Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold6
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: 1308201
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
File 11 of 11
Found at i:1190061 original size:34 final size:34
Alignment explanation
Indices: 1190023--1190088 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
1190013 TTATTTTATT
* * *
1190023 AAATATATTTAAAAATAATTTTTA-TACTAAATAA
1 AAATACATGTAAAAAT-ATTTTTACTAATAAATAA
*
1190057 AAATACATGTAATAATATTTTTACTAATAAAT
1 AAATACATGTAAAAATATTTTTACTAATAAAT
1190089 TAAATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 7 0.26
34 20 0.74
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.41
Consensus pattern (34 bp):
AAATACATGTAAAAATATTTTTACTAATAAATAA
Found at i:1191181 original size:2 final size:2
Alignment explanation
Indices: 1191174--1191229 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1191164 GTTTTAAGGG
1191174 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1191216 TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC
1191230 CCCTGTTTGG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1196335 original size:16 final size:16
Alignment explanation
Indices: 1196314--1196356 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
1196304 AGTAATTTAA
* *
1196314 ATTTTAAATTTGATTT
1 ATTTTAAATTTGAATC
1196330 ATTTTAAATTTGAATC
1 ATTTTAAATTTGAATC
*
1196346 ATTTTGAATTT
1 ATTTTAAATTT
1196357 AAATTGTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (16 bp):
ATTTTAAATTTGAATC
Found at i:1196462 original size:3 final size:3
Alignment explanation
Indices: 1196454--1196490 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1196444 GATGTTACTC
1196454 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1196491 CTTATGTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1198947 original size:149 final size:148
Alignment explanation
Indices: 1198674--1198968 Score: 398
Period size: 149 Copynumber: 2.0 Consensus size: 148
1198664 TTTAGCTAAA
* * * *
1198674 TACATATTTATAAAAATTATTTACTAAATTTAGTATTTAAATTCATTTTTTAATATTACAAATCT
1 TACATATTTATAAAAACTATTTACTAAATTTAATATTTAAATTCATTTTTTAATATCACAAATCG
* * *
1198739 ATTCAATTGAAGCTCCTAATTAGACTTATTGAATAACTAATTTGACTTTTAATTCGATTTTCAAA
66 ATTCAATTGAA-CTACTAATTAAACTTATTGAATAACTAATTTAACTTTTAATTCGATTTTCAAA
1198804 TATTACTATTACTACACAAT
130 TATTAC-ATTACTACACAAT
*
1198824 TACATATTTATATAAACTATTTACTAAATTTAATATTTAAATTCA-TTTTTAATATCACAAATCG
1 TACATATTTATAAAAACTATTTACTAAATTTAATATTTAAATTCATTTTTTAATATCACAAATCG
* * * *
1198888 ATTTAATTG-CCATAACTAATTAAACTTATTGAATAA-TCAATTTAACTTTTAATTTGATTTTTA
66 ATTCAATTGAAC-T-ACTAATTAAACTTATTGAATAACT-AATTTAACTTTTAATTCGATTTTCA
* *
1198951 AATGTTGCATTACTACAC
128 AATATTACATTACTACAC
1198969 GAGTGTATAG
Statistics
Matches: 128, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
147 1 0.01
148 12 0.09
149 73 0.57
150 42 0.33
ACGTcount: A:0.39, C:0.12, G:0.04, T:0.45
Consensus pattern (148 bp):
TACATATTTATAAAAACTATTTACTAAATTTAATATTTAAATTCATTTTTTAATATCACAAATCG
ATTCAATTGAACTACTAATTAAACTTATTGAATAACTAATTTAACTTTTAATTCGATTTTCAAAT
ATTACATTACTACACAAT
Found at i:1199013 original size:2 final size:2
Alignment explanation
Indices: 1199006--1199033 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1198996 AAAACTTAAA
1199006 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
1199034 CCATTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1201346 original size:2 final size:2
Alignment explanation
Indices: 1201339--1201363 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1201329 GAAATTTATT
1201339 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1201364 GTGTGTTTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1203003 original size:2 final size:2
Alignment explanation
Indices: 1202998--1203028 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1202988 TTTAGCTTAA
1202998 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1203029 GTCTTTGAAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1203381 original size:3 final size:3
Alignment explanation
Indices: 1203375--1203421 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
1203365 CTTCTTCTTC
1203375 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1203422 GAAATCTAAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1204364 original size:2 final size:2
Alignment explanation
Indices: 1204357--1204397 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1204347 TGAAAGACAA
1204357 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1204398 ATTTGTGGCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1204810 original size:61 final size:61
Alignment explanation
Indices: 1204665--1204841 Score: 189
Period size: 61 Copynumber: 2.9 Consensus size: 61
1204655 TTTCAAAATT
* * * *
1204665 TAATAGTTTAATAAATATGAATTTTGAATTTTAATATTAATAAATTTTTTTA-TTTTTGAAAAT
1 TAATA-TTTAATAAATTTAAATTTTGAATTTTAATATTTAT-AA-TTTTTTACTTTTTGAAAAA
* * *
1204728 TGACATTTAATATATTTAAATTTTGAATTTTAATATTTATAATTTCTTTACTTTTT-AAAAA
1 TAATATTTAATAAATTTAAATTTTGAATTTTAATATTTATAATTT-TTTACTTTTTGAAAAA
* * ** *
1204789 TAATATTTAACAAATTTAAATTTTGAATCTTAGCATCTATAATTTTTT-CTTTT
1 TAATATTTAATAAATTTAAATTTTGAATTTTAATATTTATAATTTTTTACTTTT
1204842 ATCTTCAAAT
Statistics
Matches: 97, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
59 5 0.05
60 6 0.06
61 47 0.48
62 36 0.37
63 3 0.03
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (61 bp):
TAATATTTAATAAATTTAAATTTTGAATTTTAATATTTATAATTTTTTACTTTTTGAAAAA
Found at i:1208546 original size:72 final size:74
Alignment explanation
Indices: 1208426--1208577 Score: 211
Period size: 72 Copynumber: 2.1 Consensus size: 74
1208416 TTTATTATTA
*
1208426 AATAAATTTCATTTACCCTAAATTTTTCAATAAAATTAAAATTCTTATTTACAAATGTGATAAAT
1 AATAAATTTCATTTAACCTAAATTTTTCAATAAAATTAAAATTCTTATTTACAAATGTGATAAAT
*
1208491 TGTGTTATG
66 TGTATTATG
* * *
1208500 AATAAA-TTCATTTAACC-AAATCTTTT-AATATAATTAAAATTTTTATTTATAAATGTGATAAA
1 AATAAATTTCATTTAACCTAAAT-TTTTCAATAAAATTAAAATTCTTATTTACAAATGTGATAAA
* *
1208562 TTTTATTATT
65 TTGTATTATG
1208572 AATAAA
1 AATAAA
1208578 AAATATTTAA
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
72 50 0.71
73 14 0.20
74 6 0.09
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (74 bp):
AATAAATTTCATTTAACCTAAATTTTTCAATAAAATTAAAATTCTTATTTACAAATGTGATAAAT
TGTATTATG
Found at i:1208990 original size:26 final size:25
Alignment explanation
Indices: 1208940--1209009 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 25
1208930 AATGAACATG
*
1208940 ATTATTTAAAAAATATGAAATAATTTT
1 ATTATTTAAAATA-AT-AAATAATTTT
1208967 -TTAATTTAAAATAATAAATAAATTTT
1 ATT-ATTTAAAATAATAAAT-AATTTT
*
1208993 ATTATATAAAATTAATA
1 ATTATTTAAAA-TAATA
1209010 GCATATGACA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
25 4 0.11
26 17 0.46
27 16 0.43
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (25 bp):
ATTATTTAAAATAATAAATAATTTT
Found at i:1209225 original size:17 final size:17
Alignment explanation
Indices: 1209203--1209235 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1209193 TTATTTATTA
1209203 ATAAATA-ATTATTTAAC
1 ATAAATATATT-TTTAAC
1209220 ATAAATATATTTTTAA
1 ATAAATATATTTTTAA
1209236 TATTTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
ATAAATATATTTTTAAC
Found at i:1210599 original size:22 final size:22
Alignment explanation
Indices: 1210556--1210599 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1210546 GTATCATATA
* *
1210556 AAAAATAAATATGATAACAAGT
1 AAAAATAAATATGAGAAAAAGT
1210578 AAAAA-AAATAGTGAGAAAAAGT
1 AAAAATAAATA-TGAGAAAAAGT
1210600 GTTCTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.66, C:0.02, G:0.14, T:0.18
Consensus pattern (22 bp):
AAAAATAAATATGAGAAAAAGT
Found at i:1213098 original size:15 final size:15
Alignment explanation
Indices: 1213064--1213143 Score: 53
Period size: 14 Copynumber: 5.5 Consensus size: 15
1213054 AACATCAAAT
1213064 TAAT-TAATAT-TTA
1 TAATATAATATATTA
*
1213077 AAATATAATATATTA
1 TAATATAATATATTA
* *
1213092 TAATATAAAATTAATA
1 TAATATAATA-TATTA
* *
1213108 TTAATAAAATATTTTA
1 -TAATATAATATATTA
*
1213124 -AATATAAT-TAATA
1 TAATATAATATATTA
1213137 TAA-ATAA
1 TAATATAA
1213144 AAATATATTA
Statistics
Matches: 51, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
13 10 0.20
14 15 0.29
15 11 0.22
16 7 0.14
17 8 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAATATAATATATTA
Found at i:1213118 original size:22 final size:22
Alignment explanation
Indices: 1213042--1213119 Score: 61
Period size: 22 Copynumber: 3.5 Consensus size: 22
1213032 ATTTTAAATG
* *
1213042 TAATAAGAATATAACATCAA-AT
1 TAATAA-AATATAAAATTAATAT
* *
1213064 TAATTAATATTTAAAATATAATA-
1 TAA-TAAAATATAAAAT-TAATAT
* *
1213087 TATTATAATATAAAATTAATAT
1 TAATAAAATATAAAATTAATAT
1213109 TAATAAAATAT
1 TAATAAAATAT
1213120 TTTAAATATA
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
21 5 0.12
22 29 0.69
23 7 0.17
24 1 0.02
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (22 bp):
TAATAAAATATAAAATTAATAT
Found at i:1213121 original size:46 final size:43
Alignment explanation
Indices: 1213069--1213154 Score: 118
Period size: 46 Copynumber: 1.9 Consensus size: 43
1213059 CAAATTAATT
* *
1213069 AATATTTAAAATATAATATATTATAATATAAAATTAATATTAATAA
1 AATATTTAAAATATAAT-TAATATAA-ATAAAAAT-ATATTAATAA
*
1213115 AATATTTTAAATATAATTAATATAAATAAAAATATATTAA
1 AATATTTAAAATATAATTAATATAAATAAAAATATATTAA
1213155 CACAATAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 7 0.19
44 7 0.19
45 7 0.19
46 16 0.43
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (43 bp):
AATATTTAAAATATAATTAATATAAATAAAAATATATTAATAA
Found at i:1213730 original size:16 final size:16
Alignment explanation
Indices: 1213693--1213730 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1213683 TCTAAATTTT
1213693 TTAATATAAATAAATA
1 TTAATATAAATAAATA
*
1213709 TAAATATAAA-AAATA
1 TTAATATAAATAAATA
1213724 TGTAATA
1 T-TAATA
1213731 AATTATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (16 bp):
TTAATATAAATAAATA
