCAAAAATCGAGTTGCG
1 AATTCAAAAATCGAGTTGCG
* * *
1399419 AAGTCGAAAATCGAGTTACG
1 AATTCAAAAATCGAGTTGCG
*
1399439 AATTCAGAAATCGAGTTGCG
1 AATTCAAAAATCGAGTTGCG
1399459 AATT
1 AATT
1399463 TGAAATTCAG
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
19 4 0.08
20 49 0.92
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (20 bp):
AATTCAAAAATCGAGTTGCG
Found at i:1399498 original size:20 final size:20
Alignment explanation
Indices: 1399473--1399517 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1399463 TGAAATTCAG
*
1399473 TGCGATTTACAGATTCGCAT
1 TGCGATTTACAAATTCGCAT
*
1399493 TGCGATTTACAAATTCGCGT
1 TGCGATTTACAAATTCGCAT
1399513 TGCGA
1 TGCGA
1399518 ATTTGGAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (20 bp):
TGCGATTTACAAATTCGCAT
Found at i:1401157 original size:19 final size:19
Alignment explanation
Indices: 1401133--1401170 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1401123 GAATTTAAAG
*
1401133 TTAGTAATAGTAGTAATTA
1 TTAGTAATACTAGTAATTA
1401152 TTAGTAATACTAGTAATTA
1 TTAGTAATACTAGTAATTA
1401171 CTAAGTGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.13, T:0.42
Consensus pattern (19 bp):
TTAGTAATACTAGTAATTA
Found at i:1405106 original size:30 final size:30
Alignment explanation
Indices: 1405070--1405142 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
1405060 TCCGAAGAAC
1405070 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1405100 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
1405130 CTGTCCATAGGTC
1 CTATCCAGAGGTC
1405143 CCGAAGAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1405159 original size:30 final size:30
Alignment explanation
Indices: 1405116--1405209 Score: 80
Period size: 31 Copynumber: 3.1 Consensus size: 30
1405106 AGAGGTCATA
* * *
1405116 AAGATCCTCGGTAACTGTCCATAGGTCCCG
1 AAGAACCTAGGTAACTGTCCATATGTCCCG
* * * *
1405146 AAGAACCTAGGTAAACTATTCATATGTTCCT
1 AAGAACCTAGGT-AACTGTCCATATGTCCCG
* * *
1405177 TAGAACATAGGTATACTGTCCATATGTCTCG
1 AAGAACCTAGGTA-ACTGTCCATATGTCCCG
1405208 AA
1 AA
1405210 AGACATAGGT
Statistics
Matches: 47, Mismatches: 15, Indels: 3
0.72 0.23 0.05
Matches are distributed among these distances:
30 11 0.23
31 36 0.77
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (30 bp):
AAGAACCTAGGTAACTGTCCATATGTCCCG
Found at i:1406005 original size:21 final size:21
Alignment explanation
Indices: 1405979--1406023 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1405969 GATTTCTGGG
* *
1405979 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1406000 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1406021 CAA
1 CAA
1406024 ACGAACAAAA
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1407887 original size:103 final size:103
Alignment explanation
Indices: 1407703--1407928 Score: 391
Period size: 103 Copynumber: 2.2 Consensus size: 103
1407693 GTCAAGGGTC
1407703 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
1407768 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
* *
1407806 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
1407871 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
1407909 TATGTGGTCCTT-ATGGACAT
1 TATGTGGTCCTTCA-GGACAT
1407929 TATTATATGG
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
103 115 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:1407967 original size:23 final size:23
Alignment explanation
