Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
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: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 6 of 144
Found at i:1191723 original size:27 final size:28
Alignment explanation
Indices: 1191666--1191738 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 28
1191656 AAAGATTTAT
* * *
1191666 AAAATTCATAATAGAAAATATAAACTTATA
1 AAAATTCA-AA-AAAAAATATAAAATCATA
1191696 AAAATTCAAAAAAAAATA-AAAATCATA
1 AAAATTCAAAAAAAAATATAAAATCATA
1191723 AAATATTCAAAAAAAA
1 AAA-ATTCAAAAAAAA
1191739 TTTCAAAATG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
27 10 0.26
28 19 0.49
29 2 0.05
30 8 0.21
ACGTcount: A:0.68, C:0.07, G:0.01, T:0.23
Consensus pattern (28 bp):
AAAATTCAAAAAAAAATATAAAATCATA
Found at i:1192272 original size:33 final size:33
Alignment explanation
Indices: 1192235--1192304 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 33
1192225 TAAATGTAAC
1192235 TTAACAAGCAAATGACTCT-AAATAATAACAAAA
1 TTAACAA-CAAATGACTCTAAAATAATAACAAAA
* *
1192268 TT---AACAAATGTCTTTAAAATAATAACAAAA
1 TTAACAACAAATGACTCTAAAATAATAACAAAA
1192298 TTAACAA
1 TTAACAA
1192305 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
29 9 0.29
30 18 0.58
33 4 0.13
ACGTcount: A:0.57, C:0.13, G:0.04, T:0.26
Consensus pattern (33 bp):
TTAACAACAAATGACTCTAAAATAATAACAAAA
Found at i:1192275 original size:29 final size:30
Alignment explanation
Indices: 1192243--1192304 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
1192233 ACTTAACAAG
1192243 CAAATGACTCT-AAATAATAACAAAATTAA
1 CAAATGACTCTAAAATAATAACAAAATTAA
* *
1192272 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGACTCTAAAATAATAACAAAATTAA
1192302 CAA
1 CAA
1192305 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 9 0.30
30 21 0.70
ACGTcount: A:0.58, C:0.13, G:0.03, T:0.26
Consensus pattern (30 bp):
CAAATGACTCTAAAATAATAACAAAATTAA
Found at i:1192359 original size:22 final size:22
Alignment explanation
Indices: 1192334--1192376 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1192324 TATCCAAACA
1192334 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* **
1192356 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
1192377 AATAGGAAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:1192380 original size:11 final size:11
Alignment explanation
Indices: 1192341--1192381 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
1192331 ACAATAACAA
1192341 CAAAATAGTAG
1 CAAAATAGTAG
* *
1192352 CAACATAATAG
1 CAAAATAGTAG
*
1192363 TAAAATAGTAG
1 CAAAATAGTAG
1192374 CAAAATAG
1 CAAAATAG
1192382 GAAGAAAACA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:1199711 original size:42 final size:42
Alignment explanation
Indices: 1199638--1199742 Score: 115
Period size: 42 Copynumber: 2.5 Consensus size: 42
1199628 ACGGCTTGGA
* * * *
1199638 CACACGCTCATGTCCTTGCCGGTGTGGCTCACATGGCCTA-GG
1 CACACGCCCATGTCCTTGCCGATGTGACTCACACGGCC-AGGG
*
1199680 CACATGCCCATGTCCTTGCTC-ATGTGACTCACACGGCCAGGG
1 CACACGCCCATGTCCTTGC-CGATGTGACTCACACGGCCAGGG
*
1199722 TACACGCCCATGTCCTCTGCC
1 CACACGCCCATGTCCT-TGCC
1199743 CGTGTGGTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
41 1 0.02
42 48 0.91
43 4 0.08
ACGTcount: A:0.16, C:0.37, G:0.24, T:0.23
Consensus pattern (42 bp):
CACACGCCCATGTCCTTGCCGATGTGACTCACACGGCCAGGG
Found at i:1213359 original size:53 final size:53
Alignment explanation
Indices: 1213226--1213434 Score: 246
Period size: 53 Copynumber: 4.0 Consensus size: 53
1213216 GGCACTAAAG
* * *
1213226 AAGACCATATCGTGTAAGACAGTAACTAGTGGGTTATGGCATCATATGG---A
1 AAGACCATATCGTGTAAGACCGTAACTGGTGAGTTATGGCATCATATGGAAAA
* * *
1213276 AAGATCATATCGTGTAAGACCATAATTGGTGAGTTATGGCATCATATGGAAAA
1 AAGACCATATCGTGTAAGACCGTAACTGGTGAGTTATGGCATCATATGGAAAA
* * * *
1213329 AAGACCGTATCGTGTCAGACCGTAACTGGTGGGTTATGGCATCATATGGAAAG
1 AAGACCATATCGTGTAAGACCGTAACTGGTGAGTTATGGCATCATATGGAAAA
* * * * * *
1213382 AAGATCATATCATATAAGATCGTAACTTGTGAGTTATGACATCATAT-GAAAA
1 AAGACCATATCGTGTAAGACCGTAACTGGTGAGTTATGGCATCATATGGAAAA
1213434 A
1 A
1213435 CATTTAAGGA
Statistics
Matches: 133, Mismatches: 23, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
50 43 0.32
52 5 0.04
53 85 0.64
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.27
Consensus pattern (53 bp):
AAGACCATATCGTGTAAGACCGTAACTGGTGAGTTATGGCATCATATGGAAAA
Found at i:1217156 original size:30 final size:30
Alignment explanation
Indices: 1217121--1217177 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1217111 TAGGCATTTC
* *
1217121 CACACGGGCTTGG-CACACGCCCGTGTGAGA
1 CACACGAGC-TGGCCACACGCCCATGTGAGA
1217151 CACACGAGCTGGCCACACGCCCATGTG
1 CACACGAGCTGGCCACACGCCCATGTG
1217178 CCAACCAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 21 0.88
ACGTcount: A:0.21, C:0.37, G:0.30, T:0.12
Consensus pattern (30 bp):
CACACGAGCTGGCCACACGCCCATGTGAGA
Found at i:1225409 original size:37 final size:37
Alignment explanation
Indices: 1225364--1225441 Score: 108
Period size: 37 Copynumber: 2.1 Consensus size: 37
1225354 AACTCAACTC
*
1225364 TAAA-TAAGGTCTTGTTTGATA-ACCGATTGAAAAA-AT
1 TAAATTAAGGCCTTGTTTGATAGACC-ATT-AAAAAGAT
1225400 TAAATTAAGGCCTTGTTTGATAGACCATTAAAAAGAT
1 TAAATTAAGGCCTTGTTTGATAGACCATTAAAAAGAT
1225437 TAAAT
1 TAAAT
1225442 CAATTGAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
36 9 0.24
37 26 0.68
38 3 0.08
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.33
Consensus pattern (37 bp):
TAAATTAAGGCCTTGTTTGATAGACCATTAAAAAGAT
Found at i:1230240 original size:24 final size:23
Alignment explanation
Indices: 1230171--1230247 Score: 73
Period size: 24 Copynumber: 3.3 Consensus size: 23
1230161 GCATAGATGT
*
1230171 AAACCCTATATGTTTTATACATGC
1 AAACCCTATATG-TTTATATATGC
* * * * *
1230195 GAACTCTACAAGTTTTTATATGC
1 AAACCCTATATGTTTATATATGC
1230218 AAACCCTATATGTCTTATATATGC
1 AAACCCTATATGT-TTATATATGC
*
1230242 GAACCC
1 AAACCC
1230248 CCATGTTATA
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
23 18 0.45
24 22 0.55
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.35
Consensus pattern (23 bp):
AAACCCTATATGTTTATATATGC
Found at i:1232948 original size:12 final size:12
Alignment explanation
Indices: 1232931--1232962 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
1232921 GGCTATTCTG
1232931 TTCTTTTGAGTA
1 TTCTTTTGAGTA
1232943 TTCTTTTGAGTA
1 TTCTTTTGAGTA
1232955 TTCTTTTG
1 TTCTTTTG
1232963 GCTTGTCTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.12, C:0.09, G:0.16, T:0.62
Consensus pattern (12 bp):
TTCTTTTGAGTA
Found at i:1234109 original size:21 final size:21
Alignment explanation
Indices: 1234075--1234128 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
1234065 AGTCTATGGT
*
1234075 CAAGCTAG-GTCTAAGAAAGA
1 CAAGCTTGAGTCTAAGAAAGA
1234095 CAAGCTTGAGTCTAAGAAAGA
1 CAAGCTTGAGTCTAAGAAAGA
*
1234116 CAAACTTGAGTCT
1 CAAGCTTGAGTCT
1234129 TCTGAGTTCG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 7 0.23
21 24 0.77
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (21 bp):
CAAGCTTGAGTCTAAGAAAGA
Found at i:1235644 original size:28 final size:28
Alignment explanation
Indices: 1235598--1235654 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
1235588 TATAGTTTTT
1235598 ATAATAATTATAAAGGTTATAATAATAA
1 ATAATAATTATAAAGGTTATAATAATAA
*
1235626 ATAATATATTATAAA-GTTATTATAATAA
1 ATAATA-ATTATAAAGGTTATAATAATAA
1235654 A
1 A
1235655 AACAAACATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (28 bp):
ATAATAATTATAAAGGTTATAATAATAA
Found at i:1236600 original size:43 final size:43
Alignment explanation
Indices: 1236539--1236659 Score: 156
Period size: 43 Copynumber: 2.8 Consensus size: 43
1236529 ATAGGACTCT
* *
1236539 GATATCTGTTTTCGTGTAAGACCACGTCTGGGAC-GTCGACATC
1 GATATCTGATTACGTGTAAGACCACGTCTGGGACAGT-GACATC
* *
1236582 GATATCTGATTACATGTAAGACC-CTGTCTGGGACAGTGGCATC
1 GATATCTGATTACGTGTAAGACCAC-GTCTGGGACAGTGACATC
* *
1236625 GATATGTGATTACGTATAAGACCACGTCTGGGACA
1 GATATCTGATTACGTGTAAGACCACGTCTGGGACA
1236660 ATGGCATTGT
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
42 1 0.01
43 64 0.94
44 3 0.04
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (43 bp):
GATATCTGATTACGTGTAAGACCACGTCTGGGACAGTGACATC
Found at i:1246924 original size:17 final size:18
Alignment explanation
Indices: 1246897--1246932 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
1246887 TTTAGTTATA
1246897 TTTAGTTTTCGATATGTT
1 TTTAGTTTTCGATATGTT
1246915 TTTA-TTTTCGATATGTT
1 TTTAGTTTTCGATATGTT
1246932 T
1 T
1246933 CATTTAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.17, C:0.06, G:0.14, T:0.64
Consensus pattern (18 bp):
TTTAGTTTTCGATATGTT
Found at i:1247599 original size:17 final size:17
Alignment explanation
Indices: 1247577--1247612 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1247567 TTTGATTTTG
1247577 TTTTACTATTATTAAAA
1 TTTTACTATTATTAAAA
*
1247594 TTTTACTATTATTGAAA
1 TTTTACTATTATTAAAA
1247611 TT
1 TT
1247613 AGTATTGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTTACTATTATTAAAA
Found at i:1258481 original size:15 final size:15
Alignment explanation
Indices: 1258458--1258491 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1258448 CAAAATCAAG
*
1258458 ATTTTTACAACATTC
1 ATTTGTACAACATTC
*
1258473 ATTTGTACAATATTC
1 ATTTGTACAACATTC
1258488 ATTT
1 ATTT
1258492 TTGTTTTAAT
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:0.32, C:0.15, G:0.03, T:0.50
Consensus pattern (15 bp):
ATTTGTACAACATTC
Found at i:1260303 original size:29 final size:29
Alignment explanation
Indices: 1260271--1260380 Score: 87
Period size: 29 Copynumber: 3.6 Consensus size: 29
1260261 TAATAAAAAT
1260271 ATATAATTTAATAAAATTCTTAATATTAA
1 ATATAATTTAATAAAATTCTTAATATTAA
* *
1260300 ATATTAATTTACTAAAA-TCATAATATATAA
1 ATA-TAATTTAATAAAATTCTTAATAT-TAA
* ** *
1260330 TACTATAAAATATAATTTAAAATAATTATTATTAA
1 -A-TAT--AATTTAA--TAAAATTCTTAATATTAA