Found at i:1214197 original size:20 final size:19
Alignment explanation
Indices: 1214158--1214197 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1214148 GTTTCATATT
*
1214158 ATATTTGTATTATATAATC
1 ATATTTGTATTAAATAATC
*
1214177 ATATTGTGTATTAAATTATC
1 ATATT-TGTATTAAATAATC
1214197 A
1 A
1214198 AATCTAATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (19 bp):
ATATTTGTATTAAATAATC
Found at i:1214974 original size:15 final size:16
Alignment explanation
Indices: 1214946--1214980 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1214936 GTTAATGCTA
1214946 TTATTTTATATTATAT
1 TTATTTTATATTATAT
*
1214962 TTATTTTAT-TTATTT
1 TTATTTTATATTATAT
1214977 TTAT
1 TTAT
1214981 GCCGTGTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTATTTTATATTATAT
Found at i:1215525 original size:21 final size:21
Alignment explanation
Indices: 1215479--1215517 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1215469 CTTAATATGA
*
1215479 AATAAAAATGAATATAAATAT
1 AATATAAATGAATATAAATAT
1215500 AATATAAATGAAT-TAAAT
1 AATATAAATGAATATAAAT
1215518 TTTGATATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (21 bp):
AATATAAATGAATATAAATAT
Found at i:1218007 original size:15 final size:17
Alignment explanation
Indices: 1217987--1218021 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
1217977 TTACTCATAT
1217987 TTTTTCTTC-C-CTTTC
1 TTTTTCTTCTCTCTTTC
1218002 TTTTTCTTCTCTCTTTC
1 TTTTTCTTCTCTCTTTC
1218019 TTT
1 TTT
1218022 CTTCACTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 1 0.06
17 8 0.44
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTCTTCTCTCTTTC
Found at i:1218314 original size:31 final size:31
Alignment explanation
Indices: 1218250--1218334 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 31
1218240 TAACATGAAT
* * * *
1218250 ATTTTTAATATTTTTAAAATTAAA--TTAAA
1 ATTTTAAATATTATAAAAATTAAAAATAAAA
*
1218279 ATTTTAAA-ATTTTAAAAATATAAAAATAAAA
1 ATTTTAAATATTATAAAAAT-TAAAAATAAAA
1218310 ATTTTAAATTATTATAAAAATTAAA
1 ATTTTAAA-TATTATAAAAATTAAA
1218335 TTCATATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
28 10 0.21
29 11 0.23
31 12 0.26
32 4 0.09
33 10 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
ATTTTAAATATTATAAAAATTAAAAATAAAA
Found at i:1218821 original size:15 final size:15
Alignment explanation
Indices: 1218760--1218822 Score: 51
Period size: 15 Copynumber: 4.1 Consensus size: 15
1218750 AAATTAGTTA
*
1218760 ATTATTTAAATAAAT
1 ATTATTAAAATAAAT
1218775 A-TA-TAAAATAACAT
1 ATTATTAAAATAA-AT
*
1218789 A-TGTTAAAATTTTAAAT
1 ATTATTAAAA---TAAAT
1218806 ATTATTAAAATAAAT
1 ATTATTAAAATAAAT
1218821 AT
1 AT
1218823 AAAAATAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
13 7 0.18
14 6 0.15
15 13 0.33
17 3 0.08
18 10 0.26
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (15 bp):
ATTATTAAAATAAAT
Found at i:1221467 original size:5 final size:5
Alignment explanation
Indices: 1221452--1221490 Score: 60
Period size: 5 Copynumber: 7.6 Consensus size: 5
1221442 AAGGACTCTC
*
1221452 AGTTGG AGTTG AGTTG AGTTG AGTTG AGTTG AGATG AGT
1 AGTT-G AGTTG AGTTG AGTTG AGTTG AGTTG AGTTG AGT
1221491 CTTATCAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 27 0.87
6 4 0.13
ACGTcount: A:0.23, C:0.00, G:0.41, T:0.36
Consensus pattern (5 bp):
AGTTG
Found at i:1233108 original size:33 final size:32
Alignment explanation
Indices: 1233070--1233950 Score: 604
Period size: 33 Copynumber: 27.8 Consensus size: 32
1233060 TCTCTTCTCA
1233070 AAGTCCACAACTCCGTGGCACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTCCTTTT
* *
1233103 AAGTCCACAACTCCGTGACACCTTTTTCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
* * * **
1233135 CAAAGCCCACAACTCTGTGGCATCTTTTCCTTCA
1 --AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
**
1233169 AAGTCCACAACTCTATGGCACCTTATTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTCCTTTT
* * *
1233202 AAGTCTACAATTCTGTGGCACCTTTT--TTTCT
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTT-T
* * * **
1233233 CAAAGCCCACAACTTCGTGGCATCTTTTCCTTCA
1 --AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
*
1233267 AAGTCCACAACTCCGTGCCACCTTATTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTCCTTTT
* ** *
1233300 AAGTTCATTACTCCGTAGCACCTTTT-CTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
* * **
1233331 CAAAGTCCACAACTCCGTGGTATCTTTTCCTTCA
1 --AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
* *
1233365 AAGTCCACAACTCTGTGGCACTTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTCCTTTT
** * * *
1233398 AAGTTTACAAATCCGTGGCACATTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCAC-CTTTTCCTTTT
* *
1233431 AAAG-CTCACAACTCCGTGGCATCTTTTTCTTTT
1 -AAGTC-CACAACTCCGTGGCACCTTTTCCTTTT
1233464 AAGTCCACAACTCCGTGGCA-C----CCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
* * **
1233491 AAGTTCATAACTCTATGGCACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTCCTTTT
* *
1233524 AAGTCCATAACTCCGTGGCACCTTTTTCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
* *
1233556 CAAAG-CTCACAACTCTGTGGCATCTTTTCCTTTT
1 --AAGTC-CACAACTCCGTGGCACCTTTTCCTTTT
* * * *
1233590 AATTCTACAACTTCGTGGCA-C----CCTTTC
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
* ** *
1233617 AAGTCCATAACTCTATGTCA-C----CCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
* *
1233644 AAGTCCACAACTCTGTGGTACC---T--TTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
1233671 AAGTCCACAACTCCGTGGCACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTCCTTTT
** * * **
1233704 AAGTTTACAACTCTGTGGCACATTTTCTCTTCA
1 AAGTCCACAACTCCGTGGCACCTTTTC-CTTTT
* * *
1233737 AAG-CTCATAACTCCGTGGCATCTTTTCTTTTT
1 AAGTC-CACAACTCCGTGGCACCTTTTCCTTTT
* * *
1233769 AAGTCTACCACTCTGTGGCA-C----CCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
**
1233796 AAGTCCACAACTCTTTGGCACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTCCTTTT
* * *
1233829 AAGTCCACAACTTCGTGGCACATTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
* * * * *
1233861 AAAGCCCACAACTCTGTGCCATCTTTT-CTTTCA
1 -AAGTCCACAACTCCGTGGCACCTTTTCCTTT-T
1233894 AAGTCCACAACTCCGTGGCACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTCCTTTT
* *
1233927 AAG-CTCACAACTCTGTGACACCTT
1 AAGTC-CACAACTCCGTGGCACCTT
1233951 CCTTTAAAGC
Statistics
Matches: 662, Mismatches: 137, Indels: 98
0.74 0.15 0.11
Matches are distributed among these distances:
27 107 0.16
28 3 0.00
30 3 0.00
31 10 0.02
32 161 0.24
33 299 0.45
34 77 0.12
35 2 0.00
ACGTcount: A:0.21, C:0.30, G:0.12, T:0.37
Consensus pattern (32 bp):
AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
Found at i:1233289 original size:98 final size:99
Alignment explanation
Indices: 1233039--1233611 Score: 570
Period size: 98 Copynumber: 5.9 Consensus size: 99
1233029 TCTTTTTCCA
* * * * *
1233039 AAAGGCCACGACTCAGTGGCATCTCTT-C-TCAAAGTCCACAACTCCGTGGCACCTTGTTCCTTT
1 AAAGCCCACAACTCCGTGGCATCTTTTCCTTCAAAGTCCACAACTCCGTGGCACCTTATTCCTTT
* * *
1233102 TAAGTCCACAACTCCGTGACACCTTTTTCTTTTC
66 TAAGTCTACAATTCCGTGGCACCTTTTTCTTTTC
* **
1233136 AAAGCCCACAACTCTGTGGCATCTTTTCCTTCAAAGTCCACAACTCTATGGCACCTTATTCCTTT
1 AAAGCCCACAACTCCGTGGCATCTTTTCCTTCAAAGTCCACAACTCCGTGGCACCTTATTCCTTT
* *
1233201 TAAGTCTACAATTCTGTGGCACCTTTTT-TTCTC
66 TAAGTCTACAATTCCGTGGCACCTTTTTCTTTTC
* *
1233234 AAAGCCCACAACTTCGTGGCATCTTTTCCTTCAAAGTCCACAACTCCGTGCCACCTTATTCCTTT
1 AAAGCCCACAACTCCGTGGCATCTTTTCCTTCAAAGTCCACAACTCCGTGGCACCTTATTCCTTT
* *
1233299 TAAGT-T-CATTACTCCGTAGCACC-TTTTCTTTTC
66 TAAGTCTACA--ATTCCGTGGCACCTTTTTCTTTTC
* * * * *
1233332 AAAGTCCACAACTCCGTGGTATCTTTTCCTTCAAAGTCCACAACTCTGTGGCACTTTGTTCCTTT
1 AAAGCCCACAACTCCGTGGCATCTTTTCCTTCAAAGTCCACAACTCCGTGGCACCTTATTCCTTT
* * * *
1233397 TAAGTTTACAAATCCGTGGCACATTTTTCTTTTT
66 TAAGTCTACAATTCCGTGGCACCTTTTTCTTTTC
* * **
1233431 AAAGCTCACAACTCCGTGGCATCTTTTTCTTTTAAGTCCACAACTCCGTGGCA-C-----CCTTT
1 AAAGCCCACAACTCCGTGGCATCTTTTCCTTCAAAGTCCACAACTCCGTGGCACCTTATTCCTTT
* * ** *
1233490 TAAGT-TCATAACTCTATGGCACCTTGTTCCTTTT-
66 TAAGTCT-ACAATTCCGTGGCACCTT-TTTCTTTTC
* * * * * *
1233524 -AAGTCCATAACTCCGTGGCACCTTTTTCTTTTCAAAG-CTCACAACTCTGTGGCATCTT-TTCC
1 AAAGCCCACAACTCCGTGGCATC-TTTTC-CTTCAAAGTC-CACAACTCCGTGGCACCTTATTCC
*
1233586 TTTTAATTCTACAACTT-CGTGGCACC
63 TTTTAAGTCTACAA-TTCCGTGGCACC
1233612 CTTTCAAGTC
Statistics
Matches: 396, Mismatches: 60, Indels: 38
0.80 0.12 0.08
Matches are distributed among these distances:
92 19 0.05
93 28 0.07
94 26 0.07
95 1 0.00
96 2 0.01
97 28 0.07
98 157 0.40
99 131 0.33
100 4 0.01
ACGTcount: A:0.22, C:0.30, G:0.12, T:0.36
Consensus pattern (99 bp):
AAAGCCCACAACTCCGTGGCATCTTTTCCTTCAAAGTCCACAACTCCGTGGCACCTTATTCCTTT
TAAGTCTACAATTCCGTGGCACCTTTTTCTTTTC
Found at i:1233539 original size:126 final size:126
Alignment explanation
Indices: 1233250--1233670 Score: 419
Period size: 126 Copynumber: 3.4 Consensus size: 126
1233240 CACAACTTCG
* ** * * * * **
1233250 TGGCATCTT-TTCCTTCAAAGTCCACAACTCCGTGCCACCTTATTCCTTTT-AAGTTCATTACTC
1 TGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCTCACAACTC
* * * * *
1233313 CGTAGCA-CCTTTTCTTTTCAAAGTCCACAACTCCGTGGTATCTTTTCCTTCAAAGTCCACAACT
66 CGTGGCATCTTTTTCTTTT--AAGTCCACAACTCCGTGGCA-C----CCTTTAAAGTCCATAACT
*
1233377 CTG
124 CTA
* ** * *
1233380 TGGCACTTTGTTCCTTTTAAGTTTACAAATCCGTGGCACATTTTTCTTTTTAAAGCTCACAACTC
1 TGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCTCACAACTC
* *
1233445 CGTGGCATCTTTTTCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTTCATAACTCTA
66 CGTGGCATCTTTTTCTTTTAAGTCCACAACTCCGTGGCACCCTTTAAAGTCCATAACTCTA
* *
1233506 TGGCACCTTGTTCCTTTTAAGTCCATAACTCCGTGGCACCTTTTTCTTTTCAAAGCTCACAACTC
1 TGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCTCACAACTC
* * * * * *
1233571 TGTGGCATCTTTTCCTTTTAATTCTACAACTTCGTGGCACCCTTTCAAGTCCATAACTCTA
66 CGTGGCATCTTTTTCTTTTAAGTCCACAACTCCGTGGCACCCTTTAAAGTCCATAACTCTA
* * *
1233632 TGTCA-C-----CCTTTTAAGTCCACAACTCTGTGGTACCTTTTT
1 TGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
1233671 AAGTCCACAA
Statistics
Matches: 248, Mismatches: 40, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