Indices: 1407937--1407994 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
1407927 ATTATTATAT
1407937 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
1407960 GGCACTACGGTGCAATTCTATGT
1 GGCACTACGGTGCAATTCTACGC
*
1407983 GGCACTTCGGTG
1 GGCACTACGGTG
1407995 TATTTACATG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.19, C:0.26, G:0.29, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1416431 original size:22 final size:22
Alignment explanation
Indices: 1416401--1416459 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 22
1416391 TATTGATAGA
1416401 TATATTTTTTTGTATTTATTCTC
1 TATA-TTTTTTGTATTTATTCTC
* *
1416424 TATA--TTTTGTATTAATTTTC
1 TATATTTTTTGTATTTATTCTC
1416444 TATATCTTTTT-TATTT
1 TATAT-TTTTTGTATTT
1416460 TCGAATTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
20 18 0.60
22 4 0.13
23 8 0.27
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.69
Consensus pattern (22 bp):
TATATTTTTTGTATTTATTCTC
Found at i:1416433 original size:20 final size:20
Alignment explanation
Indices: 1416408--1416448 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1416398 AGATATATTT
*
1416408 TTTTGTATTTATTCTCTATA
1 TTTTGTATTAATTCTCTATA
*
1416428 TTTTGTATTAATTTTCTATA
1 TTTTGTATTAATTCTCTATA
1416448 T
1 T
1416449 CTTTTTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.22, C:0.07, G:0.05, T:0.66
Consensus pattern (20 bp):
TTTTGTATTAATTCTCTATA
Found at i:1416476 original size:29 final size:29
Alignment explanation
Indices: 1416426--1416483 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
1416416 TTATTCTCTA
* * *
1416426 TATTTTGTATTAATTTTCTATATCTTTTT
1 TATTTTGAATTAATATTCTATATATTTTT
1416455 TATTTTCGAATTAATATT-TATATATTTTT
1 TATTTT-GAATTAATATTCTATATATTTTT
1416484 ATCCAAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (29 bp):
TATTTTGAATTAATATTCTATATATTTTT
Found at i:1416775 original size:21 final size:22
Alignment explanation
Indices: 1416751--1416792 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1416741 TACCCTTTTA
*
1416751 AATAAAAT-AAAATGGGCAACT
1 AATAAAATGAAAAGGGGCAACT
*
1416772 AATAATATGAAAAGGGGCAAC
1 AATAAAATGAAAAGGGGCAAC
1416793 GACAATAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.55, C:0.10, G:0.19, T:0.17
Consensus pattern (22 bp):
AATAAAATGAAAAGGGGCAACT
Found at i:1428541 original size:183 final size:183
Alignment explanation
Indices: 1428236--1428600 Score: 581
Period size: 183 Copynumber: 2.0 Consensus size: 183
1428226 AATTAAATGT
*
1428236 TTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAATTTAAG
1 TTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTAAG
* * *
1428301 ATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAATTTATTTGATGTTAAATTATTAATT
66 ATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAATT
* * *
1428366 GGGTTTTAAATGGTGTGGGCTGAGCCCATATGTTATATATAATATTTTTAATA
131 AGGTTTTAAATGGTGTGGGCTGAACCCATATGTTATATATAATATATTTAATA
* *
1428419 TTTTTAATT-AAAAAATGGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTTA
1 TTTTTAATTCAAAAAA-AGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTAA
*
1428483 TATACA-TTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAA
65 GATA-ATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAA
* * *
1428547 TTAGGTTTTAAATGGTTTGGGTTGAACTCATATGTTATATATAATATATTTAAT
129 TTAGGTTTTAAATGGTGTGGGCTGAACCCATATGTTATATATAATATATTTAAT
1428601 GTTTAAAATT
