Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold223
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: 4172444
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 17292 characters in sequence are not A, C, G, or T
File 21 of 26
Found at i:3364260 original size:152 final size:147
Alignment explanation
Indices: 3363976--3364284 Score: 438
Period size: 152 Copynumber: 2.0 Consensus size: 147
3363966 ATTCAATAAT
3363976 TTTAATTTACGAAGATGAGATAAAAAGATATCAAAATATAAATTTTGAGAGCAAAATAAAATTTT
1 TTTAATTTACGAAGATGAGATAAAAAGATATCAAAATATAAATTTTGAGAGCAAAATAAAATTTT
3364041 ATTATTTTACTTAAAAGAAAGAGTTTAGGAGCCAATGAGGCTAAAAAAACATTTATGTAATTAAT
66 ATTATTTTACTTAAAAGAAAGAGTTTAGGAGCCAATGAGGCTAAAAAAACA-TTA--TAATTAAT
3364106 GTATATTGAAAGTATATTAAAA
128 GTA-ATT-AAAGTATATTAAAA
3364128 TTTAATTTACGAAGATGAGATAAAAAGATATCAAAATATAAATTTTTTGAGAGCAAAATAAAATT
1 TTTAATTTACGAAGATGAGATAAAAAGATATCAAAATATAAA--TTTTGAGAGCAAAATAAAA-T
3364193 TTTATTATTTTTTACTTAAAAGAAAGAGTTTTAGGAGCCAATGAGGGCTAAAAAAATACATTTAT
63 TTTATTA--TTTTACTTAAAAGAAAGAG-TTTAGGAGCCAATGA-GGCT-AAAAAA-ACA-TTA-
3364258 GTAATTAATGTATATTGATAAGTATAT
120 -TAATTAATGTA-ATT-A-AAGTATAT
3364285 ATAATATATA
Statistics
Matches: 147, Mismatches: 0, Indels: 10
0.94 0.00 0.06
Matches are distributed among these distances:
152 42 0.29
154 19 0.13
155 8 0.05
157 19 0.13
158 15 0.10
159 4 0.03
160 6 0.04
161 26 0.18
162 8 0.05
ACGTcount: A:0.46, C:0.05, G:0.14, T:0.35
Consensus pattern (147 bp):
TTTAATTTACGAAGATGAGATAAAAAGATATCAAAATATAAATTTTGAGAGCAAAATAAAATTTT
ATTATTTTACTTAAAAGAAAGAGTTTAGGAGCCAATGAGGCTAAAAAAACATTATAATTAATGTA
ATTAAAGTATATTAAAA
Found at i:3364677 original size:24 final size:25
Alignment explanation
Indices: 3364650--3364703 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
3364640 AAAATTTATA
*
3364650 TATATATA-ATATTTTAAATAC-GAT
1 TATA-ATACATATTTTAAACACGGAT
*
3364674 TATAATACGTATTTTAAACACGGAT
1 TATAATACATATTTTAAACACGGAT
3364699 TATAA
1 TATAA
3364704 AATTAATGCG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 3 0.12
24 15 0.58
25 8 0.31
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (25 bp):
TATAATACATATTTTAAACACGGAT
Found at i:3364872 original size:230 final size:232
Alignment explanation
Indices: 3364467--3364925 Score: 760
Period size: 230 Copynumber: 2.0 Consensus size: 232
3364457 AAAATAATAA
* * * *
3364467 TATAAAATTAATGTGATATAAAATTTAAAGTTATTTGAATAATGCTAATTAAAATTGAGAATTTA
1 TATAAAATTAATGCGATACAAAATTTAAAATTATTTGAATAACGCTAATTAAAATTGAGAATTTA
* * *
3364532 AGATATGATAAAAAAACAATAAATATAATATAATATAAAAAATAATACTAGGACGATATGAATGC
66 AGATATGACAAAAAAACAATAAATATAATATAATATAAAAAATAATACTAAGACGACATGAATGC
3364597 ACAAATGTAACAAAATTTATATTATAAAAATTATTAATATGTCAAAATTTATATATATATAATAT
131 ACAAATGTAACAAAATTTATATTATAAAAATTATTAATATGTCAAAATTTATATATATATAATAT
*
3364662 TTTAAATACGATTATAATACGTATTTTAAACACGGAT
196 TTTAAATACGATTATAATACATATTTTAAACACGGAT
3364699 TATAAAATTAATGCGATACAAAATTTAAAATTATTTGAATAACGCTAATTAAAATTGAGAATTTA
1 TATAAAATTAATGCGATACAAAATTTAAAATTATTTGAATAACGCTAATTAAAATTGAGAATTTA
* * *
3364764 ATATATGACACAAAAA-AAT-AATATAATATAATATGAAAAATAATACTAAGACGACATGAATGC
66 AGATATGACAAAAAAACAATAAATATAATATAATATAAAAAATAATACTAAGACGACATGAATGC
* * * *
3364827 ATACATGTAACAAAATTTATATTATAAATATTATTGATATGTCAAAATTTATATATATATAATAT
131 ACAAATGTAACAAAATTTATATTATAAAAATTATTAATATGTCAAAATTTATATATATATAATAT
*
3364892 TTTAAATACGATTATAATATATATTTTAAACACG
196 TTTAAATACGATTATAATACATATTTTAAACACG
3364926 AATTTTTTTC
Statistics
Matches: 211, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
230 134 0.64
231 3 0.01
232 74 0.35
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (232 bp):
TATAAAATTAATGCGATACAAAATTTAAAATTATTTGAATAACGCTAATTAAAATTGAGAATTTA
AGATATGACAAAAAAACAATAAATATAATATAATATAAAAAATAATACTAAGACGACATGAATGC
ACAAATGTAACAAAATTTATATTATAAAAATTATTAATATGTCAAAATTTATATATATATAATAT
TTTAAATACGATTATAATACATATTTTAAACACGGAT
Found at i:3364907 original size:24 final size:24
Alignment explanation
Indices: 3364878--3364926 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
3364868 TCAAAATTTA
*
3364878 TATATATATAATATTTTAAATACGAT
1 TATA-ATAT-ATATTTTAAACACGAT
3364904 TATAATATATATTTTAAACACGA
1 TATAATATATATTTTAAACACGA
3364927 ATTTTTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.64
25 4 0.18
26 4 0.18
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (24 bp):
TATAATATATATTTTAAACACGAT
Found at i:3365229 original size:18 final size:18
Alignment explanation
Indices: 3365185--3365234 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
3365175 AAGAGATAAG
*
3365185 ATATAAAATTTATATGTT
1 ATATAAAATTTATATCTT
* *
3365203 ATTTTAAATTTA-ATCTT
1 ATATAAAATTTATATCTT
3365220 AATATAAAA-TTATAT
1 -ATATAAAATTTATAT
3365235 GAATAAAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (18 bp):
ATATAAAATTTATATCTT
Found at i:3365648 original size:16 final size:15
Alignment explanation
Indices: 3365619--3365649 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
3365609 AATTTTTAGT
3365619 AATTTAATTTAGTTA
1 AATTTAATTTAGTTA
3365634 AATTTAATGTTAGTTA
1 AATTTAAT-TTAGTTA
3365650 TTATTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.52
Consensus pattern (15 bp):
AATTTAATTTAGTTA
Found at i:3366624 original size:20 final size:20
Alignment explanation
Indices: 3366601--3366644 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3366591 TATAATATAA
*
3366601 TTAAAAATT-AAGTTTAAATT
1 TTAAAAATTAAAG-TTAAAGT
*
3366621 TTAAATATTAAAGTTAAAGT
1 TTAAAAATTAAAGTTAAAGT
3366641 TTAA
1 TTAA
3366645 TTTATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (20 bp):
TTAAAAATTAAAGTTAAAGT
Found at i:3367427 original size:28 final size:25
Alignment explanation
Indices: 3367369--3367430 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
3367359 AATCAGTTAG
*
3367369 ATTAAATAATTTTTTAAAATAAAAT
1 ATTAAATAATTTTTTAAAAAAAAAT
* *
3367394 AATAAATATTTTTTTAAAAAAATTTAAT
1 ATTAAATAATTTTTTAAAAAAA---AAT
3367422 ATTAAATAA
1 ATTAAATAA
3367431 ATATTATATA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 19 0.66
28 10 0.34
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
ATTAAATAATTTTTTAAAAAAAAAT
Found at i:3368902 original size:9 final size:8
Alignment explanation
Indices: 3368870--3368899 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
3368860 AATAAATTAA
3368870 TTTATATTT
1 TTTA-ATTT
3368879 TTTAATTT
1 TTTAATTT
3368887 TTTAATTT
1 TTTAATTT
3368895 TTTAA
1 TTTAA
3368900 ATTAAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 17 0.81
9 4 0.19
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTAATTT
Found at i:3371946 original size:11 final size:11
Alignment explanation
Indices: 3371909--3371946 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
3371899 TTTACAATTT
3371909 TGAATATAACA
1 TGAATATAACA
3371920 T-AATATACATCA
1 TGAATATA-A-CA
3371932 TGAATATAACA
1 TGAATATAACA
3371943 TGAA
1 TGAA
3371947 AAAACAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
10 6 0.25
11 8 0.33
12 4 0.17
13 6 0.25
ACGTcount: A:0.53, C:0.11, G:0.08, T:0.29
Consensus pattern (11 bp):
TGAATATAACA
Found at i:3372964 original size:22 final size:22
Alignment explanation
Indices: 3372934--3372998 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 22
3372924 CATCGGCACA
*
3372934 TTAAGAAAATAGAAGCTCTCGT
1 TTAATAAAATAGAAGCTCTCGT
* *
3372956 TTAATAAAAT-GTGAGC-AT-G-
1 TTAATAAAATAG-AAGCTCTCGT
*
3372975 TTAATAAAACAGAAGCTCTCGT
1 TTAATAAAATAGAAGCTCTCGT
3372997 TT
1 TT
3372999 GACAAGGCGT
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
19 12 0.38
20 3 0.09
21 3 0.09
22 14 0.44
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (22 bp):
TTAATAAAATAGAAGCTCTCGT
Found at i:3377002 original size:17 final size:18
Alignment explanation
Indices: 3376982--3377022 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
3376972 ATAAAATCAT
3376982 TAAAAATA-CATAAAAAA
1 TAAAAATATCATAAAAAA
* *
3376999 TAAAAA-ATTATACAAAA
1 TAAAAATATCATAAAAAA
3377016 TAAAAAT
1 TAAAAAT
3377023 TAAATAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (18 bp):
TAAAAATATCATAAAAAA
Found at i:3377020 original size:16 final size:16
Alignment explanation
Indices: 3376995--3377043 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
3376985 AAATACATAA
3376995 AAAATAAAAAATTATAC
1 AAAAT-AAAAATTATAC
* *
3377012 AAAATAAAAATTAAAT
1 AAAATAAAAATTATAC
3377028 AAAATTTAAAAATTAT
1 AAAA--TAAAAATTAT
3377044 CACATGGCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 13 0.48
17 5 0.19
18 9 0.33
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATAAAAATTATAC
Found at i:3377058 original size:24 final size:24
Alignment explanation
Indices: 3377031--3377080 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
3377021 ATTAAATAAA
*
3377031 ATTTAAAAATTATCACATGGCAAT
1 ATTTAAAAATTAACACATGGCAAT
3377055 ATTTAAAAATTAACACATGGCAAT
1 ATTTAAAAATTAACACATGGCAAT
3377079 AT
1 AT
3377081 CATGAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (24 bp):
ATTTAAAAATTAACACATGGCAAT
Found at i:3377136 original size:2 final size:2
Alignment explanation
Indices: 3377126--3377173 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
3377116 TGTGTGTGTC
3377126 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3377167 TA TA TA T
1 TA TA TA T
3377174 TACGATGAGT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3378339 original size:17 final size:17
Alignment explanation
Indices: 3378317--3378350 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3378307 GATGAACCTT
3378317 TAAACTTGAATGGGTAG
1 TAAACTTGAATGGGTAG
3378334 TAAACTTGAATGGGTAG
1 TAAACTTGAATGGGTAG
3378351 CCTGATTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.29
Consensus pattern (17 bp):
TAAACTTGAATGGGTAG
Found at i:3380366 original size:21 final size:21
Alignment explanation
Indices: 3380335--3380400 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 21
3380325 TTGGTAAGTG
* *
3380335 TTTTGATTTTA-TATTTATGT
1 TTTTAATTTTATTATTTATAT
*
3380355 TTTATAATTTTATTTTTTATAT
1 TTT-TAATTTTATTATTTATAT
3380377 TTTTAATTTATTATATATTTATAT
1 TTTTAA-TT-TTAT-TATTTATAT
3380401 ATAACAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
20 3 0.08
21 10 0.27
22 12 0.32
23 4 0.11
24 8 0.22
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (21 bp):
TTTTAATTTTATTATTTATAT
Found at i:3380372 original size:15 final size:15
Alignment explanation
Indices: 3380348--3380396 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
3380338 TGATTTTATA
*
3380348 TTTATGTTTTATAAT
1 TTTATTTTTTATAAT
*
3380363 TTTATTTTTTATATT
1 TTTATTTTTTATAAT
*
3380378 TTTAATTTATTATATAT
1 TTT-ATTTTTTATA-AT
3380395 TT
1 TT
3380397 ATATATAACA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 16 0.57
16 9 0.32
17 3 0.11
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTATTTTTTATAAT
Found at i:3380380 original size:8 final size:8
Alignment explanation
Indices: 3380354--3380400 Score: 53
Period size: 8 Copynumber: 6.0 Consensus size: 8
3380344 TATATTTATG
*
3380354 TTTTATAA
1 TTTTATAT
3380362 TTTTAT-T
1 TTTTATAT
3380369 TTTTATAT
1 TTTTATAT
3380377 TTTTA-AT
1 TTTTATAT
3380384 TTATTATAT
1 TT-TTATAT
*
3380393 ATTTATAT
1 TTTTATAT
3380401 ATAACAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
7 10 0.29
8 21 0.62
9 3 0.09
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (8 bp):
TTTTATAT
Found at i:3383075 original size:4 final size:4
Alignment explanation
Indices: 3383066--3383092 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3383056 TTCATAACTA
3383066 TATC TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TAT
3383093 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.00, T:0.52
Consensus pattern (4 bp):
TATC
Found at i:3383097 original size:2 final size:2
Alignment explanation
Indices: 3383090--3383120 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3383080 TCTATCTATC
*
3383090 TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3383121 GCAGAAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3385138 original size:25 final size:26
Alignment explanation
Indices: 3385110--3385160 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
3385100 TTGAAAGATT
*
3385110 ATTTAATTATAAAAATAAT-TTTTAA
1 ATTTAATAATAAAAATAATATTTTAA
* *
3385135 ATTTTATAATAATAATAATATTTTAA
1 ATTTAATAATAAAAATAATATTTTAA
3385161 TAATATAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
ATTTAATAATAAAAATAATATTTTAA
Found at i:3385149 original size:28 final size:28
Alignment explanation
Indices: 3385113--3385193 Score: 69
Period size: 28 Copynumber: 2.9 Consensus size: 28
3385103 AAAGATTATT
* **
3385113 TAATTATAAAAATAATTTTTAAATTTTA
1 TAATAATAAAAATAATTTTTAAATAATA
*
3385141 TAATAATAATAAT-A-TTTT-AATAATA
1 TAATAATAAAAATAATTTTTAAATAATA
3385166 TAATAAGTAGTAAAATGAATTTTTAAAT
1 TAATAA-TA--AAAAT-AATTTTTAAAT
3385194 CAAGAAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
25 11 0.27
26 6 0.15
27 1 0.02
28 15 0.37
30 1 0.02
31 4 0.10
32 3 0.07
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (28 bp):
TAATAATAAAAATAATTTTTAAATAATA
Found at i:3385157 original size:19 final size:19
Alignment explanation
Indices: 3385135--3385171 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3385125 TAATTTTTAA
3385135 ATTTT-ATAATAATAATAAT
1 ATTTTAATAAT-ATAATAAT
3385154 ATTTTAATAATATAATAA
1 ATTTTAATAATATAATAA
3385172 GTAGTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTTTAATAATATAATAAT
Found at i:3385662 original size:2 final size:2
Alignment explanation
Indices: 3385657--3385684 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3385647 TATATATATA
3385657 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3385685 CAGCAAAAGT
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:3390620 original size:100 final size:101
Alignment explanation
Indices: 3390376--3390620 Score: 286
Period size: 100 Copynumber: 2.5 Consensus size: 101
3390366 GCAAACAAAT
* * * * **
3390376 AAAAAAAAACAAATTTTACTTTGTAATAGGATTAATGAATATAAAATTCAAAAAAAACATGTCTT
1 AAAAAAAAACAAATTTAACTTTGTAATAGGATTAACGAAAAAAAAATAAAAAAAAAACATGTCTT
* * *
3390441 TCAAACAAATTCTGAAGAGAAACAAGAAGAAACCAC
66 TCAAACAAATTATAAAGAAAAACAAGAAGAAACCAC
* *
3390477 AAACAAAAAA-AAAATTAACTTTGCAATAGGATTAAC--AAAAAAAATAAAATAAAAAACATGT-
1 AAA-AAAAAACAAATTTAACTTTGTAATAGGATTAACGAAAAAAAAATAAAA-AAAAAACATGTC
* *
3390538 TATTCAAACAAATTATAAAGAAAAACATGAAGAAA-GA-
64 T-TTCAAACAAATTATAAAGAAAAACAAGAAGAAACCAC
* *
3390575 AAAAAAAAACAAGTTTAAATTTGTAATAGGATTAACGAAAAAAAAA
1 AAAAAAAAACAAATTTAACTTTGTAATAGGATTAACGAAAAAAAAA
3390621 AACATGTTAT
Statistics
Matches: 121, Mismatches: 17, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
97 6 0.05
98 25 0.21
99 11 0.09
100 48 0.40
101 25 0.21
102 6 0.05
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.22
Consensus pattern (101 bp):
AAAAAAAAACAAATTTAACTTTGTAATAGGATTAACGAAAAAAAAATAAAAAAAAAACATGTCTT
TCAAACAAATTATAAAGAAAAACAAGAAGAAACCAC
Found at i:3391399 original size:24 final size:24
Alignment explanation
Indices: 3391372--3391432 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 24
3391362 TTCATCTTAT
3391372 TTTTAATTATATAATA-TATATTAA
1 TTTTAATTATATAATATTATA-TAA
3391396 TTTTATATT-TAT-ATATTATATAA
1 TTTTA-ATTATATAATATTATATAA
* *
3391419 TTTTTATCATATAA
1 TTTTAATTATATAA
3391433 AAATAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
22 2 0.06
23 13 0.42
24 13 0.42
25 3 0.10
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTAATTATATAATATTATATAA
Found at i:3392190 original size:19 final size:20
Alignment explanation
Indices: 3392148--3392190 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
3392138 TTAGATCAAG
*
3392148 TTTATTAAAATTATTATTTA
1 TTTAATAAAATTATTATTTA
*
3392168 -TTAATAAAA-TATTTTTTA
1 TTTAATAAAATTATTATTTA
3392186 TTTAA
1 TTTAA
3392191 ATTTAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTAATAAAATTATTATTTA
Found at i:3392435 original size:25 final size:25
Alignment explanation
Indices: 3392405--3392458 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
3392395 GTAAAAAACT
3392405 TTAAAATGTACATTATGATATGATA
1 TTAAAATGTACATTATGATATGATA
*
3392430 TTAAAATGTACATTATGATATGATT
1 TTAAAATGTACATTATGATATGATA
3392455 TTAA
1 TTAA
3392459 TGAGTGGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.43
Consensus pattern (25 bp):
TTAAAATGTACATTATGATATGATA
Found at i:3394084 original size:23 final size:24
Alignment explanation
Indices: 3394040--3394085 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3394030 AATTAAACAT
*
3394040 TTTTTATTCAATTTCCACACTTAA
1 TTTTGATTCAATTTCCACACTTAA
*
3394064 TTTTGATTCAATTTGCA-ACTTA
1 TTTTGATTCAATTTCCACACTTA
3394086 TCTTTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.28, C:0.17, G:0.04, T:0.50
Consensus pattern (24 bp):
TTTTGATTCAATTTCCACACTTAA
Found at i:3394726 original size:25 final size:25
Alignment explanation
Indices: 3394672--3394733 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
3394662 ATTTTAAAAA
* *
3394672 TATATTTTTATGTTTTATATCGTAT
1 TATATTTTTATATTTTATATCATAT
*
3394697 CATATTTTTATTATTTTATAT-ATAT
1 TATATTTTTA-TATTTTATATCATAT
*
3394722 TATATTTATATA
1 TATATTTTTATA
