Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009072.1 Hibiscus syriacus cultivar Beakdansim tig00112503_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: 2600608
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 13
Found at i:1177798 original size:141 final size:141
Alignment explanation
Indices: 1177544--1177825 Score: 510
Period size: 141 Copynumber: 2.0 Consensus size: 141
1177534 AGAATTATTA
* **
1177544 AAATATATGGTAAACAAAGAAATGAACCTAATCAAATGTATATACAATAAATATAATATATGGAT
1 AAATATATGGTAAACAAAGAAACGAACCTAATCAAATGTATATACAATAAATATAATATATAAAT
* *
1177609 ACACCAAATGCTTAAATATGTATGGAAAACAAATCCAAAGAATCAATCACATGCAAATGTAAAGG
66 ACACCAAATGATTAAATATGTATGGAAAACAAATCCAAAGAATCAATCACATGCAAATATAAAGG
1177674 AATATGGAGAC
131 AATATGGAGAC
*
1177685 AAATATATGGTAAACAAAGAAACGAACCTAATCAAATTTATATACAATAAATATAATATATAAAT
1 AAATATATGGTAAACAAAGAAACGAACCTAATCAAATGTATATACAATAAATATAATATATAAAT
1177750 ACACCAAATGATTAAATATGTATGGAAAACAAATCCAAAGAATCAATCACATGCAAATATAAAGG
66 ACACCAAATGATTAAATATGTATGGAAAACAAATCCAAAGAATCAATCACATGCAAATATAAAGG
1177815 AATATGGAGAC
131 AATATGGAGAC
1177826 TAAACAAATG
Statistics
Matches: 135, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
141 135 1.00
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.23
Consensus pattern (141 bp):
AAATATATGGTAAACAAAGAAACGAACCTAATCAAATGTATATACAATAAATATAATATATAAAT
ACACCAAATGATTAAATATGTATGGAAAACAAATCCAAAGAATCAATCACATGCAAATATAAAGG
AATATGGAGAC
Found at i:1178693 original size:16 final size:15
Alignment explanation
Indices: 1178666--1178695 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1178656 AAAATTTTTA
1178666 TTTAATTTTTAATTT
1 TTTAATTTTTAATTT
1178681 TTTAATGTTTTAATT
1 TTTAAT-TTTTAATT
1178696 GATTTTTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTAATTTTTAATTT
Found at i:1181093 original size:35 final size:33
Alignment explanation
Indices: 1180973--1181099 Score: 119
Period size: 35 Copynumber: 3.6 Consensus size: 33
1180963 GTTCAGTTCT
* *
1180973 GATCAAGCTGATAATTTCTTATATAGGTTCAACACC
1 GATCAA-CTGGTAATTCCTTATATAGGTTC-A-ACC
* * *
1181009 GATCAACTGGTAACTCCTTATGGTAGGTTTAACTC
1 GATCAACTGGTAATTCCTTAT-ATAGGTTCAAC-C
* *
1181044 GGTCAAACTAGTAATTCCTTATATAGGTTCAGACC
1 GATC-AACTGGTAATTCCTTATATAGGTTCA-ACC
1181079 GATCGAACTGGTAATTCCTTA
1 GATC-AACTGGTAATTCCTTA
1181100 CAGATCTAAG
Statistics
Matches: 74, Mismatches: 13, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
34 2 0.03
35 43 0.58
36 29 0.39
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (33 bp):
GATCAACTGGTAATTCCTTATATAGGTTCAACC
Found at i:1182022 original size:3 final size:3
Alignment explanation
Indices: 1182014--1182046 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1182004 TGAGTGTTAC
1182014 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1182047 GTTTTGACCC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1184266 original size:31 final size:31
Alignment explanation
Indices: 1184216--1184286 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
1184206 TTTTATATAT
1184216 ATATAATATTAATAAATTTAATTTAAATAAAA
1 ATAT-ATATTAATAAATTTAATTTAAATAAAA
* * * * *
1184248 ATATATATTTATATATTTAATTTATATATAT
1 ATATATATTAATAAATTTAATTTAAATAAAA
1184279 ATATATAT
1 ATATATAT
1184287 ACCCGGCCCG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 30 0.88
32 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
ATATATATTAATAAATTTAATTTAAATAAAA
Found at i:1184320 original size:12 final size:12
Alignment explanation
Indices: 1184305--1184339 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1184295 CGATTCTCGG
1184305 CCCAATACCCGA
1 CCCAATACCCGA
*
1184317 CCCAATACCCGG
1 CCCAATACCCGA
*
1184329 CCTAATACCCG
1 CCCAATACCCG
1184340 TTTAAATAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.29, C:0.49, G:0.11, T:0.11
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:1185530 original size:28 final size:24
Alignment explanation
Indices: 1185492--1185555 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 24
1185482 TATATGATAT
1185492 AAAATTAAATATCTATAATATAATATTAA
1 AAAATT-AATAT-T-TAAT-TAAT-TTAA
*
1185521 AAAATTAATATTTAATTTATTTAA
1 AAAATTAATATTTAATTAATTTAA
1185545 AAAATTAATAT
1 AAAATTAATAT
1185556 AAAAATTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
24 15 0.44
25 3 0.09
26 4 0.12
27 1 0.03
28 5 0.15
29 6 0.18
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
AAAATTAATATTTAATTAATTTAA
Found at i:1185556 original size:64 final size:64
Alignment explanation
Indices: 1185488--1185643 Score: 239
Period size: 64 Copynumber: 2.5 Consensus size: 64
1185478 AATTTATATG
1185488 ATATAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTA
1 ATATAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTA
* *
1185552 ATATAAAAATT-AATATCTATAATAAAATATTAAAAATTTAATATTTAATTTATTTAAAAAATTA
1 ATAT-AAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTA
*
1185616 ATATTAATATTAAA-ATC-A-AATATAATAT
1 ATA-TAAAATTAAATATCTATAATATAATAT
1185644 AAATTAAATA
Statistics
Matches: 85, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
62 9 0.11
63 1 0.01
64 66 0.78
65 9 0.11
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (64 bp):
ATATAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTA
Found at i:1185610 original size:32 final size:32
Alignment explanation
Indices: 1185516--1185616 Score: 100
Period size: 32 Copynumber: 3.2 Consensus size: 32
1185506 ATAATATAAT
*
1185516 ATTAAAAAATTAATATTTAATTTATTTAAAAA
1 ATTAAAAATTTAATATTTAATTTATTTAAAAA
* * * * *
1185548 ATT---AATATAAAAATTAATATCTATAATAAAAT
1 ATTAAAAATTTAATATTTAAT-T-TAT-TTAAAAA
1185580 ATTAAAAATTTAATATTTAATTTATTTAAAAA
1 ATTAAAAATTTAATATTTAATTTATTTAAAAA
1185612 ATTAA
1 ATTAA
1185617 TATTAATATT
Statistics
Matches: 52, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
29 11 0.21
30 1 0.02
31 3 0.06
32 21 0.40
33 3 0.06
34 1 0.02
35 12 0.23
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (32 bp):
ATTAAAAATTTAATATTTAATTTATTTAAAAA
Found at i:1185652 original size:16 final size:18
Alignment explanation
Indices: 1185609--1185656 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
1185599 ATTTATTTAA
1185609 AAAATT-AATATTAATATT
1 AAAATTAAATA-TAATATT
*
1185627 AAAATCAAATATAATA-T
1 AAAATTAAATATAATATT
1185644 -AAATTAAATATAA
1 AAAATTAAATATAA
1185657 AACCTCTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 12 0.44
17 1 0.04
18 10 0.37
19 4 0.15
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAATTAAATATAATATT
Found at i:1187239 original size:14 final size:14
Alignment explanation
Indices: 1187201--1187229 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1187191 AGATGACAAA
1187201 CAAAACCAATTAAT
1 CAAAACCAATTAAT
1187215 CAAAACCAATTAAT
1 CAAAACCAATTAAT
1187229 C
1 C
1187230 TAAGCTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.21
Consensus pattern (14 bp):
CAAAACCAATTAAT
Found at i:1190665 original size:28 final size:27
Alignment explanation
Indices: 1190612--1190669 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
1190602 ATTAAAAATT
* *
1190612 AAATATAATTAAAATCGAACTTAATATA
1 AAATATAATCAAAATCGAACTAAATA-A
*
1190640 AAATATAATCAAAATAC-ATCTAAATAA
1 AAATATAATCAAAAT-CGAACTAAATAA
1190667 AAA
1 AAA
1190670 CTACATGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 4 0.15
28 21 0.81
29 1 0.04
ACGTcount: A:0.62, C:0.09, G:0.02, T:0.28
Consensus pattern (27 bp):
AAATATAATCAAAATCGAACTAAATAA
Found at i:1190939 original size:20 final size:20
Alignment explanation
Indices: 1190907--1190950 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1190897 AGAACATTAC
**
1190907 TATTAATTATTATTTTATAT
1 TATTAATTATTATACTATAT
1190927 TATT-ATTATTTATACTATAT
1 TATTAATTA-TTATACTATAT
1190947 TATT
1 TATT
1190951 TAAATTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTAATTATTATACTATAT
Found at i:1191238 original size:20 final size:21
Alignment explanation
Indices: 1191213--1191255 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1191203 TTATCAAAAT
* *
1191213 TTTAATAT-ATTTTAATCATA
1 TTTAATATAATTTGAATAATA
1191233 TTTAATATAATTTGAATAATA
1 TTTAATATAATTTGAATAATA
1191254 TT
1 TT
1191256 ATTTTTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (21 bp):
TTTAATATAATTTGAATAATA
Found at i:1192709 original size:64 final size:62
Alignment explanation
Indices: 1192640--1192813 Score: 197
Period size: 64 Copynumber: 2.7 Consensus size: 62
1192630 TGGAACACTT
* * *
1192640 AGTGCATCGGTGCACTAAGTGTGCATCGATGCATCAAATGCATTCGAAGTTTTGA-AAAAGCCTG
1 AGTGCATCGATGCA-T-AGTGTGCATCGATGCATCAAATGCATTCGAAGTTTTCATAAAA-CCAG
* * *
1192704 AGTGCATCGATGCATGGTATGTGCATCGATGCATCAAATACATTCGATGTTTTCATTAAAACCAG
1 AGTGCATCGATGCATAG--TGTGCATCGATGCATCAAATGCATTCGAAGTTTTCA-TAAAACCAG
* *
1192769 AGTGCATCGATGCATGGAGAGTGCATCGATGCATGAAATGCATTC
1 AGTGCATCGATGCAT--AGTGTGCATCGATGCATCAAATGCATTC
1192814 AATGTTCAAT
Statistics
Matches: 94, Mismatches: 10, Indels: 11
0.82 0.09 0.10
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 46 0.49
65 41 0.44
66 4 0.04
67 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (62 bp):
AGTGCATCGATGCATAGTGTGCATCGATGCATCAAATGCATTCGAAGTTTTCATAAAACCAG
Found at i:1192791 original size:19 final size:19
Alignment explanation
Indices: 1192767--1192803 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1192757 CATTAAAACC
1192767 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
1192786 AGAGTGCATCGATGCATG
1 AGAGTGCATCGATGCATG
1192804 AAATGCATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.16, G:0.35, T:0.22
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:1192802 original size:65 final size:64
Alignment explanation
Indices: 1192660--1192869 Score: 223
Period size: 65 Copynumber: 3.2 Consensus size: 64
1192650 TGCACTAAGT
* * *
1192660 GTGCATCGATGCATCAAATGCATTCGAAGTTTTGA--AAAAGCCTGAGTGCATCGATGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATTAAAA-CCAGAGTGCATCGATGCATGG-A