120 30 0.12
125 1 0.00
126 132 0.53
130 8 0.03
131 51 0.21
132 16 0.06
133 10 0.04
ACGTcount: A:0.21, C:0.29, G:0.12, T:0.38
Consensus pattern (126 bp):
TGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCTCACAACTC
CGTGGCATCTTTTTCTTTTAAGTCCACAACTCCGTGGCACCCTTTAAAGTCCATAACTCTA
Found at i:1233694 original size:27 final size:27
Alignment explanation
Indices: 1233459--1233692 Score: 137
Period size: 27 Copynumber: 8.0 Consensus size: 27
1233449 GCATCTTTTT
1233459 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * **
1233486 CTTTTAAGTTCATAACTCTATGGCACCTTGTTC
1 CTTTTAAGTCCACAACTCCGTGGCA-C-----C
*
1233519 CTTTTAAGTCCATAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1233546 TTTTTCTTTTCAAAG-CTCACAACTCTGTGGCATCTTTTC
1 -----CTTTT--AAGTC-CACAACTCCGTGGCA-C----C
* * *
1233585 CTTTTAATTCTACAACTTCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * ** *
1233612 CTTTCAAGTCCATAACTCTATGTCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1233639 CTTTTAAGTCCACAACTCTGTGGTACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1233666 TTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1233693 TTGTTCCTTT
Statistics
Matches: 158, Mismatches: 29, Indels: 40
0.70 0.13 0.18
Matches are distributed among these distances:
27 88 0.56
28 1 0.01
31 1 0.01
32 20 0.13
33 25 0.16
34 21 0.13
35 1 0.01
39 1 0.01
ACGTcount: A:0.22, C:0.30, G:0.12, T:0.35
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:1233796 original size:125 final size:125
Alignment explanation
Indices: 1233640--1233915 Score: 383
Period size: 125 Copynumber: 2.2 Consensus size: 125
1233630 TATGTCACCC
* *
1233640 TTTTAAGTCCACAACTCTGTGGTACCTTTTTAAGTCCACAACTCCGTGGCACCTTGTTCCTTTTA
1 TTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCTTGTTCCTTTTA
** * * *
1233705 AGTTTACAAC-TCTGTGGCACATTTTCTCTTCAAAGCTCATAACTCCGTGGCATCTTTTCT
66 AGTCCACAACTTC-GTGGCACATTTTCTCTTCAAAGCCCACAACTCCGTGCCATCTTTTCT
* * **
1233765 TTTTAAGTCTACCACTCTGTGGCACCCTTTTAAGTCCACAACTCTTTGGCACCTTGTTCCTTTTA
1 TTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCTTGTTCCTTTTA
* * *
1233830 AGTCCACAACTTCGTGGCACATTTTCTTTTTAAAGCCCACAACTCTGTGCCATCTTTTCT
66 AGTCCACAACTTCGTGGCACATTTTCTCTTCAAAGCCCACAACTCCGTGCCATCTTTTCT
** *
1233890 TTCAAAGTCCACAACTCCGTGGCACC
1 TTTTAAGTCCACAACTCTGTGGCACC
1233916 TTGTTCCTTT
Statistics
Matches: 131, Mismatches: 19, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
125 129 0.98
126 2 0.02
ACGTcount: A:0.21, C:0.29, G:0.13, T:0.37
Consensus pattern (125 bp):
TTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCTTGTTCCTTTTA
AGTCCACAACTTCGTGGCACATTTTCTCTTCAAAGCCCACAACTCCGTGCCATCTTTTCT
Found at i:1233808 original size:27 final size:27
Alignment explanation
Indices: 1233765--1233817 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
1233755 CATCTTTTCT
* *
1233765 TTTTAAGTCTACCACTCTGTGGCACCC
1 TTTTAAGTCCACAACTCTGTGGCACCC
*
1233792 TTTTAAGTCCACAACTCTTTGGCACC
1 TTTTAAGTCCACAACTCTGTGGCACC
1233818 TTGTTCCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.21, C:0.32, G:0.13, T:0.34
Consensus pattern (27 bp):
TTTTAAGTCCACAACTCTGTGGCACCC
Found at i:1233936 original size:65 final size:65
Alignment explanation
Indices: 1233667--1233964 Score: 210
Period size: 65 Copynumber: 4.7 Consensus size: 65
1233657 TGTGGTACCT
* * * ** *
1233667 TTTTAAG-TCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTTTACAACTCTGTGGCACATTTTC
1 TTTTAAGCT-CACAACTCTGTGCCACCTTGTTCCTTTAAAGTCCACAACTCCGTGGCACATTTTC
1233731 TC
65 -C
** * * * * * * * * *
1233733 TTCAAAGCTCATAACTCCGTGGCATCTT-TTCTTTTTAAGTCTACCACTCTGTGGCAC-----CC
1 TTTTAAGCTCACAACTCTGTGCCACCTTGTTCCTTTAAAGTCCACAACTCCGTGGCACATTTTCC
* * * *
1233792 TTTTAAG-TCCACAACTCTTTGGCACCTTGTTCCTTTTAAGTCCACAACTTCGTGGCACATTTTC
1 TTTTAAGCT-CACAACTCTGTGCCACCTTGTTCCTTTAAAGTCCACAACTCCGTGGCACATTTTC
*
1233856 T
65 C
* * *
1233857 TTTTAAAGCCCACAACTCTGTGCCATCTT-TT-CTTTCAAAGTCCACAACTCCGTGGCACCTTGT
1 TTTT-AAGCTCACAACTCTGTGCCACCTTGTTCCTTT-AAAGTCCACAACTCCGTGGCACATT-T
1233920 TCC
63 TCC
*
1233923 TTTTAAGCTCACAACTCTGTGACACC---TTCCTTTAAAG-CCACA
1 TTTTAAGCTCACAACTCTGTGCCACCTTGTTCCTTTAAAGTCCACA
1233965 CGAGCTAGTG
Statistics
Matches: 189, Mismatches: 30, Indels: 30
0.76 0.12 0.12
Matches are distributed among these distances:
58 1 0.01
59 21 0.11
60 25 0.13
62 5 0.03
63 6 0.03
64 8 0.04
65 74 0.39
66 48 0.25
67 1 0.01
ACGTcount: A:0.21, C:0.30, G:0.12, T:0.36
Consensus pattern (65 bp):
TTTTAAGCTCACAACTCTGTGCCACCTTGTTCCTTTAAAGTCCACAACTCCGTGGCACATTTTCC
Found at i:1234174 original size:32 final size:33
Alignment explanation
Indices: 1234089--1234271 Score: 175
Period size: 32 Copynumber: 5.7 Consensus size: 33
1234079 AACCTTTTTC
* * *
1234089 AAAGCCCACACAAATTGGTGGCAACTC-TCTTCA
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTT-A
* *
1234122 AAAACCCACACAAGTTGGTGGCAACCCTTCTT-
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTTA
* * *
1234154 AAAGTCCACACCAGTCGGTGGCAACCC--CTTC
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTTA
*
1234185 AAAGCCCACACAAG-CTGGTGGCAACCCTTC-TC
1 AAAGCCCACACAAGTC-GGTGGCAACCCTTCTTA
* *
1234217 AAAGCTCACATAAG-CTGGTGGCAACCCTT-TTA
1 AAAGCCCACACAAGTC-GGTGGCAACCCTTCTTA
*
1234249 AAAGCCCACACAAGTTGGTGGCA
1 AAAGCCCACACAAGTCGGTGGCA
1234272 TCTCTTTCTA
Statistics
Matches: 128, Mismatches: 15, Indels: 15
0.81 0.09 0.09
Matches are distributed among these distances:
30 4 0.03
31 23 0.18
32 72 0.56
33 25 0.20
34 4 0.03
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.19
Consensus pattern (33 bp):
AAAGCCCACACAAGTCGGTGGCAACCCTTCTTA
Found at i:1234204 original size:63 final size:63
Alignment explanation
Indices: 1234087--1234271 Score: 212
Period size: 63 Copynumber: 2.9 Consensus size: 63
1234077 GAAACCTTTT
* ** * *
1234087 TCAAAGCCCACACAAATTGGTGGCAACTCTCTTCAAAAACCCACACAAGTTGGTGGCAACCCTTC
1 TCAAAGCTCACACAAGCTGGTGGCAAC-CCCTTC-AAAGCCCACACAAGTTGGTGGCAACCCTTC
* * *
1234152 TTAAAG-TCCACACCAG-TCGGTGGCAACCCCTTCAAAGCCCACACAAGCTGGTGGCAACCCTTC
1 TCAAAGCT-CACACAAGCT-GGTGGCAACCCCTTCAAAGCCCACACAAGTTGGTGGCAACCCTTC
* * *
1234215 TCAAAGCTCACATAAGCTGGTGGCAACCCTTTTAAAAGCCCACACAAGTTGGTGGCA
1 TCAAAGCTCACACAAGCTGGTGGCAACCC-CTTCAAAGCCCACACAAGTTGGTGGCA
1234272 TCTCTTTCTA
Statistics
Matches: 102, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
63 50 0.49
64 32 0.31
65 20 0.20
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.19
Consensus pattern (63 bp):
TCAAAGCTCACACAAGCTGGTGGCAACCCCTTCAAAGCCCACACAAGTTGGTGGCAACCCTTC
Found at i:1234285 original size:95 final size:96
Alignment explanation
Indices: 1234085--1234285 Score: 237
Period size: 95 Copynumber: 2.1 Consensus size: 96
1234075 GAGAAACCTT
* *
1234085 TTTCAAAGCCCACACAAATTGGTGGCAACTCTCTTCAAAAACCCACACAAGTTGGTGGCAACCCT
1 TTTCAAAGCCCACACAAACTGGTGGCAACTCTCTTCAAAAACCCACACAAGCTGGTGGCAACCCT
* *
1234150 TCTTAAAGTCCACACCAGTCGGTGGCAACCC
66 TCTTAAAGCCCACACAAGTCGGTGGCAACCC
* * * * * *
1234181 CTTCAAAGCCCACACAAGCTGGTGGCAAC-C-CTTCTCAAAGCTCACATAAGCTGGTGGCAACCC
1 TTTCAAAGCCCACACAAACTGGTGGCAACTCTCTTC-AAAAACCCACACAAGCTGGTGGCAACCC
* * *
1234244 TT-TTAAAAGCCCACACAAGTTGGTGGCATCTC
65 TTCTT-AAAGCCCACACAAGTCGGTGGCAACCC
*
1234276 TTTCTAAGCC
1 TTTCAAAGCC
1234286 TAATATCGCT
Statistics
Matches: 88, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
94 6 0.07
95 56 0.64
96 26 0.30
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (96 bp):
TTTCAAAGCCCACACAAACTGGTGGCAACTCTCTTCAAAAACCCACACAAGCTGGTGGCAACCCT
TCTTAAAGCCCACACAAGTCGGTGGCAACCC
Found at i:1234522 original size:43 final size:43
Alignment explanation
Indices: 1234470--1234557 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 43
1234460 CATTTCTTTC
*
1234470 TAAGTCCAATGTCATTGGCCTTGAATCAACACATTGGCACCTT
1 TAAGTCCAATATCATTGGCCTTGAATCAACACATTGGCACCTT
* * * *
1234513 TAAGTCCAATATCTTTGGCCTTGAATTAGCATATTGGCACCTT
1 TAAGTCCAATATCATTGGCCTTGAATCAACACATTGGCACCTT
1234556 TA
1 TA
1234558 TCATCATTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (43 bp):
TAAGTCCAATATCATTGGCCTTGAATCAACACATTGGCACCTT
Found at i:1234535 original size:190 final size:191
Alignment explanation
Indices: 1234185--1234562 Score: 541
Period size: 190 Copynumber: 2.0 Consensus size: 191
1234175 CAACCCCTTC
*
1234185 AAAGCCCACACAAGCTGGTGGCAACCCTTCTCAAAGCTCACATAAGCTGGTGGCAACCCTTTTAA
1 AAAGCCCACACAAGCTGGTGGCAACCCTTCTCAAAGCTCACACAAGCTGGTGGCAACCCTTTTAA
* *
1234250 AAGCCCACACAAGTTGGTGGCATCTCTTTCTAAGCCTAATATCGCTAGCCTTGAATCAACACGTT
66 AAGCCCACACAAGTTGGTGGCATCTCTTTCTAAGCCTAATATCACTAGCCTTGAATCAACACATT
*
1234315 GGCACCTTTAAGTCCAATATTACTGGCCTTGAATCATCATATTGGCACATTTACCATCTTT
131 GGCACCTTTAAGTCCAATATTACTGGCCTTGAATCAGCATATTGGCACATTTACCATCTTT
* * *
1234376 AAAGCCTACACAAG-TCGGTGGCAA-CTTTCTCAAAGC-CTACACAAGCTGGTGGTAACCCTTTT
1 AAAGCCCACACAAGCT-GGTGGCAACCCTTCTCAAAGCTC-ACACAAGCTGGTGGCAACCCTTTT
* * * * *
1234438 AAAAGCCCATACAAGTTGGTGGCATTTCTTTCTAAGTCC-AATGTCATTGGCCTTGAATCAACAC
64 AAAAGCCCACACAAGTTGGTGGCATCTCTTTCTAAG-CCTAATATCACTAGCCTTGAATCAACAC
* * * *
1234502 ATTGGCACCTTTAAGTCCAATATCT-TTGGCCTTGAATTAGCATATTGGCACCTTTATCATC
128 ATTGGCACCTTTAAGTCCAATAT-TACTGGCCTTGAATCAGCATATTGGCACATTTACCATC
1234563 ATTCTCATCT
Statistics
Matches: 167, Mismatches: 16, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
189 1 0.01
190 142 0.85
191 24 0.14
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (191 bp):
AAAGCCCACACAAGCTGGTGGCAACCCTTCTCAAAGCTCACACAAGCTGGTGGCAACCCTTTTAA
AAGCCCACACAAGTTGGTGGCATCTCTTTCTAAGCCTAATATCACTAGCCTTGAATCAACACATT
GGCACCTTTAAGTCCAATATTACTGGCCTTGAATCAGCATATTGGCACATTTACCATCTTT
Found at i:1234816 original size:52 final size:51
Alignment explanation
Indices: 1234591--1235083 Score: 354
Period size: 52 Copynumber: 9.5 Consensus size: 51
1234581 AATGTTTTTT
*** * ** * *
1234591 GCCTTGAATCAATGCATTGGCACCTTCATC--TTTAAGTCTGATATCGCTA
1 GCCTTGAATCAGCACATTGGCACCTTTATCATTTTAAGTCCAACATCGCTG
* * * * * **
1234640 GCCTTGAATCAGCATATTGGTATCTTTAACATTCCTAAG-CCTAATGTCGCTG
1 GCCTTGAATCAGCACATTGGCACCTTTATCATT-TTAAGTCC-AACATCGCTG