1260365 ATATAATTTAATAAAA
1 ATATAATTTAATAAAA
1260381 ATATATAATT
Statistics
Matches: 63, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
29 16 0.25
30 15 0.24
31 8 0.13
32 2 0.03
33 8 0.13
34 1 0.02
35 8 0.13
36 5 0.08
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (29 bp):
ATATAATTTAATAAAATTCTTAATATTAA
Found at i:1260357 original size:112 final size:116
Alignment explanation
Indices: 1260233--1260447 Score: 357
Period size: 112 Copynumber: 1.9 Consensus size: 116
1260223 TTAATCATAT
*
1260233 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTC-T-TAA-T
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCATATAATT
*
1260295 ATT-AAATATTAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 ATTCAAATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
1260345 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCAATATAAT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTC-ATATAAT
**
1260410 TATTCTTATATGAATTTACTAAAATCATAATATATAAT
65 TATTCAAATATGAATTTACTAAAATCATAATATATAAT
1260448 NNNNNNNNNN
Statistics
Matches: 94, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
112 56 0.60
114 1 0.01
115 3 0.03
116 4 0.04
117 30 0.32
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (116 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCATATAATT
ATTCAAATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:1260400 original size:10 final size:10
Alignment explanation
Indices: 1260338--1260410 Score: 50
Period size: 10 Copynumber: 7.9 Consensus size: 10
1260328 AATACTATAA
1260338 AATATAATTT
1 AATATAATTT
*
1260348 AAAATAA-TT
1 AATATAATTT
*
1260357 -AT-T-ATTA
1 AATATAATTT
1260364 AATATAATTT
1 AATATAATTT
**
1260374 AATA-AAAAT
1 AATATAATTT
1260383 -ATATAATTT
1 AATATAATTT
* *
1260392 AATAAAATTC
1 AATATAATTT
1260402 AATATAATT
1 AATATAATT
1260411 ATTCTTATAT
Statistics
Matches: 46, Mismatches: 11, Indels: 12
0.67 0.16 0.17
Matches are distributed among these distances:
6 1 0.02
7 2 0.04
8 6 0.13
9 9 0.20
10 28 0.61
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (10 bp):
AATATAATTT
Found at i:1270541 original size:15 final size:14
Alignment explanation
Indices: 1270500--1270547 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
1270490 TGATTTGTGT
1270500 AAACTTAATTAATC
1 AAACTTAATTAATC
* *
1270514 AAAATTAATTTAATT
1 AAACTTAA-TTAATC
1270529 AAACTTTAATTAATC
1 AAAC-TTAATTAATC
1270544 AAAC
1 AAAC
1270548 CATAATCACA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 7 0.25
15 17 0.61
16 4 0.14
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (14 bp):
AAACTTAATTAATC
Found at i:1270843 original size:11 final size:11
Alignment explanation
Indices: 1270827--1270851 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1270817 ACGTGGCATA
1270827 AATGATGTCAT
1 AATGATGTCAT
1270838 AATGATGTCAT
1 AATGATGTCAT
1270849 AAT
1 AAT
1270852 CTAAAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (11 bp):
AATGATGTCAT
Found at i:1279824 original size:39 final size:39
Alignment explanation
Indices: 1279770--1279894 Score: 160
Period size: 39 Copynumber: 3.2 Consensus size: 39
1279760 AGGAGTACCA
*
1279770 AAGTACAACAAGGGCACGTATATGCGAACAAGGGTACTG
1 AAGTACAACAAGGGCACGTATGTGCGAACAAGGGTACTG
* * **
1279809 AAGTACAACAAGGGCATGTATGTGCGAGCAAGTATACTG
1 AAGTACAACAAGGGCACGTATGTGCGAACAAGGGTACTG
* * * * *
1279848 AAGTATAACAGGGGCACATATGTGCGAACAGGGGTACCG
1 AAGTACAACAAGGGCACGTATGTGCGAACAAGGGTACTG
1279887 AAGTACAA
1 AAGTACAA
1279895 TAGTTATCTA
Statistics
Matches: 71, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 71 1.00
ACGTcount: A:0.38, C:0.17, G:0.29, T:0.17
Consensus pattern (39 bp):
AAGTACAACAAGGGCACGTATGTGCGAACAAGGGTACTG
Found at i:1291773 original size:33 final size:33
Alignment explanation
Indices: 1291731--1291797 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
1291721 GAAAGGGAGA
*
1291731 AAAATCTAGATATCATTCTTTAGTTCTGTAGAC
1 AAAATCTAGATATCATTCTTGAGTTCTGTAGAC
1291764 AAAATCTAGATATCATTCTTGAGTTCTGTAGAC
1 AAAATCTAGATATCATTCTTGAGTTCTGTAGAC
1291797 A
1 A
1291798 TACAAAAACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.37
Consensus pattern (33 bp):
AAAATCTAGATATCATTCTTGAGTTCTGTAGAC
Found at i:1304766 original size:118 final size:118
Alignment explanation
Indices: 1304558--1304790 Score: 385
Period size: 118 Copynumber: 2.0 Consensus size: 118
1304548 AACCAAGGCT
*
1304558 CAAAATTGAATGATATGGTTATTTCGATATCAATGACTAAATTGAATAAAATGTAAAAATTTAGA
1 CAAAATTGAAAGATATGGTTATTTCGATATCAATGACTAAATTGAATAAAATGTAAAAATTTAGA
* * *
1304623 GGTATCAAAAAATAAGATTTTTTAGGCTCATTCATGTCATGGTATAATGTGTA
66 GGTATCAAAAAATAAGATTATTTAGGCTCATCCATGTCATGGCATAATGTGTA
* * * *
1304676 CAAAATTGAAAGATATGGTTATTTCGATTTTAATGACTAAATTGAATAAAATGTAAAACTTTAGG
1 CAAAATTGAAAGATATGGTTATTTCGATATCAATGACTAAATTGAATAAAATGTAAAAATTTAGA
*
1304741 GGTATCAAAAAATAAGATTATTTAGGTTCATCCATGTCATGGCATAATGT
66 GGTATCAAAAAATAAGATTATTTAGGCTCATCCATGTCATGGCATAATGT
1304791 ATAAATGTTT
Statistics
Matches: 106, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
118 106 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.35
Consensus pattern (118 bp):
CAAAATTGAAAGATATGGTTATTTCGATATCAATGACTAAATTGAATAAAATGTAAAAATTTAGA
GGTATCAAAAAATAAGATTATTTAGGCTCATCCATGTCATGGCATAATGTGTA
Found at i:1307242 original size:5 final size:5
Alignment explanation
Indices: 1307232--1307265 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
1307222 ACCCTCTCTT
1307232 TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCT
1 TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCT
1307266 TCTCCTCCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (5 bp):
TTCTC
Found at i:1308006 original size:28 final size:28
Alignment explanation
Indices: 1307974--1308084 Score: 141
Period size: 28 Copynumber: 4.0 Consensus size: 28
1307964 ACTGTACTGG
1307974 TTACTGTATTGGGCTAAGGCCCACACTA
1 TTACTGTATTGGGCTAAGGCCCACACTA
**
1308002 TTACTGTATTGGGCTAAGGCCTTCACTA
1 TTACTGTATTGGGCTAAGGCCCACACTA
* * * *
1308030 TTATTGTATTAGGCTAAGGCCCACATTG
1 TTACTGTATTGGGCTAAGGCCCACACTA
* * *
1308058 TTATTGTTTTGGGGTAAGGCCCACACT
1 TTACTGTATTGGGCTAAGGCCCACACT
1308085 GTACTGTTAC
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 71 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.34
Consensus pattern (28 bp):
TTACTGTATTGGGCTAAGGCCCACACTA
Found at i:1309440 original size:26 final size:28
Alignment explanation
Indices: 1309396--1309449 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
1309386 TTTGCCATAG
*
1309396 AGGCTATCCCTTCATCATT-TTCCACAA
1 AGGCTATCCCTTCATCATTGTGCCACAA
* *
1309423 AGGCTTTCCTTTCA-CATTGTGCCACAA
1 AGGCTATCCCTTCATCATTGTGCCACAA
1309450 GGTGTTCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.24, C:0.31, G:0.11, T:0.33
Consensus pattern (28 bp):
AGGCTATCCCTTCATCATTGTGCCACAA
Found at i:1311982 original size:8 final size:8
Alignment explanation
Indices: 1311966--1312001 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
1311956 TACACAGTGC
1311966 TAGTATTT
1 TAGTATTT
*
1311974 TAGTCTTT
1 TAGTATTT
1311982 TAGTATTT
1 TAGTATTT
1311990 TAGTATTT
1 TAGTATTT
1311998 TAGT
1 TAGT
1312002 GAGTATCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.22, C:0.03, G:0.14, T:0.61
Consensus pattern (8 bp):
TAGTATTT
Found at i:1321111 original size:9 final size:9
Alignment explanation
Indices: 1321097--1321121 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1321087 CATATATACA
1321097 TTTCATCAC
1 TTTCATCAC
1321106 TTTCATCAC
1 TTTCATCAC
1321115 TTTCATC
1 TTTCATC
1321122 CAAATACCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.32, G:0.00, T:0.48
Consensus pattern (9 bp):
TTTCATCAC
Found at i:1323685 original size:95 final size:95
Alignment explanation
Indices: 1323522--1324471 Score: 1900
Period size: 95 Copynumber: 10.0 Consensus size: 95
1323512 ATTTGTTAAG
1323522 TAATTATTTATCTGAAATTATTTATTTATTCAAAGGTACTTAGTATATTAGGGAGTGATGCCCCT
1 TAATTATTTATCTGAAATTATTTATTTATTCAAAGGTACTTAGTATATTAGGGAGTGATGCCCCT
1323587 AATAGAATATCGAGACAGGTGAGACTGGAA
66 AATAGAATATCGAGACAGGTGAGACTGGAA
1323617 TAATTATTTATCTGAAATTATTTATTTATTCAAAGGTACTTAGTATATTAGGGAGTGATGCCCCT
1 TAATTATTTATCTGAAATTATTTATTTATTCAAAGGTACTTAGTATATTAGGGAGTGATGCCCCT
1323682 AATAGAATATCGAGACAGGTGAGACTGGAA
66 AATAGAATATCGAGACAGGTGAGACTGGAA
1323712 TAATTATTTATCTGAAATTATTTATTTATTCAAAGGTACTTAGTATATTAGGGAGTGATGCCCCT
1 TAATTATTTATCTGAAATTATTTATTTATTCAAAGGTACTTAGTATATTAGGGAGTGATGCCCCT
1323777 AATAGAATATCGAGACAGGTGAGACTGGAA
66 AATAGAATATCGAGACAGGTGAGACTGGAA
1323807 TAATTATTTATCTGAAATTATTTATTTATTCAAAGGTACTTAGTATATTAGGGAGTGATGCCCCT
1 TAATTATTTATCTGAAATTATTTATTTATTCAAAGGTACTTAGTATATTAGGGAGTGATGCCCCT
1323872 AATAGAATATCGAGACAGGTGAGACTGGAA
66 AATAGAATATCGAGACAGGTGAGACTGGAA
1323902 TAATTATTTATCTGAAATTATTTATTTATTCAAAGGTACTTAGTATATTAGGGAGTGATGCCCCT
1 TAATTATTTATCTGAAATTATTTATTTATTCAAAGGTACTTAGTATATTAGGGAGTGATGCCCCT
1323967 AATAGAATATCGAGACAGGTGAGACTGGAA
66 AATAGAATATCGAGACAGGTGAGACTGGAA
1323997 TAATTATTTATCTGAAATTATTTATTTATTCAAAGGTACTTAGTATATTAGGGAGTGATGCCCCT
1 TAATTATTTATCTGAAATTATTTATTTATTCAAAGGTACTTAGTATATTAGGGAGTGATGCCCCT
1324062 AATAGAATATCGAGACAGGTGAGACTGGAA
66 AATAGAATATCGAGACAGGTGAGACTGGAA
1324092 TAATTATTTATCTGAAATTATTTATTTATTCAAAGGTACTTAGTATATTAGGGAGTGATGCCCCT
1 TAATTATTTATCTGAAATTATTTATTTATTCAAAGGTACTTAGTATATTAGGGAGTGATGCCCCT
1324157 AATAGAATATCGAGACAGGTGAGACTGGAA
66 AATAGAATATCGAGACAGGTGAGACTGGAA
1324187 TAATTATTTATCTGAAATTATTTATTTATTCAAAGGTACTTAGTATATTAGGGAGTGATGCCCCT
1 TAATTATTTATCTGAAATTATTTATTTATTCAAAGGTACTTAGTATATTAGGGAGTGATGCCCCT
1324252 AATAGAATATCGAGACAGGTGAGACTGGAA
66 AATAGAATATCGAGACAGGTGAGACTGGAA
1324282 TAATTATTTATCTGAAATTATTTATTTATTCAAAGGTACTTAGTATATTAGGGAGTGATGCCCCT
1 TAATTATTTATCTGAAATTATTTATTTATTCAAAGGTACTTAGTATATTAGGGAGTGATGCCCCT
1324347 AATAGAATATCGAGACAGGTGAGACTGGAA
66 AATAGAATATCGAGACAGGTGAGACTGGAA