*
1192723 T
64 G
*
1192724 GTGCATCGATGCATCAAATACATTCGATGTTTTCATTAAAACCAGAGTGCATCGATGCATGGAG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATTAAAACCAGAGTGCATCGATGCATGGAG
* * * **
1192788 AGTGCATCGATGCATGAAATGCATTCAATG--TTCAATTTATTCCATG-GTGCATCGATGCATGG
1 -GTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATTAAAACCA-GAGTGCATCGATGCATGG
1192850 ATTG
63 A--G
*
1192854 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
1192870 CTTAAAAAAT
Statistics
Matches: 126, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
63 3 0.02
64 57 0.45
65 61 0.48
66 5 0.04
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCATTAAAACCAGAGTGCATCGATGCATGGAG
Found at i:1195562 original size:21 final size:22
Alignment explanation
Indices: 1195481--1195584 Score: 138
Period size: 23 Copynumber: 4.7 Consensus size: 22
1195471 AAATCCCGAC
1195481 GGATGCATCGATGCACATTCAA
1 GGATGCATCGATGCACATTCAA
*
1195503 GGAGTGCATCGGTGCACATTCAA
1 GGA-TGCATCGATGCACATTCAA
* * *
1195526 GGAGTGCATCGGTGCACCTTCAT
1 GGA-TGCATCGATGCACATTCAA
*
1195549 GG-TGTATCGATGCACATTCAA
1 GGATGCATCGATGCACATTCAA
1195570 GGATGCATCGATGCA
1 GGATGCATCGATGCA
1195585 TTGTTAAGTG
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
21 17 0.24
22 14 0.19
23 41 0.57
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (22 bp):
GGATGCATCGATGCACATTCAA
Found at i:1205092 original size:16 final size:16
Alignment explanation
Indices: 1205052--1205094 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
1205042 TTCATAAATC
*
1205052 CAAAATCCAACAATCCA
1 CAAAATCAAAC-ATCCA
1205069 CAAAATCAAACATCCA
1 CAAAATCAAACATCCA
1205085 -AAATATCAAA
1 CAAA-ATCAAA
1205095 AGTGTTGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 3 0.12
16 11 0.46
17 10 0.42
ACGTcount: A:0.58, C:0.28, G:0.00, T:0.14
Consensus pattern (16 bp):
CAAAATCAAACATCCA
Found at i:1207058 original size:20 final size:21
Alignment explanation
Indices: 1207012--1207072 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
1207002 TCCCCTGTGG
1207012 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
1207035 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
1207055 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
1207073 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:1212960 original size:77 final size:77
Alignment explanation
Indices: 1212769--1212973 Score: 267
Period size: 76 Copynumber: 2.7 Consensus size: 77
1212759 CCGTTGTACA
* * * * *
1212769 AGGGGGGAATCGGTACCCCCT-TGGGGGGG-ATCGGTTCCCTCCAAGCATACTGGAATTCTCAGA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCAGA
**
1212832 GCAAAACTGTTT
66 GCAAAACCATTT
1212844 AGGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCT-AGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCA-G
*
1212907 GGCCAAAACCATTT
65 AG-CAAAACCATTT
* *
1212921 A-GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCAATCTG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTG
1212974 TAATTTTTGG
Statistics
Matches: 115, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
75 26 0.23
76 51 0.44
77 38 0.33
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.23
Consensus pattern (77 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCAGA
GCAAAACCATTT
Found at i:1213461 original size:21 final size:20
Alignment explanation
Indices: 1213435--1213554 Score: 100
Period size: 21 Copynumber: 5.8 Consensus size: 20
1213425 CATATTCGCA
1213435 TTGCGATAGTCCAAGTTCACG
1 TTGCGATAGTCCAAGTTC-CG
* *
1213456 TTGCGATAGTCGAAGTTCGCA
1 TTGCGATAGTCCAAGTTC-CG
** *
1213477 TTGCGATTTTCCAAATT-CG
1 TTGCGATAGTCCAAGTTCCG
*
1213496 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTC-CG
*
1213517 TTGCGATTTATTCCAAGTT-CG
1 TTGCGA--TAGTCCAAGTTCCG
* *
1213538 TTGTGATAGTCGAAGTT
1 TTGCGATAGTCCAAGTT
1213555 AGTCCAAAAT
Statistics
Matches: 78, Mismatches: 17, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
19 23 0.29
21 46 0.59
23 9 0.12
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (20 bp):
TTGCGATAGTCCAAGTTCCG
Found at i:1213481 original size:42 final size:40
Alignment explanation
Indices: 1213429--1213554 Score: 171
Period size: 42 Copynumber: 3.0 Consensus size: 40
1213419 GATTTACATA
*
1213429 TTCGCATTGCGATAGTCCAAGTTCACGTTGCGATAGTCGAAG
1 TTCGCATTGCGATATTCCAAGTT--CGTTGCGATAGTCGAAG
* *
1213471 TTCGCATTGCGATTTTCCAAATTCGTTGCGATAGTCGAAG
1 TTCGCATTGCGATATTCCAAGTTCGTTGCGATAGTCGAAG
* *
1213511 TTCGCGTTGCGATTTATTCCAAGTTCGTTGTGATAGTCGAAG
1 TTCGCATTGCGA--TATTCCAAGTTCGTTGCGATAGTCGAAG
1213553 TT
1 TT
1213555 AGTCCAAAAT
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
40 28 0.37
42 47 0.63
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (40 bp):
TTCGCATTGCGATATTCCAAGTTCGTTGCGATAGTCGAAG
Found at i:1213662 original size:6 final size:6
Alignment explanation
Indices: 1213651--1213683 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
1213641 GACACGTATT
1213651 ACCACG ACCACG ACC-CGG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCAC-G ACCACG ACCACG ACC
1213684 CGAGACGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 1 0.04
6 23 0.92
7 1 0.04
ACGTcount: A:0.30, C:0.52, G:0.18, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1213674 original size:18 final size:18
Alignment explanation
Indices: 1213651--1213685 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1213641 GACACGTATT
1213651 ACCACGACCACGACCCGG
1 ACCACGACCACGACCCGG
1213669 ACCACGACCACGACCCG
1 ACCACGACCACGACCCG
1213686 AGACGAGACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.51, G:0.20, T:0.00
Consensus pattern (18 bp):
ACCACGACCACGACCCGG
Found at i:1214185 original size:5 final size:5
Alignment explanation
Indices: 1214175--1214217 Score: 59
Period size: 5 Copynumber: 8.6 Consensus size: 5
1214165 CGTCGCAGTC
* * *
1214175 CGTCT CGTCT CATCT CGCCT CGTCT CATCT CGTCT CGTCT CGT
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGT
1214218 GGTCATGGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.05, C:0.42, G:0.16, T:0.37
Consensus pattern (5 bp):
CGTCT
Found at i:1214196 original size:15 final size:15
Alignment explanation
Indices: 1214178--1214215 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
1214168 CGCAGTCCGT
1214178 CTCGTCTCATCTCGC
1 CTCGTCTCATCTCGC
*
1214193 CTCGTCTCATCTCGT
1 CTCGTCTCATCTCGC
1214208 CTCGTCTC
1 CTCGTCTC
1214216 GTGGTCATGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.05, C:0.45, G:0.13, T:0.37
Consensus pattern (15 bp):
CTCGTCTCATCTCGC
Found at i:1214528 original size:82 final size:82
Alignment explanation
Indices: 1214325--1214585 Score: 441
Period size: 82 Copynumber: 3.2 Consensus size: 82
1214315 TGCAATTTTG
1214325 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAT
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGG-A-
* *
1214390 AAATCACAACGCGAACTTT
64 AAATCGCAACGCGAACTTC
* *
1214409 GACTATCGTAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACAAATTTGGAAA
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
1214474 ATCGCAACGCGAACTTC
66 ATCGCAACGCGAACTTC
* *
1214491 GACTATCGCAACGAATTTGGAATAAATCACAATGCGAACTTCGACTATCGCAACGAATTTGGAAA
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
*
1214556 ATCGCAATGCGAACTTC
66 ATCGCAACGCGAACTTC
1214573 GACTATCGCAACG
1 GACTATCGCAACG
1214586 CGAACTTGGA
Statistics
Matches: 168, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
82 107 0.64
83 1 0.01
84 60 0.36
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.22
Consensus pattern (82 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
ATCGCAACGCGAACTTC
Found at i:1214595 original size:42 final size:42
Alignment explanation
Indices: 1214325--1214585 Score: 431
Period size: 42 Copynumber: 6.3 Consensus size: 42
1214315 TGCAATTTTG
1214325 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
1214367 GACTATCGCAACGAATTTGGAATAAATCACAACGCGAACTTT
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
1214409 GACTATCGTAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
1214451 GACTATCGCAACAAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
1214491 GACTATCGCAACGAATTTGGAATAAATCACAATGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
1214533 GACTATCGCAACGAATTTGG-A-AAATCGCAATGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1214573 GACTATCGCAACG
1 GACTATCGCAACG
1214586 CGAACTTGGA
Statistics
Matches: 206, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
40 69 0.33
41 3 0.01
42 134 0.65
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.22
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:1214595 original size:124 final size:124
Alignment explanation
Indices: 1214325--1214585 Score: 445
Period size: 124 Copynumber: 2.1 Consensus size: 124
1214315 TGCAATTTTG
1214325 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAT
1 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAT
* *
1214390 AAATCACAACGCGAACTTTGACTATCGTAACGAATTTGGAATAAATCGCAACGCGAACTTC
64 AAATCACAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
1214451 GACTATCGCAACAAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
1 GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
* *
1214516 ATCACAATGCGAACTTCGACTATCGCAACGAATTTGG-A-AAATCGCAATGCGAACTTC
66 ATCACAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1214573 GACTATCGCAACG
1 GACTATCGCAACG
1214586 CGAACTTGGA
Statistics
Matches: 129, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
122 30 0.23
123 1 0.01
124 78 0.60
125 1 0.01
126 19 0.15
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.22
Consensus pattern (124 bp):
GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
ATCACAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:1214648 original size:21 final size:21
Alignment explanation
Indices: 1214619--1214668 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
1214609 AATATGTAAA