Statistics
Matches: 167, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
182 6 0.04
183 160 0.96
184 1 0.01
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.47
Consensus pattern (183 bp):
TTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTAAG
ATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAATT
AGGTTTTAAATGGTGTGGGCTGAACCCATATGTTATATATAATATATTTAATA
Found at i:1438405 original size:15 final size:15
Alignment explanation
Indices: 1438381--1438423 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1438371 AAATTATTAA
*
1438381 ATTAATTTATAAAAC
1 ATTAAATTATAAAAC
* *
1438396 ATTAAATTATAGAAT
1 ATTAAATTATAAAAC
1438411 ATTAAATGTATAA
1 ATTAAAT-TATAA
1438424 TTATGAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (15 bp):
ATTAAATTATAAAAC
Found at i:1438437 original size:23 final size:23
Alignment explanation
Indices: 1438411--1438473 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
1438401 ATTATAGAAT
1438411 ATTAAATGTATAATTATGAA-TTA
1 ATTAAATGTATAATTAT-AATTTA
** * *
1438434 ATTAAAAATTTAAATATAATTTA
1 ATTAAATGTATAATTATAATTTA
1438457 ATTAAAATGTATAATTA
1 ATT-AAATGTATAATTA
1438474 CCTAACTATT
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
22 2 0.07
23 19 0.63
24 9 0.30
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (23 bp):
ATTAAATGTATAATTATAATTTA
Found at i:1443067 original size:15 final size:14
Alignment explanation
Indices: 1443027--1443075 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
1443017 CAATGTGATT
* *
1443027 TGTGAATATGCTTT
1 TGTGAAAATGCTTA
*
1443041 TATGAAAATGCTTGA
1 TGTGAAAATGCTT-A
*
1443056 TGTGAAAGTGCTTA
1 TGTGAAAATGCTTA
1443070 TGTGAA
1 TGTGAA
1443076 CAAGATATAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
14 18 0.62
15 11 0.38
ACGTcount: A:0.31, C:0.06, G:0.24, T:0.39
Consensus pattern (14 bp):
TGTGAAAATGCTTA
Found at i:1443072 original size:14 final size:15
Alignment explanation
Indices: 1443043--1443075 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1443033 TATGCTTTTA
1443043 TGAAAATGCTTGATG
1 TGAAAATGCTTGATG
*
1443058 TGAAAGTGCTT-ATG
1 TGAAAATGCTTGATG
1443072 TGAA
1 TGAA
1443076 CAAGATATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.33
Consensus pattern (15 bp):
TGAAAATGCTTGATG
Found at i:1443232 original size:21 final size:21
Alignment explanation
Indices: 1443183--1443260 Score: 104
Period size: 21 Copynumber: 3.6 Consensus size: 21
1443173 TCGAGGGTCT
1443183 TATGTGGTCCTTCGGGACAAA
1 TATGTGGTCCTTCGGGACAAA
1443204 CCTATGTGGTCCTTCGGGACAAA
1 --TATGTGGTCCTTCGGGACAAA
*
1443227 TATGTGG-CACTTCGAGACAAA
1 TATGTGGTC-CTTCGGGACAAA
*
1443248 TATGTGGTACTTC
1 TATGTGGTCCTTC
1443261 AGTGCAAATT
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
20 1 0.02
21 29 0.57
23 21 0.41
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (21 bp):
TATGTGGTCCTTCGGGACAAA
Found at i:1443268 original size:21 final size:20
Alignment explanation
Indices: 1443183--1443274 Score: 67
Period size: 21 Copynumber: 4.2 Consensus size: 20
1443173 TCGAGGGTCT
* *
1443183 TATGTGGTCCTTCGGGACAAA
1 TATGTGGTACTTCAGG-CAAA
* *
1443204 CCTATGTGGTCCTTCGGGACAAA
1 --TATGTGGTACTTCAGG-CAAA
* *
1443227 TATGTGGCACTTCGAGACAAA
1 TATGTGGTACTTC-AGGCAAA
1443248 TATGTGGTACTTCAGTGCAAA
1 TATGTGGTACTTCAG-GCAAA
1443269 TTATGT
1 -TATGT
1443275 AAGCTATGGT
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
20 2 0.03