1324377 TAATTATTTATCTGAAATTATTTATTTATTCAAAGGTACTTAGTATATTAGGGAGTGATGCCCCT
1 TAATTATTTATCTGAAATTATTTATTTATTCAAAGGTACTTAGTATATTAGGGAGTGATGCCCCT
1324442 AATAGAATATCGAGACAGGTGAGACTGGAA
66 AATAGAATATCGAGACAGGTGAGACTGGAA
1324472 GGGTGACTTA
Statistics
Matches: 855, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 855 1.00
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.35
Consensus pattern (95 bp):
TAATTATTTATCTGAAATTATTTATTTATTCAAAGGTACTTAGTATATTAGGGAGTGATGCCCCT
AATAGAATATCGAGACAGGTGAGACTGGAA
Found at i:1330106 original size:20 final size:20
Alignment explanation
Indices: 1330061--1330106 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
1330051 AGAGATAAAG
1330061 AATAAAAATTAGAAAATCAA
1 AATAAAAATTAGAAAATCAA
*
1330081 ATTAAAAA-TAGCAAAAAT-AA
1 AATAAAAATTAG--AAAATCAA
1330101 AATAAA
1 AATAAA
1330107 GCAAAGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 14 0.64
21 5 0.23
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.20
Consensus pattern (20 bp):
AATAAAAATTAGAAAATCAA
Found at i:1332041 original size:25 final size:22
Alignment explanation
Indices: 1331987--1332041 Score: 56
Period size: 26 Copynumber: 2.3 Consensus size: 22
1331977 AATTTCAATT
1331987 AAAAATTTATTTAATAATTAAA
1 AAAAATTTATTTAATAATTAAA
*
1332009 AATTAAATTTATTATAAATATTTAAA
1 AA--AAATTTATT-T-AATAATTAAA
1332035 ACAAAAT
1 A-AAAAT
1332042 ATTAATATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
22 2 0.07
24 9 0.33
25 5 0.19
26 10 0.37
27 1 0.04
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAAATTTATTTAATAATTAAA
Found at i:1339129 original size:38 final size:38
Alignment explanation
Indices: 1339078--1339154 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
1339068 GCTCGAGCCC
*
1339078 TCTTGTTTCATTCTCATACACCTCAATATTTCTGGGGA
1 TCTTGTTTCATTCTCATACACCTCAATAGTTCTGGGGA
1339116 TCTTGTTTCATTCTCATACACCTCAATAGTTCTGGGGA
1 TCTTGTTTCATTCTCATACACCTCAATAGTTCTGGGGA
1339154 T
1 T
1339155 ATTCAGTCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (38 bp):
TCTTGTTTCATTCTCATACACCTCAATAGTTCTGGGGA
Found at i:1339600 original size:33 final size:33
Alignment explanation
Indices: 1339560--1339628 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
1339550 GAAACACCAT
* *
1339560 CACCACCCACAAATACTGAACCACATATTGAAC
1 CACCACCCACAAATACTGAACCACATAATAAAC
*
1339593 CACCACCCATAAATACTGAACCACATAATAAAC
1 CACCACCCACAAATACTGAACCACATAATAAAC
1339626 CAC
1 CAC
1339629 ATATTGAACC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.45, C:0.36, G:0.04, T:0.14
Consensus pattern (33 bp):
CACCACCCACAAATACTGAACCACATAATAAAC
Found at i:1344262 original size:17 final size:17
Alignment explanation
Indices: 1344231--1344263 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1344221 ATAAAAATTC
1344231 CCCAACAACATTAGAAG
1 CCCAACAACATTAGAAG
1344248 CCCAA-AACATATAGAA
1 CCCAACAACAT-TAGAA
1344264 CATACTACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.52, C:0.27, G:0.09, T:0.12
Consensus pattern (17 bp):
CCCAACAACATTAGAAG
Found at i:1365597 original size:35 final size:35
Alignment explanation
Indices: 1365524--1365599 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 35
1365514 GTTATCGGCT
* *
1365524 AGTCCTTCAAGGTGACACCATGATGACAATATATA
1 AGTCCTTCAAGGTGACACCATGATAACAATATACA
* **
1365559 AGTCCTTCGAGGTGACACCATG-TAAACGGTATACA
1 AGTCCTTCAAGGTGACACCATGAT-AACAATATACA
1365594 AGTCCT
1 AGTCCT
1365600 ATGGGGAAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 1 0.03
35 34 0.97
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (35 bp):
AGTCCTTCAAGGTGACACCATGATAACAATATACA
Found at i:1372646 original size:18 final size:18
Alignment explanation
Indices: 1372623--1372659 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1372613 TCTATAATGA
1372623 TAGAATTTATTACTACAT
1 TAGAATTTATTACTACAT
1372641 TAGAATTTATTACTACAT
1 TAGAATTTATTACTACAT
1372659 T
1 T
1372660 CTCATATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (18 bp):
TAGAATTTATTACTACAT
Found at i:1377312 original size:16 final size:16
Alignment explanation
Indices: 1377277--1377335 Score: 84
Period size: 16 Copynumber: 3.7 Consensus size: 16
1377267 TTATAATTTA
*
1377277 TTAAATAAAA-AGTAT
1 TTAAATAAAATATTAT
*
1377292 CTTAATTAAAATATTAT
1 -TTAAATAAAATATTAT
1377309 TTAAATAAAATATTAT
1 TTAAATAAAATATTAT
1377325 TTAAATAAAAT
1 TTAAATAAAAT
1377336 GTTTAAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
16 35 0.90
17 4 0.10
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (16 bp):
TTAAATAAAATATTAT
Found at i:1377317 original size:32 final size:30
Alignment explanation
Indices: 1377263--1377343 Score: 85
Period size: 32 Copynumber: 2.7 Consensus size: 30
1377253 GACAAGCTTA
*
1377263 TTAATTATAATTTATTAAATAAAA-AGTAT
1 TTAATTAAAATTTATTAAATAAAATAGTAT
*
1377292 CTTAATTAAAATATTATTTAAATAAAATATTAT
1 -TTAATTAAAAT-TTA-TTAAATAAAATAGTAT
* *
1377325 TTAAATAAAATGT-TTAAAT
1 TTAATTAAAATTTATTAAAT
1377344 TTCACATGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
29 6 0.14
30 10 0.23
31 4 0.09
32 20 0.45
33 4 0.09
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.44
Consensus pattern (30 bp):
TTAATTAAAATTTATTAAATAAAATAGTAT
Found at i:1393112 original size:49 final size:48
Alignment explanation
Indices: 1393059--1393208 Score: 133
Period size: 49 Copynumber: 3.1 Consensus size: 48
1393049 TCATTATTTA
* *
1393059 GCTCTTATGAGCTTCACGTTTATGGCTCGTATAAGCTTCCTGATTAATG
1 GCTCTTATGAGCTTC-CGTTTATGGCTCGCATGAGCTTCCTGATTAATG
*** * *** *
1393108 GCTCTCCGGAGCTACCCAATATTGGCTCGCATGAGCTTCCCGATT-ATG
1 GCTCTTATGAGCTTCCGTTTA-TGGCTCGCATGAGCTTCCTGATTAATG
* *
1393156 GCTCTTATGAGCTTCTCGTTACATGGCTCACATGAGCTTCCTG-TTATATG
1 GCTCTTATGAGCTTC-CGTT-TATGGCTCGCATGAGCTTCCTGATTA-ATG
1393206 GCT
1 GCT
1393209 TTAAAGAGCT
Statistics
Matches: 76, Mismatches: 20, Indels: 9
0.72 0.19 0.09
Matches are distributed among these distances:
48 19 0.25
49 50 0.66
50 7 0.09
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (48 bp):
GCTCTTATGAGCTTCCGTTTATGGCTCGCATGAGCTTCCTGATTAATG
Found at i:1393157 original size:24 final size:24
Alignment explanation
Indices: 1393065--1393196 Score: 88
Period size: 24 Copynumber: 5.4 Consensus size: 24
1393055 TTTAGCTCTT
* * *
1393065 ATGAGCTTCACGTTTATGGCTCGT
1 ATGAGCTTCCCGATTATGGCTCGC
* * *
1393089 ATAAGCTTCCTGATTAATGGCTCTC
1 ATGAGCTTCCCGATT-ATGGCTCGC
** * *
1393114 CGGAGCTACCC-AATATTGGCTCGC
1 ATGAGCTTCCCGATTA-TGGCTCGC
**
1393138 ATGAGCTTCCCGATTATGGCTCTT
1 ATGAGCTTCCCGATTATGGCTCGC
* *
1393162 ATGAGCTTCTCG-TTACATGGCTCAC
1 ATGAGCTTCCCGATT--ATGGCTCGC
1393187 ATGAGCTTCC
1 ATGAGCTTCC
1393197 TGTTATATGG
Statistics
Matches: 80, Mismatches: 23, Indels: 9
0.71 0.21 0.08
Matches are distributed among these distances:
23 3 0.04
24 45 0.56
25 32 0.40
ACGTcount: A:0.20, C:0.27, G:0.21, T:0.33
Consensus pattern (24 bp):
ATGAGCTTCCCGATTATGGCTCGC
Found at i:1393190 original size:25 final size:23
Alignment explanation
Indices: 1393130--1393208 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 23
1393120 TACCCAATAT
*
1393130 TGGCTCGCATGAGCTTCCCGATT-A
1 TGGCTCACATGAGCTT-CCG-TTAA
**
1393154 TGGCTCTTATGAGCTTCTCGTTACA
1 TGGCTCACATGAGCTTC-CGTTA-A
1393179 TGGCTCACATGAGCTTCCTGTTATA
1 TGGCTCACATGAGCTTCC-GTTA-A
1393204 TGGCT
1 TGGCT
1393209 TTAAAGAGCT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
23 3 0.07
24 17 0.37
25 26 0.57
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.35
Consensus pattern (23 bp):
TGGCTCACATGAGCTTCCGTTAA
Found at i:1396462 original size:20 final size:20
Alignment explanation
Indices: 1396434--1396474 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1396424 AAGTAATTTA
* *
1396434 AATTGAGCTTAAACGAGCTG
1 AATTAAGCTCAAACGAGCTG
*
1396454 AATTAAGCTCAAGCGAGCTG
1 AATTAAGCTCAAACGAGCTG
1396474 A
1 A
1396475 TTGGAGCTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (20 bp):
AATTAAGCTCAAACGAGCTG
Found at i:1397761 original size:7 final size:6
Alignment explanation
Indices: 1397705--1397767 Score: 60
Period size: 6 Copynumber: 10.7 Consensus size: 6
1397695 TCTCTTTTGA
* *
1397705 TTTTTC TTCTTTC --TTTC TTTTTC TTTTTC ATTTTTA TTTTT- ATTTTC
1 TTTTTC TT-TTTC TTTTTC TTTTTC TTTTTC -TTTTTC TTTTTC TTTTTC
*
1397752 TTTTTC CTTTTC TTTT
1 TTTTTC TTTTTC TTTT
1397768 GTCTCTTTAC
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
4 4 0.09
5 4 0.09
6 30 0.64
7 9 0.19
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTTC
Found at i:1401528 original size:50 final size:50
Alignment explanation
Indices: 1400562--1401485 Score: 1713
Period size: 50 Copynumber: 18.4 Consensus size: 50
1400552 TGTGAGCCAG
* ** *
1400562 TGTAAGACCATGTCTGGGACATGGCATTGGCATCGTTGAGATTATAAGAGGTCCCA
1 TGTAAGACCATGTCTGGGGCATGGTGTTGGCA-C--TGAG---ATGAGAGGTCCCA
1400618 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
1400668 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
1400718 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
1400768 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
1400818 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
1400868 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
1400918 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
1400968 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
1401018 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
1401068 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
1401118 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
1401168 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
1401218 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
1401268 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
1401318 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
1401368 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
* * * *
1401418 TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCC
1 TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
