Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 161 of 210
Found at i:48581191 original size:20 final size:20
Alignment explanation
Indices: 48581155--48581202 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
48581145 CATAAATTTT
* * *
48581155 AAATTTTAAATTTTAAATTA
1 AAATTTTAAAATGTAAATCA
*
48581175 AAATTTTAAAATGTAAATCC
1 AAATTTTAAAATGTAAATCA
48581195 AAATTTTA
1 AAATTTTA
48581203 GTTACGAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (20 bp):
AAATTTTAAAATGTAAATCA
Found at i:48582340 original size:27 final size:28
Alignment explanation
Indices: 48582297--48582356 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 28
48582287 TAGTTTACCC
* * *
48582297 TTATTTTAAATATTTTAATAATTAAATT
1 TTATTTAAAATATTTTAAAAACTAAATT
48582325 TTATTTAAAATA-TTTAAAAACTAAATT
1 TTATTTAAAATATTTTAAAAACTAAATT
48582352 TTATT
1 TTATT
48582357 AATTAATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 18 0.62
28 11 0.38
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (28 bp):
TTATTTAAAATATTTTAAAAACTAAATT
Found at i:48585833 original size:24 final size:24
Alignment explanation
Indices: 48585803--48585871 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
48585793 CAAGTGAAAA
48585803 AATAATAATATAGT-ATAACTTTTA-
1 AATAATAATATA-TAATAA-TTTTAG
* *
48585827 AGTAATAATACATAATAATTTTAG
1 AATAATAATATATAATAATTTTAG
* *
48585851 AATAATAATATACAATGATTT
1 AATAATAATATATAATAATTT
48585872 CGAAAATATG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
23 6 0.16
24 31 0.84
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (24 bp):
AATAATAATATATAATAATTTTAG
Found at i:48585975 original size:3 final size:3
Alignment explanation
Indices: 48585967--48586014 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
48585957 ATAGTACATA
*
48585967 AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
48586015 TAAATGGTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:48586477 original size:13 final size:12
Alignment explanation
Indices: 48586456--48586504 Score: 62
Period size: 13 Copynumber: 3.9 Consensus size: 12
48586446 CATTTTTTTC
*
48586456 AAAACGAAAAGAA
1 AAAAAGAAAA-AA
48586469 AAAAAGAAAAAA
1 AAAAAGAAAAAA
*
48586481 ATAAAAGAAAAAT
1 A-AAAAGAAAAAA
48586494 AAAAAGAAAAA
1 AAAAAGAAAAA
48586505 TAGAGAGCCC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
12 13 0.39
13 20 0.61
ACGTcount: A:0.84, C:0.02, G:0.10, T:0.04
Consensus pattern (12 bp):
AAAAAGAAAAAA
Found at i:48586498 original size:12 final size:12
Alignment explanation
Indices: 48586462--48586506 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
48586452 TTTCAAAACG
48586462 AAAAGAAAAA-A
1 AAAAGAAAAATA
*
48586473 AGAA-AAAAAT-
1 AAAAGAAAAATA
48586483 AAAAGAAAAATA
1 AAAAGAAAAATA
48586495 AAAAGAAAAATA
1 AAAAGAAAAATA
48586507 GAGAGCCCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
10 8 0.28
11 9 0.31
12 12 0.41
ACGTcount: A:0.84, C:0.00, G:0.09, T:0.07
Consensus pattern (12 bp):
AAAAGAAAAATA
Found at i:48592250 original size:15 final size:17
Alignment explanation
Indices: 48592232--48592277 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
48592222 AACTTCCTTA
48592232 ACTAACTAACTG-CTT-
1 ACTAACTAACTGACTTG
48592247 ACTAACT-ACTGACTTG
1 ACTAACTAACTGACTTG
*