21 31 0.52
22 6 0.10
23 21 0.35
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.30
Consensus pattern (20 bp):
TATGTGGTACTTCAGGCAAA
Found at i:1443269 original size:42 final size:44
Alignment explanation
Indices: 1443182--1443274 Score: 104
Period size: 44 Copynumber: 2.1 Consensus size: 44
1443172 GTCGAGGGTC
* *
1443182 TTATGTGGTCCTTCGGGACAAACCTATGTGGTCCTTCGGGACAAA
1 TTATGTGGTCCTTCGAGACAAA-CTATGTGGTACTTCGGGACAAA
*
1443227 -TATGTGG-CACTTCGAGACAAA-TATGTGGTACTTCAGTG-CAAA
1 TTATGTGGTC-CTTCGAGACAAACTATGTGGTACTTC-GGGACAAA
1443269 TTATGT
1 TTATGT
1443275 AAGCTATGGT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
42 16 0.38
43 8 0.19
44 18 0.43
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (44 bp):
TTATGTGGTCCTTCGAGACAAACTATGTGGTACTTCGGGACAAA
Found at i:1451878 original size:34 final size:34
Alignment explanation
Indices: 1451813--1451880 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
1451803 GTATATAGTA
* * * *
1451813 TAATTATCATATATTTTCATGTTACTCTTCAGCC
1 TAATAATCATATAATTTCATGCTAATCTTCAGCC
*
1451847 TAATAATCATATAATTTCATGCTAATTTTCAGCC
1 TAATAATCATATAATTTCATGCTAATCTTCAGCC
1451881 AAGGGTTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (34 bp):
TAATAATCATATAATTTCATGCTAATCTTCAGCC
Found at i:1456226 original size:2 final size:2
Alignment explanation
Indices: 1456219--1456243 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1456209 ACAGTTCTTT
1456219 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1456244 TTTATACGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1462015 original size:33 final size:33
Alignment explanation
Indices: 1461978--1462045 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
1461968 TGGATGTTGT
1461978 TTATGCTTTGAAAATGCAGAGCCAGAAGTTTGG
1 TTATGCTTTGAAAATGCAGAGCCAGAAGTTTGG
1462011 TTATGCTTTGAAAATGCAGAGCCAGAAGTTTGG
1 TTATGCTTTGAAAATGCAGAGCCAGAAGTTTGG
1462044 TT
1 TT
1462046 CTTTTGCAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.32
Consensus pattern (33 bp):
TTATGCTTTGAAAATGCAGAGCCAGAAGTTTGG
Found at i:1474920 original size:21 final size:20
Alignment explanation
Indices: 1474894--1474933 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
1474884 TAAAGCAGGG
1474894 CATGATAATACATGGTATTAT
1 CATGATAATACAT-GTATTAT
1474915 CATGATAATACATGTATTA
1 CATGATAATACATGTATTA
1474934 AACCAAAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (20 bp):
CATGATAATACATGTATTAT
Found at i:1477938 original size:2 final size:2
Alignment explanation
Indices: 1477931--1477969 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1477921 TGTACACCAC
*
1477931 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1477970 CCCAGGCCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1478098 original size:12 final size:12
Alignment explanation
Indices: 1478081--1478105 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1478071 TCTTATTGGT
1478081 CGTCAAGTGTTC
1 CGTCAAGTGTTC
1478093 CGTCAAGTGTTC
1 CGTCAAGTGTTC
1478105 C
1 C
1478106 ATAGATCGTT
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:0.28, G:0.24, T:0.32
Consensus pattern (12 bp):
CGTCAAGTGTTC
Found at i:1479057 original size:24 final size:24
Alignment explanation
Indices: 1479005--1479085 Score: 134
Period size: 24 Copynumber: 3.5 Consensus size: 24
1478995 TCCCCTTGAA
1479005 GTGCATCGATGCATTC--T-ACA-
1 GTGCATCGATGCATTCTTTAACAT