*
1401468 CGTAAGACCATGTCTGGG
1 TGTAAGACCATGTCTGGG
1401486 ATATGGCATG
Statistics
Matches: 859, Mismatches: 9, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
50 825 0.96
53 4 0.00
55 1 0.00
56 29 0.03
ACGTcount: A:0.22, C:0.18, G:0.35, T:0.24
Consensus pattern (50 bp):
TGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGGTCCCA
Found at i:1401583 original size:49 final size:50
Alignment explanation
Indices: 1400613--1401598 Score: 338
Period size: 50 Copynumber: 19.7 Consensus size: 50
1400603 TTATAAGAGG
** ** ** * * **
1400613 TCCCATGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCAACAGGAGAAC
** ** ** * * **
1400663 TCCCATGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCAACAGGAGAAC
** ** ** * * **
1400713 TCCCATGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCAACAGGAGAAC
** ** ** * * **
1400763 TCCCATGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCAACAGGAGAAC
** ** ** * * **
1400813 TCCCATGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCAACAGGAGAAC
** ** ** * * **
1400863 TCCCATGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCAACAGGAGAAC
** ** ** * * **
1400913 TCCCATGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCAACAGGAGAAC
** ** ** * * **
1400963 TCCCATGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCAACAGGAGAAC
** ** ** * * **
1401013 TCCCATGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCAACAGGAGAAC
** ** ** * * **
1401063 TCCCATGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCAACAGGAGAAC
** ** ** * * **
1401113 TCCCATGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCAACAGGAGAAC
** ** ** * * **
1401163 TCCCATGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCAACAGGAGAAC
** ** ** * * **
1401213 TCCCATGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCAACAGGAGAAC
** ** ** * * **
1401263 TCCCATGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCAACAGGAGAAC
** ** ** * * **
1401313 TCCCATGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCAACAGGAGAAC
** ** ** * * **
1401363 TCCCATGTAAGACCATGTCTGGGGCATGGTGTTGGCACTGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCAACAGGAGAAC
* * * * * **
1401413 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCAACAGGAGAAC
** * * * *
1401463 TCCCCCGTAAGACCATGTCTGGGATATGGCATGGGAACCAATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCAACAGGAGAAC
* **
1401513 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCA-GTACAGGA-AAC
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCAACAGGAGAAC
* * *
1401561 ATCTCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 -TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCA
1401599 TGTTATTATC
Statistics
Matches: 909, Mismatches: 26, Indels: 3
0.97 0.03 0.00
Matches are distributed among these distances:
48 3 0.00
49 37 0.04
50 869 0.96
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCAACAGGAGAAC
Found at i:1403801 original size:59 final size:59
Alignment explanation
Indices: 1403705--1403827 Score: 219
Period size: 59 Copynumber: 2.1 Consensus size: 59
1403695 AAGAGAAGAA
* *
1403705 AGAAATTTTTGCTTTCTTTACAATTTGGTCCTTTCACCAAAAATTCACTATTTTCACCT
1 AGAAAGTTTTGCTTTCTTTACAATTTGGTCCTCTCACCAAAAATTCACTATTTTCACCT
*
1403764 AGAAAGTTTTGCTTTTTTTACAATTTGGTCCTCTCACCAAAAATTCACTATTTTCACCT
1 AGAAAGTTTTGCTTTCTTTACAATTTGGTCCTCTCACCAAAAATTCACTATTTTCACCT
1403823 AGAAA
1 AGAAA
1403828 TCAAAAGAAT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.41
Consensus pattern (59 bp):
AGAAAGTTTTGCTTTCTTTACAATTTGGTCCTCTCACCAAAAATTCACTATTTTCACCT
Found at i:1407171 original size:16 final size:16
Alignment explanation
Indices: 1407150--1407180 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1407140 AGTCCCAAAC
1407150 TATTGTAAACATCAGT
1 TATTGTAAACATCAGT
1407166 TATTGTAAACATCAG
1 TATTGTAAACATCAG
1407181 ATAGGTTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (16 bp):
TATTGTAAACATCAGT
Found at i:1411490 original size:40 final size:40
Alignment explanation
Indices: 1411446--1411524 Score: 95
Period size: 40 Copynumber: 2.0 Consensus size: 40
1411436 GCGTTTTTAA
1411446 AAAAGCGCCGCTAATACTTAATCTTTAGCGGCATTTTTTT
1 AAAAGCGCCGCTAATACTTAATCTTTAGCGGCATTTTTTT
* * * * * * *
1411486 AAAAGTGTCGCTAATGCTTGATTTTTAGTGGCGTTTTTT
1 AAAAGCGCCGCTAATACTTAATCTTTAGCGGCATTTTTT
1411525 ATCCAAACGC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (40 bp):
AAAAGCGCCGCTAATACTTAATCTTTAGCGGCATTTTTTT
Found at i:1412233 original size:25 final size:22
Alignment explanation
Indices: 1412193--1412245 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 22
1412183 CACTTCACTC
1412193 TTTTTTTTATTCGAATTTCTCTCT
1 TTTTTTTTATTCGAATTTCT-T-T
1412217 TTTTTTTTAACTT-GAATTTCTTT
1 TTTTTTTT-A-TTCGAATTTCTTT
1412240 TTTTTT
1 TTTTTT
1412246 ACTTCATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
23 7 0.26
24 9 0.33
25 9 0.33
26 2 0.07
ACGTcount: A:0.13, C:0.11, G:0.04, T:0.72
Consensus pattern (22 bp):
TTTTTTTTATTCGAATTTCTTT
Found at i:1417911 original size:17 final size:17
Alignment explanation
Indices: 1417891--1417964 Score: 60
Period size: 17 Copynumber: 4.4 Consensus size: 17
1417881 TGTGTTGCGC
1417891 TTATATACGAGCTGTGT
1 TTATATACGAGCTGTGT
* * *
1417908 TTATATGCTAGCTTTGT
1 TTATATACGAGCTGTGT
* * *
1417925 TTATATGCAAGTTGTGT
1 TTATATACGAGCTGTGT
* *
1417942 TTATA-AGAGAGCTATGT
1 TTATATA-CGAGCTGTGT
1417959 TTATAT
1 TTATAT
1417965 GCTAACTGTG
Statistics
Matches: 44, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
17 44 1.00
ACGTcount: A:0.26, C:0.08, G:0.20, T:0.46
Consensus pattern (17 bp):
TTATATACGAGCTGTGT
Found at i:1417929 original size:34 final size:34
Alignment explanation
Indices: 1417891--1417983 Score: 98
Period size: 34 Copynumber: 2.7 Consensus size: 34
1417881 TGTGTTGCGC
* * * *
1417891 TTATATACGAGCTGTGTTTATATGCTAGCTTTGT
1 TTATATGCAAGCTGTGTTTATATGCGAGCTATGT
* * *
1417925 TTATATGCAAGTTGTGTTTATAAGAGAGCTATGT
1 TTATATGCAAGCTGTGTTTATATGCGAGCTATGT
*
1417959 TTATATGCTAA-CTGTGTTCATATGC
1 TTATATGC-AAGCTGTGTTTATATGC
1417984 AAACTATTTC
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
34 45 0.96
35 2 0.04
ACGTcount: A:0.25, C:0.11, G:0.20, T:0.44
Consensus pattern (34 bp):
TTATATGCAAGCTGTGTTTATATGCGAGCTATGT
Found at i:1417976 original size:17 final size:17
Alignment explanation
Indices: 1417902--1417988 Score: 68
Period size: 17 Copynumber: 5.1 Consensus size: 17
1417892 TATATACGAG
*
1417902 CTGTGTTTATATGCTAG
1 CTGTGTTTATATGCTAA
*
1417919 CTTTGTTTATATGC-AA
1 CTGTGTTTATATGCTAA
* * ** *
1417935 GTTGTGTTTATAAGAGAG
1 -CTGTGTTTATATGCTAA
*
1417953 CTATGTTTATATGCTAA
1 CTGTGTTTATATGCTAA
* *
1417970 CTGTGTTCATATGCAAA
1 CTGTGTTTATATGCTAA
1417987 CT
1 CT
1417989 ATTTCAATGT
Statistics
Matches: 52, Mismatches: 16, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
16 1 0.02
17 50 0.96
18 1 0.02
ACGTcount: A:0.25, C:0.11, G:0.20, T:0.44
Consensus pattern (17 bp):
CTGTGTTTATATGCTAA
Found at i:1418043 original size:68 final size:68
Alignment explanation
Indices: 1417971--1418124 Score: 218
Period size: 68 Copynumber: 2.3 Consensus size: 68
1417961 ATATGCTAAC
* * ** * *
1417971 TGTGTTCATATGCAAACTATTTCAATGTGTGGATTGTGTAAATATGCTACCTGTGATAATGTGCA
1 TGTGTTTATATGCAAACTATGTCAATGTGTGGACCGTGTAAATATGCAACCTGTGACAATGTGCA
1418036 TGT
66 TGT
* * * *
1418039 TGTGTTTATATGTAAACTGTGTCAATGTGTGGACCGTGTAAATATGCAAGCTGTGACAATGTGCG
1 TGTGTTTATATGCAAACTATGTCAATGTGTGGACCGTGTAAATATGCAACCTGTGACAATGTGCA
1418104 TGT
66 TGT
1418107 TGTGTTTATATGCAAACT
1 TGTGTTTATATGCAAACT
1418125 CTCACTATAA
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
68 75 1.00
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (68 bp):
TGTGTTTATATGCAAACTATGTCAATGTGTGGACCGTGTAAATATGCAACCTGTGACAATGTGCA
TGT
Found at i:1418118 original size:34 final size:34
Alignment explanation
Indices: 1417971--1418124 Score: 105
Period size: 34 Copynumber: 4.5 Consensus size: 34
1417961 ATATGCTAAC
* * ** *
1417971 TGTGTTCATATGCAAACTATTTCAATGTGTG-GAT
1 TGTGTTTATATGCAAACTGTGACAATGTGCGTG-T
** * * * *
1418005 TGTGTAAATATGCTACCTGTGATAATGTGCATGT
1 TGTGTTTATATGCAAACTGTGACAATGTGCGTGT
* * * *
1418039 TGTGTTTATATGTAAACTGTGTCAATGTGTG-GAC
1 TGTGTTTATATGCAAACTGTGACAATGTGCGTG-T
* ** *
1418073 CGTGTAAATATGCAAGCTGTGACAATGTGCGTGT
1 TGTGTTTATATGCAAACTGTGACAATGTGCGTGT
1418107 TGTGTTTATATGCAAACT
1 TGTGTTTATATGCAAACT
1418125 CTCACTATAA
Statistics
Matches: 85, Mismatches: 32, Indels: 6
0.69 0.26 0.05
Matches are distributed among these distances:
33 1 0.01
34 82 0.96
35 2 0.02
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (34 bp):
TGTGTTTATATGCAAACTGTGACAATGTGCGTGT
Found at i:1418326 original size:26 final size:26
Alignment explanation
Indices: 1418275--1418326 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1418265 GTTTATGTAG
* *
1418275 GAGCTTTTTGTAAAGTAATTACGTGC
1 GAGCTCTTTGTAAAGTAATTAAGTGC
1418301 GAGCTCTTTGTAAAGT-ATCTAAGTGC
1 GAGCTCTTTGTAAAGTAAT-TAAGTGC
1418327 AACCTGGTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 2 0.09
26 21 0.91
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (26 bp):
GAGCTCTTTGTAAAGTAATTAAGTGC
Found at i:1422556 original size:12 final size:12
Alignment explanation
Indices: 1422539--1422563 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1422529 TGTAAATGAA
1422539 TCATTTCCATTT
1 TCATTTCCATTT
1422551 TCATTTCCATTT
1 TCATTTCCATTT
1422563 T
1 T
1422564 GGAAGCCTAT
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:0.24, G:0.00, T:0.60
Consensus pattern (12 bp):
TCATTTCCATTT
Found at i:1428836 original size:54 final size:54
Alignment explanation
Indices: 1428778--1428901 Score: 178
Period size: 54 Copynumber: 2.3 Consensus size: 54
1428768 CTAACTTGCT
* *
1428778 AAACAGACTAGTGAAC-TTCTAGTTCGCAACTCAACTAGTAAACACTAGCTCGCC
1 AAACAGACTAGTGAACTTTC-AATTCGCAACTCAACTAGAAAACACTAGCTCGCC
* * *