3394734 ATCGTAATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 2 0.06
25 20 0.65
26 9 0.29
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (25 bp):
TATATTTTTATATTTTATATCATAT
Found at i:3395930 original size:2 final size:2
Alignment explanation
Indices: 3395925--3395962 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3395915 CCCCCCCCCC
3395925 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT -T CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
3395963 AGGTTTCCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3398487 original size:44 final size:44
Alignment explanation
Indices: 3398422--3398518 Score: 167
Period size: 44 Copynumber: 2.2 Consensus size: 44
3398412 TTTTCAATAC
*
3398422 AGCTTTAATCACCTCTCCTGTTTATGGGCCCTAGTTATATCATTA
1 AGCTTTTA-CACCTCTCCTGTTTATGGGCCCTAGTTATATCATTA
*
3398467 TGCTTTTACACCTCTCCTGTTTATGGGCCCTAGTTATATCATTA
1 AGCTTTTACACCTCTCCTGTTTATGGGCCCTAGTTATATCATTA
3398511 AGCTTTTA
1 AGCTTTTA
3398519 ACTACTCCTT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
44 43 0.88
45 6 0.12
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.42
Consensus pattern (44 bp):
AGCTTTTACACCTCTCCTGTTTATGGGCCCTAGTTATATCATTA
Found at i:3414762 original size:4 final size:4
Alignment explanation
Indices: 3414753--3414779 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3414743 ACCGTGATGT
3414753 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
3414780 TGTCAGAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:3415152 original size:20 final size:19
Alignment explanation
Indices: 3415124--3415163 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3415114 TTGTTTAATT
3415124 AAAACAATTTTAAATATTAA
1 AAAACAA-TTTAAATATTAA
* *
3415144 AAAATAATTTCAATATTAA
1 AAAACAATTTAAATATTAA
3415163 A
1 A
3415164 TGGGTAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAACAATTTAAATATTAA
Found at i:3415393 original size:18 final size:18
Alignment explanation
Indices: 3415372--3415410 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
3415362 TTGTATTAAA
*
3415372 TATATTAATAATACATAT
1 TATATTAACAATACATAT
*
3415390 TATATTTACAATACATAT
1 TATATTAACAATACATAT
3415408 TAT
1 TAT
3415411 GTAATCGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (18 bp):
TATATTAACAATACATAT
Found at i:3416699 original size:2 final size:2
Alignment explanation
Indices: 3416694--3416742 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
3416684 CACACACCCC
3416694 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3416736 TA TA TA T
1 TA TA TA T
3416743 TAAACATATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3420081 original size:17 final size:18
Alignment explanation
Indices: 3420061--3420096 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3420051 AAAATCGATT
3420061 ATTTA-TTTAAATTTAAA
1 ATTTATTTTAAATTTAAA
*
3420078 ATTTATTTTATATTTAAA
1 ATTTATTTTAAATTTAAA
3420096 A
1 A
3420097 ATATTAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTATTTTAAATTTAAA
Found at i:3420288 original size:3 final size:3
Alignment explanation
Indices: 3420280--3420323 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
3420270 TGGATTAGAC
3420280 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 TT
3420324 TTAAGGGCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3421000 original size:20 final size:20
Alignment explanation
Indices: 3420961--3421002 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
3420951 ATGTTATAAT
**
3420961 TTTATTTAAAATATTTTATA
1 TTTATTTAAAATATAATATA
*
3420981 TTTATTTAAATTATAATATA
1 TTTATTTAAAATATAATATA
3421001 TT
1 TT
3421003 AATAATTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTATTTAAAATATAATATA
Found at i:3421061 original size:21 final size:21
Alignment explanation
Indices: 3421032--3421072 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3421022 ATTATAAAAT
3421032 ATATCTTTATTATATTATATC
1 ATATCTTTATTATATTATATC
* *
3421053 ATATTTTTATTATTTTATAT
1 ATATCTTTATTATATTATAT
3421073 TATTAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (21 bp):
ATATCTTTATTATATTATATC
Found at i:3426903 original size:29 final size:29
Alignment explanation
Indices: 3426842--3426897 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
3426832 AATTTATAAG
*
3426842 AAATGATAAAAATTTAAATTTTTAATTTC
1 AAATGATAAAAATTTAAATTCTTAATTTC
* *
3426871 AAATGATCAATATTT-AATTCTTAATTT
1 AAATGATAAAAATTTAAATTCTTAATTT
3426898 ATAAATAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (29 bp):
AAATGATAAAAATTTAAATTCTTAATTTC
Found at i:3428343 original size:16 final size:16
Alignment explanation
Indices: 3428309--3428354 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
3428299 TAATGATAAC
3428309 TATTTTTTA-AATTAA
1 TATTTTTTATAATTAA
*
3428324 -ATTTTTTATCATTAA
1 TATTTTTTATAATTAA
*
3428339 TATTTATTATAATTAA
1 TATTTTTTATAATTAA
3428355 AATACAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 8 0.31
15 5 0.19
16 13 0.50
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTTTTTATAATTAA
Found at i:3428774 original size:85 final size:84
Alignment explanation
Indices: 3428618--3428788 Score: 254
Period size: 85 Copynumber: 2.0 Consensus size: 84
3428608 GTTCTTTGTG
* * *
3428618 TTAGTAATATAGTTGTTTATAATAAATTGTTTGTTACTTTGGACTCAAACTCAATGGTTTGCGTA
1 TTAGTAATACAGGTGTTTATAATAAATTGTTTGTTACTTTGGACTCAAACTCAATGGGTTGCGTA
*
3428683 TGGTGAGATTTTGGCAAAT
66 TGGTGAGATTTCGGCAAAT
* * *
3428702 TTAGTAATACAGGTGTTTAATCATAAATTGTTTTTTACTTTGGACTCAAACTCAATGGGTTGGGT
1 TTAGTAATACAGGTGTTT-ATAATAAATTGTTTGTTACTTTGGACTCAAACTCAATGGGTTGCGT
3428767 A-GCGTGAGATTTCGGCAAAT
65 ATG-GTGAGATTTCGGCAAAT
3428787 TT
1 TT
3428789 TCTAAATTCG
Statistics
Matches: 78, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
84 17 0.22
85 61 0.78
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (84 bp):
TTAGTAATACAGGTGTTTATAATAAATTGTTTGTTACTTTGGACTCAAACTCAATGGGTTGCGTA
TGGTGAGATTTCGGCAAAT
Found at i:3428920 original size:18 final size:18
Alignment explanation
Indices: 3428899--3428933 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3428889 TTAATTAGAT
3428899 TAAAAATAATGATTATAA
1 TAAAAATAATGATTATAA
* *
3428917 TAAAATTAATTATTATA
1 TAAAAATAATGATTATA
3428934 TCGATGAAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
TAAAAATAATGATTATAA
Found at i:3429915 original size:13 final size:13
Alignment explanation
Indices: 3429893--3429945 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
3429883 TTATTTTTAA
*
3429893 AATATTTATATTT
1 AATATATATATTT
*
3429906 AATATATATATAT
1 AATATATATATTT
3429919 ACATTATATATATTTT
1 A-A-TATATATA-TTT
*
3429935 AATATAAATAT
1 AATATATATAT
3429946 AAAATACAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
13 13 0.39
14 8 0.24
15 9 0.27
16 3 0.09
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (13 bp):
AATATATATATTT
Found at i:3429969 original size:24 final size:25
Alignment explanation
Indices: 3429931--3429977 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
3429921 ATTATATATA
3429931 TTTTAATATAAATATAAAATACAAT
1 TTTTAATATAAATATAAAATACAAT
* *
3429956 TTTTAA-ATATATATCAAATACA
1 TTTTAATATAAATATAAAATACA
3429978 TTTATTCGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.40
Consensus pattern (25 bp):
TTTTAATATAAATATAAAATACAAT
Found at i:3431364 original size:23 final size:25
Alignment explanation
Indices: 3431312--3431364 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 25
3431302 TTTAAGGGAA
*
3431312 ATTAATTATTTGTTTAAAAAATTAAAG
1 ATTAATTATTTGTTAAAAAAATT--AG
3431339 ATTAATTATTT-TTAAAAAAATT-G
1 ATTAATTATTTGTTAAAAAAATTAG
3431362 ATT
1 ATT
3431365 TTTTTGAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 4 0.16
26 10 0.40
27 11 0.44
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (25 bp):
ATTAATTATTTGTTAAAAAAATTAG
Found at i:3432156 original size:21 final size:21
Alignment explanation
Indices: 3432113--3432172 Score: 84
Period size: 21 Copynumber: 2.8 Consensus size: 21
3432103 ATTTCGATAA
3432113 TATAATAATAAAATTTAATTAT
1 TATAATAATAAAA-TTAATTAT
* *
3432135 TATAATAGTAAAATTGATTAT
1 TATAATAATAAAATTAATTAT
*
3432156 TATAATATTAAAATTAA
1 TATAATAATAAAATTAA
3432173 AATTAATGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 22 0.65
22 12 0.35
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (21 bp):
TATAATAATAAAATTAATTAT
Found at i:3432700 original size:19 final size:20
Alignment explanation
Indices: 3432676--3432713 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3432666 TCCTTTAATT
3432676 ATTTATATATA-AAATATTA
1 ATTTATATATATAAATATTA
*
3432695 ATTTATATTTATAAATATT
1 ATTTATATATATAAATATT