*
1214619 TCGCATTGCGATAGTCCAAGT
1 TCGCGTTGCGATAGTCCAAGT
*
1214640 TCGCGTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCCAAGT
1214661 TCGCGTTG
1 TCGCGTTG
1214669 TGAATCTGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.18, C:0.22, G:0.30, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCCAAGT
Found at i:1229162 original size:20 final size:21
Alignment explanation
Indices: 1229134--1229172 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1229124 GGTAAAACAC
*
1229134 TACCTAAAACATT-ATTTTTT
1 TACCGAAAACATTAATTTTTT
*
1229154 TACCGAAAATATTAATTTT
1 TACCGAAAACATTAATTTT
1229173 GCTACCTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.38, C:0.13, G:0.03, T:0.46
Consensus pattern (21 bp):
TACCGAAAACATTAATTTTTT
Found at i:1232071 original size:20 final size:18
Alignment explanation
Indices: 1232046--1232085 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
1232036 AAATTACATC
1232046 AAAAATAGATCATAATCGAT
1 AAAAATAGATCA-AATC-AT
*
1232066 AAAAATGGATCAAATCAT
1 AAAAATAGATCAAATCAT
1232084 AA
1 AA
1232086 GATAAAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 4 0.21
20 11 0.58
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.23
Consensus pattern (18 bp):
AAAAATAGATCAAATCAT
Found at i:1242109 original size:20 final size:21
Alignment explanation
Indices: 1242084--1242142 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
1242074 GGCTGCTGGA
1242084 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
1242104 AACCGGTTCTGACCGG-TTTC
1 AACCGGTTCTAACCGGTTTTC
*
1242124 AACCGGTTCGAACCGGTTT
1 AACCGGTTCTAACCGGTTT
1242143 GACCGGTCTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 26 0.76
21 8 0.24
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.31
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:1242120 original size:10 final size:10
Alignment explanation
Indices: 1242105--1242174 Score: 62
Period size: 10 Copynumber: 7.3 Consensus size: 10
1242095 CCGGTTTTCA
1242105 ACCGGTTCTG
1 ACCGGTTCTG
*
1242115 ACCGGTT-TCA
1 ACCGGTTCT-G
1242125 ACCGGTTC-G
1 ACCGGTTCTG
1242134 AACCGGTT-TG
1 -ACCGGTTCTG
1242144 ACCGG-TCTG
1 ACCGGTTCTG
1242153 AACCGGTT-TG
1 -ACCGGTTCTG
1242163 ACCGG-TCTG
1 ACCGGTTCTG
1242172 ACC
1 ACC
1242175 CGACCCGACC
Statistics
Matches: 50, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
8 2 0.04
9 18 0.36
10 29 0.58
11 1 0.02
ACGTcount: A:0.16, C:0.30, G:0.29, T:0.26
Consensus pattern (10 bp):
ACCGGTTCTG
Found at i:1242149 original size:19 final size:20
Alignment explanation
Indices: 1242105--1242172 Score: 90
Period size: 19 Copynumber: 3.5 Consensus size: 20
1242095 CCGGTTTTCA
*
1242105 ACCGGTTCTG-ACCGGTTTCA
1 ACCGGTTCTGAACCGGTTT-G
1242125 ACCGGTTC-GAACCGGTTTG
1 ACCGGTTCTGAACCGGTTTG
1242144 ACCGG-TCTGAACCGGTTTG
1 ACCGGTTCTGAACCGGTTTG
1242163 ACCGG-TCTGA
1 ACCGGTTCTGA
1242173 CCCGACCCGA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
18 2 0.04
19 27 0.60
20 16 0.36
ACGTcount: A:0.16, C:0.28, G:0.29, T:0.26
Consensus pattern (20 bp):
ACCGGTTCTGAACCGGTTTG
Found at i:1242173 original size:9 final size:9
Alignment explanation
Indices: 1242135--1242174 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
1242125 ACCGGTTCGA
*
1242135 ACCGGTTTG
1 ACCGGTCTG
1242144 ACCGGTCTG
1 ACCGGTCTG
*
1242153 AACCGGTTTG
1 -ACCGGTCTG
1242163 ACCGGTCTG
1 ACCGGTCTG
1242172 ACC
1 ACC
1242175 CGACCCGACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.25
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:1242198 original size:17 final size:17
Alignment explanation
Indices: 1242176--1242230 Score: 101
Period size: 17 Copynumber: 3.2 Consensus size: 17
1242166 GGTCTGACCC
*
1242176 GACCCGACCCGATCGTT
1 GACCCGACCCGACCGTT
1242193 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
1242210 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
1242227 GACC
1 GACC
1242231 GTTGACCGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.18, C:0.45, G:0.24, T:0.13
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:1242218 original size:22 final size:22
Alignment explanation
Indices: 1242170--1242237 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 22
1242160 TTGACCGGTC
*
1242170 TGACCCGACCCGACCCGATCGT
1 TGACCCGACCCGACCCGACCGT
1242192 T-----GACCCGACCCGACCGT
1 TGACCCGACCCGACCCGACCGT
*
1242209 TGACCCGACCCGACCGTTGACCGT
1 TGACCCGACCCGACC--CGACCGT
1242233 TGACC
1 TGACC
1242238 GTTGACTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
17 16 0.43
22 10 0.27
24 11 0.30
ACGTcount: A:0.18, C:0.44, G:0.24, T:0.15
Consensus pattern (22 bp):
TGACCCGACCCGACCCGACCGT
Found at i:1249416 original size:9 final size:9
Alignment explanation
Indices: 1249402--1249459 Score: 53
Period size: 10 Copynumber: 6.0 Consensus size: 9
1249392 GGCTGCTGGA
1249402 AACCGGTTT
1 AACCGGTTT
1249411 AACCGGTTTT
1 AACCGG-TTT
1249421 CAACCGGTTCT
1 -AACCGGTT-T
*
1249432 GACCGGTTT
1 AACCGGTTT
* *
1249441 GACCGGTTCG
1 AACCGGTT-T
1249451 AACCGGTTT
1 AACCGGTTT
1249460 GACCTGTCTG
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
9 15 0.37
10 19 0.46
11 7 0.17
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.31
Consensus pattern (9 bp):
AACCGGTTT
Found at i:1249427 original size:20 final size:21
Alignment explanation
Indices: 1249402--1249459 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 21
1249392 GGCTGCTGGA
1249402 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
1249422 AACCGGTTCTGACCGG-TTT-
1 AACCGGTTCTAACCGGTTTTC
* *
1249441 GACCGGTTCGAACCGGTTT
1 AACCGGTTCTAACCGGTTT
1249460 GACCTGTCTG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 13 0.41
20 13 0.41
21 6 0.19
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.31
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:1249438 original size:10 final size:10
Alignment explanation
Indices: 1249423--1249472 Score: 54
Period size: 9 Copynumber: 5.3 Consensus size: 10
1249413 CCGGTTTTCA
1249423 ACCGGTTCTG
1 ACCGGTTCTG
1249433 ACCGGTT-TG
1 ACCGGTTCTG
1249442 ACCGGTTC-G
1 ACCGGTTCTG
1249451 AACCGGTT-TG
1 -ACCGGTTCTG
*
1249461 ACCTG-TCTG
1 ACCGGTTCTG
1249470 ACC
1 ACC
1249473 CGACCTGACC
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
8 1 0.03
9 19 0.54
10 15 0.43
ACGTcount: A:0.14, C:0.30, G:0.28, T:0.28
Consensus pattern (10 bp):
ACCGGTTCTG
Found at i:1249447 original size:19 final size:19
Alignment explanation
Indices: 1249423--1249472 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
1249413 CCGGTTTTCA
1249423 ACCGGTTCTGACCGGTTTG
1 ACCGGTTCTGACCGGTTTG
1249442 ACCGGTTC-GAACCGGTTTG
1 ACCGGTTCTG-ACCGGTTTG
*
1249461 ACCTG-TCTGACC
1 ACCGGTTCTGACC
1249473 CGACCTGACC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.14, C:0.30, G:0.28, T:0.28
Consensus pattern (19 bp):
ACCGGTTCTGACCGGTTTG
Found at i:1249494 original size:5 final size:5
Alignment explanation
Indices: 1249486--1249548 Score: 63
Period size: 5 Copynumber: 11.8 Consensus size: 5
1249476 CCTGACCGTT
** *
1249486 GACCC GACCC GACCC GATCGTT GACCC GACCC GACCC GACCGTT GACCC
1 GACCC GACCC GACCC GA-C-CC GACCC GACCC GACCC GACC--C GACCC
1249535 GACCC GACCC GACC
1 GACCC GACCC GACC
1249549 GTTGACCGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
5 40 0.83
6 2 0.04
7 6 0.12
ACGTcount: A:0.19, C:0.51, G:0.22, T:0.08
Consensus pattern (5 bp):
GACCC
Found at i:1249495 original size:22 final size:22
Alignment explanation
Indices: 1249469--1249555 Score: 156
Period size: 22 Copynumber: 4.0 Consensus size: 22
1249459 TGACCTGTCT
*
1249469 GACCCGACCTGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
1249491 GACCCGACCCGATCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
1249513 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
1249535 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
1249556 GTTTACCGTT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 62 1.00
ACGTcount: A:0.18, C:0.47, G:0.23, T:0.11
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:1249557 original size:7 final size:7
Alignment explanation
Indices: 1249545--1249575 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1249535 GACCCGACCC
1249545 GACCGTT
1 GACCGTT
1249552 GACCGTT
1 GACCGTT
*
1249559 TACCGTT
1 GACCGTT
1249566 GACCGTT
1 GACCGTT
1249573 GAC
1 GAC
1249576 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.16, C:0.29, G:0.26, T:0.29
Consensus pattern (7 bp):
GACCGTT
Found at i:1251083 original size:13 final size:13
Alignment explanation
Indices: 1251065--1251094 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1251055 TAGTCGAGGG
1251065 ACTCAACAAAGCA
1 ACTCAACAAAGCA
1251078 ACTCAACAAAGCA
1 ACTCAACAAAGCA
1251091 ACTC
1 ACTC
1251095 CATATAGTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.50, C:0.33, G:0.07, T:0.10
Consensus pattern (13 bp):
ACTCAACAAAGCA
Found at i:1252278 original size:13 final size:14
Alignment explanation
Indices: 1252252--1252280 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1252242 TACTTTTATC
1252252 ATTTTTTCACATTT
1 ATTTTTTCACATTT
1252266 ATTTTTTCA-ATTT
1 ATTTTTTCACATTT
1252279 AT
1 AT
1252281 CAATTATCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.66
Consensus pattern (14 bp):
ATTTTTTCACATTT
Found at i:1255406 original size:14 final size:14
Alignment explanation
Indices: 1255371--1255406 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
1255361 CAACGTCTAC
1255371 ATTAAGTAGAACTT
1 ATTAAGTAGAACTT
*
1255385 ATTAAAGTCGAACTT
1 ATT-AAGTAGAACTT
1255400 ATTAAGT
1 ATTAAGT
1255407 GTCATCAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (14 bp):
ATTAAGTAGAACTT
Found at i:1255719 original size:53 final size:54
Alignment explanation
Indices: 1255657--1255766 Score: 204
Period size: 54 Copynumber: 2.1 Consensus size: 54
1255647 TACATAAAAT
*
1255657 TTAAAATATAATATTAATG-AAAAAATACATCATCACATTCGAAATACGAACTA