1428832 AAACAGACTAGTGAACTTTCAATTTGCAACTTAACTGGAAAACACTAGCTCGCC
1 AAACAGACTAGTGAACTTTCAATTCGCAACTCAACTAGAAAACACTAGCTCGCC
*
1428886 AAACAGACTGGTGAAC
1 AAACAGACTAGTGAAC
1428902 CCACTTGCAA
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 60 0.95
55 3 0.05
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (54 bp):
AAACAGACTAGTGAACTTTCAATTCGCAACTCAACTAGAAAACACTAGCTCGCC
Found at i:1430988 original size:18 final size:18
Alignment explanation
Indices: 1430967--1431002 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1430957 AGATTCGCCA
*
1430967 ATCATGTTATTATTGATT
1 ATCAAGTTATTATTGATT
1430985 ATCAAGTTATTATTGATT
1 ATCAAGTTATTATTGATT
1431003 CCATTTGTGT
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:0.06, G:0.11, T:0.53
Consensus pattern (18 bp):
ATCAAGTTATTATTGATT
Found at i:1438466 original size:25 final size:25
Alignment explanation
Indices: 1438438--1438487 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
1438428 AGTAGTTCTT
*
1438438 GCTGACTGGTTATGTTAGTGTAAGA
1 GCTGACTGGTTATGTTAGTGGAAGA
*
1438463 GCTGACTTGTTATGTTAGTGGAAGA
1 GCTGACTGGTTATGTTAGTGGAAGA
1438488 TCGGAAGATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.24, C:0.08, G:0.32, T:0.36
Consensus pattern (25 bp):
GCTGACTGGTTATGTTAGTGGAAGA
Found at i:1452696 original size:36 final size:35
Alignment explanation
Indices: 1452643--1452714 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 35
1452633 CGACATCGTC
1452643 TTTCCATACGATCAATAATTAAATAAATAAAAAGA
1 TTTCCATACGATCAATAATTAAATAAATAAAAAGA
*
1452678 TNTTCCCTACGATCAATAATTAAATAAATAAAAAGA
1 T-TTCCATACGATCAATAATTAAATAAATAAAAAGA
1452714 T
1 T
1452715 ATAATATTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 1 0.03
36 34 0.97
ACGTcount: A:0.51, C:0.12, G:0.06, T:0.29
Consensus pattern (35 bp):
TTTCCATACGATCAATAATTAAATAAATAAAAAGA
Found at i:1464472 original size:11 final size:11
Alignment explanation
Indices: 1464456--1464492 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
1464446 CATTCAATAA
*
1464456 CATAAACAAAT
1 CATAAATAAAT
1464467 CATAAATAAAT
1 CATAAATAAAT
1464478 CATAAATAAAT
1 CATAAATAAAT
1464489 CATA
1 CATA
1464493 TACATACATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.62, C:0.14, G:0.00, T:0.24
Consensus pattern (11 bp):
CATAAATAAAT
Found at i:1465589 original size:40 final size:40
Alignment explanation
Indices: 1465545--1465627 Score: 114
Period size: 40 Copynumber: 2.1 Consensus size: 40
1465535 GTAAATGAGT
** *
1465545 TCAGGAGTATTGAAGTACAAATAGAGG-CACGTATGTGCAA
1 TCAGGAGTACCGAAGTACAAACAG-GGACACGTATGTGCAA
*
1465585 TCAGGGGTACCGAAGTACAAACAGGGACACGTATGTGCAA
1 TCAGGAGTACCGAAGTACAAACAGGGACACGTATGTGCAA
1465625 TCA
1 TCA
1465628 TTCAATTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
39 2 0.05
40 36 0.95
ACGTcount: A:0.36, C:0.17, G:0.28, T:0.19
Consensus pattern (40 bp):
TCAGGAGTACCGAAGTACAAACAGGGACACGTATGTGCAA
Found at i:1467538 original size:363 final size:362
Alignment explanation
Indices: 1466873--1467601 Score: 1262
Period size: 363 Copynumber: 2.0 Consensus size: 362
1466863 ATAGCACCAC
*
1466873 TATTAGGATACCATGCTTAATCGATAACCATTCGACAAGTAGCAACCATCGCAACAATGTTTCCG
1 TATTAGGATACCATGCCTAATCGATAACCATTCGACAAGTAGCAACCATCGCAACAATGTTTCCG
* *
1466938 TGAGAGTAAAAACCATTGTAATCTGCATATGGCACTCTAGAAACAAAACTAGATACAGACCCTAA
66 TGAGAATAAAAACCATTGTAATCTGCATATAGCACTCTAGAAACAAAACTAGATACAGACCCTAA
** *
1467003 AGAGTTGAGCGGTGGAGATGAAGAGACATTAGGGGGAGATGAGGAGACACGGGAAAATAACCCAC
131 AGAGTTGAAAGGTGGAGATGAAGAGACATTAAGGGGAGATGAGGAGACACGGGAAAATAACCCAC
1467068 CAAAAAATGGTAGAAGAAAAGGCACGAGCAGACGGTAAGAAAGAAACACAAGCAGACCCAAACCC
196 CAAAAAATGGTAGAAGAAAAGGCACGAGCAGACGGTAAGAAAGAAACACAAGCAGACCCAAACCC
*
1467133 TAATGAATTATGTGGATCACGCTCAGCGTAACAATATTGGGCCGAAACAGGCTAAGAAGAACGGG
261 TAATGAATTATGTGGATCACGCTCAGCGTAACAATATTGGGCCGAAACAGGCTAAGAACAACGGG
*
1467198 CCTGAAAATTACTACCTAAATTGGGCTCAACATAACAA
326 CCTG-AAACTACTACCTAAATTGGGCTCAACATAACAA
** *
1467236 TATTAGGATACCATGCCTAATCGATAACTGTTCGACAAGTAGCAACCGTCGCAACAATGTTTCCG
1 TATTAGGATACCATGCCTAATCGATAACCATTCGACAAGTAGCAACCATCGCAACAATGTTTCCG
* * **
1467301 TGAGAATAAGAACCGTTGTAATCTGCATATAGCACTCTAGAAACAAAACTAGATATGGACCCTAA
66 TGAGAATAAAAACCATTGTAATCTGCATATAGCACTCTAGAAACAAAACTAGATACAGACCCTAA
* *
1467366 AGAGTTGAAAGGTTGAGATGAAGAGACATTAAGGGGAGATGAGGGGACACGGGAAAATGAA-CCA
131 AGAGTTGAAAGGTGGAGATGAAGAGACATTAAGGGGAGATGAGGAGACACGGGAAAAT-AACCCA
**
1467430 CCAAAAAATGGTAGAAGAAAAGGCACGAGCAGACGGTAAGAAAGAAACATGAGCAGACCCAAACC
195 CCAAAAAATGGTAGAAGAAAAGGCACGAGCAGACGGTAAGAAAGAAACACAAGCAGACCCAAACC
1467495 CTAATGAATTATGTGGATCACGCTCAGCGTAACAATATTGGGCCGAAACAGGCTAAGAACAACGG
260 CTAATGAATTATGTGGATCACGCTCAGCGTAACAATATTGGGCCGAAACAGGCTAAGAACAACGG
1467560 GCCTGAAACTACTACCTAAATTGGGCTCAACATAACAA
325 GCCTGAAACTACTACCTAAATTGGGCTCAACATAACAA
1467598 TATT
1 TATT
1467602 GAGCCAATGT
Statistics
Matches: 346, Mismatches: 19, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
362 36 0.10
363 308 0.89
364 2 0.01
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.18
Consensus pattern (362 bp):
TATTAGGATACCATGCCTAATCGATAACCATTCGACAAGTAGCAACCATCGCAACAATGTTTCCG
TGAGAATAAAAACCATTGTAATCTGCATATAGCACTCTAGAAACAAAACTAGATACAGACCCTAA
AGAGTTGAAAGGTGGAGATGAAGAGACATTAAGGGGAGATGAGGAGACACGGGAAAATAACCCAC
CAAAAAATGGTAGAAGAAAAGGCACGAGCAGACGGTAAGAAAGAAACACAAGCAGACCCAAACCC
TAATGAATTATGTGGATCACGCTCAGCGTAACAATATTGGGCCGAAACAGGCTAAGAACAACGGG
CCTGAAACTACTACCTAAATTGGGCTCAACATAACAA
Found at i:1469608 original size:26 final size:26
Alignment explanation
Indices: 1469562--1469611 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1469552 TTGAATAAAA
*
1469562 AGGGGTCGCTAAGTGTAGATTCCCCG
1 AGGGGTCGCTAAGTCTAGATTCCCCG
*
1469588 AGGGGTTGCTAAGTACT-GATTCCC
1 AGGGGTCGCTAAGT-CTAGATTCCC
1469612 AAAATTATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 20 0.95
27 1 0.05
ACGTcount: A:0.20, C:0.22, G:0.32, T:0.26
Consensus pattern (26 bp):
AGGGGTCGCTAAGTCTAGATTCCCCG
Found at i:1469652 original size:42 final size:42
Alignment explanation
Indices: 1469591--1469733 Score: 128
Period size: 42 Copynumber: 3.4 Consensus size: 42
1469581 TTCCCCGAGG
* *
1469591 GGTTGCTAAGTACTGATTCCCAAAATTATTGACTTTAAAGGT
1 GGTTGCTAAGTGCTGATTCCCAAAATCATTGACTTTAAAGGT
* *** * *
1469633 GGTTGCTAAGTGCTAATTCCACCGTATCCTTGACTATGAAAGG-
1 GGTTGCTAAGTGCTGATTCC-CAAAATCATTGACT-TTAAAGGT
* ** * *
1469676 GGTTGCTATGTGCTGATTCCCCGTAATCACTGAATTT-AAGGT
1 GGTTGCTAAGTGCTGATT-CCCAAAATCATTGACTTTAAAGGT
1469718 GGTTGCTAAGTGCTGA
1 GGTTGCTAAGTGCTGA
1469734 ATCCACCGAG
Statistics
Matches: 79, Mismatches: 18, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
41 4 0.05
42 34 0.43
43 33 0.42
44 8 0.10
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (42 bp):
GGTTGCTAAGTGCTGATTCCCAAAATCATTGACTTTAAAGGT
Found at i:1469680 original size:43 final size:46
Alignment explanation
Indices: 1469619--1469741 Score: 138
Period size: 43 Copynumber: 2.8 Consensus size: 46
1469609 CCCAAAATTA
1469619 TTGACT-TTAAAGGTGGTTGCTAAGTGCTAATTCCACCGT-ATC-C
1 TTGACTATTAAAGGTGGTTGCTAAGTGCTAATTCCACCGTAATCAC
* * *
1469662 TTGACTATGAAAGG-GGTTGCTATGTGCTGATTCC-CCGTAATCAC
1 TTGACTATTAAAGGTGGTTGCTAAGTGCTAATTCCACCGTAATCAC
*
1469706 -TGA--ATTTAAGGTGGTTGCTAAGTGCTGAA-TCCACCG
1 TTGACTATTAAAGGTGGTTGCTAAGTGCT-AATTCCACCG
1469742 AGTTACGGAT
Statistics
Matches: 67, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
41 6 0.09
42 20 0.30
43 34 0.51
44 7 0.10
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (46 bp):
TTGACTATTAAAGGTGGTTGCTAAGTGCTAATTCCACCGTAATCAC
Found at i:1474193 original size:7 final size:7
Alignment explanation
Indices: 1474181--1474213 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
1474171 TCCCTTTCCA
1474181 TCCCACC
1 TCCCACC
1474188 TCCCACC
1 TCCCACC
1474195 TCCCACC
1 TCCCACC
1474202 TCCCACC
1 TCCCACC
1474209 TCCCA
1 TCCCA
1474214 TCTACTCCAA
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:0.15, C:0.70, G:0.00, T:0.15
Consensus pattern (7 bp):
TCCCACC
Found at i:1476967 original size:20 final size:20
Alignment explanation
Indices: 1476893--1476978 Score: 77
Period size: 20 Copynumber: 4.2 Consensus size: 20
1476883 TTTTATAATT
*
1476893 TTTTTAAAATATAATTTTTGGAA
1 TTTTTAAAA-ATTA-TTTT-GAA
* * *
1476916 TTTCTATAAA-TATTTTGTA
1 TTTTTAAAAATTATTTTGAA
1476935 -TTTTAAAAATTATTTTGAA
1 TTTTTAAAAATTATTTTGAA
* *
1476954 TTTTTGAAATTTATTTTGAA
1 TTTTTAAAAATTATTTTGAA
1476974 TTTTT
1 TTTTT
1476979 TTAACTTTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
18 7 0.13
19 10 0.19
20 26 0.50
21 1 0.02
22 1 0.02
23 7 0.13
ACGTcount: A:0.34, C:0.01, G:0.07, T:0.58
Consensus pattern (20 bp):
TTTTTAAAAATTATTTTGAA
Found at i:1482298 original size:30 final size:31
Alignment explanation
Indices: 1482264--1482326 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
1482254 ATACTTAAAC
*
1482264 AAGCCCTTAA-ATTTTAA-TTAGTATCCAAAT
1 AAGCCATTAATATTTTAACTT-GTATCCAAAT
*
1482294 AAGCCATTAATCTTTTAACTTGTATCCAAAT
1 AAGCCATTAATATTTTAACTTGTATCCAAAT
1482325 AA
1 AA
1482327 ATCTTTAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 9 0.31
31 18 0.62
32 2 0.07
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.37
Consensus pattern (31 bp):
AAGCCATTAATATTTTAACTTGTATCCAAAT
Found at i:1482310 original size:31 final size:30
Alignment explanation
Indices: 1482275--1482343 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 30
1482265 AGCCCTTAAA
*
1482275 TTTTAATTAGTATCCAAATAAGCCATTAATC
1 TTTTAATT-GTATCCAAATAAACCATTAATC
* *
1482306 TTTTAACTTGTATCCAAATAAATCTTTAATC
1 TTTTAA-TTGTATCCAAATAAACCATTAATC
1482337 -TTTAATT
1 TTTTAATT
1482344 TATATAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 2 0.06
30 5 0.15
31 25 0.74
32 2 0.06
ACGTcount: A:0.36, C:0.14, G:0.04, T:0.45
Consensus pattern (30 bp):
TTTTAATTGTATCCAAATAAACCATTAATC
Found at i:1482826 original size:22 final size:22
Alignment explanation