3432714 GATTAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTATATATATAAATATTA
Found at i:3434624 original size:18 final size:20
Alignment explanation
Indices: 3434603--3434648 Score: 69
Period size: 18 Copynumber: 2.4 Consensus size: 20
3434593 AAATTTAATT
*
3434603 ATAAGTATAAATA-TAAAA-
1 ATAAATATAAATATTAAAAC
3434621 ATAAATATAAATATTAAAAC
1 ATAAATATAAATATTAAAAC
3434641 ATAAATAT
1 ATAAATAT
3434649 TAAAAAAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 12 0.48
19 5 0.20
20 8 0.32
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (20 bp):
ATAAATATAAATATTAAAAC
Found at i:3434646 original size:14 final size:14
Alignment explanation
Indices: 3434627--3434653 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3434617 AAAAATAAAT
3434627 ATAAATATTAAAAC
1 ATAAATATTAAAAC
3434641 ATAAATATTAAAA
1 ATAAATATTAAAA
3434654 AAAACTCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAAATATTAAAAC
Found at i:3438692 original size:17 final size:16
Alignment explanation
Indices: 3438670--3438713 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
3438660 TAAAAAATTA
3438670 TTTTAATAAATTAAGAT
1 TTTTAATAAATTAA-AT
3438687 TTTTAA-AAATTTAAAT
1 TTTTAATAAA-TTAAAT
*
3438703 ATTTAATAAAT
1 TTTTAATAAAT
3438714 ATTATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
TTTTAATAAATTAAAT
Found at i:3440565 original size:2 final size:2
Alignment explanation
Indices: 3440558--3440589 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3440548 ATTATGTAGA
3440558 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
3440590 TGCATTCTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3448008 original size:31 final size:29
Alignment explanation
Indices: 3447970--3448032 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
3447960 AATTTACTTG
*
3447970 AAATTAATTC-TAGATAAAAATATATTTTAAA
1 AAATTAATCCATA-ATAAAAA-A-ATTTTAAA
3448001 AAATTAATCCATTAATAAAAAAATTTTAAA
1 AAATTAATCCA-TAATAAAAAAATTTTAAA
3448031 AA
1 AA
3448033 CAAACTTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 10 0.34
31 10 0.34
32 7 0.24
33 2 0.07
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.35
Consensus pattern (29 bp):
AAATTAATCCATAATAAAAAAATTTTAAA
Found at i:3448240 original size:22 final size:21
Alignment explanation
Indices: 3448182--3448240 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
3448172 TTTCGTAAAG
3448182 AAAATAATTTTTAA-ATTAATT
1 AAAA-AATTTTTAATATTAATT
* *
3448203 ATAAAATTTATAAATATTAATAT
1 AAAAAATTT-TTAATATTAAT-T
3448226 AAAAAATTTTTAATA
1 AAAAAATTTTTAATA
3448241 ATTTTATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 5 0.16
21 6 0.19
22 11 0.35
23 9 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAAAAATTTTTAATATTAATT
Found at i:3448424 original size:24 final size:24
Alignment explanation
Indices: 3448397--3448457 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
3448387 TTAAATGATG
*
3448397 TTAACTTATATTATTTTA-ATTTTT
1 TTAACATATA-TATTTTATATTTTT
3448421 TTAACATATATATTTTATATTTATAT
1 TTAACATATATATTTTATATTT-T-T
*
3448447 TTAATATATAT
1 TTAACATATAT
3448458 TTAAATATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 7 0.22
24 13 0.41
25 1 0.03
26 11 0.34
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (24 bp):
TTAACATATATATTTTATATTTTT
Found at i:3448446 original size:17 final size:17
Alignment explanation
Indices: 3448426--3448472 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
3448416 TTTTTTTAAC
* *
3448426 ATATATATTTTATATTT
1 ATATATAATATATATTT
*
3448443 ATATTTAATATATATTT
1 ATATATAATATATATTT
*
3448460 AAATATAA-ATATA
1 ATATATAATATATA
3448473 AAAATATAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATATAATATATATTT
Found at i:3448894 original size:60 final size:59
Alignment explanation
Indices: 3448760--3448872 Score: 163
Period size: 60 Copynumber: 1.9 Consensus size: 59
3448750 GCACTGGTGT
* ** * *
3448760 AATTAAGCATATAGATTATTCATTTCCATTTGTTAGGATAAAGTGTTCCTGCCAAAGTGT
1 AATTAAG-ATATAGATTATTCATTTCCATTTGTTAGGACAAAGTGCCCCTACCAAAGTGG
3448820 AATTAAGCATATAGATTATTCATTTCCATTTGTTAGGACAAAGTGCCCCTACC
1 AATTAAG-ATATAGATTATTCATTTCCATTTGTTAGGACAAAGTGCCCCTACC
3448873 GTGTTGGGGA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (59 bp):
AATTAAGATATAGATTATTCATTTCCATTTGTTAGGACAAAGTGCCCCTACCAAAGTGG
Found at i:3450014 original size:66 final size:67
Alignment explanation
Indices: 3449887--3450073 Score: 313
Period size: 66 Copynumber: 2.8 Consensus size: 67
3449877 AGGTATGTTG
*
3449887 AACTTGAGCCATACCAACTTATACCAAGTCATTTTATCAGCCCTTGACCTGATTCCTAAGCATGC
1 AACTTGAGCCATACCAACTTATACCAAGTCATTTTATCAACCCTTGACCTGATTCCTAAGCATGC
3449952 TA
66 TA
* * *
3449954 AACTTGAGCCATACCAACTTATACCAAG-CATTTTATCAACCTTTGACTTGATTCCTAAGCATGT
1 AACTTGAGCCATACCAACTTATACCAAGTCATTTTATCAACCCTTGACCTGATTCCTAAGCATGC
*
3450018 TG
66 TA
*
3450020 AACTTGAGCCATACCAACTTATACCAAGTCACTTTATCAACCCTTGACCTGATT
1 AACTTGAGCCATACCAACTTATACCAAGTCATTTTATCAACCCTTGACCTGATT
3450074 GAATTCCAAA
Statistics
Matches: 111, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
66 61 0.55
67 50 0.45
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.31
Consensus pattern (67 bp):
AACTTGAGCCATACCAACTTATACCAAGTCATTTTATCAACCCTTGACCTGATTCCTAAGCATGC
TA
Found at i:3456313 original size:18 final size:18
Alignment explanation
Indices: 3456287--3456352 Score: 50
Period size: 18 Copynumber: 3.8 Consensus size: 18
3456277 AATAAAATAT
*
3456287 AAATATATAAATATTTTA
1 AAATTTATAAATATTTTA
*
3456305 AAATTTAT--ATAATTT-
1 AAATTTATAAATATTTTA
* *
3456320 AAA-TTATTAATATATTAA
1 AAATTTATAAATAT-TTTA
3456338 AAATTATATAAATAT
1 AAATT-TATAAATAT
3456353 AAAATATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
14 4 0.11
15 3 0.08
16 9 0.24
17 2 0.05
18 10 0.27
19 1 0.03
20 8 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAATTTATAAATATTTTA
Found at i:3456338 original size:32 final size:33
Alignment explanation
Indices: 3456286--3456348 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
3456276 AAATAAAATA
* *
3456286 TAAATATATAAATATTTTAAAATTTATATAATT
1 TAAATATATAAATATATTAAAAATTATATAATT
*
3456319 TAAAT-TATTAATATATTAAAAATTATATAA
1 TAAATATATAAATATATTAAAAATTATATAA
3456349 ATATAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 22 0.81
33 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (33 bp):
TAAATATATAAATATATTAAAAATTATATAATT
Found at i:3456401 original size:18 final size:17
Alignment explanation
Indices: 3456365--3456414 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
3456355 AATATTTTAA
*
3456365 ATATAAT-TATAATATG
1 ATATAATATATAATACG
3456381 ATATAATATATTAATACG
1 ATATAATATA-TAATACG
3456399 ATATAGATATACTAAT
1 ATATA-ATATA-TAAT
3456415 TATCTGTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 7 0.24
17 2 0.07
18 11 0.38
19 9 0.31
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.40
Consensus pattern (17 bp):
ATATAATATATAATACG
Found at i:3457274 original size:2 final size:2
Alignment explanation
Indices: 3457269--3457298 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3457259 TTCATATTAA
3457269 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
3457299 TTGATGTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3461716 original size:14 final size:14
Alignment explanation
Indices: 3461697--3461725 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3461687 TCATGGAAGA
3461697 CCTCTTTTCTCACC
1 CCTCTTTTCTCACC
3461711 CCTCTTTTCTCACC
1 CCTCTTTTCTCACC
3461725 C
1 C
3461726 TACTTCCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.52, G:0.00, T:0.41
Consensus pattern (14 bp):
CCTCTTTTCTCACC
Found at i:3463077 original size:20 final size:19
Alignment explanation
Indices: 3463048--3463094 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
3463038 TGTGTTATTT
*
3463048 TTTATTTAAAATATTATAAA
1 TTTATATAAAATATTAT-AA
* *
3463068 TTTATATAAATTTTTATAA
1 TTTATATAAAATATTATAA
3463087 TTTA-ATAA
1 TTTATATAA
3463095 TTAATTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 4 0.17
19 6 0.25
20 14 0.58
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTATATAAAATATTATAA
Found at i:3463405 original size:11 final size:10
Alignment explanation
Indices: 3463387--3463420 Score: 52
Period size: 11 Copynumber: 3.4 Consensus size: 10
3463377 CTGACACGTA
3463387 ATATATTTAT
1 ATATATTTAT
3463397 ATCATATTTAT
1 AT-ATATTTAT
3463408 ATAT-TTTAT
1 ATATATTTAT
3463417 ATAT
1 ATAT
3463421 TAAATATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.39
10 4 0.17
11 10 0.43
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (10 bp):