1 TTAAAATATAATATTAATGAAAAAAATACATCATCACATTAGAAATACGAACTA
1255710 TTAAAATATAATATTAATGAAAAAAATACATCATCACATTAGAAATACGAACTA
1 TTAAAATATAATATTAATGAAAAAAATACATCATCACATTAGAAATACGAACTA
1255764 TTA
1 TTA
1255767 CTCAACAATC
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
53 19 0.35
54 36 0.65
ACGTcount: A:0.54, C:0.12, G:0.05, T:0.29
Consensus pattern (54 bp):
TTAAAATATAATATTAATGAAAAAAATACATCATCACATTAGAAATACGAACTA
Found at i:1257998 original size:7 final size:7
Alignment explanation
Indices: 1257986--1258018 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
1257976 CATTAATATT
1257986 ATTATCA
1 ATTATCA
1257993 ATTATCA
1 ATTATCA
1258000 ATTATCA
1 ATTATCA
1258007 ATTATCA
1 ATTATCA
1258014 ATTAT
1 ATTAT
1258019 TATTATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (7 bp):
ATTATCA
Found at i:1258022 original size:3 final size:3
Alignment explanation
Indices: 1258014--1258075 Score: 74
Period size: 3 Copynumber: 21.0 Consensus size: 3
1258004 TCAATTATCA
*
1258014 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TGT TTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT
* *
1258059 TTT ATT TTT ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT
1258076 TCTTTTGTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
2 3 0.06
3 47 0.92
4 1 0.02
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.73
Consensus pattern (3 bp):
ATT
Found at i:1258401 original size:5 final size:5
Alignment explanation
Indices: 1258393--1258419 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1258383 AAAAGAAATC
1258393 AGAAG AGAAG AGAAG AGAAG AGAAG AG
1 AGAAG AGAAG AGAAG AGAAG AGAAG AG
1258420 TAAGCAAGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (5 bp):
AGAAG
Found at i:1266306 original size:2 final size:2
Alignment explanation
Indices: 1266295--1266339 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
1266285 TAAAGGTGAT
1266295 TA TA -A 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 TA
1266336 TA TA
1 TA TA
1266340 CATACAATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1268457 original size:41 final size:41
Alignment explanation
Indices: 1268351--1268457 Score: 103
Period size: 42 Copynumber: 2.6 Consensus size: 41
1268341 CCAAAATTGG
* *
1268351 TAAGTCCTTTGGGCCATCAGTAAGTCTTTCGAGCATGATGAT
1 TAAGTCCTTCGGGCCATCA-TAAGTCTTTCGAGCAAGATGAT
* *
1268393 TACA-TCCTTCGGGTCATTTATAAGTCTTT-GAAGCAAGATGA-
1 TA-AGTCCTTCGGGCCA-TCATAAGTCTTTCG-AGCAAGATGAT
*
1268434 TAAGTTCTTCGGGCCATCCATAAG
1 TAAGTCCTTCGGGCCAT-CATAAG
1268458 ACCTTTGGGC
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
40 2 0.04
41 18 0.34
42 30 0.57
43 3 0.06
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (41 bp):
TAAGTCCTTCGGGCCATCATAAGTCTTTCGAGCAAGATGAT
Found at i:1268668 original size:256 final size:257
Alignment explanation
Indices: 1267957--1268780 Score: 1160
Period size: 257 Copynumber: 3.2 Consensus size: 257
1267947 CATTAAGTTA
* *
1267957 TTTCACATGTTTTTC--AAAAAATGAAAAAAACGATTTCCAAAGTTACTCATTTAAATCTTTCTT
1 TTTCACATGTTTTTCGAAAAAAAT-AAGAAAACGATTTCCAAAGTTTCTCATTTAAA----T-TT
*
1268020 GAAAATTGAAATTTTTGAAAAGTAAGAAAATGATTTTCAAAGTTTCTTACCTAGTAAACTATTTC
60 GAAAATTGAAATTTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAACTATTTC
* * * *
1268085 CAAAATTGGTAAGTCCTTCGGGCCATCAGTAAATCTTTCAAGAATGATGATTAAATCCTTCGGGT
125 CAAAATTGGTAAGTCCTTCTGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
* * * * *
1268150 C-TTCTATAAGCCTTTCGAGCAAGATGATAAGTCCTTCAGGCTATCCATAAGTCCTTCGGGCAGG
190 CATT-TATAAGTCTTTCGAGCAAGATGATAAGTTCTTCGGGCCATCCATAAGACCTTCGGGCAGG
1268214 ATGT
254 ATGT
* * * * * *
1268218 TTTCACATGTTTTTCGAAAAAAATGAGAAAACAATTTCCAAAGTTTCTCATTTAGATCTAAAAAA
1 TTTCACATGTTTTTCGAAAAAAATAAGAAAACGATTTCCAAAGTTTCTCATTTAAATTTGAAAAT
* *
1268283 TGAAATTTTTGAAAAGTAAGGAAACGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAAT
66 TGAAATTTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAAT
*
1268348 TGGTAAGTCCTT-TGGGCCATCAGTAAGTCTTTCGAGCATGATGATTACATCCTTCGGGTCATTT
131 TGGTAAGTCCTTCT-GGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATTT
*
1268412 ATAAGTCTTT-GAAGCAAGATGATAAGTTCTTCGGGCCATCCATAAGACCTTTGGGCAGGATGT
195 ATAAGTCTTTCG-AGCAAGATGATAAGTTCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGT
* * *
1268475 TTTCACTTGTATTTCGAAAAAAATAAGAAAATGATTTCCAAAGTTTCTCATTTAAATTTGAAAAT
1 TTTCACATGTTTTTCGAAAAAAATAAGAAAACGATTTCCAAAGTTTCTCATTTAAATTTGAAAAT
*
1268540 TGAAATTTTTGAAAAGTAA-AAAAT-AGTTTCCAAAGTTTTTTACCTAGTAAACTATTTCCAAAA
66 TGAAATTTTTGAAAAGTAAGAAAATGA-TTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAA
*
1268603 TTGGTAAGTCCTTCTGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGTTCATTT
130 TTGGTAAGTCCTTCTGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATTT
* * * *
1268668 ATAAGTCTTTCGACCAAGATGATAAG-TCTTTCGGGACATCCATAAGACCTTCGAGCAAGATGTT
195 ATAAGTCTTTCGAGCAAGATGATAAGTTC-TTCGGGCCATCCATAAGACCTTCGGGCAGGATG--
1268732 T
257 T
* * * *
1268733 TTTTACATGTTTTTCGAAAAAAATGAGAAAATGATTTCTAAAGTTTCT
1 TTTCACATGTTTTTCGAAAAAAATAAGAAAACGATTTCCAAAGTTTCT
1268781 TACCTAGTAA
Statistics
Matches: 506, Mismatches: 46, Indels: 25
0.88 0.08 0.04
Matches are distributed among these distances:
255 3 0.01
256 153 0.30
257 254 0.50
258 47 0.09
261 15 0.03
262 27 0.05
263 7 0.01
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Consensus pattern (257 bp):
TTTCACATGTTTTTCGAAAAAAATAAGAAAACGATTTCCAAAGTTTCTCATTTAAATTTGAAAAT
TGAAATTTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAAT
TGGTAAGTCCTTCTGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATTTA
TAAGTCTTTCGAGCAAGATGATAAGTTCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGT
Found at i:1268713 original size:41 final size:42
Alignment explanation
Indices: 1268627--1268729 Score: 109
Period size: 41 Copynumber: 2.5 Consensus size: 42
1268617 TGGCCATCAG
* ** **
1268627 TAAGTCTTTCGAGCATGATGATTAAATCCTTCGGTTCATTTA
1 TAAGTCTTTCGAGCAAGATGATTAAATCCTTCGGGACATCCA
* * *
1268669 TAAGTCTTTCGACCAAGATGA-TAAGTCTTTCGGGACATCCA
1 TAAGTCTTTCGAGCAAGATGATTAAATCCTTCGGGACATCCA
* *
1268710 TAAGACCTTCGAGCAAGATG
1 TAAGTCTTTCGAGCAAGATG
1268730 TTTTTTTACA
Statistics
Matches: 50, Mismatches: 11, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
41 31 0.62
42 19 0.38
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (42 bp):
TAAGTCTTTCGAGCAAGATGATTAAATCCTTCGGGACATCCA
Found at i:1269060 original size:3 final size:3
Alignment explanation
Indices: 1269046--1269104 Score: 70
Period size: 3 Copynumber: 20.3 Consensus size: 3
1269036 TTGGACATTC
* *
1269046 TAT TAA TAT TAT TAT CAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1269092 T-T T-T TAT T-T TAT T
1 TAT TAT TAT TAT TAT T
1269105 TCTTTTGCAA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 6 0.12
3 41 0.84
4 2 0.04
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1271606 original size:13 final size:13
Alignment explanation
Indices: 1271588--1271612 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1271578 GAGACGAGAT
1271588 CTTTTAAAAATTA
1 CTTTTAAAAATTA
1271601 CTTTTAAAAATT
1 CTTTTAAAAATT
1271613 TAAATTTGTT
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:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (13 bp):
CTTTTAAAAATTA
Found at i:1276673 original size:20 final size:18
Alignment explanation
Indices: 1276650--1276686 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
1276640 TGTATTATAA
1276650 TTATTCAATAATTTATTATT
1 TTATTCAAT--TTTATTATT
1276670 TTATTCAATTTTATTAT
1 TTATTCAATTTTATTAT
1276687 ACTAATTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
20 9 0.53
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATTCAATTTTATTATT
Found at i:1276836 original size:16 final size:18
Alignment explanation
Indices: 1276803--1276841 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1276793 TCTGTTGTAA
1276803 TTTTAATTATTGTGAATT
1 TTTTAATTATTGTGAATT
*
1276821 TTTTATTTATT-T-AATT
1 TTTTAATTATTGTGAATT
1276837 TTTTA
1 TTTTA
1276842 GTATTAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
17 1 0.05
18 10 0.50
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (18 bp):
TTTTAATTATTGTGAATT
Found at i:1278962 original size:26 final size:26
Alignment explanation
Indices: 1278933--1278987 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
1278923 TTTGTTAGTG
1278933 TTTTTATTATTTAATTGTTTGAATTA
1 TTTTTATTATTTAATTGTTTGAATTA
* **
1278959 TTTTTATTATTTAGTTGTTTTTATTA
1 TTTTTATTATTTAATTGTTTGAATTA
1278985 TTT
1 TTT
1278988 GAGTTGTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.71
Consensus pattern (26 bp):
TTTTTATTATTTAATTGTTTGAATTA
Found at i:1278979 original size:17 final size:18
Alignment explanation
Indices: 1278959--1278998 Score: 73
Period size: 17 Copynumber: 2.3 Consensus size: 18
1278949 GTTTGAATTA
1278959 TTTTTATTATTT-AGTTG
1 TTTTTATTATTTGAGTTG
1278976 TTTTTATTATTTGAGTTG
1 TTTTTATTATTTGAGTTG
1278994 TTTTT
1 TTTTT
1278999 TTTCTTGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.72
Consensus pattern (18 bp):
TTTTTATTATTTGAGTTG
Found at i:1283529 original size:24 final size:24
Alignment explanation
Indices: 1283502--1283550 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
1283492 CAAAACTCTC
1283502 TTTTCCTTTGA-ACGCCCATCTCAT
1 TTTTCCTTTGAGA-GCCCATCTCAT
*
1283526 TTTTCCTTTGAGAGCCTATCTCAT
1 TTTTCCTTTGAGAGCCCATCTCAT
1283550 T
1 T
1283551 GTTCTTCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.16, C:0.29, G:0.10, T:0.45
Consensus pattern (24 bp):
TTTTCCTTTGAGAGCCCATCTCAT
Found at i:1298201 original size:17 final size:17
Alignment explanation
Indices: 1298179--1298219 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1298169 TAAATAACAA
*
1298179 ATTTATTTTTCTTTTAT
1 ATTTATTTTTATTTTAT
*
1298196 ATTTATATTTATTTTAT
1 ATTTATTTTTATTTTAT
*
1298213 TTTTATT
1 ATTTATT
1298220 ATTCGTGGAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (17 bp):