* * * ** ** *
1234692 GCCTTAAATCAGCACATTAGCACCTTTTGTCATCTTTAAGTCCAATGTTACTA
1 GCCTTGAATCAGCACATTGGCACC-TTTATCAT-TTTAAGTCCAACATCGCTG
1234745 GCCTTGAATCAGCACATTGGCACCTTCT-TC-TTTCTCAAGTCCAACATCGCTG
1 GCCTTGAATCAGCACATTGGCACCTT-TATCATTT-T-AAGTCCAACATCGCTG
* * * ** *
1234797 GCCTTGAATTAGCATATTGGCAACTTTATCATTTTTAAGTCCAATGTTGCTG
1 GCCTTGAATCAGCACATTGGCACCTTTATCA-TTTTAAGTCCAACATCGCTG
* * * *
1234849 GCCTTGAATCAGCACATTGGCA-CTTTCTTCTTTTTTAAGTCTAACATCGTTG
1 GCCTTGAATCAGCACATTGGCACCTTT-ATC-ATTTTAAGTCCAACATCGCTG
* * ** ** *
1234901 GCCTTGAATCAGCATATTGGCACATTTATCATCTTTAAGTCCAATGTTACTA
1 GCCTTGAATCAGCACATTGGCACCTTTATCAT-TTTAAGTCCAACATCGCTG
* ** **
1234953 GCCTTGAATCAGCACATTGGCACCTTTATCATCTTTAAATCCAATGTTACTG
1 GCCTTGAATCAGCACATTGGCACCTTTATCAT-TTTAAGTCCAACATCGCTG
* *
1235005 GCCTTAAATCAGCACATTGGCA-CATTATTC-TTTCTCAAGTCCAAACATCGCTG
1 GCCTTGAATCAGCACATTGGCACCTTTA-TCATTT-T-AAGTCC-AACATCGCTG
*
1235058 ACCTTGAATCAGCACATTGGCACCTT
1 GCCTTGAATCAGCACATTGGCACCTT
1235084 CAAGTTCGAT
Statistics
Matches: 351, Mismatches: 71, Indels: 39
0.76 0.15 0.08
Matches are distributed among these distances:
49 22 0.06
50 4 0.01
51 16 0.05
52 231 0.66
53 70 0.20
54 8 0.02
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.35
Consensus pattern (51 bp):
GCCTTGAATCAGCACATTGGCACCTTTATCATTTTAAGTCCAACATCGCTG
Found at i:1234863 original size:104 final size:103
Alignment explanation
Indices: 1234686--1235170 Score: 442
Period size: 104 Copynumber: 4.7 Consensus size: 103
1234676 AAGCCTAATG
* * * * * * *
1234686 TCGCTGGCCTTAAATCAGCACATTAGCACCTTTTGTCATCTTTAAGTCCAATGTTACTAGCCTTG
1 TCGCTGGCCTTGAATCAGCATATTGGCAAC-TTTATCATTTTTAAGTCCAATGTTGCTAGCCTTG
1234751 AATCAGCACATTGGCACCTTCTTCTTTCTCAAGTCCAACA
65 AATCAGCACATTGGCACCTTCTTCTTT-TCAAGTCCAACA
* *
1234791 TCGCTGGCCTTGAATTAGCATATTGGCAACTTTATCATTTTTAAGTCCAATGTTGCTGGCCTTGA
1 TCGCTGGCCTTGAATCAGCATATTGGCAACTTTATCATTTTTAAGTCCAATGTTGCTAGCCTTGA
* * *
1234856 ATCAGCACATTGGCACTTTCTTCTTTTTTAAGTCTAACA
66 ATCAGCACATTGGCACCTTCTTC-TTTTCAAGTCCAACA
* * *
1234895 TCGTTGGCCTTGAATCAGCATATTGGC-ACATTTATCATCTTTAAGTCCAATGTTACTAGCCTTG
1 TCGCTGGCCTTGAATCAGCATATTGGCAAC-TTTATCATTTTTAAGTCCAATGTTGCTAGCCTTG
* **
1234959 AATCAGCACATTGGCACCTT-TATCATCTTT-AAATCCAATG
65 AATCAGCACATTGGCACCTTCT-TC-T-TTTCAAGTCCAACA
** * * * * ** *
1234999 TTACTGGCCTTAAATCAGCACATTGGC-ACATTATTC-TTTCTCAAGTCCAAACATCGCT-GACC
1 TCGCTGGCCTTGAATCAGCATATTGGCAACTTTA-TCATTT-TTAAGTCC-AATGTTGCTAG-CC
* * *
1235061 TTGAATCAGCACATTGGCA----C--C--TTCAAGTTCGATA
62 TTGAATCAGCACATTGGCACCTTCTTCTTTTCAAGTCCAACA
** * * *
1235095 TCGCTGGCCTTGAATCAGCATATTGGCATTTTTAACATTTTTAA-ACTCAATGTCGCTAGCCTTG
1 TCGCTGGCCTTGAATCAGCATATTGGCAACTTTATCATTTTTAAGTC-CAATGTTGCTAGCCTTG
1235159 AATCAGCACATT
65 AATCAGCACATT
1235171 AGCAATCTTC
Statistics
Matches: 315, Mismatches: 51, Indels: 38
0.78 0.13 0.09
Matches are distributed among these distances:
95 27 0.09
96 35 0.11
97 6 0.02
99 1 0.00
103 8 0.03
104 181 0.57
105 57 0.18
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.35
Consensus pattern (103 bp):
TCGCTGGCCTTGAATCAGCATATTGGCAACTTTATCATTTTTAAGTCCAATGTTGCTAGCCTTGA
ATCAGCACATTGGCACCTTCTTCTTTTCAAGTCCAACA
Found at i:1234972 original size:156 final size:155
Alignment explanation
Indices: 1234637--1235080 Score: 464
Period size: 156 Copynumber: 2.8 Consensus size: 155
1234627 TCTGATATCG
* * * ** *
1234637 CTAGCCTTGAATCAGCATATTGGTATCTTTAACATTCCTAAG-CCTAATGTCGCTGGCCTTAAAT
1 CTAGCCTTGAATCAGCATATTGGCAACTTTATCATTTTTAAGTCC-AATGTTGCTGGCCTTAAAT
* * * * ** ** *
1234701 CAGCACATTAGCACCTTTTGTCATCTTTAAGTCCAATGTTACTAGCCTTGAATCAGCACATTGGC
65 CAGCACATTGGCA-CTTTT-TCTTTTTTAAGTCAAACATCGCTGGCCTTGAATCAGCACATTGGC
* *
1234766 ACCTTCTTCTTTCTCAAGTCCAACATCG
128 ACATTCTTCTTTCTCAAGTCCAACATCA
* * *
1234794 CTGGCCTTGAATTAGCATATTGGCAACTTTATCATTTTTAAGTCCAATGTTGCTGGCCTTGAATC
1 CTAGCCTTGAATCAGCATATTGGCAACTTTATCATTTTTAAGTCCAATGTTGCTGGCCTTAAATC
* * *
1234859 AGCACATTGGCACTTTCTTCTTTTTTAAGTCTAACATCGTTGGCCTTGAATCAGCATATTGGCAC
66 AGCACATTGGCACTTT-TTCTTTTTTAAGTCAAACATCGCTGGCCTTGAATCAGCACATTGGCAC
** *
1234924 ATT-TATCATCTT-T-AAGTCCAATGTTA
130 ATTCT-TC-T-TTCTCAAGTCCAACATCA
* * * * *
1234950 CTAGCCTTGAATCAGCACATTGGCACCTTTATCATCTTTAAATCCAATGTTACTGGCCTTAAATC
1 CTAGCCTTGAATCAGCATATTGGCAACTTTATCATTTTTAAGTCCAATGTTGCTGGCCTTAAATC
* * * *
1235015 AGCACATTGGCACATTATTCTTTCTCAAGTCCAAACATCGCTGACCTTGAATCAGCACATTGGCA
66 AGCACATTGGCAC-TTTTTCTTTTTTAAGT-CAAACATCGCTGGCCTTGAATCAGCACATTGGCA
1235080 C
129 C
1235081 CTTCAAGTTC
Statistics
Matches: 240, Mismatches: 40, Indels: 14
0.82 0.14 0.05
Matches are distributed among these distances:
155 1 0.00
156 135 0.56
157 100 0.42
158 4 0.02
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.35
Consensus pattern (155 bp):
CTAGCCTTGAATCAGCATATTGGCAACTTTATCATTTTTAAGTCCAATGTTGCTGGCCTTAAATC
AGCACATTGGCACTTTTTCTTTTTTAAGTCAAACATCGCTGGCCTTGAATCAGCACATTGGCACA
TTCTTCTTTCTCAAGTCCAACATCA
Found at i:1235259 original size:52 final size:52
Alignment explanation
Indices: 1235092--1235261 Score: 169
Period size: 52 Copynumber: 3.3 Consensus size: 52
1235082 TTCAAGTTCG
* * * * * * *
1235092 ATATCGCTGGCCTTGAATCAGCATATTGGCATTTTTAACATTTTTAAACTCA
1 ATATCGCTGGCCTTGAATCAGCACATTAGCATTCTTCACATCTTTAAGCCCA
* * * * * * *
1235144 ATGTCGCTAGCCTTGAATCAGCACATTAGCAATCTTCTCATCTTCAAGTCTA
1 ATATCGCTGGCCTTGAATCAGCACATTAGCATTCTTCACATCTTTAAGCCCA
* * * * *
1235196 ATGTCGTTGGCCGTGAATCAACACATTAACATTCTTCACATCTTTAAGCCCA
1 ATATCGCTGGCCTTGAATCAGCACATTAGCATTCTTCACATCTTTAAGCCCA
1235248 ATATCGCTGGCCTT
1 ATATCGCTGGCCTT
1235262 AAATTAGAAT
Statistics
Matches: 91, Mismatches: 27, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
52 91 1.00
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (52 bp):
ATATCGCTGGCCTTGAATCAGCACATTAGCATTCTTCACATCTTTAAGCCCA
Found at i:1245446 original size:17 final size:17
Alignment explanation
Indices: 1245421--1245453 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1245411 ATAAATAAAT
*
1245421 AAATTAAAATATAATTA
1 AAATAAAAATATAATTA
1245438 AAATAAAAATATAATT
1 AAATAAAAATATAATT
1245454 GCATCTCCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATAAAAATATAATTA
Found at i:1247408 original size:6 final size:6
Alignment explanation
Indices: 1247397--1247421 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1247387 TGTTAGATTG
1247397 AATCTA AATCTA AATCTA AATCTA A
1 AATCTA AATCTA AATCTA AATCTA A
1247422 TGGAAACAAA
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:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
AATCTA
Found at i:1247687 original size:16 final size:16
Alignment explanation
Indices: 1247660--1247704 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1247650 TTTTCTTGTG
*
1247660 ATAATTAAATAAAATTA
1 ATAATAAAATAAAA-TA
1247677 A-AATAAAATAAAATA
1 ATAATAAAATAAAATA
1247692 ATAATAATAATAA
1 ATAATAA-AATAA
1247705 TTTAATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 3 0.12
16 16 0.64
17 6 0.24
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
ATAATAAAATAAAATA
Found at i:1247721 original size:5 final size:5
Alignment explanation
Indices: 1247666--1247704 Score: 51
Period size: 5 Copynumber: 7.2 Consensus size: 5
1247656 TGTGATAATT
1247666 AAATA AAATTA AAATA AAATA AAATA ATAATA ATAATA A
1 AAATA AAA-TA AAATA AAATA AAATA A-AATA A-AATA A
1247705 TTTAATTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 16 0.50
6 16 0.50
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (5 bp):
AAATA
Found at i:1248660 original size:17 final size:18
Alignment explanation
Indices: 1248634--1248701 Score: 75
Period size: 19 Copynumber: 3.7 Consensus size: 18
1248624 TGACCTTTTA
* *
1248634 AAATTAAATTAAATAAAT
1 AAATTTAATTCAATAAAT
*
1248652 -AATTTAATTCAATAATT
1 AAATTTAATTCAATAAAT
*
1248669 AAATTTTAATTCAATAATT
1 AAA-TTTAATTCAATAAAT
1248688 AAATTTTAATTCAA
1 AAA-TTTAATTCAA
1248702 CACTAATAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
17 14 0.31
18 2 0.04
19 29 0.64
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATTTAATTCAATAAAT
Found at i:1248678 original size:19 final size:19
Alignment explanation
Indices: 1248654--1248701 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
1248644 AAATAAATAA
1248654 TTTAATTCAATAATTAAAT
1 TTTAATTCAATAATTAAAT
1248673 TTTAATTCAATAATTAAAT
1 TTTAATTCAATAATTAAAT
1248692 TTTAATTCAA
1 TTTAATTCAA
1248702 CACTAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (19 bp):
TTTAATTCAATAATTAAAT
Found at i:1248678 original size:24 final size:21
Alignment explanation
Indices: 1248647--1248701 Score: 82
Period size: 19 Copynumber: 2.8 Consensus size: 21
1248637 TTAAATTAAA
1248647 TAAATAATTTAATTCAATAAT
1 TAAATAATTTAATTCAATAAT
1248668 TAAAT--TTTAATTCAATAAT
1 TAAATAATTTAATTCAATAAT
1248687 TAAAT--TTTAATTCAA
1 TAAATAATTTAATTCAA
1248702 CACTAATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 29 0.85
21 5 0.15
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.45
Consensus pattern (21 bp):
TAAATAATTTAATTCAATAAT
Found at i:1248685 original size:36 final size:38
Alignment explanation
Indices: 1248631--1248701 Score: 92
Period size: 36 Copynumber: 1.9 Consensus size: 38
1248621 TAATGACCTT
1248631 TTAAAATTAAATTAAATAAAT-AA-TTTAATTCAATAA
1 TTAAAATTAAATTAAATAAATAAATTTTAATTCAATAA
* * * *
1248667 TTAAATTTTAATTCAATAATTAAATTTTAATTCAA
1 TTAAAATTAAATTAAATAAATAAATTTTAATTCAA
1248702 CACTAATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 17 0.59
37 2 0.07
38 10 0.34
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (38 bp):
TTAAAATTAAATTAAATAAATAAATTTTAATTCAATAA
Found at i:1249082 original size:6 final size:6
Alignment explanation
Indices: 1249044--1249093 Score: 52
Period size: 6 Copynumber: 8.3 Consensus size: 6
1249034 ATTATATTTG
1249044 ATTT-A ATTTAA ATTTTAA TATTTTAA A--TAA ATTTAA ATTTAA ATTTAA
1 ATTTAA ATTTAA A-TTTAA -A-TTTAA ATTTAA ATTTAA ATTTAA ATTTAA
1249092 AT
1 AT
1249094 AATTTAAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
4 4 0.10
5 4 0.10
6 19 0.47
7 6 0.15