ATATATTTAT
Found at i:3466198 original size:71 final size:71
Alignment explanation
Indices: 3466082--3466227 Score: 283
Period size: 71 Copynumber: 2.1 Consensus size: 71
3466072 CTTGTTTTTG
3466082 TTAACGTGACATTTAATTTTTAATATTTTTTATTGATATTTATATTTATATAATTTAATTATTAA
1 TTAACGTGACATTTAATTTTTAATATTTTTTATTGATATTTATATTTATATAATTTAATTATTAA
3466147 AAAATA
66 AAAATA
*
3466153 TTAACGTGATATTTAATTTTTAATATTTTTTATTGATATTTATATTTATATAATTTAATTATTAA
1 TTAACGTGACATTTAATTTTTAATATTTTTTATTGATATTTATATTTATATAATTTAATTATTAA
3466218 AAAATA
66 AAAATA
3466224 TTAA
1 TTAA
3466228 TATGACATAA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 74 1.00
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (71 bp):
TTAACGTGACATTTAATTTTTAATATTTTTTATTGATATTTATATTTATATAATTTAATTATTAA
AAAATA
Found at i:3466230 original size:27 final size:28
Alignment explanation
Indices: 3466194--3466248 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
3466184 ATTGATATTT
* **
3466194 ATATTTATATAATTTAATTAT-TAAAAA
1 ATATTAATATAACATAATTATATAAAAA
*
3466221 ATATTAATATGACATAATTATATAAAAA
1 ATATTAATATAACATAATTATATAAAAA
3466249 TTAAATATCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (28 bp):
ATATTAATATAACATAATTATATAAAAA
Found at i:3466263 original size:26 final size:27
Alignment explanation
Indices: 3466208--3466263 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 27
3466198 TTATATAATT
* *
3466208 TAATTATTAAAAAATATTAATATGACA
1 TAATTATTAAAAAATATAAATATCACA
*
3466235 TAATTA-TATAAAAAT-TAAATATCATA
1 TAATTATTA-AAAAATATAAATATCACA
3466261 TAA
1 TAA
3466264 ATAAAAGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
26 13 0.52
27 12 0.48
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (27 bp):
TAATTATTAAAAAATATAAATATCACA
Found at i:3467069 original size:15 final size:15
Alignment explanation
Indices: 3467049--3467078 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3467039 AAAAAAAATG
3467049 AAAAATAAATTATAT
1 AAAAATAAATTATAT
3467064 AAAAATAAATTATAT
1 AAAAATAAATTATAT
3467079 TGTCAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAAATAAATTATAT
Found at i:3467561 original size:18 final size:18
Alignment explanation
Indices: 3467538--3467576 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
3467528 ATTTAATTTG
3467538 TTAATAATAAAATTTTAA
1 TTAATAATAAAATTTTAA
3467556 TTAATAATAAAATTTTAA
1 TTAATAATAAAATTTTAA
3467574 TTA
1 TTA
3467577 TTTAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAATAATAAAATTTTAA
Found at i:3468091 original size:2 final size:2
Alignment explanation
Indices: 3468078--3468109 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3468068 CATCTTTTAT
*
3468078 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3468110 AACCCTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3468934 original size:3 final size:3
Alignment explanation
Indices: 3468928--3468971 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
3468918 ATTTTCATCG
3468928 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3468972 CATTATAGTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3469552 original size:25 final size:26
Alignment explanation
Indices: 3469507--3469581 Score: 66
Period size: 25 Copynumber: 2.9 Consensus size: 26
3469497 TTTATAAATA
*
3469507 ATTTATATATTTATATCTTAT-TTAT
1 ATTTATATATTTATATATTATATTAT
*
3469532 ATTTATA-ATTTTTTATATTATAATTAT
1 ATTTATATA-TTTATATATTAT-ATTAT
* *
3469559 ATTAAAATA-TTATATATTTATAT
1 ATTTATATATTTATATA-TTATAT
3469582 AAAATTTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
24 1 0.03
25 17 0.43
26 8 0.20
27 13 0.32
28 1 0.03
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTATATATTTATATATTATATTAT
Found at i:3469554 original size:15 final size:16
Alignment explanation
Indices: 3469512--3469556 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
3469502 AAATAATTTA
3469512 TATATTTAT-ATCTTATT
1 TATATTTATAAT-TT-TT
3469529 TATATTTATAATTTTT
1 TATATTTATAATTTTT
3469545 TATA-TTATAATT
1 TATATTTATAATT
3469557 ATATTAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.30
16 6 0.22
17 11 0.41
18 2 0.07
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
TATATTTATAATTTTT
Found at i:3469570 original size:19 final size:20
Alignment explanation
Indices: 3469546--3469586 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
3469536 ATAATTTTTT
3469546 ATATTATA-A-TTATATTAAA
1 ATATTATATATTTATA-TAAA
3469565 ATATTATATATTTATATAAA
1 ATATTATATATTTATATAAA
3469585 AT
1 AT
3469587 TTAAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.40
20 7 0.35
21 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTATATATTTATATAAA
Found at i:3469579 original size:27 final size:26
Alignment explanation
Indices: 3469513--3469613 Score: 75
Period size: 27 Copynumber: 3.8 Consensus size: 26
3469503 AATAATTTAT
*
3469513 ATATT-TATATCTTAT-TTATATTTATA
1 ATATTATATAT-TTATATTATA-TTAAA
* *
3469539 ATTTTTTATA-TTATAATTATATTAAA
1 ATATTATATATTTAT-ATTATATTAAA
* *
3469565 ATATTATATATTTATATAAAATTTAAA
1 ATATTATATATTTATATTATA-TTAAA
*
3469592 ATA-TAAATAATTTATATTATAT
1 ATATTATAT-ATTTATATTATAT
3469614 AAATTTTAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
25 4 0.07
26 25 0.42
27 31 0.52
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (26 bp):
ATATTATATATTTATATTATATTAAA
Found at i:3469579 original size:32 final size:30
Alignment explanation
Indices: 3469543--3469638 Score: 83
Period size: 27 Copynumber: 3.1 Consensus size: 30
3469533 TTTATAATTT
3469543 TTTATATTATAATTATATTAAAATATTATATA
1 TTTATATTATAA-TAT-TTAAAATATTATATA
*
3469575 TTTATA-TA-AA-ATTTAAAATA-TAAATAA
1 TTTATATTATAATATTTAAAATATTATAT-A
* *
3469602 TTTATATTATATAAATTTTAAATTATTTATATA
1 TTTATATTATA-ATA-TTTAAAATA-TTATATA
3469635 TTTA
1 TTTA
3469639 AATCATATTT
Statistics
Matches: 53, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
26 4 0.08
27 15 0.28
28 4 0.08
29 1 0.02
30 3 0.06
31 3 0.06
32 14 0.26
33 5 0.09
34 4 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
TTTATATTATAATATTTAAAATATTATATA
Found at i:3469612 original size:16 final size:16
Alignment explanation
Indices: 3469551--3469612 Score: 51
Period size: 16 Copynumber: 3.9 Consensus size: 16
3469541 TTTTTATATT
3469551 ATAA-TTATATTA-AA
1 ATAATTTATATTATAA
3469565 AT-ATTATATATTTATATA
1 ATAATT-TATA-TTATA-A
* *
3469583 A-AATTTAAAATATAA
1 ATAATTTATATTATAA
3469598 ATAATTTATATTATA
1 ATAATTTATATTATA
3469613 TAAATTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
13 1 0.03
14 3 0.08
15 6 0.16
16 18 0.49
17 4 0.11
18 5 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAATTTATATTATAA
Found at i:3469655 original size:17 final size:16
Alignment explanation
Indices: 3469602--3469667 Score: 50
Period size: 16 Copynumber: 4.2 Consensus size: 16
3469592 ATATAAATAA
* * *
3469602 TTTATATTATATAAAT
1 TTTAAATTATTTATAT
3469618 TTTAAATTATTTATAT
1 TTTAAATTATTTATAT
3469634 ATTTAAATCATATTT-TAT
1 -TTTAAAT--TATTTATAT
3469652 TTT-AA-TATTT-TAT
1 TTTAAATTATTTATAT
3469665 TTT
1 TTT
3469668 GTGTTTATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
13 11 0.25
16 15 0.34
17 10 0.23
18 3 0.07
19 5 0.11
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTAAATTATTTATAT
Found at i:3469659 original size:13 final size:13
Alignment explanation
Indices: 3469643--3469667 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3469633 TATTTAAATC
3469643 ATATTTTATTTTA
1 ATATTTTATTTTA
3469656 ATATTTTATTTT
1 ATATTTTATTTT
3469668 GTGTTTATAA
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
ATATTTTATTTTA
Found at i:3475477 original size:79 final size:78
Alignment explanation
Indices: 3475339--3476006 Score: 538
Period size: 79 Copynumber: 8.3 Consensus size: 78
3475329 TATTTTGGAG
* * * *
3475339 ATAAAAAC-GGGTTGGAGTATCCCCT-G-AAATAATGGGGTTGGAGTATTCTCGATGGTGAAAAA
1 ATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAA-CGGGTTGGAGTATCCCCGATGGTGAAAAA
* * *
3475401 TCGACGTGTTAAAA
65 TCGATGTTTTAGAA
*
3475415 ATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACGGTGTTGGAGTATCCCCTATGGTGAAAAA
1 ATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACGG-GTTGGAGTATCCCCGATGGTGAAAAA
*
3475480 TTGATGTTTTAGAA
65 TCGATGTTTTAGAA
** * *
3475494 ATAAAATCGGGGTTGGAGTATCCTCTCAAAAATTTAAAAATAACGGGGTTAGAGTATCTCCGATG
1 ATAAAATCGGGGTTGGAGTATCC-C-C------TCGAAAATAAC-GGGTTGGAGTATCCCCGATG
* *
3475559 GTGAAAAATCGGTATTTTAGAA
57 GTGAAAAATCGATGTTTTAGAA
* ** * *
3475581 ATAAAACCGGGGTTGGAGTATCCTTTTGAAAATAACAGGGTTGGAGTATCCCCGATTGTGAAAAA
1 ATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAAC-GGGTTGGAGTATCCCCGATGGTGAAAAA