ATTTATTTTTATTTTAT
Found at i:1301609 original size:145 final size:146
Alignment explanation
Indices: 1301346--1301639 Score: 581
Period size: 145 Copynumber: 2.0 Consensus size: 146
1301336 GGACAAAAAG
1301346 ATATTTTCACAATAAGACAGTTGGTAAGGCGCGTGTCTGATGGTTGTAACCGCCTGATGGGGACC
1 ATATTTTCACAATAAGACAGTTGGTAAGGCGCGTGTCTGATGGTTGTAACCGCCTGATGGGGACC
1301411 ACTGCCACCATTAAAGAAAGACCTCAAGCACAAAAGATACTCGAGGAGTATGATGGGTATTTTGT
66 ACTGCCACCATTAAAGAAAGACCTCAAGCACAAAAGATACTCGAGGAGTATGATGGGTATTTTGT
1301476 GTGCAAAATCCC-AGA
131 GTGCAAAATCCCAAGA
1301491 ATATTTTCACAATAAGACAGTTGGTAAGGCGCGTGTCTGATGGTTGTAACCGCCTGATGGGGACC
1 ATATTTTCACAATAAGACAGTTGGTAAGGCGCGTGTCTGATGGTTGTAACCGCCTGATGGGGACC
1301556 ACTGCCACCATTAAAGAAAGACCTCAAGCACAAAAGATACTCGAGGAGTATGATGGGTATTTTGT
66 ACTGCCACCATTAAAGAAAGACCTCAAGCACAAAAGATACTCGAGGAGTATGATGGGTATTTTGT
1301621 GTGCAAAATCCCAAGA
131 GTGCAAAATCCCAAGA
1301637 ATA
1 ATA
1301640 CCCTTAGATA
Statistics
Matches: 148, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
145 142 0.96
146 6 0.04
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.24
Consensus pattern (146 bp):
ATATTTTCACAATAAGACAGTTGGTAAGGCGCGTGTCTGATGGTTGTAACCGCCTGATGGGGACC
ACTGCCACCATTAAAGAAAGACCTCAAGCACAAAAGATACTCGAGGAGTATGATGGGTATTTTGT
GTGCAAAATCCCAAGA
Found at i:1307370 original size:24 final size:24
Alignment explanation
Indices: 1307337--1307395 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
1307327 TCGCGGACAC
*
1307337 TAAACAAACATATTGGTGAATATA
1 TAAACGAACATATTGGTGAATATA
1307361 TAAACGAACATATTGGTGAATATA
1 TAAACGAACATATTGGTGAATATA
1307385 TAAACGAACAT
1 TAAACGAACAT
1307396 GTTCATAGAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (24 bp):
TAAACGAACATATTGGTGAATATA
Found at i:1308743 original size:20 final size:19
Alignment explanation
Indices: 1308699--1308745 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
1308689 AAATTATTGG
1308699 TAAAATT-TAGTTTAAATA
1 TAAAATTATAGTTTAAATA
* *
1308717 TATAAATTATATTTTAGATA
1 TA-AAATTATAGTTTAAATA
1308737 TTAAAATTA
1 -TAAAATTA
1308746 GATATGAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 2 0.08
19 5 0.21
20 15 0.62
21 2 0.08
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (19 bp):
TAAAATTATAGTTTAAATA
Found at i:1309748 original size:13 final size:13
Alignment explanation
Indices: 1309730--1309766 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1309720 TTGCTACTTA
1309730 AGTTTTCTCTCCT
1 AGTTTTCTCTCCT
* *
1309743 AGTTTTTTCTTCT
1 AGTTTTCTCTCCT
1309756 AGTTTTCTCTC
1 AGTTTTCTCTC
1309767 ATTGGTAAGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.08, C:0.24, G:0.08, T:0.59
Consensus pattern (13 bp):
AGTTTTCTCTCCT
Found at i:1311136 original size:6 final size:6
Alignment explanation
Indices: 1311125--1311158 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1311115 CATCATCAAC
* *
1311125 ATCATT ATCATT TTCACT ATCATT ATCATT ATCA
1 ATCATT ATCATT ATCATT ATCATT ATCATT ATCA
1311159 CTGTTCAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.47
Consensus pattern (6 bp):
ATCATT
Found at i:1311146 original size:18 final size:18
Alignment explanation
Indices: 1311125--1311160 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1311115 CATCATCAAC
*
1311125 ATCATTATCATTTTCACT
1 ATCATTATCATTATCACT
1311143 ATCATTATCATTATCACT
1 ATCATTATCATTATCACT
1311161 GTTCAAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.22, G:0.00, T:0.47
Consensus pattern (18 bp):
ATCATTATCATTATCACT
Found at i:1311414 original size:24 final size:24
Alignment explanation
Indices: 1311369--1311415 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1311359 CTCGTATAAA
* *
1311369 TTGCAACGAAGTACCGCGTAGAAT
1 TTGCAACGAAGTACCACATAGAAT
* *
1311393 TTGCACCGAAGTGCCACATAGAA
1 TTGCAACGAAGTACCACATAGAA
1311416 ATATCCCGAA
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:0.34, C:0.23, G:0.23, T:0.19
Consensus pattern (24 bp):
TTGCAACGAAGTACCACATAGAAT
Found at i:1312789 original size:43 final size:46
Alignment explanation
Indices: 1312668--1312791 Score: 166
Period size: 47 Copynumber: 2.8 Consensus size: 46
1312658 ATAAAATCTT
*
1312668 TTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
1 TTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* * *
1312713 TTACTATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATAC
1 TTACCATTT-AATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
*
1312760 TTTCCA-TT-ATT-CATAAGCTCGTAAGCTTATTT
1 TTACCATTTAATTCCATAAGCTCGTAAGCTTATTT
1312792 ACATACTTAC
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
43 21 0.30
44 3 0.04
45 8 0.11
46 2 0.03
47 37 0.52
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.41
Consensus pattern (46 bp):
TTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
Found at i:1312799 original size:38 final size:41
Alignment explanation
Indices: 1312681--1312805 Score: 130
Period size: 47 Copynumber: 2.9 Consensus size: 41
1312671 CCATTTATCC
* *
1312681 CATAAGCTCGTAAGCTTATTTTACCAAAATACTTACTATTTAAATT
1 CATAAGCTCGTAAGCTTATTTTATC--AATACTTACCA-TT--ATT
*
1312727 CCATAAGCTCGTAAGCTTATTTTATCAATATACTTTCCATTATT
1 -CATAAGCTCGTAAGCTTATTTTATC-A-ATACTTACCATTATT
1312771 CATAAGCTCGTAAGCTTA-TTTA-C-ATACTTACCATT
1 CATAAGCTCGTAAGCTTATTTTATCAATACTTACCATT
1312806 CATTAACCAA
Statistics
Matches: 73, Mismatches: 4, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
38 11 0.15
41 1 0.01
42 4 0.05
43 18 0.25
44 3 0.04
46 4 0.05
47 32 0.44
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (41 bp):
CATAAGCTCGTAAGCTTATTTTATCAATACTTACCATTATT
Found at i:1317117 original size:16 final size:16
Alignment explanation
Indices: 1317098--1317131 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1317088 TTTTAACTAT
*
1317098 TGATATTTTGATTTAC
1 TGATATATTGATTTAC
*
1317114 TGATGTATTGATTTAC
1 TGATATATTGATTTAC
1317130 TG
1 TG
1317132 TTTACAAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.06, G:0.18, T:0.53
Consensus pattern (16 bp):
TGATATATTGATTTAC
Found at i:1323402 original size:2 final size:2
Alignment explanation
Indices: 1323395--1323447 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1323385 ATGATGTTAA
1323395 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
1323437 AT AT AT AT AT A
1 AT AT AT AT AT A
1323448 CAATTAGGTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1323786 original size:26 final size:26
Alignment explanation
Indices: 1323743--1323804 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
1323733 TTTATCAAAT
1323743 AAAAAAATAATTACTTAATTACA-TA
1 AAAAAAATAATTACTTAATTACATTA
* * *
1323768 AAAAAAATTATATAGTTAATTACATTT
1 AAAAAAATAAT-TACTTAATTACATTA
1323795 AAAAAAATAA
1 AAAAAAATAA
1323805 GTACCATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 10 0.32
26 11 0.35
27 10 0.32
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (26 bp):
AAAAAAATAATTACTTAATTACATTA
Found at i:1325870 original size:147 final size:143
Alignment explanation
Indices: 1325510--1325873 Score: 356
Period size: 143 Copynumber: 2.5 Consensus size: 143
1325500 TGTGTCTGCA
* * * * * *
1325510 AATTCCAATAGCTTGAGTTGTCAATCACCTTTAGGAACCAATGGTATTTTGAA-TA-GTTATATC
1 AATTCCAATAGCTTAAGTAGTCAATCACCTTTAGGAACCAATGATATTCTGAATTATG-GA-ATG
* * * * *
1325573 TTGAATTGTTTCTAGGATGTGATGATAAATCGTATGAACTTTTAAGACCTTTTTCTTCTAAACAT
64 TTGAAATGTTGCTAGCATGTGAAGATAAATCATATGAACTTTTAAGACCTTTTTCTTCTAAACAT
1325638 CACTCCGAGTATGCT
129 CACTCCGAGTATGCT
* * * * * * * *
1325653 AATTCCAATAGCTCAAGTAGTCAATCCCCTTTCGAAATCAGT-ACTATTCTGAATTGTGGATTGT
1 AATTCCAATAGCTTAAGTAGTCAATCACCTTTAGGAACCAATGA-TATTCTGAATTATGGAATGT
* ** * ** **
1325717 TAAAATGTTGCTAGCATGTGAAAGATAAATCATATGAACTTTTAAGGGCTTTTGTCTTTTGGATG
65 TGAAATGTTGCTAGCATGTG-AAGATAAATCATATGAACTTTTAAGACCTTTT-TCTTCTAAACA
*
1325782 TCACTCTGAGTATGCT
128 TCACTCCGAGTATGCT
* * * *
1325798 AATTCTCCAATAGCTTTAGTAGTCAATCACTTTTAGGTACCACTGATATTCTGAATTATGGAATG
1 AA-T-TCCAATAGCTTAAGTAGTCAATCACCTTTAGGAACCAATGATATTCTGAATTATGGAATG
1325863 TTGAAATGTTG
64 TTGAAATGTTG
1325874 TTACTTGCTA
Statistics
Matches: 173, Mismatches: 40, Indels: 12
0.77 0.18 0.05
Matches are distributed among these distances:
143 60 0.35
144 30 0.17
145 24 0.14
146 1 0.01
147 57 0.33
148 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (143 bp):
AATTCCAATAGCTTAAGTAGTCAATCACCTTTAGGAACCAATGATATTCTGAATTATGGAATGTT
GAAATGTTGCTAGCATGTGAAGATAAATCATATGAACTTTTAAGACCTTTTTCTTCTAAACATCA
CTCCGAGTATGCT
Found at i:1332712 original size:22 final size:21
Alignment explanation
Indices: 1332660--1332700 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1332650 TAAAAATTCT
*
1332660 AAAAAGAA-AAAAGAGCATAG
1 AAAAACAAGAAAAGAGCATAG
1332680 AAAAACAAGAAAAGAGCATAG
1 AAAAACAAGAAAAGAGCATAG
1332701 GAAAGCAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.68, C:0.07, G:0.20, T:0.05
Consensus pattern (21 bp):
AAAAACAAGAAAAGAGCATAG
Found at i:1333886 original size:34 final size:34
Alignment explanation
Indices: 1333838--1333902 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
1333828 AATACCCTAA
*
1333838 TTAGTGTAAACCCTATACATAATGAACAAAATTC
1 TTAGCGTAAACCCTATACATAATGAACAAAATTC
1333872 TTAGCGTAAACCCTATACATAATGAACAAAA
1 TTAGCGTAAACCCTATACATAATGAACAAAA
1333903 ATATTATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.46, C:0.18, G:0.09, T:0.26
Consensus pattern (34 bp):
TTAGCGTAAACCCTATACATAATGAACAAAATTC
Found at i:1354889 original size:17 final size:17
Alignment explanation
Indices: 1354867--1354920 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
1354857 AATGTTAATA
1354867 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
1354884 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
1354901 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
1354918 TTT
1 TTT
1354921 TATAATGTAT
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:1356525 original size:21 final size:21