Indices: 1482796--1482851 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
1482786 ATTTCCTCTC
**
1482796 AATTCCTCTCAATTTTTTTCCAA
1 AATT-CTCTCAATTTCCTTCCAA
1482819 AATTCTCTCAATTTCCTTCCAA
1 AATTCTCTCAATTTCCTTCCAA
1482841 AATTCTCTCAA
1 AATTCTCTCAA
1482852 ATCCATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 27 0.87
23 4 0.13
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTCTCTCAATTTCCTTCCAA
Found at i:1482899 original size:22 final size:22
Alignment explanation
Indices: 1482874--1482924 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
1482864 TTTCAATTTC
1482874 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
*
1482896 CTCTTAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
*
1482918 CCCTCAA
1 CTCTCAA
1482925 ATCCATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.27, C:0.33, G:0.00, T:0.39
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Found at i:1482905 original size:73 final size:73
Alignment explanation
Indices: 1482794--1482960 Score: 282
Period size: 73 Copynumber: 2.3 Consensus size: 73
1482784 ATATTTCCTC
** *
1482794 TCAA-TTCCTCTCAATTTTTTTCCAAAATTCTCTCAATTTCCTTCCAAAATTCTCTCAAATCCAT
1 TCAATTTCCTCTCAATTTCCTTCCAAAATTCTCTCAATTTCCTTCCAAAATTCCCTCAAATCCAT
1482858 ATTTAATT
66 ATTTAATT
*
1482866 TCAATTTCCTCTCAATTTCCTTCCAAAATTCTCTTAATTTCCTTCCAAAATTCCCTCAAATCCAT
1 TCAATTTCCTCTCAATTTCCTTCCAAAATTCTCTCAATTTCCTTCCAAAATTCCCTCAAATCCAT
*
1482931 ATTTGATT
66 ATTTAATT
1482939 TCAATTTCCTCTCAATTTCCTT
1 TCAATTTCCTCTCAATTTCCTT
1482961 TTTTAAAATA
Statistics
Matches: 89, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
72 4 0.04
73 85 0.96
ACGTcount: A:0.27, C:0.28, G:0.01, T:0.44
Consensus pattern (73 bp):
TCAATTTCCTCTCAATTTCCTTCCAAAATTCTCTCAATTTCCTTCCAAAATTCCCTCAAATCCAT
ATTTAATT
Found at i:1496120 original size:7 final size:7
Alignment explanation
Indices: 1496108--1496133 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1496098 TAGTCGATTG
1496108 GTATTTA
1 GTATTTA
1496115 GTATTTA
1 GTATTTA
1496122 GTATTTA
1 GTATTTA
1496129 GTATT
1 GTATT
1496134 ATTATGTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:1497284 original size:42 final size:44
Alignment explanation
Indices: 1497233--1497320 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 44
1497223 TTATTTGTAC
*
1497233 AAATATTTTGA-ATATTTTGATATTATTTTTATGT-A-AAAATAG
1 AAATATTTTGAGATATTTTGATATTA-TTTGATGTAATAAAATAG
* *
1497275 AAATTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAG
1 AAATATTTTGAGATATTTTGATATTATTTGATGTAATAAAATAG
1497319 AA
1 AA
1497321 GTTTATTCCT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
42 17 0.43
43 14 0.35
44 9 0.22
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (44 bp):
AAATATTTTGAGATATTTTGATATTATTTGATGTAATAAAATAG
Found at i:1497357 original size:23 final size:23
Alignment explanation
Indices: 1497331--1497415 Score: 98
Period size: 23 Copynumber: 3.4 Consensus size: 23
1497321 GTTTATTCCT
*
1497331 AACCCTAACCAAATTTAATTAAA
1 AACCCTAACCAAACTTAATTAAA
*
1497354 AACCCTAACCTAACTTAATTAAA
1 AACCCTAACCAAACTTAATTAAA
1497377 AACCCTAACCTTGACTAAACTTAATTAAA
1 AACCCTAA-C----C-AAACTTAATTAAA
1497406 AACCCTAACC
1 AACCCTAACC
1497416 CTAACCCAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
23 29 0.55
24 2 0.04
28 2 0.04
29 20 0.38
ACGTcount: A:0.47, C:0.27, G:0.01, T:0.25
Consensus pattern (23 bp):
AACCCTAACCAAACTTAATTAAA
Found at i:1497361 original size:29 final size:29
Alignment explanation
Indices: 1497328--1497513 Score: 222
Period size: 29 Copynumber: 6.6 Consensus size: 29
1497318 GAAGTTTATT
1497328 CCTAACCCTAACCAAATTTAATTAAAAAC
1 CCTAACCCTAACCAAATTTAATTAAAAAC
1497357 CCTAA-CCTAA-C----TTAATTAAAAAC
1 CCTAACCCTAACCAAATTTAATTAAAAAC
* * * *
1497380 CCTAACCTTGACTAAACTTAATTAAAAAC
1 CCTAACCCTAACCAAATTTAATTAAAAAC
* * *
1497409 CCTAACCCTAACCCAATTAAATTTAAAAC
1 CCTAACCCTAACCAAATTTAATTAAAAAC
* *
1497438 CGTAACCCTAACCTAATTTAATTAAAAAC
1 CCTAACCCTAACCAAATTTAATTAAAAAC
* *
1497467 CCTAACCCTAACCCAATTCAATTAAAAAC
1 CCTAACCCTAACCAAATTTAATTAAAAAC
1497496 CCTAACCCTAACCCAAAT
1 CCTAACCCTAA-CCAAAT
1497514 CCAATTTTAT
Statistics
Matches: 132, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
23 17 0.13
24 3 0.02
27 1 0.01
28 5 0.04
29 101 0.77
30 5 0.04
ACGTcount: A:0.45, C:0.30, G:0.01, T:0.24
Consensus pattern (29 bp):
CCTAACCCTAACCAAATTTAATTAAAAAC
Found at i:1497556 original size:19 final size:20
Alignment explanation
Indices: 1497527--1497650 Score: 119
Period size: 18 Copynumber: 6.7 Consensus size: 20
1497517 ATTTTATATA
1497527 ATTTGATAATTTTACTAACC
1 ATTTGATAATTTTACTAACC
1497547 ATTT-ATAATTTTA-TATA--
1 ATTTGATAATTTTACTA-ACC
1497564 ATTTGATAATTTTACTAACC
1 ATTTGATAATTTTACTAACC
*
1497584 A-TTAATAATTTTA-TATA--
1 ATTTGATAATTTTACTA-ACC
1497601 ATTTGATAATTTTACTAACC
1 ATTTGATAATTTTACTAACC
*
1497621 A-TTAATAATTTTA-TATA--
1 ATTTGATAATTTTACTA-ACC
1497638 ATTTGATAATTTT
1 ATTTGATAATTTT
1497651 GTAACCCGCT
Statistics
Matches: 88, Mismatches: 4, Indels: 26
0.75 0.03 0.22
Matches are distributed among these distances:
17 6 0.07
18 38 0.43
19 38 0.43
20 6 0.07
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.51
Consensus pattern (20 bp):
ATTTGATAATTTTACTAACC
Found at i:1497558 original size:37 final size:37
Alignment explanation
Indices: 1497516--1497650 Score: 261
Period size: 37 Copynumber: 3.6 Consensus size: 37
1497506 ACCCAAATCC
*
1497516 AATTTTATATAATTTGATAATTTTACTAACCATTTAT
1 AATTTTATATAATTTGATAATTTTACTAACCATTAAT
1497553 AATTTTATATAATTTGATAATTTTACTAACCATTAAT
1 AATTTTATATAATTTGATAATTTTACTAACCATTAAT
1497590 AATTTTATATAATTTGATAATTTTACTAACCATTAAT
1 AATTTTATATAATTTGATAATTTTACTAACCATTAAT
1497627 AATTTTATATAATTTGATAATTTT
1 AATTTTATATAATTTGATAATTTT
1497651 GTAACCCGCT
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 97 1.00
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.51
Consensus pattern (37 bp):
AATTTTATATAATTTGATAATTTTACTAACCATTAAT
Found at i:1498313 original size:124 final size:124
Alignment explanation
Indices: 1498152--1498377 Score: 380
Period size: 124 Copynumber: 1.8 Consensus size: 124
1498142 CCCAAACATG
*
1498152 CTACTGTAGCAAAAGCGCGCCCATGAGGCCACGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGCCCACGAGGCCACGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* * *
1498217 TAGAAGTGATTTTATACTATTTGGTCAGAAAAGTCAAAAAAATTTATTTCTTACATGAC
66 TAAAAGCGATTTTATACTATTTGCTCAGAAAAGTCAAAAAAATTTATTTCTTACATGAC
* * * *
1498276 CTACTGTAGCAAAAGCGCGTCCACGAGGCCGCTATTTCACAAATTCTTCTCGAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGCCCACGAGGCCACGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1498341 TAAAAGCGATTTTATACTATTTGCTCAGAAAAGTCAA
66 TAAAAGCGATTTTATACTATTTGCTCAGAAAAGTCAA
1498378 CTCGAAATTA
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
124 94 1.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.29
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGCCCACGAGGCCACGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAAAAGCGATTTTATACTATTTGCTCAGAAAAGTCAAAAAAATTTATTTCTTACATGAC
Found at i:1504684 original size:51 final size:51
Alignment explanation
Indices: 1504619--1504755 Score: 175
Period size: 51 Copynumber: 2.7 Consensus size: 51
1504609 TATGGTAATT
*
1504619 AATCTTAGAAGATATGATATTATAATCTTAGAGATCTTAGATATGATATGG
1 AATCTTAGAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGG
* * * ** * * **
1504670 AATCTTATAAGATATTATTTTATAAGATTACATATCTTATCTAAGATATGG
1 AATCTTAGAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGG
*
1504721 AATCTTAGAAGATATGATATTATATTCTTAGAGAT
1 AATCTTAGAAGATATGATATTATAATCTTAGAGAT
1504756 TTGATGGTAG
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
51 68 1.00
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (51 bp):
AATCTTAGAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGG
Found at i:1507436 original size:66 final size:66
Alignment explanation
Indices: 1507354--1507484 Score: 253
Period size: 66 Copynumber: 2.0 Consensus size: 66
1507344 TACTAAAGAA
*
1507354 GCCTGTCAGATTGAAGCCTGGTTGGCCCGATAGCGAAGAGATGGCAACTTAGGCTAATATGGTAA
1 GCCTGTCAGATTGAAGCCTGGTTGGCCCGATAGCGAAGAGATGGCAACTTAAGCTAATATGGTAA
1507419 C
66 C
1507420 GCCTGTCAGATTGAAGCCTGGTTGGCCCGATAGCGAAGAGATGGCAACTTAAGCTAATATGGTAA
1 GCCTGTCAGATTGAAGCCTGGTTGGCCCGATAGCGAAGAGATGGCAACTTAAGCTAATATGGTAA
1507485 TTAATCTTAG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (66 bp):
GCCTGTCAGATTGAAGCCTGGTTGGCCCGATAGCGAAGAGATGGCAACTTAAGCTAATATGGTAA
C
Found at i:1507552 original size:51 final size:51
Alignment explanation
Indices: 1507487--1507623 Score: 175
Period size: 51 Copynumber: 2.7 Consensus size: 51
1507477 TATGGTAATT
*
1507487 AATCTTAGAAGATATGATATTATAATCTTAGAGATCTTAGATATGATATGG
1 AATCTTAGAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGG
* * * ** * * **
1507538 AATCTTATAAGATATTATTTTATAAGATTACATATCTTATCTAAGATATGG
1 AATCTTAGAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGG
*
1507589 AATCTTAGAAGATATGATATTATATTCTTAGAGAT
1 AATCTTAGAAGATATGATATTATAATCTTAGAGAT
1507624 TTGATGGTAG
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
51 68 1.00
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (51 bp):
AATCTTAGAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGG
Found at i:1509496 original size:47 final size:46
Alignment explanation
Indices: 1509373--1509498 Score: 112
Period size: 49 Copynumber: 2.7 Consensus size: 46
1509363 CTTTTATTTG
* * * *
1509373 TTATTTATCTATT-ATTCATTTAATCAATTAGAGATAAAATAATTA
1 TTATTTATCTCTTAATTAATTAAATTAATTAGAGATAAAATAATTA
* * * * *
1509418 TT-TTTATTATCATTTAATTATTTTAATTTAATTAGCGATAATATAATTA
1 TTATTTA-TCTC--TTAATTA-ATTAAATTAATTAGAGATAAAATAATTA
1509467 TTATTTATCTCTTAATTAACTTAAATTAATTA
1 TTATTTATCTCTTAATTAA-TTAAATTAATTA
1509499 AAATATGATG
Statistics
Matches: 62, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