3475646 TCGATGTTTGTA-AA
65 TCGATGTTT-TAGAA
* * * * * *
3475660 ATAAAACCGGGATTAGAGTATCCCCTAGAAAATTGAAAAATAACGGGGCTGGAGTATCCCTGATG
1 ATAAAATCGGGGTTGGAGTATCCCC-------TCG-AAAATAAC-GGGTTGGAGTATCCCCGATG
*
3475725 GTGAAAAATCGATATTTTAGAA
57 GTGAAAAATCGATGTTTTAGAA
* * * * * * * **
3475747 ATAAAATCAGGGTTTGAGTATCCCCTCAAAAATAATGAGGTTAGAGTATCTCTGATTATGAAAAA
1 ATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACG-GGTTGGAGTATCCCCGATGGTGAAAAA
* *
3475812 TTGATGTTTTGGAA
65 TCGATGTTTTAGAA
* * * ** * * *
3475826 GTAAAACCGGAGTTAAAGTATCCCTTCGAAAATAGCGAGGTTGAAGTATCCCCGATGGTGAAAAA
1 ATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACG-GGTTGGAGTATCCCCGATGGTGAAAAA
* *
3475891 TCGATGTTTTGGAT
65 TCGATGTTTTAGAA
* * *** * *
3475905 GTAAAA-CTGAGGTTGGAGTATCCCCTCGAAAATAGTTAGGTTGGAGTATCCCCAATGATGAAAA
1 ATAAAATC-GGGGTTGGAGTATCCCCTCGAAAATA-ACGGGTTGGAGTATCCCCGATGGTGAAAA
*
3475969 ATC-AGTATTTTAGAA
64 ATCGA-TGTTTTAGAA
*
3475984 ATAAAATCGGGGTTTGAGTATCC
1 ATAAAATCGGGGTTGGAGTATCC
3476007 TCGGGATGAA
Statistics
Matches: 478, Mismatches: 86, Indels: 53
0.77 0.14 0.09
Matches are distributed among these distances:
76 7 0.01
77 17 0.04
78 6 0.01
79 306 0.64
80 5 0.01
81 1 0.00
86 5 0.01
87 129 0.27
88 2 0.00
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (78 bp):
ATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACGGGTTGGAGTATCCCCGATGGTGAAAAAT
CGATGTTTTAGAA
Found at i:3475592 original size:87 final size:86
Alignment explanation
Indices: 3475443--3475779 Score: 393
Period size: 87 Copynumber: 4.0 Consensus size: 86
3475433 TATCCCCTCG
* * * * *
3475443 AAAATAACGGTGTTGGAGTATCCCCTATGGTGAAAAATTGATGTTTTAGAAATAAAATCGGGGTT
1 AAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGATATTTTAGAAATAAAACCGGGGTT
*
3475508 GGAGTATCCTCTCAAAAATTTA
66 GGAGTATCCCCT-AAAAATTTA
* * *
3475530 AAAATAACGGGGTTAGAGTATCTCCGATGGTGAAAAATCGGTATTTTAGAAATAAAACCGGGGTT
1 AAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGATATTTTAGAAATAAAACCGGGGTT
*
3475595 GGAGTAT--CCT-----TTTG
66 GGAGTATCCCCTAAAAATTTA
* * * *
3475609 AAAATAACAGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTGTA-AAATAAAACCGGGAT
1 AAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGATATTT-TAGAAATAAAACCGGGGT
* *
3475673 TAGAGTATCCCCTAGAAAATTGA
65 TGGAGTATCCCCTA-AAAATTTA
* * * *
3475696 AAAATAACGGGGCTGGAGTATCCCTGATGGTGAAAAATCGATATTTTAGAAATAAAATCAGGGTT
1 AAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGATATTTTAGAAATAAAACCGGGGTT
*
3475761 TGAGTATCCCCTCAAAAAT
66 GGAGTATCCCCT-AAAAAT
3475780 AATGAGGTTA
Statistics
Matches: 210, Mismatches: 29, Indels: 22
0.80 0.11 0.08
Matches are distributed among these distances:
79 64 0.30
80 2 0.01
81 3 0.01
85 2 0.01
86 2 0.01
87 136 0.65
88 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (86 bp):
AAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGATATTTTAGAAATAAAACCGGGGTT
GGAGTATCCCCTAAAAATTTA
Found at i:3475664 original size:166 final size:166
Alignment explanation
Indices: 3475365--3476006 Score: 602
Period size: 166 Copynumber: 3.9 Consensus size: 166
3475355 GTATCCCCTG
* ** * *
3475365 AAATAATGGGGTTGGAGTAT-TCTCGATGGTGAAAAATCGACGTGTTAAAAATAAAATCGGGGTT
1 AAATAACGGGGTTGGAGTATCTC-CGATGGTGAAAAATCGATATTTTAGAAATAAAATCGGGGTT
* *
3475429 GGAGTATCCCCTCGAAAATAACGGTGTTGGAGTATCCCCTATGGTGAAAAATTGATGTTTTAGAA
65 GGAGTATCCCCTCGAAAATAACGGTGTTGGAGTATCCCCGATGGTGAAAAATCGATGTTTTAGAA
* * * * *
3475494 ATAAAATCGGGGTTGGAGTATCCTCTCA-AAAATTTAA
130 ATAAAACCGGGATTAGAGTATCCCCT-AGAAAATTGAA
* * *
3475531 AAATAACGGGGTTAGAGTATCTCCGATGGTGAAAAATCGGTATTTTAGAAATAAAACCGGGGTTG
1 AAATAACGGGGTTGGAGTATCTCCGATGGTGAAAAATCGATATTTTAGAAATAAAATCGGGGTTG
** * *
3475596 GAGTATCCTTTTGAAAATAACAGG-GTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTGTA-A
66 GAGTATCCCCTCGAAAATAAC-GGTGTTGGAGTATCCCCGATGGTGAAAAATCGATGTTT-TAGA
3475659 AATAAAACCGGGATTAGAGTATCCCCTAGAAAATTGAA
129 AATAAAACCGGGATTAGAGTATCCCCTAGAAAATTGAA
* *
3475697 AAATAACGGGGCTGGAGTATC-CCTGATGGTGAAAAATCGATATTTTAGAAATAAAATCAGGGTT
1 AAATAACGGGGTTGGAGTATCTCC-GATGGTGAAAAATCGATATTTTAGAAATAAAATCGGGGTT
* * * * * * ** * *
3475761 TGAGTATCCCCTCAAAAATAATGAG-GTTAGAGTATCTCTGATTATGAAAAATTGATGTTTTGGA
65 GGAGTATCCCCTCGAAAATAACG-GTGTTGGAGTATCCCCGATGGTGAAAAATCGATGTTTTAGA
* * *
3475825 AGTAAAACC-GGAGTTAAAGTAT-CCCT------TCG-A
129 AATAAAACCGGGA-TTAGAGTATCCCCTAGAAAATTGAA
* * * * * * ** *
3475855 AAATAGCGAGGTTGAAGTATCCCCGATGGTGAAAAATCGATGTTTTGGATGTAAAA-CTGAGGTT
1 AAATAACGGGGTTGGAGTATCTCCGATGGTGAAAAATCGATATTTTAGAAATAAAATC-GGGGTT
* * * *
3475919 GGAGTATCCCCTCGAAAAT-A-GTTAGGTTGGAGTATCCCCAATGATGAAAAATC-AGTATTTTA
65 GGAGTATCCCCTCGAAAATAACGGT--GTTGGAGTATCCCCGATGGTGAAAAATCGA-TGTTTTA
* * *
3475981 GAAATAAAATCGGGGTTTGAGTATCC
127 GAAATAAAACCGGGATTAGAGTATCC
3476007 TCGGGATGAA
Statistics
Matches: 395, Mismatches: 65, Indels: 39
0.79 0.13 0.08
Matches are distributed among these distances:
156 1 0.00
157 3 0.01
158 110 0.28
159 7 0.02
165 12 0.03
166 256 0.65
167 6 0.02
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (166 bp):
AAATAACGGGGTTGGAGTATCTCCGATGGTGAAAAATCGATATTTTAGAAATAAAATCGGGGTTG
GAGTATCCCCTCGAAAATAACGGTGTTGGAGTATCCCCGATGGTGAAAAATCGATGTTTTAGAAA
TAAAACCGGGATTAGAGTATCCCCTAGAAAATTGAA
Found at i:3475926 original size:245 final size:244
Alignment explanation
Indices: 3475373--3476006 Score: 611
Period size: 245 Copynumber: 2.6 Consensus size: 244
3475363 TGAAATAATG
* * * * * * * *
3475373 GGGTTGGAGTATTCTCGATGGTGAAAAATCGACGTGTT-AAAAATAAAATCGGGGTTGGAGTATC
1 GGGTTGAAGTATCCCCGATGGTGAAAAATCGATGT-TTGTAAAATAAAACCGGGATTAGAGTATC
* * * *
3475437 CCCTCG-----AAAATAACGGTGTTGGAGTATCCCCTATGGTGAAAAATTGATGTTTTAGAAATA
65 CCCTAGAAAATAAAATAACGGGGTTGGAGTAT-CCCTATGGTGAAAAATCGATATTTTAGAAATA
* * * *
3475497 AAATCGGGGTTGGAGTATCCTCTCAAAAATTTAAAAATAACGGGGTTAGAGTATCTCCGATGGTG
129 AAATCGGGGTTTGAGTATCCCCTCAAAAA-TT--AAAT-A-GAGGTTAGAGTATCTCCGATGATG
* * ** * *
3475562 AAAAATCGGTATTTTAGAAATAAAACCGGGGTTGGAGTATCCTTTTGAAAATAACA
189 AAAAATCGATATTTTAGAAATAAAACCGGAGTTAAAGTATCCCTTCGAAAATAACA
* *
3475618 GGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTGTAAAATAAAACCGGGATTAGAGTATCC
1 GGGTTGAAGTATCCCCGATGGTGAAAAATCGATGTTTGTAAAATAAAACCGGGATTAGAGTATCC
*
3475683 CCTAGAAAATTGAAAAATAACGGGGCTGGAGTATCCCTGATGGTGAAAAATCGATATTTTAGAAA
66 CCTAGAAAA-T--AAAATAACGGGGTTGGAGTATCCCT-ATGGTGAAAAATCGATATTTTAGAAA
* * *
3475748 TAAAATCAGGGTTTGAGTATCCCCTCAAAAA-T-AAT-GAGGTTAGAGTATCTCTGATTATGAAA
127 TAAAATCGGGGTTTGAGTATCCCCTCAAAAATTAAATAGAGGTTAGAGTATCTCCGATGATGAAA
* * * * *
3475810 AATTGATGTTTTGGAAGTAAAACCGGAGTTAAAGTATCCCTTCGAAAATAGC-
192 AATCGATATTTTAGAAATAAAACCGGAGTTAAAGTATCCCTTCGAAAATAACA
* ** * *
3475862 GAGGTTGAAGTATCCCCGATGGTGAAAAATCGATGTTT-TGGATGTAAAACTGAGG-TTGGAGTA
1 G-GGTTGAAGTATCCCCGATGGTGAAAAATCGATGTTTGT-AAAATAAAACCG-GGATTAGAGTA
* * * * *
3475925 TCCCCTCGAAAAT--AGTTA---GGTTGGAGTATCCCCAATGATGAAAAATC-AGTATTTTAGAA
63 TCCCCTAGAAAATAAAATAACGGGGTTGGAGTAT-CCCTATGGTGAAAAATCGA-TATTTTAGAA
3475984 ATAAAATCGGGGTTTGAGTATCC
126 ATAAAATCGGGGTTTGAGTATCC
3476007 TCGGGATGAA
Statistics
Matches: 329, Mismatches: 45, Indels: 38
0.80 0.11 0.09
Matches are distributed among these distances:
236 1 0.00
237 54 0.16
238 3 0.01
240 3 0.01
244 5 0.02
245 182 0.55
246 2 0.01
248 3 0.01
251 1 0.00
252 4 0.01
253 71 0.22
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (244 bp):
GGGTTGAAGTATCCCCGATGGTGAAAAATCGATGTTTGTAAAATAAAACCGGGATTAGAGTATCC
CCTAGAAAATAAAATAACGGGGTTGGAGTATCCCTATGGTGAAAAATCGATATTTTAGAAATAAA
ATCGGGGTTTGAGTATCCCCTCAAAAATTAAATAGAGGTTAGAGTATCTCCGATGATGAAAAATC
GATATTTTAGAAATAAAACCGGAGTTAAAGTATCCCTTCGAAAATAACA
Found at i:3478333 original size:50 final size:50
Alignment explanation
Indices: 3478279--3478413 Score: 164
Period size: 50 Copynumber: 2.7 Consensus size: 50
3478269 AAAAATACCT
* * * *
3478279 GAATGTATTGATACATTGAGAAACGTATCAATACATCTGGGTAAAACCCA
1 GAATGTATCGATACAATGAAAAACGTATCAATACATCTAGGTAAAACCCA
* * *
3478329 GAATGTATCGATATAATGAAAAATGTATCAATACATCTAGGTAAAATCCA
1 GAATGTATCGATACAATGAAAAACGTATCAATACATCTAGGTAAAACCCA
* * *
3478379 GAATGTATC-ATTACAATGAACAATGTATCGATACA
1 GAATGTATCGA-TACAATGAAAAACGTATCAATACA
3478414 AATTGTGAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
49 1 0.01
50 73 0.99
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (50 bp):
GAATGTATCGATACAATGAAAAACGTATCAATACATCTAGGTAAAACCCA
Found at i:3480457 original size:3 final size:3
Alignment explanation
Indices: 3480449--3480475 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3480439 TATATCAACT
3480449 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