Alignment explanation
Indices: 1356499--1356592 Score: 136
Period size: 21 Copynumber: 4.5 Consensus size: 21
1356489 TATGCCATCT
*
1356499 CCGCAGGGTTACATTTCGAGC
1 CCGCAGGGTTACATTCCGAGC
1356520 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
1356541 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCGAGC
* *
1356562 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCGAGC
1356583 CCGCAGGGTT
1 CCGCAGGGTT
1356593 TTATACCATA
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
20 2 0.03
21 64 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.33, G:0.28, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:1357174 original size:33 final size:34
Alignment explanation
Indices: 1357115--1357211 Score: 124
Period size: 33 Copynumber: 2.9 Consensus size: 34
1357105 AAATGTTTTT
*
1357115 AAAATACAAATTATATTATTCAAAATTTAAAATA
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* * *
1357149 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* * *
1357182 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCAAAATTTAA
1357212 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCAAAATTTAAAATA
Found at i:1357218 original size:34 final size:32
Alignment explanation
Indices: 1357113--1357218 Score: 122
Period size: 34 Copynumber: 3.2 Consensus size: 32
1357103 ATAAATGTTT
*
1357113 TTAAAATACAAATTATATTATTCAAAATTTAAAA
1 TTAAAATAAAAATTATATTATTC-AAATTT-AAA
* *
1357147 TAAAAATAAAAATAATATTATTCAAATTTAAA
1 TTAAAATAAAAATTATATTATTCAAATTTAAA
* *
1357179 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTC-AAATTTAA-A
1357214 TTAAA
1 TTAAA
1357219 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (32 bp):
TTAAAATAAAAATTATATTATTCAAATTTAAA
Found at i:1357839 original size:128 final size:128
Alignment explanation
Indices: 1357611--1358109 Score: 872
Period size: 128 Copynumber: 3.9 Consensus size: 128
1357601 TTACCTGATT
* *
1357611 TACTGATATATCTAGTATCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *** * *
1357676 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCTTGAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
1357739 TACTGATATATCTAGTGTCCCCAAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
1357804 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
1357867 TACTGATATATCTAGTGTCCCCGAGGGACATAAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
1357932 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCTTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
1357995 TACTGATATATCTAGTGTCCCTGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1358060 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATA
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATA
1358110 ATACTCCGAT
Statistics
Matches: 354, Mismatches: 17, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
128 354 1.00
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:1372898 original size:22 final size:22
Alignment explanation
Indices: 1372870--1372925 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
1372860 GGGTCTATAC
*
1372870 GGTCCTTCGGGACATACTCATA
1 GGTCCTTCGGGACATACTCACA
1372892 GGTCCTTCGGGACATACTCACA
1 GGTCCTTCGGGACATACTCACA
1372914 GGTCCTTCGGGA
1 GGTCCTTCGGGA
1372926 TATATTTTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.20, C:0.29, G:0.27, T:0.25
Consensus pattern (22 bp):
GGTCCTTCGGGACATACTCACA
Found at i:1380031 original size:3 final size:3
Alignment explanation
Indices: 1380016--1380095 Score: 151
Period size: 3 Copynumber: 26.7 Consensus size: 3
1380006 AATTTTAATT
*
1380016 TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1380064 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1380096 TCATTAATAT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1381864 original size:21 final size:22
Alignment explanation
Indices: 1381817--1381864 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
1381807 GTATGTACAT
* * *
1381817 ATTGTAAATGTTATTATTTTAT
1 ATTGTAAATATTATTATTATAC
*
1381839 GTTGTAAATATT-TTATTATAC
1 ATTGTAAATATTATTATTATAC
1381860 ATTGT
1 ATTGT
1381865 TATTGTTTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.56
Consensus pattern (22 bp):
ATTGTAAATATTATTATTATAC
Found at i:1382461 original size:16 final size:16
Alignment explanation
Indices: 1382423--1382461 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1382413 CATACCAGCT
1382423 TTTTTGTCTAAAAAATA
1 TTTTT-TCTAAAAAATA
* *
1382440 ATTTTTCTTAAAAATA
1 TTTTTTCTAAAAAATA
1382456 TTTTTT
1 TTTTTT
1382462 AAAAGACGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (16 bp):
TTTTTTCTAAAAAATA
Found at i:1384500 original size:3 final size:3
Alignment explanation
Indices: 1384494--1384534 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1384484 AAAAAATTGA
1384494 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1384535 ATTTTAGTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1385008 original size:11 final size:11
Alignment explanation
Indices: 1384967--1385009 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
1384957 TAAACACCCG
*
1384967 AAATGCCACTA
1 AAATCCCACTA
*
1384978 AAATCCTACTA
1 AAATCCCACTA
*
1384989 AAATACCACTA
1 AAATCCCACTA
1385000 AAATCCCACT
1 AAATCCCACT
1385010 TAAACACCAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.47, C:0.30, G:0.02, T:0.21
Consensus pattern (11 bp):
AAATCCCACTA
Found at i:1385018 original size:22 final size:22
Alignment explanation
Indices: 1384972--1385018 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1384962 ACCCGAAATG
* *
1384972 CCACTAAAATCCTACTAAAATA
1 CCACTAAAATCCCACTAAAACA
*
1384994 CCACTAAAATCCCACTTAAACA
1 CCACTAAAATCCCACTAAAACA
1385016 CCA
1 CCA
1385019 TTATTTGGGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.34, G:0.00, T:0.19
Consensus pattern (22 bp):
CCACTAAAATCCCACTAAAACA
Found at i:1386541 original size:104 final size:101
Alignment explanation
Indices: 1386394--1386595 Score: 287
Period size: 104 Copynumber: 2.0 Consensus size: 101
1386384 TGTCTTGTGT
*
1386394 CACGTGTAATACACTAATTATTGTACTAAAGTGGCTTTACATTTAATATTACATATAAAATCTTA
1 CACGTGTAATACACTAATTATTGTACTAAAGTGGCCTTACATTTAATATTACATATAAAATCTTA
* *
1386459 TTATATATATGTCTTATATGGAATCATTAAGTGTTCTC
66 -T-TATATATGTCTTATATGGAAGCATTAAATGTTCTC
* * * * *
1386497 CACGTGTAATATACTAATTATGTGTGCTAAAGTGGCCTTGCATTTAATATTATATATACAATCTT
1 CACGTGTAATACACTAATTAT-TGTACTAAAGTGGCCTTACATTTAATATTACATATAAAATCTT
* *
1386562 ATTATATATGTTTTGTATGGAAGCATTAAATGTT
65 ATTATATATGTCTTATATGGAAGCATTAAATGTT
1386596 TTGATATATG
Statistics
Matches: 88, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
102 28 0.32
103 21 0.24
104 39 0.44
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (101 bp):
CACGTGTAATACACTAATTATTGTACTAAAGTGGCCTTACATTTAATATTACATATAAAATCTTA
TTATATATGTCTTATATGGAAGCATTAAATGTTCTC
Found at i:1389843 original size:15 final size:15
Alignment explanation
Indices: 1389823--1389851 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1389813 TAATAGCTAG
1389823 CTATCGTTTTTTGTC
1 CTATCGTTTTTTGTC
1389838 CTATCGTTTTTTGT
1 CTATCGTTTTTTGT
1389852 GATATCACGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.17, G:0.14, T:0.62
Consensus pattern (15 bp):
CTATCGTTTTTTGTC
Found at i:1389857 original size:15 final size:15
Alignment explanation
Indices: 1389824--1389857 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1389814 AATAGCTAGC
*
1389824 TATCGTTTTTTGTCC
1 TATCGTTTTTTGTCA
*
1389839 TATCGTTTTTTGTGA
1 TATCGTTTTTTGTCA
1389854 TATC
1 TATC
1389858 ACGATACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.15, G:0.15, T:0.59
Consensus pattern (15 bp):
TATCGTTTTTTGTCA
Found at i:1391196 original size:3 final size:3
Alignment explanation
Indices: 1391188--1391268 Score: 83
Period size: 3 Copynumber: 26.3 Consensus size: 3
1391178 TTATATTAAA
* * * * *
1391188 ATT ATT ATT ATT AAT ATA ACT ATT A-T ATT ATA ATAC ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT
1391233 ATAT ATT ATT ATT ATT ATT ATTT ATT ATT ATT ATT A
1 AT-T ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT A
1391269 ATGTTACATA
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
2 2 0.03
3 55 0.85
4 8 0.12
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:1391212 original size:32 final size:32
Alignment explanation
Indices: 1391170--1391285 Score: 115
Period size: 35 Copynumber: 3.5 Consensus size: 32
1391160 TTGTCCGGGT
* *
1391170 TATAAATATTATATTAAAATTATTATTATTAA
1 TATAACTATTATATTATAATTATTATTATTAA
*
1391202 TATAACTATTATATTATAATACATTATTATTATA
1 TATAACTATTATATTATAAT-TATTATTATTA-A
* * *
1391236 TATTATTATTATTATTATTTATTATTATTATTAA
1 TATAACTATTA-TATTA-TAATTATTATTATTAA
* *
1391270 TGTTACATATTATATT
1 TATAAC-TATTATATT
1391286 TTACAGGCCC
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
32 18 0.26
33 10 0.14
34 19 0.27
35 20 0.29
36 3 0.04
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (32 bp):
TATAACTATTATATTATAATTATTATTATTAA
Found at i:1391267 original size:16 final size:17
Alignment explanation
Indices: 1391188--1391268 Score: 89
Period size: 16 Copynumber: 4.9 Consensus size: 17
1391178 TTATATTAAA
*
1391188 ATTATTATTATTAATAT
1 ATTATTATTATTATTAT
* *
1391205 AACTATTA-TATTATAAT
1 -ATTATTATTATTATTAT
*
1391222 A-CATTATTATTA-TAT
1 ATTATTATTATTATTAT
1391237 ATTATTATTATTATTAT
1 ATTATTATTATTATTAT
1391254 -TTATTATTATTATTA
1 ATTATTATTATTATTA
1391269 ATGTTACATA
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
15 7 0.13
16 31 0.57
17 10 0.19
18 6 0.11
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTATTATTATTATTAT
Found at i:1394570 original size:21 final size:21
Alignment explanation
Indices: 1394546--1394601 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
1394536 CAAAACCGGG
1394546 AGACATGAAGACCATTCATAA
1 AGACATGAAGACCATTCATAA
*
1394567 AGACATGAAGACCCTTCATAA
1 AGACATGAAGACCATTCATAA
1394588 AGACATGAAGACCA
1 AGACATGAAGACCA