1479025 GTGCATCGATGCATTCTTTAACAT
1 GTGCATCGATGCATTCTTTAACAT
1479049 GTGCATCGATGCATTCTTTAACAT
1 GTGCATCGATGCATTCTTTAACAT
1479073 GTGCATCGATGCA
1 GTGCATCGATGCA
1479086 CTACCCATGC
Statistics
Matches: 57, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
20 16 0.28
22 1 0.02
23 3 0.05
24 37 0.65
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (24 bp):
GTGCATCGATGCATTCTTTAACAT
Found at i:1481720 original size:27 final size:27
Alignment explanation
Indices: 1481690--1481746 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
1481680 CTTTGAGTAA
1481690 GGATTAAAAATGATCTTTAAAAGATTT
1 GGATTAAAAATGATCTTTAAAAGATTT
1481717 GGATTAAAAATGATCTTTAAAAGATTT
1 GGATTAAAAATGATCTTTAAAAGATTT
1481744 GGA
1 GGA
1481747 ACAGTAAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.44, C:0.04, G:0.18, T:0.35
Consensus pattern (27 bp):
GGATTAAAAATGATCTTTAAAAGATTT
Found at i:1481905 original size:21 final size:21
Alignment explanation
Indices: 1481879--1481920 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1481869 TTTGAATATT
*
1481879 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1481900 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1481921 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:1481982 original size:21 final size:21
Alignment explanation
Indices: 1481949--1481988 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1481939 TTTTTGCCGA
*
1481949 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
1481971 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
1481989 AGATATGACT
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:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:1483624 original size:23 final size:20
Alignment explanation
Indices: 1483572--1483646 Score: 64
Period size: 19 Copynumber: 3.6 Consensus size: 20
1483562 AATGAAGGTA
*
1483572 TGCATCGATGCA-CTATACAG
1 TGCATCGATGCATCTAT-CGG
* *
1483592 TGTATAGATGCATTCCCTATCGG
1 TGCATCGATGCA-T--CTATCGG
*
1483615 TGCATCGATGCA-CTATCTG
1 TGCATCGATGCATCTATCGG
1483634 TGCATCGATGCAT
1 TGCATCGATGCAT
1483647 AAATGACATT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
19 18 0.41
20 10 0.23
23 12 0.27
24 4 0.09
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (20 bp):
TGCATCGATGCATCTATCGG
Found at i:1483636 original size:19 final size:19
Alignment explanation
Indices: 1483608--1483645 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1483598 GATGCATTCC
1483608 CTATCGGTGCATCGATGCA
1 CTATCGGTGCATCGATGCA
*
1483627 CTATCTGTGCATCGATGCA
1 CTATCGGTGCATCGATGCA
1483646 TAAATGACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (19 bp):
CTATCGGTGCATCGATGCA
Found at i:1485704 original size:7 final size:7
Alignment explanation
Indices: 1485626--1485703 Score: 124
Period size: 7 Copynumber: 11.4 Consensus size: 7
1485616 GTTGGAGAAG
1485626 AGAA-GA
1 AGAATGA
1485632 AG-ATGA
1 AGAATGA
1485638 AGAATGA
1 AGAATGA
1485645 AGAATGA
1 AGAATGA
1485652 AGAATGA
1 AGAATGA
1485659 AGAATGA
1 AGAATGA
1485666 AGAATGA
1 AGAATGA
1485673 AGAATGA
1 AGAATGA
*
1485680 AGAGTGA
1 AGAATGA
1485687 AGAATGA
1 AGAATGA
*
1485694 AGAGTGA
1 AGAATGA
1485701 AGA
1 AGA
1485704 GATATTTGGA
Statistics
Matches: 67, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
5 1 0.01
6 6 0.09
7 60 0.90
ACGTcount: A:0.55, C:0.00, G:0.32, T:0.13
Consensus pattern (7 bp):
AGAATGA
Found at i:1495259 original size:18 final size:16