8 7 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
ATTTAA
Found at i:1249084 original size:31 final size:30
Alignment explanation
Indices: 1249044--1249103 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
1249034 ATTATATTTG
* *
1249044 ATTTAATTTAAATTTTAATATTTTAAATAA
1 ATTTAATTTAAATTTAAATAATTTAAATAA
1249074 ATTTAAATTTAAATTTAAATAATTTAAATA
1 ATTT-AATTTAAATTTAAATAATTTAAATA
1249104 TCAAATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
ATTTAATTTAAATTTAAATAATTTAAATAA
Found at i:1249131 original size:22 final size:21
Alignment explanation
Indices: 1249048--1249131 Score: 71
Period size: 22 Copynumber: 3.7 Consensus size: 21
1249038 TATTTGATTT
*
1249048 AATTTAAATTTTAATATTTTAAATA
1 AATTTAAA--TTAAAATTTT-AA-A
*
1249073 AATTTAAATTTAAA-TTTAAA
1 AATTTAAATTAAAATTTTAAA
*
1249093 TAATTTAAATATCAAATTTTAAA
1 -AATTTAAAT-TAAAATTTTAAA
1249116 AATTTAAAATTAAAAT
1 AATTT-AAATTAAAAT
1249132 GATTTATATT
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
20 1 0.02
21 11 0.22
22 17 0.33
23 14 0.27
25 8 0.16
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (21 bp):
AATTTAAATTAAAATTTTAAA
Found at i:1249147 original size:17 final size:18
Alignment explanation
Indices: 1249125--1249164 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
1249115 AAATTTAAAA
*
1249125 TTAAAATGATTT-ATATT
1 TTAAAATAATTTAATATT
1249142 TTAAAATAATTTAATATT
1 TTAAAATAATTTAATATT
1249160 TTAAA
1 TTAAA
1249165 TAGATAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TTAAAATAATTTAATATT
Found at i:1249483 original size:24 final size:24
Alignment explanation
Indices: 1249453--1249498 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
1249443 ATGCGGGTCC
1249453 TTTTTTATAAATATAAATATAATT
1 TTTTTTATAAATATAAATATAATT
1249477 TTTTTTATAAATATAAATATAA
1 TTTTTTATAAATATAAATATAA
1249499 ATAAATGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TTTTTTATAAATATAAATATAATT
Found at i:1249543 original size:26 final size:26
Alignment explanation
Indices: 1249458--1249545 Score: 70
Period size: 26 Copynumber: 3.2 Consensus size: 26
1249448 GGTCCTTTTT
*
1249458 TATAAATATAAATATAATTTTTTTTATAAA
1 TATAAACATAAATATAA--TTTTTT-T-AA
* * **
1249488 TATAAATATAAATA-AATGTTTAAAA
1 TATAAACATAAATATAATTTTTTTAA
*
1249513 TTATAGACATAAATATAATTTTTTTAA
1 -TATAAACATAAATATAATTTTTTTAA
1249540 TATAAA
1 TATAAA
1249546 AAAAATTTAT
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
25 2 0.04
26 17 0.36
27 12 0.26
29 2 0.04
30 14 0.30
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.44
Consensus pattern (26 bp):
TATAAACATAAATATAATTTTTTTAA
Found at i:1249594 original size:14 final size:15
Alignment explanation
Indices: 1249547--1249624 Score: 81
Period size: 14 Copynumber: 5.1 Consensus size: 15
1249537 TAATATAAAA
* *
1249547 AAAATTTATAATATG
1 AAAATTTAAAATATT
1249562 AAAATATTATAAATATT
1 AAAAT-TTA-AAATATT
1249579 AAAATTTAAAAT-TT
1 AAAATTTAAAATATT
1249593 AAAATTTAAAAT-TT
1 AAAATTTAAAATATT
1249607 -AAATTTATTAAATATT
1 AAAATTTA--AAATATT
1249623 AA
1 AA
1249625 TTTATTATAT
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
13 7 0.13
14 16 0.29
15 13 0.24
16 8 0.15
17 11 0.20
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (15 bp):
AAAATTTAAAATATT
Found at i:1249612 original size:6 final size:7
Alignment explanation
Indices: 1249547--1249613 Score: 73
Period size: 7 Copynumber: 9.1 Consensus size: 7
1249537 TAATATAAAA
1249547 AAAATTT
1 AAAATTT
* *
1249554 ATAATATG
1 AAAAT-TT
1249562 AAAATATT
1 AAAAT-TT
1249570 ATAAATATT
1 A-AAAT-TT
1249579 AAAATTT
1 AAAATTT
1249586 AAAATTT
1 AAAATTT
1249593 AAAATTT
1 AAAATTT
1249600 AAAATTT
1 AAAATTT
1249607 -AAATTT
1 AAAATTT
1249613 A
1 A
1249614 TTAAATATTA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
6 6 0.11
7 27 0.51
8 12 0.23
9 8 0.15
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (7 bp):
AAAATTT
Found at i:1249626 original size:15 final size:17
Alignment explanation
Indices: 1249608--1249643 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
1249598 TTAAAATTTA
1249608 AATTTATTA-A-ATATT
1 AATTTATTATATATATT
1249623 AATTTATTATATATATT
1 AATTTATTATATATATT
1249640 AATT
1 AATT
1249644 AAATTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.47
16 1 0.05
17 9 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTTATTATATATATT
Found at i:1249725 original size:42 final size:43
Alignment explanation
Indices: 1249679--1249761 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 43
1249669 GTATATTAAA
* *
1249679 TATATTATTATAATCATAT-TTAAATATATTAT-TTTATATTTT
1 TATATAATTATAAT-ATATATTAAATATATCATATTTATATTTT
* * *
1249721 TATATAATTTTTATATTTATTAAATATATCATATTTATATT
1 TATATAATTATAATATATATTAAATATATCATATTTATATT
1249762 ATATTTTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
41 3 0.09
42 23 0.68
43 8 0.24
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (43 bp):
TATATAATTATAATATATATTAAATATATCATATTTATATTTT
Found at i:1249732 original size:11 final size:11
Alignment explanation
Indices: 1249716--1249785 Score: 50
Period size: 12 Copynumber: 5.9 Consensus size: 11
1249706 ATTATTTTAT
1249716 ATTTTTATATA
1 ATTTTTATATA
*
1249727 ATTTTTATATTT
1 ATTTTTATA-TA
** *
1249739 ATTAAATATATC
1 ATT-TTTATATA
*
1249751 ATATTTATATTA
1 ATTTTTATA-TA
1249763 TATTTTTATATA
1 -ATTTTTATATA
1249775 ATATTTTATAT
1 AT-TTTTATAT
1249786 TAATAAATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 9
0.71 0.14 0.14
Matches are distributed among these distances:
11 15 0.33
12 18 0.40
13 12 0.27
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (11 bp):
ATTTTTATATA
Found at i:1249760 original size:13 final size:12
Alignment explanation
Indices: 1249678--1249785 Score: 58
Period size: 13 Copynumber: 9.5 Consensus size: 12
1249668 TGTATATTAA
1249678 ATATAT-TA-TT
1 ATATATATATTT
1249688 ATA-ATCATATTT
1 ATATAT-ATATTT
*
1249700 AAATATATTATTT
1 ATATATA-TATTT
1249713 -TATAT-T-TTT
1 ATATATATATTT
1249722 ATATA-AT-TTT
1 ATATATATATTT
* *
1249732 -TATATTTATTAA
1 ATATATATATT-T
1249744 ATATATCATATTT
1 ATATAT-ATATTT
1249757 ATAT-TATATTT
1 ATATATATATTT
*
1249768 TTATATAATATTT
1 ATATAT-ATATTT
1249781 -TATAT
1 ATATAT
1249786 TAATAAATTT
Statistics
Matches: 77, Mismatches: 7, Indels: 26
0.70 0.06 0.24
Matches are distributed among these distances:
9 9 0.12
10 13 0.17
11 13 0.17
12 16 0.21
13 22 0.29
14 4 0.05
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (12 bp):
ATATATATATTT
Found at i:1250669 original size:13 final size:15
Alignment explanation
Indices: 1250635--1250664 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1250625 ATTTCAAGAG
*
1250635 ATTTTCTAAAATTTT
1 ATTTTATAAAATTTT
1250650 ATTTTATAAAATTTT
1 ATTTTATAAAATTTT
1250665 TTTATTTATT
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:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTTATAAAATTTT
Found at i:1250870 original size:25 final size:25
Alignment explanation
Indices: 1250803--1250897 Score: 94
Period size: 25 Copynumber: 3.9 Consensus size: 25
1250793 TGTTTTATAA
*
1250803 AAATAATTAAAATATTATA-ATATAT
1 AAATTATTAAAATATTATATA-ATAT
1250828 AAA--A--AATAATATTAATATAATAT
1 AAATTATTAA-AATATT-ATATAATAT
1250851 AAATTTATTAAAAT-TTATATAATAT
1 AAA-TTATTAAAATATTATATAATAT
*
1250876 AAATTATTAATATATTATATAA
1 AAATTATTAAAATATTATATAA
1250898 ATATGGTAAA
Statistics
Matches: 60, Mismatches: 1, Indels: 18
0.76 0.01 0.23
Matches are distributed among these distances:
21 2 0.03
22 6 0.10
23 11 0.18
24 10 0.17
25 23 0.38
26 3 0.05
27 3 0.05
28 2 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
AAATTATTAAAATATTATATAATAT
Found at i:1251747 original size:4 final size:5
Alignment explanation
Indices: 1251722--1251755 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
1251712 TATAATGCAA
1251722 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAA
1251756 ACAATCACCT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 19 0.70
6 4 0.15
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:1253579 original size:2 final size:2
Alignment explanation
Indices: 1253572--1253609 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1253562 ATTATGAAGG
1253572 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
1253610 TATCAAAACC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1256152 original size:21 final size:21
Alignment explanation
Indices: 1256126--1256179 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
1256116 ACTTATGAAC
1256126 TAAAAACCAAACCAAATTCAA
1 TAAAAACCAAACCAAATTCAA
* * * *
1256147 TAAAAACTAAGCCAAATTTAG
1 TAAAAACCAAACCAAATTCAA
*
1256168 TTAAAACCAAAC
1 TAAAAACCAAAC
1256180 GGAAACCGAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.57, C:0.20, G:0.04, T:0.19
Consensus pattern (21 bp):
TAAAAACCAAACCAAATTCAA
Found at i:1264585 original size:10 final size:10
Alignment explanation
Indices: 1264570--1264599 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
1264560 CATTTGAAAA
1264570 TATAGCCGTT
1 TATAGCCGTT
1264580 TATAGCCGTT
1 TATAGCCGTT
1264590 TATAGCCGTT
1 TATAGCCGTT
1264600 ACAAGCCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (10 bp):
TATAGCCGTT
Found at i:1264646 original size:13 final size:13
Alignment explanation
Indices: 1264628--1264653 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1264618 ACATTTTGGG
1264628 ATGTATCGATACA
1 ATGTATCGATACA
1264641 ATGTATCGATACA
1 ATGTATCGATACA
1264654 TATTGTATAT
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1264648 original size:33 final size:32
Alignment explanation
Indices: 1264606--1264673 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
1264596 CGTTACAAGC
* *
1264606 CAATGTATCGATACATTTTGGGATGTATCGATA
1 CAATGTATCGATACATATT-GGATATATCGATA
*
1264639 CAATGTATCGATACATATTGTATATATCGATA
1 CAATGTATCGATACATATTGGATATATCGATA
1264671 CAA
1 CAA
1264674 ATTTGGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATATTGGATATATCGATA
Found at i:1264753 original size:20 final size:21
Alignment explanation
Indices: 1264706--1264758 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1264696 ACCAATGACC