1394602 CTTCGCATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.46, C:0.21, G:0.16, T:0.16
Consensus pattern (21 bp):
AGACATGAAGACCATTCATAA
Found at i:1394878 original size:6 final size:6
Alignment explanation
Indices: 1394846--1394870 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1394836 TAACACCTCG
1394846 TGCATT TGCATT TGCATT TGCATT T
1 TGCATT TGCATT TGCATT TGCATT T
1394871 TTCATTTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (6 bp):
TGCATT
Found at i:1394897 original size:20 final size:20
Alignment explanation
Indices: 1394856--1394897 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1394846 TGCATTTGCA
* *
1394856 TTTGCATTTGCATTTTTCAT
1 TTTGCATTTGCATCTTTAAT
1394876 TTTGCA-TTGCATGCTTTAAT
1 TTTGCATTTGCAT-CTTTAAT
1394896 TT
1 TT
1394898 AAACATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.17, C:0.14, G:0.12, T:0.57
Consensus pattern (20 bp):
TTTGCATTTGCATCTTTAAT
Found at i:1398935 original size:83 final size:81
Alignment explanation
Indices: 1398774--1398935 Score: 290
Period size: 83 Copynumber: 2.0 Consensus size: 81
1398764 GATACAGACC
1398774 AAGGCCTTGAGAATGAGCCTTACAATTAGGGTTGTGGCATTTTGAAGGCACGTACCAGTATAAGT
1 AAGGCCTTGAGAATGAGCCTTACAATTAGGGTTGTGGCATTTTGAAGGCACGTACCAGTATAAGT
1398839 TGACGTTGCGGCACAG
66 TGACGTTGCGGCACAG
1398855 AAGGCCTTGAGAATGAGCCTTACAATTAGAGGTGTTGTGGCATTTTGAAGGC-CGTACCAGTATA
1 AAGGCCTTGAGAATGAGCCTTACAATT--AGG-GTTGTGGCATTTTGAAGGCACGTACCAGTATA
1398919 AGTTGACGTTGCGGCAC
63 AGTTGACGTTGCGGCAC
1398936 TAGTGAAGGC
Statistics
Matches: 78, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
81 27 0.35
83 32 0.41
84 19 0.24
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.27
Consensus pattern (81 bp):
AAGGCCTTGAGAATGAGCCTTACAATTAGGGTTGTGGCATTTTGAAGGCACGTACCAGTATAAGT
TGACGTTGCGGCACAG
Found at i:1400298 original size:36 final size:36
Alignment explanation
Indices: 1400219--1400325 Score: 128
Period size: 36 Copynumber: 2.9 Consensus size: 36
1400209 AGCAAAGTCA
*
1400219 ATCTTAAGCCTTCACTGAAGAGTAGTGAA-TCAAAACC
1 ATCTTAATCCTTCACTGAAGAGTAGTGAAGT--AAACC
**
1400256 ATCTTAATCCTTCACCAAAGAGTAGTGAAGTAAACC
1 ATCTTAATCCTTCACTGAAGAGTAGTGAAGTAAACC
* *
1400292 ATCTTAAGT-ATTCACTGAAGAGTAGGGAAGTAAA
1 ATCTTAA-TCCTTCACTGAAGAGTAGTGAAGTAAA
1400326 TCTATTTTAA
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
36 33 0.54
37 27 0.44
38 1 0.02
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (36 bp):
ATCTTAATCCTTCACTGAAGAGTAGTGAAGTAAACC
Found at i:1400349 original size:37 final size:36
Alignment explanation
Indices: 1400219--1400351 Score: 108
Period size: 37 Copynumber: 3.6 Consensus size: 36
1400209 AGCAAAGTCA
* * *
1400219 ATCTTAAGCCTTCACTGAAGAGTAGTGAA-TCAAAACC
1 ATCTTAAGCATTCACAGAAGAGTAGGGAAGT--AAACC
* * *
1400256 ATCTTAATCCTTCACCA-AAGAGTAGTGAAGTAAACC
1 ATCTTAAGCATTCA-CAGAAGAGTAGGGAAGTAAACC
* * *
1400292 ATCTTAAGTATTCACTGAAGAGTAGGGAAGTAAATCT
1 ATCTTAAGCATTCACAGAAGAGTAGGGAAGTAAA-CC
* * *
1400329 ATTTTAAGCCTTCTCAGAAGAGT
1 ATCTTAAGCATTCACAGAAGAGT
1400352 GTTGGAGCAA
Statistics
Matches: 79, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
35 1 0.01
36 32 0.41
37 44 0.56
38 2 0.03
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (36 bp):
ATCTTAAGCATTCACAGAAGAGTAGGGAAGTAAACC
Found at i:1400722 original size:37 final size:37
Alignment explanation
Indices: 1400667--1400742 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
1400657 TCGACATTAT
1400667 AAGCAAATCAAACTTAAGCCTTCACGAAAG-AGTAGTG
1 AAGCAAATCAAACTTAAGCCTTCA-GAAAGAAGTAGTG
* *
1400704 AAGCAAATC-ATCTATAAGCCTTCATAAAGAAGTAGTG
1 AAGCAAATCAAACT-TAAGCCTTCAGAAAGAAGTAGTG
1400741 AA
1 AA
1400743 TCAAGAGAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 7 0.20
37 28 0.80
ACGTcount: A:0.45, C:0.17, G:0.17, T:0.21
Consensus pattern (37 bp):
AAGCAAATCAAACTTAAGCCTTCAGAAAGAAGTAGTG
Found at i:1400846 original size:56 final size:56
Alignment explanation
Indices: 1400748--1401459 Score: 1112
Period size: 56 Copynumber: 12.8 Consensus size: 56
1400738 GTGAATCAAG
* * * *
1400748 AGAAGA-TGTTCGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTTGC
1 AGAAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGC
*
1400802 ATAAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGC
1 AGAAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGC
*
1400858 AGAAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGGGCGAACCCGTTTGC
1 AGAAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGC
* * *
1400914 AGAAGATTATTCGAGTTTTATACTTCCTGAAAGAAGGAGGGAGCGAACCCATTTGC
1 AGAAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGC
* * *
1400970 AGAAGATTATTCAAATTCTATACTTTCTGAAAGAAAGAGGGAGCGAACCCGTTTGC
1 AGAAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGC
* *
1401026 AGAAGATTATTCGAGTTTTATACTTCCTGAAAGAAAGAGGGAGCAAACCCGTTTGC
1 AGAAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGC
* * *
1401082 AAAAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAACGAACCCGTTTGT
1 AGAAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGC
*
1401138 AGAAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAAGGAGCGAACCCGTTTGC
1 AGAAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGC
*
1401194 AGAAGATTATTCAAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGC
1 AGAAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGC
*
1401250 AGAAGATTATTCGAGTTCTATATTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGC
1 AGAAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGC
*
1401306 AGAAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCATTTGC
1 AGAAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGC
* * * *
1401362 AGAACATTATTCGAATTCTATACTTCATGAAAGAAAGA-GGAGCGAACCCGTTTGT
1 AGAAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGC
* * *
1401417 GGAAGATTGTTCGAG-TCTTATAC-TCTCTG-AAGAAATAGGGAGC
1 AGAAGATTATTCGAGTTC-TATACTTC-CTGAAAGAAAGAGGGAGC
1401460 AGACATGATT
Statistics
Matches: 605, Mismatches: 48, Indels: 9
0.91 0.07 0.01
Matches are distributed among these distances:
54 16 0.03
55 56 0.09
56 533 0.88
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (56 bp):
AGAAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGC
Found at i:1401487 original size:45 final size:45
Alignment explanation
Indices: 1401421--1401572 Score: 205
Period size: 45 Copynumber: 3.2 Consensus size: 45
1401411 GTTTGTGGAA
1401421 GATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACAT
1 GATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACAT
*
1401466 GATTGTTCGAGTCTTAAACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
1 GATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAG--AC-A----T
1401518 GAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACAT
1 G---ATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACAT
1401566 GATTGTT
1 GATTGTT
1401573 GAAAATTGTT
Statistics
Matches: 95, Mismatches: 2, Indels: 20
0.81 0.02 0.17
Matches are distributed among these distances:
45 46 0.48
47 2 0.02
48 3 0.03
52 3 0.03
53 2 0.02
55 39 0.41
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (45 bp):
GATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACAT
Found at i:1401544 original size:100 final size:99
Alignment explanation
Indices: 1401413--1401723 Score: 370
Period size: 110 Copynumber: 3.0 Consensus size: 99
1401403 GCGAACCCGT
*
1401413 TTGTGGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACATGATTGTTCGAGT
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACATGATTGTTCGAGT
* *
1401478 CTTAAACTCTCTGAAGAAATAGGGAGCAGACACGA
66 CTTATACTCTCTGAAGGAATA-GGAGCAGACACGA
*
1401513 TTGTTGAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACATGATTGTTGAAAA
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC---A----TG---A
* *
1401578 TTGTTTGAGTCTTATACTCTCTGAAGGAATAAGGAGCATACACGA
56 TTGTTCGAGTCTTATACTCTCTGAAGGAAT-AGGAGCAGACACGA
* * * **
1401623 TTGTTCAAGATTGTTTGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACCATTGTTTTTCG
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACATGATTG---TTCG
* *
1401688 AGTCTTATACTCTTTGAAGGAATAGGAGGAGACACG
63 AGTCTTATACTCTCTGAAGGAATAGGAGCAGACACG
1401724 TTGAAGATTG
Statistics
Matches: 181, Mismatches: 16, Indels: 26
0.81 0.07 0.12
Matches are distributed among these distances:
100 53 0.29
102 11 0.06
103 26 0.14
107 3 0.02
110 87 0.48
111 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (99 bp):
TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACATGATTGTTCGAGT
CTTATACTCTCTGAAGGAATAGGAGCAGACACGA
Found at i:1401664 original size:110 final size:105
Alignment explanation
Indices: 1401467--1401866 Score: 394
Period size: 110 Copynumber: 3.8 Consensus size: 105
1401457 AGCAGACATG
* * * *
1401467 ATTGTTCGAGTCTTAAACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAAATTGTTCGAG
1 ATTGTTCGAGTCTTATACTCTCTGAAGGAATAAGGAGCAGACACGATTGTTGAAGA---TT-GAG
* *
1401532 TCTTATACTCTCTGAAGAAATAGGGAGCAGACATGATTGTTGAAA
62 TCCTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG-AA
* * *
1401577 ATTGTTTGAGTCTTATACTCTCTGAAGGAATAAGGAGCATACACGATTGTTCAAGATTGTTTGAG
1 ATTGTTCGAGTCTTATACTCTCTGAAGGAATAAGGAGCAGACACGATTGTTGAAGA----TTGAG
* * *
1401642 TCTTATACTCTCTGAAGGAATAGGGAGCAGACACCATTG-T---
62 TCCTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAA
* *
1401682 -TT-TTCGAGTCTTATACTCTTTGAAGGAAT-AGGAGGAGACAC----GTTGAAGATTGAGTCCT
1 ATTGTTCGAGTCTTATACTCTCTGAAGGAATAAGGAGCAGACACGATTGTTGAAGATTGAGTCCT
* * * *
1401740 ATACTCTCTGAAGGAATAGTGAGCGGACACGTTTGTTGAA
66 ATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAA
* * * * * *
1401780 GGTTGTTCAAGTCCTATACTCTCTGAAGGAATAGGGAGC-GAACATGTTTGTTGAAGATTGAGTC
1 -ATTGTTCGAGTCTTATACTCTCTGAAGGAATAAGGAGCAG-ACACGATTGTTGAAGATTGAGTC
1401844 CTATACTCTCTGAA-AAATAGGGA
64 CTATACTCTCTGAAGAAATAGGGA
1401867 ACATGCCTAT
Statistics
Matches: 246, Mismatches: 30, Indels: 33