Alignment explanation
Indices: 1495236--1495275 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1495226 TTTTTATTTG
1495236 TTTAATAAAATATTTTAT
1 TTTAAT-AAA-ATTTTAT
*
1495254 TTTAATATAATTTTAT
1 TTTAATAAAATTTTAT
1495270 TTTAAT
1 TTTAAT
1495276 TACTTTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 13 0.62
17 2 0.10
18 6 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTAATAAAATTTTAT
Found at i:1496046 original size:2 final size:2
Alignment explanation
Indices: 1496007--1496034 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1495997 AGGCTCTTGT
1496007 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1496035 GACACCTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1499525 original size:17 final size:18
Alignment explanation
Indices: 1499493--1499526 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1499483 CCGCTACTAG
1499493 TGAACCGGTCAGAACCGC
1 TGAACCGGTCAGAACCGC
*
1499511 TGAACC-GTTAGAACCG
1 TGAACCGGTCAGAACCG
1499527 GACCGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.15
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGC
Found at i:1499551 original size:10 final size:10
Alignment explanation
Indices: 1499536--1499565 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1499526 GGACCGGCTG
1499536 AAAACCGGAA
1 AAAACCGGAA
1499546 AAAACCGG-A
1 AAAACCGGAA
1499555 AAAACCGGAA
1 AAAACCGGAA
1499565 A
1 A
1499566 TTTTGTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.60, C:0.20, G:0.20, T:0.00
Consensus pattern (10 bp):
AAAACCGGAA
Found at i:1499557 original size:9 final size:9
Alignment explanation
Indices: 1499536--1499565 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
1499526 GGACCGGCTG
1499536 AAAACCGGAA
1 AAAACCGG-A
1499546 AAAACCGGA
1 AAAACCGGA
1499555 AAAACCGGA
1 AAAACCGGA
1499564 AA
1 AA
1499566 TTTTGTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.60
10 8 0.40
ACGTcount: A:0.60, C:0.20, G:0.20, T:0.00
Consensus pattern (9 bp):
AAAACCGGA
Found at i:1500249 original size:22 final size:21
Alignment explanation
Indices: 1500224--1500264 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1500214 TATAAAAAAT
1500224 TATTTTTATTAAATATTTTTGG
1 TATTTTTATTAAAT-TTTTTGG
*
1500246 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
1500265 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:1501742 original size:15 final size:15
Alignment explanation
Indices: 1501719--1501748 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1501709 ACGAGGCTGG
1501719 AATTACAACAACAAC
1 AATTACAACAACAAC
*
1501734 AATTCCAACAACAAC
1 AATTACAACAACAAC
1501749 TATGAGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.13
Consensus pattern (15 bp):
AATTACAACAACAAC
Found at i:1502428 original size:15 final size:15
Alignment explanation
Indices: 1502383--1502425 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
1502373 TCATGGCTTT
1502383 GGCATCTTCAATTTG
1 GGCATCTTCAATTTG
*
1502398 GGCATCTTCGATTTG
1 GGCATCTTCAATTTG
1502413 GGCATC-TCAATTT
1 GGCATCTTCAATTT
1502426 TGGAGGTCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 6 0.23
15 20 0.77
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.40
Consensus pattern (15 bp):
GGCATCTTCAATTTG
Found at i:1505148 original size:29 final size:29
Alignment explanation
Indices: 1505106--1505187 Score: 119
Period size: 29 Copynumber: 2.8 Consensus size: 29