**
1264706 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
*
1264727 AGTATCGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
1264747 TGTATCGATACA
1 TGTATCGATACA
1264759 ATGTCTCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:1269334 original size:17 final size:17
Alignment explanation
Indices: 1269314--1269358 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1269304 TGAACTATTA
1269314 ATTTAATAAATTTAAAT
1 ATTTAATAAATTTAAAT
** *
1269331 ATTTAATTGATTTAGAT
1 ATTTAATAAATTTAAAT
*
1269348 ATTTGATAAAT
1 ATTTAATAAAT
1269359 ATTATTTTTT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (17 bp):
ATTTAATAAATTTAAAT
Found at i:1269994 original size:25 final size:25
Alignment explanation
Indices: 1269966--1270022 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
1269956 CTTTTTTTTC
*
1269966 TAAAAAAGATA-TTATAATTTTAAA-A
1 TAAAAAAGA-AGTTA-AATTTAAAAGA
*
1269991 TAAAAAATAAGTTAAATTTAAAAGA
1 TAAAAAAGAAGTTAAATTTAAAAGA
1270016 TAAAAAA
1 TAAAAAA
1270023 TTAATTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 9 0.32
25 19 0.68
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (25 bp):
TAAAAAAGAAGTTAAATTTAAAAGA
Found at i:1270580 original size:15 final size:14
Alignment explanation
Indices: 1270545--1270586 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
1270535 AAATCACCTT
1270545 TTTTTTTAATAAAA
1 TTTTTTTAATAAAA
* *
1270559 TATTTTTGATGAAAA
1 TTTTTTTAAT-AAAA
1270574 TTTTTTT-ATAAAA
1 TTTTTTTAATAAAA
1270587 AAATAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 4 0.17
14 10 0.42
15 10 0.42
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (14 bp):
TTTTTTTAATAAAA
Found at i:1270749 original size:14 final size:14
Alignment explanation
Indices: 1270723--1270778 Score: 67
Period size: 14 Copynumber: 3.9 Consensus size: 14
1270713 GAAATTTTAA
1270723 ATTTTTACTTTTTGTT
1 ATTTTTA-TTTTT-TT
1270739 ATTTTTATTTTTTT
1 ATTTTTATTTTTTT
**
1270753 GGTTTTATTTTTTT
1 ATTTTTATTTTTTT
*
1270767 ATTTTTAGTTTT
1 ATTTTTATTTTT
1270779 AAAGATATCA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
14 23 0.66
15 5 0.14
16 7 0.20
ACGTcount: A:0.12, C:0.02, G:0.07, T:0.79
Consensus pattern (14 bp):
ATTTTTATTTTTTT
Found at i:1270762 original size:20 final size:20
Alignment explanation
Indices: 1270737--1270779 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
1270727 TTACTTTTTG
*
1270737 TTATTTTTATT-TTTTTGGTT
1 TTATTTTT-TTATTTTTAGTT
1270757 TTATTTTTTTATTTTTAGTT
1 TTATTTTTTTATTTTTAGTT
1270777 TTA
1 TTA
1270780 AAGATATCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (20 bp):
TTATTTTTTTATTTTTAGTT
Found at i:1270826 original size:21 final size:21
Alignment explanation
Indices: 1270802--1270841 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1270792 TCAGAACTGA
1270802 GAAA-ATAAATTATAAATATTC
1 GAAATATAAATT-TAAATATTC
*
1270823 GAAATTTAAATTTAAATAT
1 GAAATATAAATTTAAATAT
1270842 ATTAAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.38
Consensus pattern (21 bp):
GAAATATAAATTTAAATATTC
Found at i:1271873 original size:16 final size:16
Alignment explanation
Indices: 1271852--1271883 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1271842 TTAGATTTTA
1271852 TTATTTAAATAAAATT
1 TTATTTAAATAAAATT
*
1271868 TTATTTAAATTAAATT
1 TTATTTAAATAAAATT
1271884 ATAAAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATTTAAATAAAATT
Found at i:1271948 original size:26 final size:26
Alignment explanation
Indices: 1271902--1271951 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1271892 ATTAATATGT
*
1271902 TATTTTAAAATATAATAAAATTTTAG
1 TATTTTAAAATAAAATAAAATTTTAG
*
1271928 TATTTTAAAA-AAAAGTTAAATTTT
1 TATTTTAAAATAAAA-TAAAATTTT
1271952 TTAAGTCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 18 0.86
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (26 bp):
TATTTTAAAATAAAATAAAATTTTAG
Found at i:1272210 original size:2 final size:2
Alignment explanation
Indices: 1272203--1272229 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1272193 TTAACAAGTG
1272203 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1272230 TCTATTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1272481 original size:14 final size:14
Alignment explanation
Indices: 1272464--1272491 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1272454 CTAAAATTAA
1272464 CTTTTAAAAAATAT
1 CTTTTAAAAAATAT
1272478 CTTTTAAAAAATAT
1 CTTTTAAAAAATAT
1272492 AAAATTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
CTTTTAAAAAATAT
Found at i:1272843 original size:30 final size:32
Alignment explanation
Indices: 1272803--1272875 Score: 105
Period size: 30 Copynumber: 2.3 Consensus size: 32
1272793 AATAATCATT
1272803 AAAATATTATTAATATTAATATAA-TATT-TA
1 AAAATATTATTAATATTAATATAATTATTATA
* * *
1272833 AAAATTTTATTTATATTAATATAATTATTATT
1 AAAATATTATTAATATTAATATAATTATTATA
1272865 AAAATATTATT
1 AAAATATTATT
1272876 TTACAATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 22 0.59
31 4 0.11
32 11 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
AAAATATTATTAATATTAATATAATTATTATA
Found at i:1272940 original size:25 final size:25
Alignment explanation
Indices: 1272912--1272960 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1272902 CATAAAATAG
*
1272912 AAATATTAATTATTAATA-TATTAAA
1 AAATATTAATCATTAA-ACTATTAAA
*
1272937 AAATATTTATCATTAAACTATTAA
1 AAATATTAATCATTAAACTATTAA
1272961 TTTTCAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (25 bp):
AAATATTAATCATTAAACTATTAAA
Found at i:1273021 original size:19 final size:19
Alignment explanation
Indices: 1272987--1273023 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1272977 AGTAATATTT
1272987 TAACAATATTATTTAATAC
1 TAACAATATTATTTAATAC
1273006 TAAC-ATATTATATTAATA
1 TAACAATATTAT-TTAATA
1273024 TTAAATACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (19 bp):
TAACAATATTATTTAATAC
Found at i:1273186 original size:28 final size:27
Alignment explanation
Indices: 1273155--1273209 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
1273145 TAAAATACTG
1273155 ATAATACTATAATTTA-TTATTAAAATAA
1 ATAATA-T-TAATTTATTTATTAAAATAA
*
1273183 ATAATATTATTTTATTTTATTAAAATA
1 ATAATATTAATTTA-TTTATTAAAATA
1273210 TTACATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 6 0.25
27 1 0.04
28 17 0.71
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (27 bp):
ATAATATTAATTTATTTATTAAAATAA
Found at i:1273194 original size:25 final size:24
Alignment explanation
Indices: 1273155--1273225 Score: 63
Period size: 28 Copynumber: 2.8 Consensus size: 24
1273145 TAAAATACTG
* *
1273155 ATAATACTATAATTTATTATTAAA
1 ATAATAATATTATTTATTATTAAA
1273179 ATAAATAATATTATTTTATTTTATTAAA
1 AT-AATAATATTA-TTTA--TTATTAAA
*
1273207 ATATTACATATT-TTTATTA
1 ATAATA-ATATTATTTATTA
1273226 ATAATAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
24 5 0.13
25 8 0.21
26 8 0.21
27 3 0.08
28 15 0.38
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (24 bp):
ATAATAATATTATTTATTATTAAA
Found at i:1274106 original size:33 final size:33
Alignment explanation
Indices: 1274069--1274135 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1274059 TTCAACGATT
1274069 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1274102 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1274135 T
1 T
1274136 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1274107 original size:13 final size:13
Alignment explanation
Indices: 1274089--1274113 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1274079 CATAAAATGT
1274089 TGTATCGATACAA
1 TGTATCGATACAA
1274102 TGTATCGATACA
1 TGTATCGATACA
1274114 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1274114 original size:404 final size:406
Alignment explanation
Indices: 1273362--1274167 Score: 1483
Period size: 404 Copynumber: 2.0 Consensus size: 406
1273352 CTCTATTGAT
* *
1273362 TGTAGACACCTCATTTTGTCCGGGTCAATTTTCGACAATTTGAATCCTAGCTAGTAGGTGGAGGA
1 TGTAGACACCTCATTTTGTCCGGGCCAATTTTCGACAATTTGAAGCCTAGCTAGTAGGTGGAGGA
*
1273427 TTCGACTTATGTGGGGACGAATTCGCCGGGCGCCGCTGGCGCCCGGCGAAAATGGTTTTTTAGAT
66 TTCGACTTATGTGGGGACGAATTCGCCGGGCGCCGCTGGCGCCCGGCAAAAATGGTTTTTTAGAT
*
1273492 TTTTATAACTTTTTGTTAAGCTCGAATTCATTTCTCATCGTCCCTAGTCGAGATAGGGTGTTTCG
131 TTTTATAACTTTTTGTTAAGCTCGAATTCATTTCCCATCGTCCCTAGTCGAGATAGGGTGTTTCG
1273557 AAGGCAAAAAGGATGAAAAAATCACATTTTGGTCCAAATGTATCGATACATTGTTATAATGTATC
196 AAGGCAAAAAGGATGAAAAAATCACATTTTGGTCCAAATGTATCGATACATTGTTATAATGTATC
1273622 GATACAAGGTCCCAACGATCAAAAATTTTGAATTTCAACGATTTGTATCGATACATAAAATGTTG
261 GATACAAGGTCCCAACGATCAAAAATTTTGAATTTCAACGATTTGTATCGATACATAAAATGTTG
* *
1273687 TATCGATACAATGTATTGATACATATTTTTTT-TATCGATACAATTTAAGCTACTGCC-AAAGAA
326 TATCGATACAATGTATCGATACATATTTTTTTGTATCGATACAATTTAAGCTACTGCCAAAAAAA
1273750 ATGTATCGATACCTTG
391 ATGTATCGATACCTTG
* *
1273766 TGTAGACACTTCATTTTGTCCGGGCCAATTTTTGACAATTTGAAGCCTAGCTAGTAGGTGGAGGA
1 TGTAGACACCTCATTTTGTCCGGGCCAATTTTCGACAATTTGAAGCCTAGCTAGTAGGTGGAGGA
1273831 TTCGACTTATGTGGGGACGAATTCGCCGGGCGCCAGC-GGCGCCCGGCAAAAATGGTTTTTTAGA
66 TTCGACTTATGTGGGGACGAATTCGCCGGGCGCC-GCTGGCGCCCGGCAAAAATGGTTTTTTAGA
*
1273895 TTTTTATAACTTTTTGTTAAGCTCGAATTCATTTCCCGTCGTCCCTAGTCGAGATAGGGTGTTTC
130 TTTTTATAACTTTTTGTTAAGCTCGAATTCATTTCCCATCGTCCCTAGTCGAGATAGGGTGTTTC
*
1273960 GAAGGCAAAAATGATGAAAAAATCACATTTTGGTCCAAATGTATCGATACATTGTTATAATGTAT
195 GAAGGCAAAAAGGATGAAAAAATCACATTTTGGTCCAAATGTATCGATACATTGTTATAATGTAT
*
1274025 CGATACAAGGTCCCAACGGTCAAAAATTTTGAATTTCAACGATTTGTATCGATACATAAAATGTT
260 CGATACAAGGTCCCAACGATCAAAAATTTTGAATTTCAACGATTTGTATCGATACATAAAATGTT
1274090 GTATCGATACAATGTATCGATACATATTTTTTTGTATCGATACAATTTAAGCTACTGCCAAAAAA
325 GTATCGATACAATGTATCGATACATATTTTTTTGTATCGATACAATTTAAGCTACTGCCAAAAAA
1274155 AATGTATCGATAC
390 AATGTATCGATAC
1274168 ATTACTCACA
Statistics
Matches: 388, Mismatches: 11, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
404 344 0.89
405 27 0.07
406 17 0.04
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (406 bp):
TGTAGACACCTCATTTTGTCCGGGCCAATTTTCGACAATTTGAAGCCTAGCTAGTAGGTGGAGGA