3480476 CTATCAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3483589 original size:20 final size:20
Alignment explanation
Indices: 3483564--3483606 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
3483554 TTATACTCAT
*
3483564 TTATTATA-ATTATATTTAAA
1 TTATTATATATT-TATATAAA
3483584 TTATTATATATTTATATAAA
1 TTATTATATATTTATATAAA
3483604 TTA
1 TTA
3483607 ATTTTAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTATTATATATTTATATAAA
Found at i:3483631 original size:15 final size:14
Alignment explanation
Indices: 3483594--3483636 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
3483584 TTATTATATA
*
3483594 TTTATATAAATTAAT
1 TTTATATAAATT-TT
3483609 TTTA-ATAAATTTT
1 TTTATATAAATTTT
3483622 TATTATATAAATTTT
1 T-TTATATAAATTTT
3483637 GAAACTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 2 0.08
14 10 0.40
15 13 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTATATAAATTTT
Found at i:3484742 original size:17 final size:17
Alignment explanation
Indices: 3484705--3484757 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
3484695 AAATATTTCG
*
3484705 AATTAAAT-ATTAATA-
1 AATTAAATAAATAATAT
3484720 AA-TAAATAAATAATAT
1 AATTAAATAAATAATAT
3484736 AATTAAAATAAA-AATAT
1 AATT-AAATAAATAATAT
3484753 AATTA
1 AATTA
3484758 CATCTTTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.15
15 8 0.24
16 3 0.09
17 10 0.30
18 7 0.21
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AATTAAATAAATAATAT
Found at i:3485799 original size:14 final size:13
Alignment explanation
Indices: 3485775--3485824 Score: 75
Period size: 13 Copynumber: 3.8 Consensus size: 13
3485765 TTATTACTTA
3485775 TAAAATTTTTAAT
1 TAAAATTTTTAAT
*
3485788 TAAAATTTTTTAT
1 TAAAATTTTTAAT
3485801 GTAAAATTTTTAAT
1 -TAAAATTTTTAAT
3485815 T-AAATTTTTA
1 TAAAATTTTTA
3485825 TGTGTAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
12 9 0.26
13 13 0.38
14 12 0.35
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (13 bp):
TAAAATTTTTAAT
Found at i:3485805 original size:27 final size:28
Alignment explanation
Indices: 3485775--3485851 Score: 104
Period size: 27 Copynumber: 2.8 Consensus size: 28
3485765 TTATTACTTA
3485775 TAAAATTTTTAATTAAAATTTTT-TATG
1 TAAAATTTTTAATTAAAATTTTTATATG
*
3485802 TAAAATTTTTAATT-AAATTTTTATGTG
1 TAAAATTTTTAATTAAAATTTTTATATG
* *
3485829 TAAAATTTTCAGTTAAACATTTT
1 TAAAATTTTTAATTAAA-ATTTT
3485852 ACAAATATGA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 8 0.18
27 29 0.66
28 2 0.05
29 5 0.11
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (28 bp):
TAAAATTTTTAATTAAAATTTTTATATG
Found at i:3485837 original size:14 final size:13
Alignment explanation
Indices: 3485775--3485837 Score: 60
Period size: 13 Copynumber: 4.7 Consensus size: 13
3485765 TTATTACTTA
3485775 TAAAATTTTTAAT-
1 TAAAATTTTT-ATG
3485788 TAAAATTTTTTATG
1 TAAAA-TTTTTATG
3485802 TAAAATTTTTAAT-
1 TAAAATTTTT-ATG
3485815 T-AAATTTTTATGTG
1 TAAAATTTTTA--TG
3485829 TAAAATTTT
1 TAAAATTTT
3485838 CAGTTAAACA
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
11 1 0.02
12 8 0.19
13 14 0.33
14 13 0.30
15 7 0.16
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (13 bp):
TAAAATTTTTATG
Found at i:3485864 original size:28 final size:28
Alignment explanation
Indices: 3485841--3485904 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
3485831 AAATTTTCAG
3485841 TTAAACATTT-TACAAATATGATTTTAAA
1 TTAAAC-TTTCTACAAATATGATTTTAAA
**
3485869 TTAAACTTTCTACAAATAAAACTTTT-AA
1 TTAAACTTTCTACAAATATGA-TTTTAAA
3485897 TTAAACTT
1 TTAAACTT
3485905 CCATAAGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 3 0.09
28 25 0.78
29 4 0.12
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.42
Consensus pattern (28 bp):
TTAAACTTTCTACAAATATGATTTTAAA
Found at i:3485921 original size:27 final size:27
Alignment explanation
Indices: 3485862--3485932 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
3485852 ACAAATATGA
*
3485862 TTTTAAATTAAACTTTCTACAAATAAAAC
1 TTTT-AATTAAAC-TTCCACAAATAAAAC
* *
3485891 TTTTAATTAAACTTCCATAAGTAAAAC
1 TTTTAATTAAACTTCCACAAATAAAAC
3485918 TTTTAATTAAACTTC
1 TTTTAATTAAACTTC
3485933 TTGCATGTAG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
27 27 0.69
28 8 0.21
29 4 0.10
ACGTcount: A:0.44, C:0.14, G:0.01, T:0.41
Consensus pattern (27 bp):
TTTTAATTAAACTTCCACAAATAAAAC
Found at i:3485998 original size:27 final size:26
Alignment explanation
Indices: 3485918--3486001 Score: 71
Period size: 27 Copynumber: 3.1 Consensus size: 26
3485908 TAAGTAAAAC
*
3485918 TTTTAATTAAACTTCTTGCATGTAGAA-T
1 TTTTAATT-AACTTCTT--ATATAGAATT
* * * *
3485946 CTTTAATTAAATTTTTACATATGAATT
1 TTTTAATTAACTTCTTATATA-GAATT
3485973 TTTTAATTAACCTTCTTATATAGAATT
1 TTTTAATTAA-CTTCTTATATAGAATT
3486000 TT
1 TT
3486002 AATTAAACTT
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
25 3 0.07
26 3 0.07
27 23 0.52
28 15 0.34
ACGTcount: A:0.33, C:0.10, G:0.06, T:0.51
Consensus pattern (26 bp):
TTTTAATTAACTTCTTATATAGAATT
Found at i:3486032 original size:55 final size:53
Alignment explanation
Indices: 3485918--3486041 Score: 137
Period size: 55 Copynumber: 2.3 Consensus size: 53
3485908 TAAGTAAAAC
*
3485918 TTTTAATTAAACTTCTTGCATGTAGAATCTTTAATTAAATTTTTACATATGAATT
1 TTTTAATTAAACTTCTT-CATATAGAATCTTTAATTAAATTTTTACATATGAA-T
* *
3485973 TTTTAATTAACCTTCTT-ATATAGAAT-TTTAATTAAACTTATATATATATATGAGA-
1 TTTTAATTAAACTTCTTCATATAGAATCTTTAATTAAA-TT-T-T-TACATATGA-AT
3486028 TTTTAATTAAACTT
1 TTTTAATTAAACTT
3486042 TATATATATA
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
52 10 0.17
53 10 0.17
54 1 0.02
55 30 0.50
56 8 0.13
57 1 0.02
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (53 bp):
TTTTAATTAAACTTCTTCATATAGAATCTTTAATTAAATTTTTACATATGAAT
Found at i:3486047 original size:25 final size:26
Alignment explanation
Indices: 3485947--3486050 Score: 70
Period size: 27 Copynumber: 3.8 Consensus size: 26
3485937 ATGTAGAATC
* * *
3485947 TTTAATTAAATTTTTACATATGA-ATTT
1 TTTAATTAAACTTATATATATGAGA--T
* *
3485974 TTTAATTAACCTTCT-TATAT-AGAAT
1 TTTAATTAAACTTATATATATGAG-AT
3485999 TTTAATTAAACTTATATATATATATGAGAT
1 TTTAATTAAAC---T-TATATATATGAGAT
3486029 TTTAATTAAACTTTATATATAT
1 TTTAATTAAAC-TTATATATAT
3486051 ATATATAGAA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
25 12 0.19
26 4 0.06
27 22 0.35
28 2 0.03
29 2 0.03
30 18 0.29
31 2 0.03
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (26 bp):
TTTAATTAAACTTATATATATGAGAT
Found at i:3486048 original size:31 final size:29
Alignment explanation
Indices: 3485989--3486054 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 29
3485979 TTAACCTTCT
3485989 TATATA-GAATTTTAATTAAACTTATATA
1 TATATATGAATTTTAATTAAACTTATATA
3486017 TATATATGAGATTTTAATTAAACTTTATATA
1 TATATATGA-ATTTTAATTAAAC-TTATATA
3486048 TATATAT
1 TATATAT
3486055 ATAGAATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
28 6 0.17
29 2 0.06
30 13 0.37
31 14 0.40
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (29 bp):
TATATATGAATTTTAATTAAACTTATATA
Found at i:3488062 original size:15 final size:15
Alignment explanation
Indices: 3488044--3488083 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
3488034 TTTATAATTC
*
3488044 AAAATAATTCAATCT
1 AAAATAATTCAACCT
*
3488059 AAAATAATTTAACCT
1 AAAATAATTCAACCT
3488074 AAAATCAATT
1 AAAAT-AATT
3488084 TGATTCACCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAATAATTCAACCT
Found at i:3488464 original size:27 final size:26
Alignment explanation
Indices: 3488434--3488493 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
3488424 TCCCACTCTC
*
3488434 TTCTTTTTCTAAATCCATCGACAACTT
1 TTCTTTTTCTAAACCCATCGACAA-TT
* *
3488461 TTCTCCTTTCTAAACCCATCTACAATT
1 TTCT-TTTTCTAAACCCATCGACAATT
3488488 TCTCTT
1 T-TCTT
3488494 AAAGAAGGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
27 7 0.26
28 20 0.74
ACGTcount: A:0.23, C:0.30, G:0.02, T:0.45
Consensus pattern (26 bp):
TTCTTTTTCTAAACCCATCGACAATT
Found at i:3490007 original size:17 final size:17
Alignment explanation
Indices: 3489987--3490021 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3489977 ATGCCTTTGG
*
3489987 TATTTTATTTAATTTAA
1 TATTATATTTAATTTAA
*
3490004 TATTATATTTTATTTAA
1 TATTATATTTAATTTAA
3490021 T
1 T
3490022 TTAATGTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTATATTTAATTTAA
Found at i:3490165 original size:30 final size:30
Alignment explanation
Indices: 3490126--3490187 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
3490116 ATGTTTTATC
* *
3490126 TTATTTTTTTATTATTTTTATTTA-TTTAAA