44 4 0.06
45 4 0.06
47 20 0.32
48 3 0.05
49 27 0.44
50 4 0.06
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (46 bp):
TTATTTATCTCTTAATTAATTAAATTAATTAGAGATAAAATAATTA
Found at i:1509785 original size:46 final size:46
Alignment explanation
Indices: 1509718--1509811 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
1509708 AGTTTGATTC
1509718 GTGGATATTTGTAAAATTCTAAATCTTCATCAATGCCATCAACTTG
1 GTGGATATTTGTAAAATTCTAAATCTTCATCAATGCCATCAACTTG
1509764 GTGGATATTTGTAAAATTCTAAATCTTCATCAATGCCATCAACTTG
1 GTGGATATTTGTAAAATTCTAAATCTTCATCAATGCCATCAACTTG
1509810 GT
1 GT
1509812 TATCAGCATG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (46 bp):
GTGGATATTTGTAAAATTCTAAATCTTCATCAATGCCATCAACTTG
Found at i:1511660 original size:25 final size:24
Alignment explanation
Indices: 1511609--1511678 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 24
1511599 GAGCGATAAA
* * *
1511609 CGGTAAGTTCCTCCGAGCTGAATAT
1 CGGTAAGCTCCTACGAGCT-AAAAT
1511634 CGGTAAGCTCCTACGAGCTACAAAT
1 CGGTAAGCTCCTACGAGCTA-AAAT
* *
1511659 CGGTAAACTCATACGAGCTA
1 CGGTAAGCTCCTACGAGCTA
1511679 TGGTGAGTCT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
24 1 0.03
25 38 0.97
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (24 bp):
CGGTAAGCTCCTACGAGCTAAAAT
Found at i:1516692 original size:46 final size:44
Alignment explanation
Indices: 1516622--1516709 Score: 104
Period size: 46 Copynumber: 2.0 Consensus size: 44
1516612 ATAGATAATC
* * * *
1516622 TCAGTTTGGGCCTAAACCCTTTTCATTACCAGTATCAGTATTAGCA
1 TCAGTTTAGGCCTAAACCCATTTCAGTAACAGTA--AGTATTAGCA
* *
1516668 TCAGTTTAGGCCTTAGCCCATTTCAGTAACAGTAAGTATTAG
1 TCAGTTTAGGCCTAAACCCATTTCAGTAACAGTAAGTATTAG
1516710 GGCCTTAGCC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
44 8 0.22
46 28 0.78
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (44 bp):
TCAGTTTAGGCCTAAACCCATTTCAGTAACAGTAAGTATTAGCA
Found at i:1516714 original size:34 final size:34
Alignment explanation
Indices: 1516676--1516756 Score: 135
Period size: 34 Copynumber: 2.4 Consensus size: 34
1516666 CATCAGTTTA
*
1516676 GGCCTTAGCCCATTTCAGTAACAGTAAGTATTAG
1 GGCCTTAGCCCATTTCAGTAACAGTAAGCATTAG
*
1516710 GGCCTTAGCCCATTTCGGTAACAGTAAGCATTAG
1 GGCCTTAGCCCATTTCAGTAACAGTAAGCATTAG
*
1516744 GGCTTTAGCCCAT
1 GGCCTTAGCCCAT
1516757 CATAGTACAG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.28
Consensus pattern (34 bp):
GGCCTTAGCCCATTTCAGTAACAGTAAGCATTAG
Found at i:1517254 original size:18 final size:18
Alignment explanation
Indices: 1517231--1517271 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1517221 TATGTTGTAT
1517231 GCCCATATGGGCCCACAC-
1 GCCCATAT-GGCCCACACG
*
1517249 GCCCATGTGGCCCACACG
1 GCCCATATGGCCCACACG
1517267 GCCCA
1 GCCCA
1517272 AACTGGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.20, C:0.46, G:0.24, T:0.10
Consensus pattern (18 bp):
GCCCATATGGCCCACACG
Found at i:1525573 original size:18 final size:17
Alignment explanation
Indices: 1525527--1525580 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 17
1525517 TTTCCAGTTC
*
1525527 TCAATTCAAACTTACTT
1 TCAATTCAAATTTACTT
*
1525544 TCATTTCAAAATTTACTT
1 TCAATTC-AAATTTACTT
*
1525562 TCAATATCAAATTCACTT
1 TCAAT-TCAAATTTACTT
1525580 T
1 T
1525581 TTCATTCACT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 6 0.19
18 23 0.74
19 2 0.06
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.44
Consensus pattern (17 bp):
TCAATTCAAATTTACTT
Found at i:1527424 original size:40 final size:40
Alignment explanation
Indices: 1527380--1527641 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
1527370 GCTCCTCGTT
* *
1527380 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
1527420 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
1527460 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
1527499 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
1527538 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
1527577 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
1527618 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
1527642 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:1535511 original size:79 final size:81
Alignment explanation
Indices: 1535409--1535592 Score: 222
Period size: 79 Copynumber: 2.3 Consensus size: 81
1535399 GCTCCTCGTT
* *
1535409 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAACC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTC-GGATCTTAACC
*
1535471 CGGAT-TTAGTAAC-TCGCA
63 CGGATATT-GTAACTTAGCA
**
1535489 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAACCCGG
*
1535553 ATATTGTCACTTAGCA
66 ATATTGTAACTTAGCA
1535569 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
1535593 CATCATTCAA
Statistics
Matches: 92, Mismatches: 6, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
78 14 0.15
79 56 0.61
80 22 0.24
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATTGTAACTTAGCA
Found at i:1535526 original size:39 final size:41
Alignment explanation
Indices: 1535409--1535592 Score: 199
Period size: 40 Copynumber: 4.6 Consensus size: 41
1535399 GCTCCTCGTT
* *
1535409 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAATCTCGCA
* *
1535449 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAA-CTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
1535489 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGT-ATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
* * *
1535528 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTAATC-TCGCA
1535569 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
1535593 CATCATTCAA
Statistics
Matches: 128, Mismatches: 7, Indels: 19
0.83 0.05 0.12
Matches are distributed among these distances:
38 3 0.02
39 48 0.38
40 66 0.52
41 11 0.09
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (41 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
Found at i:1540298 original size:39 final size:39
Alignment explanation
Indices: 1540237--1540314 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
1540227 ATAGAAATAT
1540237 AGAAATAGAATCATTAAAAAATG-TTTTTCTCCAAAATGG
1 AGAAATAGAATCATTAAAAAATGATTTTTCT-CAAAATGG
* ***
1540276 AGAAATGGAATCATTTGGAAATGAATTTTTCTCAAAATG
1 AGAAATAGAATCATTAAAAAATG-ATTTTTCTCAAAATG
1540315 AAAATAAGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 19 0.58
40 7 0.21
41 7 0.21
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.32
Consensus pattern (39 bp):
AGAAATAGAATCATTAAAAAATGATTTTTCTCAAAATGG
Found at i:1542407 original size:11 final size:11
Alignment explanation
Indices: 1542387--1542416 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
1542377 TTAAAATTAA
1542387 AAAAAGTATTTT
1 AAAAA-TATTTT
1542399 AAAAATATTTT
1 AAAAATATTTT
1542410 AAAAATA
1 AAAAATA
1542417 AAAAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:1545306 original size:36 final size:36
Alignment explanation
Indices: 1545265--1545337 Score: 112
Period size: 36 Copynumber: 2.0 Consensus size: 36
1545255 GCATATTGTG
*
1545265 ACCCAACATA-TTTTGAAAGTGTTGTCAATAAGGCAA
1 ACCCAACA-AGTTTTGAAAGTGTTGCCAATAAGGCAA
*
1545301 ACCCAACAAGTTTTGAAAGTGTTGCCAATGAGGCAA
1 ACCCAACAAGTTTTGAAAGTGTTGCCAATAAGGCAA
1545337 A
1 A
1545338 ATGGAAAGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 1 0.03
36 33 0.97
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (36 bp):
ACCCAACAAGTTTTGAAAGTGTTGCCAATAAGGCAA
Found at i:1546850 original size:25 final size:25
Alignment explanation
Indices: 1546818--1546868 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1546808 AGATATCAAA
1546818 TAGTAAGTATGTATTAAACTGAAAG
1 TAGTAAGTATGTATTAAACTGAAAG
1546843 TAGTAAGTATGTATTAAACTGAAAG
1 TAGTAAGTATGTATTAAACTGAAAG
1546868 T
1 T
1546869 GTCCTTTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.33
Consensus pattern (25 bp):
TAGTAAGTATGTATTAAACTGAAAG
Found at i:1552870 original size:2 final size:2
Alignment explanation
Indices: 1552865--1552895 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1552855 TTATGCTCAT
1552865 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1552896 TTTCTTCTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1553828 original size:73 final size:74
Alignment explanation
Indices: 1553713--1553858 Score: 249
Period size: 73 Copynumber: 2.0 Consensus size: 74
1553703 CATCAGTGGT
*
1553713 AATGTTATGCATTATTTCTTTTGGCTATTTCTTGGTTTCTTCTAAGCACTATCATGGTGATGGTA
1 AATGTTATGCATTATTTCTTTTGCCTATTTCTTGGTTTCTTCTAAGCACTATCATGGTGATGGTA
1553778 ATAATTTTC
66 ATAATTTTC
** *
1553787 AATGTTATGTTTTATTTC-TTTGCCTATTTCTTGGTTTCTTCTAAGCACTATTATGGTGATGGTA
1 AATGTTATGCATTATTTCTTTTGCCTATTTCTTGGTTTCTTCTAAGCACTATCATGGTGATGGTA
1553851 ATAATTTT
66 ATAATTTT
1553859 TAAGTTTGCC
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
73 52 0.76
74 16 0.24
ACGTcount: A:0.21, C:0.12, G:0.16, T:0.51
Consensus pattern (74 bp):
AATGTTATGCATTATTTCTTTTGCCTATTTCTTGGTTTCTTCTAAGCACTATCATGGTGATGGTA
ATAATTTTC
Found at i:1568571 original size:25 final size:25
Alignment explanation
Indices: 1568538--1568674 Score: 100
Period size: 25 Copynumber: 5.4 Consensus size: 25
1568528 AGCACATAAA
1568538 CGGGAAGCTCAAGAGAGCCATTAAT
1 CGGGAAGCTCAAGAGAGCCATTAAT
* * * * *
1568563 TGGGGAGCTCATGCGAGCCAAT-AT
1 CGGGAAGCTCAAGAGAGCCATTAAT
**
1568587 CGGGAAGCTCCGGAGAGCCATTAAT
1 CGGGAAGCTCAAGAGAGCCATTAAT
* * *
1568612 CAGGAAGCTCATGAAAGAGCCTTTAAT
1 CGGGAAGCTCA--AGAGAGCCATTAAT
**
1568639 TAGGAAGCTCCAA-AGAGCCA-TATAT
1 CGGGAAGCT-CAAGAGAGCCATTA-AT
*
1568664 CGGGACGCTCA
1 CGGGAAGCTCA
1568675 TAAGAGCTAC
Statistics
Matches: 86, Mismatches: 21, Indels: 11
0.73 0.18 0.09
Matches are distributed among these distances:
24 22 0.26
25 42 0.49
26 1 0.01
27 19 0.22
28 2 0.02
ACGTcount: A:0.32, C:0.22, G:0.28, T:0.18
Consensus pattern (25 bp):
CGGGAAGCTCAAGAGAGCCATTAAT
Found at i:1573056 original size:25 final size:25
Alignment explanation