1505096 AAACTAAATT
*
1505106 GATGTCATTACTTACATAATTTAAGTAAA
1 GATGTCATTGCTTACATAATTTAAGTAAA
* *
1505135 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATAATTTAAGTAAA
*
1505164 GATGTCAATGCTTACATCAATTTA
1 GATGTCATTGCTTACAT-AATTTA
1505188 GTTAGGTGAG
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 42 0.89
30 5 0.11
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.39
Consensus pattern (29 bp):
GATGTCATTGCTTACATAATTTAAGTAAA
Found at i:1507626 original size:174 final size:176
Alignment explanation
Indices: 1507318--1507672 Score: 651
Period size: 174 Copynumber: 2.0 Consensus size: 176
1507308 ATGAAACTTC
*
1507318 TTGGTGCATGGGTCATTTTGGAATTCTGTTTTCTTTCTTTTAATTTTTAATCGGATTTTCGGTCC
1 TTGGTGCATGGGTCATTTTGGAATTCTGTTTTCTTTCTTTTAATTTGTAATCGGATTTTCGGTCC
1507383 TATATATATATATTTATACTTTCTCTCTCTTCAATGGTTTAAACATAGATTAATCATGTTCACGT
66 ---ATATATATATTTATACTTTCTCTCTCTTCAATGGTTTAAACATAGATTAATCATGTTCACGT
1507448 GTATTTTTGGGTAAATTACAAGTTTCTCAGCTTAA-TTTTTTGCTCTTT
128 GTATTTTTGGGTAAATTACAAGTTTCTCAGCTTAATTTTTTTGCTCTTT
1507496 TTGGTGCATGGGTCATTTTGGAATTCTGTTTTCTTTCTTTTAATTTGTAATCGGATTTTCGGTCC
1 TTGGTGCATGGGTCATTTTGGAATTCTGTTTTCTTTCTTTTAATTTGTAATCGGATTTTCGGTCC
1507561 -TATATATATTTATACTTTCTCTCTCTTCAATGGTTTAAACATAGATTAATCATGTTCACGTGTA
66 ATATATATATTTATACTTTCTCTCTCTTCAATGGTTTAAACATAGATTAATCATGTTCACGTGTA
*
1507625 TTTTTGGGTAAATTACAAGTTTCTCAGCTTAATTTTTTTTCTCTTT
131 TTTTTGGGTAAATTACAAGTTTCTCAGCTTAATTTTTTTGCTCTTT
1507671 TT
1 TT
1507673 TATTTTGGTT
Statistics
Matches: 174, Mismatches: 2, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
174 96 0.55
175 14 0.08
178 64 0.37
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.50
Consensus pattern (176 bp):
TTGGTGCATGGGTCATTTTGGAATTCTGTTTTCTTTCTTTTAATTTGTAATCGGATTTTCGGTCC
ATATATATATTTATACTTTCTCTCTCTTCAATGGTTTAAACATAGATTAATCATGTTCACGTGTA
TTTTTGGGTAAATTACAAGTTTCTCAGCTTAATTTTTTTGCTCTTT
Found at i:1508052 original size:37 final size:37
Alignment explanation
Indices: 1508011--1508083 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
1508001 GGTATGTTCA
*
1508011 TAATTTTTTTTATAAAAATGTCTAATCATAAAATCAT
1 TAATTTTTTTTACAAAAATGTCTAATCATAAAATCAT
*
1508048 TAATTTTTTTTACAAAAATGTCTAATCATAACATCA
1 TAATTTTTTTTACAAAAATGTCTAATCATAAAATCA
1508084 CTAAGTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.44
Consensus pattern (37 bp):
TAATTTTTTTTACAAAAATGTCTAATCATAAAATCAT
Found at i:1509996 original size:21 final size:21
Alignment explanation
Indices: 1509957--1509996 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1509947 ATGTGTTGTA
*
1509957 TGATAATAATCTATGAGATAT
1 TGATAATAATCTATAAGATAT
1509978 TGATAATAAGTC-ATAAGAT
1 TGATAATAA-TCTATAAGAT
1509997 TTCATACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.45, C:0.05, G:0.15, T:0.35
Consensus pattern (21 bp):
TGATAATAATCTATAAGATAT
Found at i:1510209 original size:15 final size:14
Alignment explanation
Indices: 1510191--1510237 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
1510181 ATCATATGAA
*
1510191 ATGTGATAGAGAGCT
1 ATGTGATA-AGAACT
1510206 ATGTGA-AAGAACT
1 ATGTGATAAGAACT
*
1510219 ATGTGATATGAA-T
1 ATGTGATAAGAACT
1510232 ATGTGA
1 ATGTGA
1510238 ATGTGTAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 18 0.62
14 5 0.17
15 6 0.21
ACGTcount: A:0.38, C:0.04, G:0.28, T:0.30
Consensus pattern (14 bp):
ATGTGATAAGAACT