1 TTATATTTTTATT-TTTATATTTATTTTAAA
3490156 TTATATTTTTATTTTTATATTTATTTTAAA
1 TTATATTTTTATTTTTATATTTATTTTAAA
3490186 TT
1 TT
3490188 TTTTTAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 9 0.31
30 20 0.69
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (30 bp):
TTATATTTTTATTTTTATATTTATTTTAAA
Found at i:3490188 original size:25 final size:26
Alignment explanation
Indices: 3490137--3490190 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
3490127 TATTTTTTTA
*
3490137 TTATTTTTATTTATTTAAATTATATTT
1 TTATTTTTA-TTATTTAAATTAAATTT
**
3490164 TTATTTTTA-TATTTATTTTAAATTT
1 TTATTTTTATTATTTAAATTAAATTT
3490189 TT
1 TT
3490191 TTAAAATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 15 0.62
27 9 0.38
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (26 bp):
TTATTTTTATTATTTAAATTAAATTT
Found at i:3490202 original size:39 final size:38
Alignment explanation
Indices: 3490126--3490207 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 38
3490116 ATGTTTTATC
* * *
3490126 TTATTTTTTTATTATTTTTATTTATTTAAATTATATTT
1 TTATTTTTATATTATTTTAATTTATTTAAAATATATTT
*
3490164 TTATTTTTATATTTATTTTAAATTTTTTTAAAAT-TATTT
1 TTATTTTTATA-TTATTTT-AATTTATTTAAAATATATTT
3490203 TTATT
1 TTATT
3490208 ACGAAAATAC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 10 0.26
39 17 0.45
40 11 0.29
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (38 bp):
TTATTTTTATATTATTTTAATTTATTTAAAATATATTT
Found at i:3491015 original size:14 final size:13
Alignment explanation
Indices: 3490998--3491031 Score: 59
Period size: 14 Copynumber: 2.5 Consensus size: 13
3490988 ATAATTAATT
3490998 AAATATAAAAATA
1 AAATATAAAAATA
3491011 CAAATATAAAAATA
1 -AAATATAAAAATA
3491025 AAATATA
1 AAATATA
3491032 TAATCATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATATAAAAATA
Found at i:3491181 original size:23 final size:24
Alignment explanation
Indices: 3491140--3491192 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
3491130 ATTTTTTTAA
*
3491140 ATATTTAATAAAATTAAAAT-ATT
1 ATATATAATAAAATTAAAATAATT
3491163 ATATATAA-AAAATTAAAAATAATT
1 ATATATAATAAAATT-AAAATAATT
*
3491187 AAATAT
1 ATATAT
3491193 TATTTTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 6 0.23
23 12 0.46
24 8 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
ATATATAATAAAATTAAAATAATT
Found at i:3491192 original size:24 final size:22
Alignment explanation
Indices: 3491149--3491192 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
3491139 AATATTTAAT
*
3491149 AAAATTAAAATATTATATATAA
1 AAAATTAAAATATTAAATATAA
3491171 AAAATTAAAAATAATTAAATAT
1 AAAATT-AAAAT-ATTAAATAT
3491193 TATTTTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 5 0.26
24 8 0.42
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAATTAAAATATTAAATATAA
Found at i:3491643 original size:42 final size:37
Alignment explanation
Indices: 3491590--3491668 Score: 104
Period size: 38 Copynumber: 2.0 Consensus size: 37
3491580 TTTAATTACT
*
3491590 TTTTAAAATTTTATTAAATTATTTTTTAAATATAAATATAA
1 TTTTAAAA-TTT-TT-AATTATTATTT-AATATAAATATAA
3491631 TTTTAATAATTTTTAATTATTATTTAATATAAATATAA
1 TTTTAA-AATTTTTAATTATTATTTAATATAAATATAA
3491669 ATATTTGTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
38 13 0.36
39 10 0.28
40 2 0.06
41 9 0.25
42 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (37 bp):
TTTTAAAATTTTTAATTATTATTTAATATAAATATAA
Found at i:3491718 original size:30 final size:30
Alignment explanation
Indices: 3491606--3491718 Score: 88
Period size: 31 Copynumber: 3.7 Consensus size: 30
3491596 AATTTTATTA
* *
3491606 AATTATTTTTTAA-ATATAAATATAATTTT
1 AATTATTTTTTAATAAATAAATATAAATTT
* * * *
3491635 AA-TAATTTTTAATTATTATTTAATATAAATAT
1 AATTATTTTTTAA-TA--AATAAATATAAATTT
* *
3491667 AAATATTTGTTT-ATAATATAAATAGAAATTT
1 AATTATTT-TTTAATAA-ATAAATATAAATTT
3491698 AATTATTTTTTAATAAATAAA
1 AATTATTTTTTAATAAATAAA
3491719 AGTTTAATAA
Statistics
Matches: 64, Mismatches: 12, Indels: 15
0.70 0.13 0.16
Matches are distributed among these distances:
28 9 0.14
29 2 0.03
30 10 0.16
31 21 0.33
32 14 0.22
33 5 0.08
34 3 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (30 bp):
AATTATTTTTTAATAAATAAATATAAATTT
Found at i:3491733 original size:26 final size:26
Alignment explanation
Indices: 3491684--3491733 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
3491674 TGTTTATAAT
* *
3491684 ATAAATAGAAATTTAATTATTTTTTA
1 ATAAATAGAAATTTAATAAATTTTTA
3491710 ATAAATA-AAAGTTTAATAAATTTT
1 ATAAATAGAAA-TTTAATAAATTTT
3491734 AATTATTATT
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):
ATAAATAGAAATTTAATAAATTTTTA
Found at i:3491862 original size:16 final size:16
Alignment explanation
Indices: 3491791--3491866 Score: 59
Period size: 16 Copynumber: 4.8 Consensus size: 16
3491781 ATAAAATATA
*
3491791 AATTTTATTTATTTAT
1 AATTTAATTTATTTAT
* *
3491807 TATTTATATATATTT-T
1 AATTTA-ATTTATTTAT
*
3491823 AATTTAA-TAATTT-T
1 AATTTAATTTATTTAT
* *
3491837 AAAATTAATTTTTTTAT
1 -AATTTAATTTATTTAT
3491854 AATTTAATTTATT
1 AATTTAATTTATT
3491867 ATTACAATTA
Statistics
Matches: 45, Mismatches: 11, Indels: 8
0.70 0.17 0.12
Matches are distributed among these distances:
14 5 0.11
15 7 0.16
16 25 0.56
17 8 0.18
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
AATTTAATTTATTTAT
Found at i:3491911 original size:6 final size:6
Alignment explanation
Indices: 3491900--3491959 Score: 50
Period size: 6 Copynumber: 9.5 Consensus size: 6
3491890 ATATTTCATA
* * *
3491900 TTAATT TTAATT TTATTATT TTAATAT TTAATT TTACTA TT-ATT ATTATTT
1 TTAATT TTAATT TTA--ATT TTAAT-T TTAATT TTAATT TTAATT -TTAATT
3491951 TTAATT TTA
1 TTAATT TTA
3491960 TTAAAATTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
5 1 0.02
6 28 0.65
7 8 0.19
8 6 0.14
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (6 bp):
TTAATT
Found at i:3491953 original size:24 final size:23
Alignment explanation
Indices: 3491898--3491959 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 23
3491888 ATATATTTCA
* *
3491898 TATTAATTTTAATTTTATTATTT
1 TATTATTTTTAATTTTACTATTT
*
3491921 TA--ATATTTAATTTTACTATTAT
1 TATTATTTTTAATTTTACTATT-T
3491943 TATTATTTTTAATTTTA
1 TATTATTTTTAATTTTA
3491960 TTAAAATTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
21 15 0.47
22 3 0.09
23 2 0.06
24 12 0.38
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (23 bp):
TATTATTTTTAATTTTACTATTT
Found at i:3492142 original size:15 final size:17
Alignment explanation
Indices: 3492112--3492148 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
3492102 CCTTTTCTTT
3492112 AATAATTAATTATATAA
1 AATAATTAATTATATAA
3492129 AATAATT-A-TATATAA
1 AATAATTAATTATATAA
*
3492144 CATAA
1 AATAA
3492149 ATAGAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 11 0.58
16 1 0.05
17 7 0.37
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
AATAATTAATTATATAA
Found at i:3496168 original size:6 final size:6
Alignment explanation
Indices: 3496157--3496215 Score: 82
Period size: 6 Copynumber: 9.8 Consensus size: 6
3496147 GCCAAATGTT
* * *
3496157 ATATAC ATATAC ATATAC ATATAC ATATAC ATAAAC ATATAC TTACAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
*
3496205 ATATAA ATATA
1 ATATAC ATATA
3496216 TATTCATTCC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (6 bp):
ATATAC
Found at i:3500650 original size:17 final size:18
Alignment explanation
Indices: 3500628--3500666 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
3500618 TTTTGAGATT
*
3500628 TTAA-TTTAAATTTTTAA
1 TTAATTTTAAATTTTAAA
3500645 TTAATTTTAAATTTTAAA
1 TTAATTTTAAATTTTAAA
3500663 TTAA
1 TTAA
3500667 ATTCGATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAATTTTAAATTTTAAA
Found at i:3502657 original size:21 final size:20
Alignment explanation
Indices: 3502633--3502673 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
3502623 ATTTTTTATT
3502633 TAAATTATTATAAATTGAATA
1 TAAATTATTATAAATT-AATA
* *
3502654 TAAATTTTTATATATTAATA
1 TAAATTATTATAAATTAATA
3502674 ATTCATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
TAAATTATTATAAATTAATA
Found at i:3503026 original size:21 final size:21
Alignment explanation
Indices: 3502971--3503028 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
3502961 CTAAAAAAGG
*
3502971 TTTAAATAAGA-ATTT-TATT
1 TTTAAATAATATATTTATATT
** *
3502990 TTTAAAATTTTTTATTTATATT
1 TTT-AAATAATATATTTATATT
3503012 TTTAAATAATATATTTA
1 TTTAAATAATATATTTA
3503029 AATAGATTGA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
19 3 0.10
20 4 0.14
21 15 0.52
22 7 0.24
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTAAATAATATATTTATATT
Done.