0.80 0.10 0.11
Matches are distributed among these distances:
94 39 0.16
95 1 0.00
98 7 0.03
100 2 0.01
101 25 0.10
102 17 0.07
103 25 0.10
104 2 0.01
105 7 0.03
106 29 0.12
109 1 0.00
110 88 0.36
111 3 0.01
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.30
Consensus pattern (105 bp):
ATTGTTCGAGTCTTATACTCTCTGAAGGAATAAGGAGCAGACACGATTGTTGAAGATTGAGTCCT
ATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAA
Found at i:1401691 original size:48 final size:48
Alignment explanation
Indices: 1401637--1401866 Score: 155
Period size: 55 Copynumber: 4.6 Consensus size: 48
1401627 TCAAGATTGT
***
1401637 TTGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACCATTG-TTT
1 TTGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACCATTGAAGA
* * *
1401684 TTCGAGTCTTATACTCTTTGAAGGAATA-GGAGGAGACA-CGTTGAAGA
1 TT-GAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACCATTGAAGA
* * * ** *
1401731 TTGAGTCCTATACTCTCTGAAGGAATAGTGAGCGGACACGTTTGTTGAAGG
1 TTGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACAC---CATTGAAGA
* ***
1401782 TTGTTCAAGTCCTATACTCTCTGAAGGAATAGGGAGC-GAACATGTTTGTTGAAGA
1 TTG----AGTCTTATACTCTCTGAAGGAATAGGGAGCAG-ACA---CCATTGAAGA
* *
1401837 TTGAGTCCTATACTCTCTGAA-AAATAGGGA
1 TTGAGTCTTATACTCTCTGAAGGAATAGGGA
1401867 ACATGCCTAT
Statistics
Matches: 151, Mismatches: 17, Indels: 27
0.77 0.09 0.14
Matches are distributed among these distances:
46 27 0.18
47 20 0.13
48 24 0.16
50 8 0.05
51 28 0.19
54 1 0.01
55 43 0.28
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (48 bp):
TTGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACCATTGAAGA
Found at i:1402123 original size:3 final size:3
Alignment explanation
Indices: 1402106--1402177 Score: 65
Period size: 3 Copynumber: 23.3 Consensus size: 3
1402096 ATTATATTAA
* * * *
1402106 ATT A-T ATT TTT ATT ATT ATT ATT ATT ATA ATT ATT AAAT ATAT ATAC
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT AT-T AT-T
*
1402153 ATT ATT ATT ATT ATT ACT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
1402178 ATGTTACATA
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
2 2 0.04
3 46 0.82
4 8 0.14
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:1404063 original size:87 final size:83
Alignment explanation
Indices: 1403912--1404081 Score: 295
Period size: 87 Copynumber: 2.0 Consensus size: 83
1403902 TTTTTAAATA
1403912 ATCGAATATTCTTCATCTTCTAAAGGTTGGGTAATTTTTAAATCTATATTGGTGCTTTTGAATAT
1 ATCGAATATTCTTCATCTTCTAAAGGTTGGGTAATTTTTAAATCTATATTGGTGCTTTTGAATAT
1403977 GATGAAATTCATATGTTG
66 GATGAAATTCATATGTTG
*
1403995 ATCGAATATTCTTCATCTTTCTAAAGGTTGGGTAATTTTAATTTAATCTATATTGGTGCTTTTGA
1 ATCGAATATTCTTCATC-TTCTAAAGGTTGGGTAA-TTT--TTAAATCTATATTGGTGCTTTTGA
1404060 ATATGATGAAATTCATATGTTG
62 ATATGATGAAATTCATATGTTG
1404082 CTATTTTTTG
Statistics
Matches: 82, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
83 17 0.21
84 17 0.21
85 3 0.04
87 45 0.55
ACGTcount: A:0.29, C:0.09, G:0.16, T:0.45
Consensus pattern (83 bp):
ATCGAATATTCTTCATCTTCTAAAGGTTGGGTAATTTTTAAATCTATATTGGTGCTTTTGAATAT
GATGAAATTCATATGTTG
Found at i:1405825 original size:85 final size:85
Alignment explanation
Indices: 1405677--1405896 Score: 264
Period size: 85 Copynumber: 2.6 Consensus size: 85
1405667 ATACAATCAC
* * * *
1405677 GACACACGAATGTGTGTCATCTT-TTTTAATGACGTGTGCTTCAATGACACGCAATGTAAGTCAT
1 GACACACAAATGTGTGTCATCTTAATTT-ATGACGGGGGCTTCAATGACACGCAATGTAAGTCAT
* *
1405741 ACATGTGTATCATAAATTTAT
65 AAATGTGCATCATAAATTTAT
* *
1405762 GACACACAAATGTGTGTCATCTTAATTTATGACGGGGGCTTCAATGACGCTCAATG-AACGTCAT
1 GACACACAAATGTGTGTCATCTTAATTTATGACGGGGGCTTCAATGACACGCAATGTAA-GTCAT
* *
1405826 AAATGTGCGTCATAGATTTAT
65 AAATGTGCATCATAAATTTAT
* * * * *
1405847 GACACACAATTGTGTGTCATCTGAGATTCATGTCGGTGGCTTCAATGACA
1 GACACACAAATGTGTGTCATCTTA-ATTTATGACGGGGGCTTCAATGACA
1405897 AGAAAATGTG
Statistics
Matches: 116, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
84 2 0.02
85 90 0.78
86 24 0.21
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (85 bp):
GACACACAAATGTGTGTCATCTTAATTTATGACGGGGGCTTCAATGACACGCAATGTAAGTCATA
AATGTGCATCATAAATTTAT
Found at i:1406268 original size:42 final size:43
Alignment explanation
Indices: 1406209--1406292 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 43
1406199 TCTAAACTCA
* * *
1406209 AAAAGTAACAATTCACAAATACA-CAAAATTAACATATTAAAAC
1 AAAAGTAACAATCCACAAATAAATC-AAACTAACATATTAAAAC
1406252 AAAA-TAACAATCCACAAATAAATCAAACTAACATATTAAAA
1 AAAAGTAACAATCCACAAATAAATCAAACTAACATATTAAAA
1406293 ACAATCTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 32 0.86
43 5 0.14
ACGTcount: A:0.62, C:0.17, G:0.01, T:0.20
Consensus pattern (43 bp):
AAAAGTAACAATCCACAAATAAATCAAACTAACATATTAAAAC
Found at i:1407963 original size:52 final size:54
Alignment explanation
Indices: 1407902--1408008 Score: 175
Period size: 52 Copynumber: 2.0 Consensus size: 54
1407892 GATTTTTCAA
1407902 ATGTTATCGAAATTTG-AAATTATCAAA-TT-CTAATTATGGGAATGGGAATTTT
1 ATGTTATCGAAA-TTGAAAATTATCAAATTTACTAATTATGGGAATGGGAATTTT
1407954 ATGTTATCGAAATTGAAAATTATCAAATTTACCTAATTATGGGAATGGGAATTTT
1 ATGTTATCGAAATTGAAAATTATCAAATTTA-CTAATTATGGGAATGGGAATTTT
1408009 TTATTAATTA
Statistics
Matches: 51, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
51 3 0.06
52 23 0.45
53 2 0.04
55 23 0.45
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (54 bp):
ATGTTATCGAAATTGAAAATTATCAAATTTACTAATTATGGGAATGGGAATTTT
Found at i:1410921 original size:440 final size:436
Alignment explanation
Indices: 1410063--1410939 Score: 1677
Period size: 440 Copynumber: 2.0 Consensus size: 436
1410053 TAACAACCAT
1410063 GGAAGACTGTTTTGTTAAGAATTGCAAGGAAGGAGGCAATTTAATAAAGATATTTGACGAAATCA
1 GGAAGACTGTTTTGTTAAGAATTGCAAGGAAGGAGGCAATTTAATAAAGATATTTGACGAAATCA
1410128 TAGGAAACTTATATCTGGTGATGTAATTGTTTGAAGAATGTATGATTTCTGGAAATTCCATCACA
66 TAGGAAACTTATATCTGGTGATGTAATTGTTTGAAGAATGTATGATTTCTGGAAATTCCATCACA
1410193 TCACACTGATCTAGATAAAAAGAAGGGTAAGCTACATCAGATACCATCAAATTTTAGGCATTGTA
131 TCACACTGATCTAGATAAAAAGAAGGGTAAGCTACATCAGATACCATCAAATTTTAGGCATTGTA
1410258 TCGTTTAAACTACTAAAGTTTCAATTTTACAAATTATAGCACAAAACTTTGATTTTATTACAATT
196 TCGTTTAAACTACTAAAGTTTCAATTTTACAAATTATAGCACAAAACTTTGATTTTATTACAATT
1410323 ATATCACTAAACCGTTAAAGCGTTAACAACATACAACGTGGCTGCCAACTATCGAATTAAATACC
261 ATATCACTAAACCGTTAAAGCGTTAACAACATACAACGTGGCTGCCAACTATCGAATTAAATACC
1410388 TCACCAAATAAACGTCGTTTTGATCGACTGTTAACAATTTAACGGCCTAGTGGTATAATTGAAAT
326 TCACCAAATAAACGTCGTTTTGATCGACTGTTAACAATTTAACGGCCTAGTGGTATAATTGAAAT
1410453 GAAAATAAAAGTTCAAGTTATAATTGGTAAAATTAAAAGTTTAGTG
391 GAAAATAAAAGTTCAAGTTATAATTGGTAAAATTAAAAGTTTAGTG
1410499 GGAAGACTGTTTTGTTAAGAATTGCAAGGAAGGAGGCAATTTAATAAAGATATTTGACGAAATCA
1 GGAAGACTGTTTTGTTAAGAATTGCAAGGAAGGAGGCAATTTAATAAAGATATTTGACGAAATCA
1410564 TTAGGAAACTTATATCTGGTGATGTAATTGTTTGAAGAATGTATGATTTCTGGAAATTCCATCAA
66 -TAGGAAACTTATATCTGGTGATGTAATTGTTTGAAGAATGTATGATTTCTGGAAATTCCATC-A
1410629 CATCACACCTGATCTAGATAAAAAGAAGGGTAAGCTACATCAGATACCATCAAATTTTAGGCATT
129 CATCACA-CTGATCTAGATAAAAAGAAGGGTAAGCTACATCAGATACCATCAAATTTTAGGCATT
1410694 GTATCGTTTAAACTACTAAAGTTTCAATTTTACAAATTATAGCACAAAACTTTGATTTTTATTAC
193 GTATCGTTTAAACTACTAAAGTTTCAATTTTACAAATTATAGCACAAAACTTTGA-TTTTATTAC
*
1410759 AATTATATCACTAAACCGTTAAATCGTTAACAACAATACAACGTGGCTGCCAACTATCGAATTAA
257 AATTATATCACTAAACCGTTAAAGCGTTAACAAC-ATACAACGTGGCTGCCAACTATCGAATTAA
1410824 ATACCTCACCAAAT-AACGTCGTTTTGATCCGACTGTTAAC-ATTTAACGGCCTAGTGGTATAAT
321 ATACCTCACCAAATAAACGTCGTTTTGAT-CGACTGTTAACAATTTAACGGCCTAGTGGTATAAT
1410887 TGAAATGAAAATAAAAGTTCAAGTTATAATTGGTAAAATTAAAAGTTTAGTG
385 TGAAATGAAAATAAAAGTTCAAGTTATAATTGGTAAAATTAAAAGTTTAGTG
1410939 G
1 G
1410940 TATAAACGAT
Statistics
Matches: 434, Mismatches: 1, Indels: 8
0.98 0.00 0.02
Matches are distributed among these distances:
436 65 0.15
437 62 0.14
438 8 0.02
439 112 0.26
440 132 0.30
441 55 0.13
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (436 bp):
GGAAGACTGTTTTGTTAAGAATTGCAAGGAAGGAGGCAATTTAATAAAGATATTTGACGAAATCA
TAGGAAACTTATATCTGGTGATGTAATTGTTTGAAGAATGTATGATTTCTGGAAATTCCATCACA
TCACACTGATCTAGATAAAAAGAAGGGTAAGCTACATCAGATACCATCAAATTTTAGGCATTGTA
TCGTTTAAACTACTAAAGTTTCAATTTTACAAATTATAGCACAAAACTTTGATTTTATTACAATT
ATATCACTAAACCGTTAAAGCGTTAACAACATACAACGTGGCTGCCAACTATCGAATTAAATACC
TCACCAAATAAACGTCGTTTTGATCGACTGTTAACAATTTAACGGCCTAGTGGTATAATTGAAAT
GAAAATAAAAGTTCAAGTTATAATTGGTAAAATTAAAAGTTTAGTG
Found at i:1411539 original size:17 final size:19
Alignment explanation
Indices: 1411512--1411546 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1411502 ATGAAATGTT
1411512 AAAATTCAAAT-ACTTAAA
1 AAAATTCAAATGACTTAAA
1411530 AAAATT-AAATGACTTAA
1 AAAATTCAAATGACTTAA
1411547 TCAAATGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.60, C:0.09, G:0.03, T:0.29
Consensus pattern (19 bp):
AAAATTCAAATGACTTAAA
Found at i:1416686 original size:4 final size:4
Alignment explanation
Indices: 1416677--1416707 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
1416667 TTTGTCCCTT
1416677 TTTA TTTA TTTA TTTA TTTA TTTA TTT- TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1416708 AAAAATGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:1417695 original size:13 final size:12
Alignment explanation
Indices: 1417677--1417706 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
1417667 ATTCTTTATT
1417677 AAAAATTAATAAA
1 AAAAATTAA-AAA
1417690 AAAAATTAAAAA
1 AAAAATTAAAAA
1417702 AAAAA
1 AAAAA
1417707 CAATAAGTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (12 bp):
AAAAATTAAAAA
Found at i:1420052 original size:2 final size:2
Alignment explanation
Indices: 1420045--1420118 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
1420035 ATTATATTAA
1420045 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
1420087 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
1420119 TTGTATTGTC
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.