Found at i:1520723 original size:21 final size:22
Alignment explanation
Indices: 1520679--1520724 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1520669 GATTTCTGGG
* *
1520679 CAAGGGGAAATCGGTACCCATT
1 CAAGGGGAAACCGATACCCATT
*
1520701 CAAGGGG-AACCGATACCCCTT
1 CAAGGGGAAACCGATACCCATT
1520722 CAA
1 CAA
1520725 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.33, C:0.28, G:0.24, T:0.15
Consensus pattern (22 bp):
CAAGGGGAAACCGATACCCATT
Found at i:1522438 original size:22 final size:22
Alignment explanation
Indices: 1522406--1522486 Score: 135
Period size: 22 Copynumber: 3.6 Consensus size: 22
1522396 ATCATTATAT
*
1522406 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
1522428 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
*
1522450 GGCACTTCGGTGTAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
1522473 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
1522487 TTTATACGAG
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 41 0.75
23 14 0.25
ACGTcount: A:0.19, C:0.26, G:0.30, T:0.26
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:1525680 original size:21 final size:22
Alignment explanation
Indices: 1525636--1525681 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1525626 GATTTCTGGG
* *
1525636 CAAGGGGAAATCGGTACCCATT
1 CAAGGGGAAACCGATACCCATT
*
1525658 CAAGGGG-AACCGATACCCCTT
1 CAAGGGGAAACCGATACCCATT
1525679 CAA
1 CAA
1525682 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.33, C:0.28, G:0.24, T:0.15
Consensus pattern (22 bp):
CAAGGGGAAACCGATACCCATT
Found at i:1527377 original size:13 final size:13
Alignment explanation
Indices: 1527359--1527421 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
1527349 TTATATGGCA
1527359 CTACGGTGCAATT
1 CTACGGTGCAATT
1527372 CTACGG-GC-A--
1 CTACGGTGCAATT
*
1527381 CTTCGGTGCAATT
1 CTACGGTGCAATT
1527394 CTACGG-GC-A--
1 CTACGGTGCAATT
*
1527403 CTTCGGTGCAATT
1 CTACGGTGCAATT
1527416 CTACGG
1 CTACGG
1527422 GGCACTTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 10 0.26
10 4 0.11
11 4 0.11
12 4 0.11
13 16 0.42
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:1527442 original size:22 final size:22
Alignment explanation
Indices: 1527355--1527435 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
1527345 ATCATTATAT
*
1527355 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
1527377 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
1527399 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
1527422 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
1527436 TTATACGAGC
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 42 0.74
23 15 0.26
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.25
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:1550725 original size:37 final size:38
Alignment explanation
Indices: 1550666--1550750 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 38
1550656 ATCCCATTAT
1550666 TATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC-
1 TATTTTTCAAACAAACATCTACCAAACTTTGAAAAACA
* * *
1550702 TATTTTTCAAATAAACATTTACCAAACTTTGAAAATCA
1 TATTTTTCAAACAAACATCTACCAAACTTTGAAAAACA
*
1550740 TTTTTTTCAAA
1 TATTTTTCAAA
1550751 GTTGGTTACC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 8 0.19
37 25 0.58
38 10 0.23
ACGTcount: A:0.42, C:0.18, G:0.02, T:0.38
Consensus pattern (38 bp):
TATTTTTCAAACAAACATCTACCAAACTTTGAAAAACA
Done.