TTCGACTTATGTGGGGACGAATTCGCCGGGCGCCGCTGGCGCCCGGCAAAAATGGTTTTTTAGAT
TTTTATAACTTTTTGTTAAGCTCGAATTCATTTCCCATCGTCCCTAGTCGAGATAGGGTGTTTCG
AAGGCAAAAAGGATGAAAAAATCACATTTTGGTCCAAATGTATCGATACATTGTTATAATGTATC
GATACAAGGTCCCAACGATCAAAAATTTTGAATTTCAACGATTTGTATCGATACATAAAATGTTG
TATCGATACAATGTATCGATACATATTTTTTTGTATCGATACAATTTAAGCTACTGCCAAAAAAA
ATGTATCGATACCTTG
Found at i:1274196 original size:13 final size:13
Alignment explanation
Indices: 1274178--1274202 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1274168 ATTACTCACA
1274178 TGTATCGATACAT
1 TGTATCGATACAT
1274191 TGTATCGATACA
1 TGTATCGATACA
1274203 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1281524 original size:14 final size:13
Alignment explanation
Indices: 1281497--1281530 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
1281487 TAATCTTCAC
1281497 AAAAAAAAACAAA
1 AAAAAAAAACAAA
*
1281510 AAAAAATAAATAAA
1 AAAAAA-AAACAAA
1281524 AAAAAAA
1 AAAAAAA
1281531 GGGAAAAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.91, C:0.03, G:0.00, T:0.06
Consensus pattern (13 bp):
AAAAAAAAACAAA
Found at i:1282516 original size:31 final size:30
Alignment explanation
Indices: 1282478--1282660 Score: 215
Period size: 31 Copynumber: 5.9 Consensus size: 30
1282468 ATACCTTTTT
*
1282478 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
1 AAAGTCCACGACTCAGTGGC-ATCTTTTCTC
* * *
1282509 AAAGTCCACGACTCAGTGGTAATCTCTGCTC
1 AAAGTCCACGACTCAGTGG-CATCTTTTCTC
*
1282540 AAAGTCCACGACTCAGTGGCATCTTTTTCTTT
1 AAAGTCCACGACTCAGTGGCATC-TTTTC-TC
1282572 AAAGTCCACGACTCAGTGGCAT-TTTGTCTC
1 AAAGTCCACGACTCAGTGGCATCTTT-TCTC
*
1282602 AAAGTCCACGACTCAGTGGCATTTTTTCTTC
1 AAAGTCCACGACTCAGTGGCATCTTTTC-TC
* * * *
1282633 AAAGCCCACAACTCCGTGGCACCTTTTC
1 AAAGTCCACGACTCAGTGGCATCTTTTC
1282661 CTTTAAAGCC
Statistics
Matches: 134, Mismatches: 12, Indels: 12
0.85 0.08 0.08
Matches are distributed among these distances:
30 31 0.23
31 80 0.60
32 23 0.17
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.30
Consensus pattern (30 bp):
AAAGTCCACGACTCAGTGGCATCTTTTCTC
Found at i:1282635 original size:93 final size:93
Alignment explanation
Indices: 1282475--1282685 Score: 264
Period size: 93 Copynumber: 2.3 Consensus size: 93
1282465 CAAATACCTT
1282475 TTTAAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGTAATCTCTGCTC
1 TTTAAAGTCCACGACTCAGTGGC-ATCTCTTCTCAAAGTCCACGACTCAGTGGTAATCTCTGCTC
* * * *
1282540 AAAGTCCACGACTCAGTGGCATCTTTTTC
65 AAAGCCCACAACTCAGTGGCACCTTTTCC
* * * * *
1282569 TTTAAAGTCCACGACTCAGTGGCAT-TTTGTCTCAAAGTCCACGACTCAGTGG-CATTTTTTCTT
1 TTTAAAGTCCACGACTCAGTGGCATCTCT-TCTCAAAGTCCACGACTCAGTGGTAATCTCTGC-T
*
1282632 CAAAGCCCACAACTCCGTGGCACCTTTTCC
64 CAAAGCCCACAACTCAGTGGCACCTTTTCC
* * *
1282662 TTTAAAGCCCACAACTCCGTGGCA
1 TTTAAAGTCCACGACTCAGTGGCA
1282686 CCTTTTTCCC
Statistics
Matches: 102, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
92 7 0.07
93 72 0.71
94 23 0.23
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (93 bp):
TTTAAAGTCCACGACTCAGTGGCATCTCTTCTCAAAGTCCACGACTCAGTGGTAATCTCTGCTCA
AAGCCCACAACTCAGTGGCACCTTTTCC
Found at i:1282768 original size:34 final size:33
Alignment explanation
Indices: 1282540--1283256 Score: 857
Period size: 34 Copynumber: 21.3 Consensus size: 33
1282530 ATCTCTGCTC
* * * *
1282540 AAAGTCCACGACTCAGTGGCATCTTTTTC-TTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
* * * *
1282572 AAAGTCCACGACTCAGTGGCA--TTTTGTC--TC
1 AAAGCCCACAACTCCGTGGCACCTTTT-TCTTTT
* * * * *
1282602 AAAGTCCACGACTCAGTGGCA-TTTTTTC-TTC
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
*
1282633 AAAGCCCACAACTCCGTGGCACC-TTTTCCTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
1282665 AAAGCCCACAACTCCGTGGCACCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTT--CTTTT
* *
1282700 CAAAACCCACAACTCCGTGGCACC-TTTTCCTTT
1 -AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
1282733 AAAGCCCACAACTCCGTGGCACCTTTTTCTGTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCT-TTT
1282767 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT--CTTTT
*
1282803 CAAAGCCCACAACTCCGTGGCACC-TTTTCCTTT
1 -AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
*
1282836 AAAGCCCACAACTCTGTGGCACCTTTTTCTGTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCT-TTT
1282870 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT--CTTTT
*
1282906 CAAAGCCCACAACTCCGTGGCACC-TTTTCCTTT
1 -AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
1282939 AAAGCCCACAACTCCGTGGCACCTTTTTCTGTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCT-TTT
1282973 AAAGCCCACAACTCCGTGGCACTCTTTTTTCCTTTT
1 AAAGCCCACAACTCCGTGGCAC-C-TTTTT-CTTTT
*
1283009 CAAAGCCCACAACTCCGTGGCACTTTTTTCTTTT
1 -AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
*
1283043 AAAGCCCACAACTCCGTGGCACC-TTTTCCTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
*
1283075 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
*
1283108 CAAAGCCCACAACTCCGTGGCACCTTCTTCTTTT
1 -AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
*
1283142 CAAAGCCCACAACTCCGTGGCACTTTTTTCTTTT
1 -AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
1283176 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT--CTTTT
* * *
1283212 -AAGTCCACAACTCCGTGGCATCTTTCTCCCTTTCT
1 AAAGCCCACAACTCCGTGGCACCTTT-T-TCTTT-T
1283247 AAAGCCCACA
1 AAAGCCCACA
1283257 CAAGTCGGTG
Statistics
Matches: 620, Mismatches: 29, Indels: 68
0.86 0.04 0.09
Matches are distributed among these distances:
30 28 0.05
31 31 0.05
32 144 0.23
33 82 0.13
34 157 0.25
35 55 0.09
36 51 0.08
37 72 0.12
ACGTcount: A:0.21, C:0.34, G:0.13, T:0.32
Consensus pattern (33 bp):
AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
Found at i:1282817 original size:103 final size:103
Alignment explanation
Indices: 1282600--1283256 Score: 1005
Period size: 103 Copynumber: 6.4 Consensus size: 103
1282590 GCATTTTGTC
* * * * * * *
1282600 TCAAAGTCCACGACTCAGTGGCA-TTTTTTCTTCAAAGCCCACAACTCCGTGGCACC-TTTTC-C
1 TCAAAGCCCACAACTCCGTGGCACCTTTTCCTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTG
1282662 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCCCTTT
66 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT
*
1282699 TCAAAACCCACAACTCCGTGGCACCTTTTCCTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTG
1 TCAAAGCCCACAACTCCGTGGCACCTTTTCCTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTG
1282764 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT
66 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT
*
1282802 TCAAAGCCCACAACTCCGTGGCACCTTTTCCTTTAAAGCCCACAACTCTGTGGCACCTTTTTCTG
1 TCAAAGCCCACAACTCCGTGGCACCTTTTCCTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTG
1282867 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT
66 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT
1282905 TCAAAGCCCACAACTCCGTGGCACCTTTTCCTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTG
1 TCAAAGCCCACAACTCCGTGGCACCTTTTCCTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTG
*
1282970 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTTCCTTT
66 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT
* *
1283008 TCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACC-TTTTC-
1 TCAAAGCCCACAACTCCGTGGCAC-CTTTTCCTTTAAAGCCCACAACTCCGTGGCACCTTTTTCT
* *
1283071 CTTTAAAGCCCACAACTCCGTGGCAC-CTTCTT--CTTT
65 GTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT
* *
1283107 TCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTC
1 TCAAAGCCCACAACTCCGTGGCACCTT-TTCCTTT-AAAGCCCACAACTCCGTGGCACCTTTTTC
1283172 T-TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT
64 TGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT
* *
1283211 T--AAGTCCACAACTCCGTGGCATCTTTCTCCCTTTCTAAAGCCCACA
1 TCAAAGCCCACAACTCCGTGGCACCTTT-T-CC-TT-TAAAGCCCACA
1283257 CAAGTCGGTG
Statistics
Matches: 520, Mismatches: 22, Indels: 27
0.91 0.04 0.05
Matches are distributed among these distances:
98 2 0.00
99 54 0.10
100 52 0.10
101 41 0.08
102 78 0.15
103 244 0.47
104 48 0.09
105 1 0.00
ACGTcount: A:0.21, C:0.35, G:0.12, T:0.32
Consensus pattern (103 bp):
TCAAAGCCCACAACTCCGTGGCACCTTTTCCTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTG
TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT
Found at i:1283290 original size:34 final size:34
Alignment explanation
Indices: 1283247--1283311 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
1283237 CTCCCTTTCT
1283247 AAAGCCCACACAAGTCGGTGGCAACCCTTCTTCC
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTTCC
1283281 AAAGCCCACACAAGTCGGTGGCAACCCTTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCT
1283312 AAGCCCAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.28, C:0.37, G:0.18, T:0.17
Consensus pattern (34 bp):
AAAGCCCACACAAGTCGGTGGCAACCCTTCTTCC
Found at i:1283529 original size:49 final size:49
Alignment explanation
Indices: 1283311--1284230 Score: 1199
Period size: 49 Copynumber: 18.7 Consensus size: 49
1283301 GCAACCCTTC
* * *
1283311 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
*
1283363 TAAGTCCAATGTAGCTAGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
1283406 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
* * *
1283458 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
1283507 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
1283556 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * *
1283605 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
1283654 TAAGACCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * *
1283703 TAAGTCCAATGTGGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * *
1283752 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCATCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
1283801 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCGT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
1283850 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
1283899 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * * *
1283948 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
1283997 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-CTTGCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTT-CATCTT
* * *
1284046 TAAGTCC-ATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
1284094 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * *
1284143 TCAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
*
1284195 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
1284231 ACATCCTTTT
Statistics
Matches: 750, Mismatches: 103, Indels: 30
0.85 0.12 0.03
Matches are distributed among these distances:
43 39 0.05
45 1 0.00
48 40 0.05
49 552 0.74
50 3 0.00
51 2 0.00
52 113 0.15
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.31
Consensus pattern (49 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
Found at i:1285197 original size:33 final size:33
Alignment explanation
Indices: 1285160--1285226 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1285150 TTCAACGATT
1285160 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1285193 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1285226 T
1 T
1285227 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1285198 original size:13 final size:13
Alignment explanation
Indices: 1285180--1285204 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1285170 CATAAAATGT
1285180 TGTATCGATACAA
1 TGTATCGATACAA
1285193 TGTATCGATACA
1 TGTATCGATACA
1285205 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1285287 original size:13 final size:13
Alignment explanation
Indices: 1285269--1285293 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1285259 ATTACTCACA
1285269 TGTATCGATACAT
1 TGTATCGATACAT
1285282 TGTATCGATACA
1 TGTATCGATACA
1285294 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1285430 original size:52 final size:52
Alignment explanation
Indices: 1285302--1285422 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
1285292 CACTGATCTT
*
1285302 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1285354 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1285406 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
1285423 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1288559 original size:52 final size:53
Alignment explanation
Indices: 1288497--1288636 Score: 169
Period size: 52 Copynumber: 2.7 Consensus size: 53
1288487 TACGACACCT
*** * *
1288497 TGTATCGATACACCGAT-CTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACCGATAAAATGTATCAATACATGCAAGCAAATTTGCCCAGA
**
1288549 TGTATCGATACA-TTATAAAATGTATCAATACATGCAAGCAAATTTGCCCAGA
1 TGTATCGATACACCGATAAAATGTATCAATACATGCAAGCAAATTTGCCCAGA
* * *
1288601 TGTATCGATACA-CTATTAAATGTATCGATACATGCA
1 TGTATCGATACACCGATAAAATGTATCAATACATGCA
1288637 GATAAATTTT
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
51 2 0.03
52 75 0.97
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (53 bp):
TGTATCGATACACCGATAAAATGTATCAATACATGCAAGCAAATTTGCCCAGA
Found at i:1288644 original size:52 final size:52
Alignment explanation
Indices: 1288517--1288645 Score: 197
Period size: 52 Copynumber: 2.5 Consensus size: 52
1288507 CACCGATCTT
* *
1288517 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGACAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
1288569 TGTATCAATACATGCA-AGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGA-CAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1288621 TGTATCGATACATGCAGATAAATTT
1 TGTATCGATACATGCAGACAAATTT
1288646 TCATATTTCG
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
52 68 0.99
53 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGACAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1289534 original size:20 final size:20
Alignment explanation
Indices: 1289497--1289536 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1289487 TAAACCTTGA
*
1289497 TCATGCATTTCGGCTATGTT
1 TCATGCATTTCAGCTATGTT
1289517 TCATGCATTTACAG-TATGTT
1 TCATGCATTT-CAGCTATGTT
1289537 CAGCACCTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.20, C:0.17, G:0.17, T:0.45
Consensus pattern (20 bp):
TCATGCATTTCAGCTATGTT
Found at i:1293011 original size:7 final size:7
Alignment explanation
Indices: 1292996--1293030 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
1292986 TTTTCATAGA
*
1292996 TAAAATT
1 TAAATTT
1293003 TAAATTT
1 TAAATTT
1293010 TAAATTT
1 TAAATTT
1293017 TAAATTT
1 TAAATTT
1293024 TAAATTT
1 TAAATTT
1293031 ATTTTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
TAAATTT
Found at i:1294598 original size:22 final size:22
Alignment explanation
Indices: 1294556--1294598 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1294546 TCGTGTTCAT
*
1294556 ATTATTTTTTATCAGTGTTTTA
1 ATTATTTTTTATCAGTATTTTA
*
1294578 ATTATTTTCTTAT-ATTATTTT
1 ATTATTTT-TTATCAGTATTTT
1294599 TCTTGTTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (22 bp):
ATTATTTTTTATCAGTATTTTA
Found at i:1297525 original size:15 final size:15
Alignment explanation
Indices: 1297490--1297587 Score: 69
Period size: 17 Copynumber: 6.3 Consensus size: 15
1297480 TATTAGACAA
*
1297490 TATATATACTAAAAT
1 TATATATACTAATAT
1297505 CATATATATACTAATAT
1 --TATATATACTAATAT
*
1297522 TATATATATATATATAT
1 TATATATA-CTA-ATAT
*
1297539 TTTATATAC--ATAT
1 TATATATACTAATAT
1297552 TATATATACTGGAGAT-T
1 TATATATACT--A-ATAT
*
1297569 TATATATGCTAA-AT
1 TATATATACTAATAT
1297583 TATAT
1 TATAT
1297588 TTATAAATAA
Statistics
Matches: 67, Mismatches: 6, Indels: 19
0.73 0.07 0.21
Matches are distributed among these distances:
13 12 0.18
14 7 0.10
15 9 0.13
16 2 0.03
17 35 0.52
18 2 0.03
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (15 bp):
TATATATACTAATAT
Found at i:1297534 original size:13 final size:13
Alignment explanation
Indices: 1297506--1297559 Score: 60
Period size: 13 Copynumber: 4.4 Consensus size: 13
1297496 TACTAAAATC
*
1297506 ATATATATACTA-
1 ATATATATATTAT
1297518 ATAT-TATA-TAT
1 ATATATATATTAT
*
1297529 ATATATATATTTT
1 ATATATATATTAT
*
1297542 ATATACATATTAT
1 ATATATATATTAT
1297555 ATATA
1 ATATA
1297560 CTGGAGATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
10 2 0.06
11 8 0.22
12 8 0.22
13 18 0.50
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (13 bp):
ATATATATATTAT
Found at i:1297575 original size:2 final size:2
Alignment explanation
Indices: 1297506--1297559 Score: 53
Period size: 2 Copynumber: 28.5 Consensus size: 2
1297496 TACTAAAATC
*
1297506 AT AT AT AT ACT A- AT AT -T AT AT AT AT AT AT AT AT -T TT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1297546 AC AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT A
1297560 CTGGAGATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
1 4 0.09
2 38 0.86
3 2 0.05
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1298787 original size:21 final size:21
Alignment explanation
Indices: 1298761--1298802 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1298751 AAAAATTAAT
*
1298761 TTTAT-ATTAATATTTATATAA
1 TTTATAATTAA-ATTTAAATAA
1298782 TTTATAATTAAATTTAAATAA
1 TTTATAATTAAATTTAAATAA
1298803 AAATTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTATAATTAAATTTAAATAA
Found at i:1304617 original size:21 final size:20
Alignment explanation
Indices: 1304593--1304632 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1304583 AAATCAAATA
1304593 TATATTTAATTAATTATTTAC
1 TATATTTAA-TAATTATTTAC
*
1304614 TATATTTAATATTTATTTA
1 TATATTTAATAATTATTTA
1304633 ATATTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (20 bp):
TATATTTAATAATTATTTAC
Found at i:1304660 original size:21 final size:20
Alignment explanation
Indices: 1304624--1304676 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1304614 TATATTTAAT
1304624 ATTTATTTAATATTAAAATA
1 ATTTATTTAATATTAAAATA
*
1304644 ATTTTTTTAAGTATTAAAA-A
1 ATTTATTTAA-TATTAAAATA
*
1304664 TTTTATTTTAATA
1 ATTTA-TTTAATA
1304677 AATTAATTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
ATTTATTTAATATTAAAATA
Found at i:1307899 original size:10 final size:10
Alignment explanation
Indices: 1307884--1307964 Score: 50
Period size: 10 Copynumber: 8.4 Consensus size: 10
1307874 ATTAATATTG
1307884 TATTTATATA
1 TATTTATATA
1307894 TATTTATATA
1 TATTTATATA
1307904 T-TTTCATCATA
1 TATTT-AT-ATA
1307915 T-TTTA-ATCA
1 TATTTATAT-A
1307924 TATTT-TA-A
1 TATTTATATA
* *
1307932 AATAT-TATA
1 TATTTATATA
1307941 TATTTATATA
1 TATTTATATA
*
1307951 AATTT-TGATA
1 TATTTAT-ATA
1307961 TATT
1 TATT
1307965 AAATTTATAA
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
8 8 0.14
9 10 0.18
10 32 0.56
11 7 0.12
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (10 bp):
TATTTATATA
Found at i:1307917 original size:11 final size:11
Alignment explanation
Indices: 1307901--1307931 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1307891 ATATATTTAT
*
1307901 ATATTTTCATC
1 ATATTTTAATC
1307912 ATATTTTAATC
1 ATATTTTAATC
1307923 ATATTTTAA
1 ATATTTTAA
1307932 AATATTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (11 bp):
ATATTTTAATC
Found at i:1308169 original size:23 final size:25
Alignment explanation
Indices: 1308143--1308201 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 25
1308133 TAAACTCAAA
1308143 TATAAAATTTA-TTTATATT-ATAT
1 TATAAAATTTATTTTATATTAATAT
1308166 TATAAAATTTATTTTATATTAATAT
1 TATAAAATTTATTTTATATTAATAT
1308191 T-TATAAATTTA
1 TATA-AAATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
23 11 0.33
24 10 0.30
25 12 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATAAAATTTATTTTATATTAATAT
Found at i:1308192 original size:17 final size:19
Alignment explanation
Indices: 1308152--1308195 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1308142 ATATAAAATT
1308152 TATTTATATTATATTATAA
1 TATTTATATTATATTATAA
* *
1308171 AATTTATTTTATA-T-TAA
1 TATTTATATTATATTATAA
1308188 TATTTATA
1 TATTTATA
1308196 AATTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 9 0.43
18 1 0.05
19 11 0.52
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TATTTATATTATATTATAA
Done.