Indices: 1573016--1573071 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
1573006 TTAATAGATT
* *
1573016 AAAAAAGTTCACGTTTTTTTATGTAA
1 AAAAAAGTTCAAGTTTTTTAAT-TAA
1573042 AAAAAAGTT-AAGTTTTTTAATTAA
1 AAAAAAGTTCAAGTTTTTTAATTAA
1573066 AAAAAA
1 AAAAAA
1573072 CTTTTTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 9 0.32
25 10 0.36
26 9 0.32
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.38
Consensus pattern (25 bp):
AAAAAAGTTCAAGTTTTTTAATTAA
Found at i:1573057 original size:24 final size:26
Alignment explanation
Indices: 1573016--1573071 Score: 73
Period size: 24 Copynumber: 2.2 Consensus size: 26
1573006 TTAATAGATT
*
1573016 AAAAAAGTTCACGTTTTTTT-ATGTAA
1 AAAAAAGTTCAAGTTTTTTTAAT-TAA
1573042 AAAAAAGTT-AAG-TTTTTTAATTAA
1 AAAAAAGTTCAAGTTTTTTTAATTAA
1573066 AAAAAA
1 AAAAAA
1573072 CTTTTTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 15 0.54
25 4 0.14
26 9 0.32
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.38
Consensus pattern (26 bp):
AAAAAAGTTCAAGTTTTTTTAATTAA
Found at i:1574693 original size:172 final size:173
Alignment explanation
Indices: 1574394--1574718 Score: 458
Period size: 172 Copynumber: 1.9 Consensus size: 173
1574384 TACTTTTCCT
*
1574394 TCAACATCTTCTAATATTATACACATACTTAGTAAAATATAAAAATTGTTTTCATAATTATACAC
1 TCAACATCTTCTAATATTATACACATACTTAGTAAAATATAAAAATTATTTTCATAATTATACAC
*
1574459 TTTATTTGATTTGAGTTTAAGTTCAGCTCAAGCACGAGGCTAAGTCAAGTTTGAGCTCTTGATTT
66 TTTATTTGATTTGAGTTTAAGTTCAGCTCAAGCACGAAGCTAAGTCAAGTTTGAGCTCTTGATTT
1574524 GACTTAATGATAATCAGGCCTATTCAAGTTTAGCTACTGCTTC
131 GACTTAATGATAATCAGGCCTATTCAAGTTTAGCTACTGCTTC
* * * * ** * * * **
1574567 TCAATATCTTCTAGTTTTATACACATATTTAGTAAAATAT-AATTTTATTTTTATATTTTTACGT
1 TCAACATCTTCTAATATTATACACATACTTAGTAAAATATAAAAATTATTTTCATAATTATACAC
* ** *
1574631 TTTATTT-AGTTTGAGTTTAAGTTCCGC-CAAGCTTGAAGCTAATTCAAGTTTAGAGCTCTTGAT
66 TTTATTTGA-TTTGAGTTTAAGTTCAGCTCAAGCACGAAGCTAAGTCAAGTTT-GAGCTCTTGAT
1574694 TTGACTTAATGATAATCAGGCCTAT
129 TTGACTTAATGATAATCAGGCCTAT
1574719 CCGAGTTGAG
Statistics
Matches: 133, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
171 21 0.16
172 76 0.57
173 36 0.27
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (173 bp):
TCAACATCTTCTAATATTATACACATACTTAGTAAAATATAAAAATTATTTTCATAATTATACAC
TTTATTTGATTTGAGTTTAAGTTCAGCTCAAGCACGAAGCTAAGTCAAGTTTGAGCTCTTGATTT
GACTTAATGATAATCAGGCCTATTCAAGTTTAGCTACTGCTTC
Found at i:1578951 original size:28 final size:28
Alignment explanation
Indices: 1578915--1578978 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
1578905 TATAATACCC
*
1578915 AGGTAGCAGAGCCGACCATATATCATTT
1 AGGTGGCAGAGCCGACCATATATCATTT
* *
1578943 AGGTGGCAGAGTCGATCATATATCATTT
1 AGGTGGCAGAGCCGACCATATATCATTT
1578971 AGGTGGCA
1 AGGTGGCA
1578979 AAATCGATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.27
Consensus pattern (28 bp):
AGGTGGCAGAGCCGACCATATATCATTT
Found at i:1578985 original size:28 final size:28
Alignment explanation
Indices: 1578931--1578993 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
1578921 CAGAGCCGAC
* *
1578931 CATATATCATTTAGGTGGCAGAGTCGAT
1 CATATATCATTTAGGTGGCAAAATCGAT
1578959 CATATATCATTTAGGTGGCAAAATCGAT
1 CATATATCATTTAGGTGGCAAAATCGAT
*
1578987 TATATAT
1 CATATAT
1578994 TCAAACTAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (28 bp):
CATATATCATTTAGGTGGCAAAATCGAT
Found at i:1583207 original size:22 final size:21
Alignment explanation
Indices: 1583179--1583220 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1583169 GTTTAGTTGA
*
1583179 TTTTTAATATATATATATTTAC
1 TTTTTAAGATATAT-TATTTAC
*
1583201 TTTTTAAGATTTATTATTTA
1 TTTTTAAGATATATTATTTA
1583221 TAAAACAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (21 bp):
TTTTTAAGATATATTATTTAC
Found at i:1583594 original size:5 final size:5
Alignment explanation
Indices: 1583584--1583611 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1583574 CCCTAAAATT
1583584 ATAAA ATAAA ATAAA ATAAA ATAAA ATA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATA
1583612 GTACAGTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:1585833 original size:58 final size:58
Alignment explanation
Indices: 1585758--1585876 Score: 168
Period size: 58 Copynumber: 2.1 Consensus size: 58
1585748 TATAAATATT
* *
1585758 AAGGTCCAAGGTATGAACTTCTACTACTAAAAGTGTTATTGCATAATAATGATTGATG
1 AAGGTCCAAGGTATGAACTCCTACTACTAAAAGTGTTATTGCATAATAATGATTAATG
* ** *
1585816 AAGGTCCAAGGCT-TGAACTCCTATTGTTAAAAGTGTTATTGCGTAATAATGATTAATG
1 AAGGTCCAAGG-TATGAACTCCTACTACTAAAAGTGTTATTGCATAATAATGATTAATG
1585874 AAG
1 AAG
1585877 TCATGACAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
58 53 0.98
59 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (58 bp):
AAGGTCCAAGGTATGAACTCCTACTACTAAAAGTGTTATTGCATAATAATGATTAATG
Found at i:1593850 original size:29 final size:29
Alignment explanation
Indices: 1593817--1593879 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
1593807 TTGTGAAGAA
*
1593817 CCTAACCTTAGAACTCTTTGAAGAGAGCT
1 CCTAACCTTAGAACTCGTTGAAGAGAGCT
* *
1593846 CCTAACCTTGGAACTCGTTGAAGGGAGCT
1 CCTAACCTTAGAACTCGTTGAAGAGAGCT
*
1593875 TCTAA
1 CCTAA
1593880 TCATGAATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.27
Consensus pattern (29 bp):
CCTAACCTTAGAACTCGTTGAAGAGAGCT
Found at i:1593993 original size:28 final size:27
Alignment explanation
Indices: 1593953--1594007 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 27
1593943 ATTAATGAGA
1593953 ATTGTCCCTTTAAATAGCGGTTCAGGT
1 ATTGTCCCTTTAAATAGCGGTTCAGGT
*
1593980 NATTGTCCCTTTAAATTGCGGTTCAGGT
1 -ATTGTCCCTTTAAATAGCGGTTCAGGT
1594008 TACATTGGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.38
Consensus pattern (27 bp):
ATTGTCCCTTTAAATAGCGGTTCAGGT
Found at i:1594499 original size:29 final size:29
Alignment explanation
Indices: 1594441--1594499 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
1594431 TGAATATATA
*
1594441 TGGAACCTGTTGAAAGGAGCTCCTACCCT
1 TGGAACCTGTTGAAAGGAGCTCCTAACCT
* * *
1594470 TGGAACTTGTTGAAGGGAGCTCTTAACCT
1 TGGAACCTGTTGAAAGGAGCTCCTAACCT
1594499 T
1 T
1594500 AAAGTCATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (29 bp):
TGGAACCTGTTGAAAGGAGCTCCTAACCT
Found at i:1594643 original size:15 final size:15
Alignment explanation
Indices: 1594619--1594648 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1594609 TAAGAATGAG
*
1594619 AACTATAATTAAGGA
1 AACTAAAATTAAGGA
1594634 AACTAAAATTAAGGA
1 AACTAAAATTAAGGA
1594649 CTTCTAATTA
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:0.07, G:0.13, T:0.23
Consensus pattern (15 bp):
AACTAAAATTAAGGA
Found at i:1598061 original size:13 final size:13
Alignment explanation
Indices: 1598043--1598068 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1598033 TTTGAAGCTT
1598043 TTTTTAATTAATA
1 TTTTTAATTAATA
1598056 TTTTTAATTAATA
1 TTTTTAATTAATA
1598069 AATATATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTTAATTAATA
Found at i:1602114 original size:50 final size:52
Alignment explanation
Indices: 1601990--1602114 Score: 139
Period size: 50 Copynumber: 2.4 Consensus size: 52
1601980 GAACAAATGT
* * * *
1601990 GTTACTTAATGCA-AGACTTAATTTAATGATGCAGGCTTAAACTAACATGGGA
1 GTTACATAATGCATA-ACTTTATTTAATGATGCAGACTTAAACTAACATGGAA
** * * *
1602042 GTTACATAATGCATGTCATTATTT-ATGATGCATACTT-AACTAGCATGGAA
1 GTTACATAATGCATAACTTTATTTAATGATGCAGACTTAAACTAACATGGAA
1602092 GTTACATAATGCATAACTTTATT
1 GTTACATAATGCATAACTTTATT
1602115 ACATGCAGAA
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
50 31 0.52
51 11 0.18
52 18 0.30
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (52 bp):
GTTACATAATGCATAACTTTATTTAATGATGCAGACTTAAACTAACATGGAA
Found at i:1607773 original size:19 final size:19
Alignment explanation
Indices: 1607749--1607788 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1607739 TTATAGCATG
1607749 TTACTGTGGTCATCATCAT
1 TTACTGTGGTCATCATCAT
1607768 TTACTGTGGTCATCATCAT
1 TTACTGTGGTCATCATCAT
1607787 TT
1 TT
1607789 TCGAGAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.45
Consensus pattern (19 bp):
TTACTGTGGTCATCATCAT
Found at i:1613934 original size:30 final size:30
Alignment explanation
Indices: 1613898--1613958 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
1613888 TTTGCATACA
1613898 TAAAATCATTTTAGAAGAAGGTGAAAGAGC
1 TAAAATCATTTTAGAAGAAGGTGAAAGAGC
1613928 TAAAATCATTTTAGAAGAAGGTGAAAGAGC
1 TAAAATCATTTTAGAAGAAGGTGAAAGAGC
1613958 T
1 T
1613959 CGGATTGATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.46, C:0.07, G:0.23, T:0.25
Consensus pattern (30 bp):
TAAAATCATTTTAGAAGAAGGTGAAAGAGC
Found at i:1614067 original size:88 final size:88
Alignment explanation
Indices: 1613951--1614118 Score: 327
Period size: 88 Copynumber: 1.9 Consensus size: 88
1613941 GAAGAAGGTG
*
1613951 AAAGAGCTCGGATTGATGGGAAAAGGAGGCTCAATCCTATTATGCAAGAATTTGTGTGAAAGGAA
1 AAAGAGCTCGGATTGATGGGAAAAGGAGGCTCAATCCTATTATGCAAGAATTTGTGAGAAAGGAA
1614016 ATGATGAAATGGTTATTCTTCTA
66 ATGATGAAATGGTTATTCTTCTA
1614039 AAAGAGCTCGGATTGATGGGAAAAGGAGGCTCAATCCTATTATGCAAGAATTTGTGAGAAAGGAA
1 AAAGAGCTCGGATTGATGGGAAAAGGAGGCTCAATCCTATTATGCAAGAATTTGTGAGAAAGGAA
1614104 ATGATGAAATGGTTA
66 ATGATGAAATGGTTA
1614119 GATGCGGGAA
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 79 1.00
ACGTcount: A:0.37, C:0.10, G:0.27, T:0.26
Consensus pattern (88 bp):
AAAGAGCTCGGATTGATGGGAAAAGGAGGCTCAATCCTATTATGCAAGAATTTGTGAGAAAGGAA
ATGATGAAATGGTTATTCTTCTA
Found at i:1614612 original size:11 final size:13
Alignment explanation
Indices: 1614596--1614627 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
1614586 AATTTCATGG
1614596 AAAAATTTTG-T-
1 AAAAATTTTGTTC
1614607 AAAAATTTTGTTC
1 AAAAATTTTGTTC
1614620 AAAAATTT
1 AAAAATTT
1614628 CGACGTTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 10 0.53
12 1 0.05
13 8 0.42
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (13 bp):
AAAAATTTTGTTC
Done.