48592263 AC-AACTAACTAACTT
1 ACTAACTAACTGACTT
48592278 CCTTATAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 4 0.15
15 14 0.52
16 9 0.33
ACGTcount: A:0.37, C:0.26, G:0.07, T:0.30
Consensus pattern (17 bp):
ACTAACTAACTGACTTG
Found at i:48593273 original size:9 final size:9
Alignment explanation
Indices: 48593237--48593283 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 9
48593227 TAGATTTTAT
48593237 TTTTTATTA
1 TTTTTATTA
*
48593246 TTTGT-TT-
1 TTTTTATTA
*
48593253 TGTTTA-TA
1 TTTTTATTA
48593261 TTTTTATTA
1 TTTTTATTA
48593270 TTTTTATTA
1 TTTTTATTA
48593279 TTTTT
1 TTTTT
48593284 GTGAGATGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
7 4 0.13
8 7 0.23
9 20 0.65
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.79
Consensus pattern (9 bp):
TTTTTATTA
Found at i:48596228 original size:8 final size:8
Alignment explanation
Indices: 48596215--48596241 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
48596205 GATTCTTTGT
48596215 TTTTCGGG
1 TTTTCGGG
48596223 TTTTCGGG
1 TTTTCGGG
48596231 TTTTCGGG
1 TTTTCGGG
48596239 TTT
1 TTT
48596242 AGTTTTTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.00, C:0.11, G:0.33, T:0.56
Consensus pattern (8 bp):
TTTTCGGG
Found at i:48598205 original size:8 final size:8
Alignment explanation
Indices: 48598192--48598218 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
48598182 GATTCTTTGT
48598192 TTTTCGGG
1 TTTTCGGG
48598200 TTTTCGGG
1 TTTTCGGG
48598208 TTTTCGGG
1 TTTTCGGG
48598216 TTT
1 TTT
48598219 AGTTTTTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.00, C:0.11, G:0.33, T:0.56
Consensus pattern (8 bp):
TTTTCGGG
Found at i:48600593 original size:12 final size:12
Alignment explanation
Indices: 48600578--48600652 Score: 78
Period size: 12 Copynumber: 6.2 Consensus size: 12
48600568 TATTGGTGGA
48600578 GGTGTTGGAGGT
1 GGTGTTGGAGGT
*
48600590 GGTGTTGGTGGT
1 GGTGTTGGAGGT
* * **
48600602 GGTATAGGAATT
1 GGTGTTGGAGGT
**
48600614 GGAATTGGAGGT
1 GGTGTTGGAGGT
48600626 GGTGTTGGAGGT
1 GGTGTTGGAGGT
*
48600638 GGTGTTGGTGGT
1 GGTGTTGGAGGT
48600650 GGT
1 GGT
48600653 ATAGGAATTG
Statistics
Matches: 50, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 50 1.00
ACGTcount: A:0.12, C:0.00, G:0.53, T:0.35
Consensus pattern (12 bp):
GGTGTTGGAGGT
Found at i:48600640 original size:48 final size:48
Alignment explanation
Indices: 48600564--48600675 Score: 197
Period size: 48 Copynumber: 2.3 Consensus size: 48
48600554 ACCCTGGGAG
* * *
48600564 TTGGTATTGGTGGAGGTGTTGGAGGTGGTGTTGGTGGTGGTATAGGAA
1 TTGGAATTGGAGGTGGTGTTGGAGGTGGTGTTGGTGGTGGTATAGGAA
48600612 TTGGAATTGGAGGTGGTGTTGGAGGTGGTGTTGGTGGTGGTATAGGAA
1 TTGGAATTGGAGGTGGTGTTGGAGGTGGTGTTGGTGGTGGTATAGGAA
48600660 TTGGAATTGGAGGTGG
1 TTGGAATTGGAGGTGG
48600676 AGGTATAGGA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 61 1.00
ACGTcount: A:0.16, C:0.00, G:0.50, T:0.34
Consensus pattern (48 bp):
TTGGAATTGGAGGTGGTGTTGGAGGTGGTGTTGGTGGTGGTATAGGAA
Found at i:48600698 original size:27 final size:27
Alignment explanation
Indices: 48600644--48600698 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
48600634 AGGTGGTGTT
* **
48600644 GGTGGTGGTATAGGAATTGGAATTGGA
1 GGTGGAGGTATAGGAATTGGAAGCGGA
* *
48600671 GGTGGAGGTATAGGAGTTGGAGGCGGA
1 GGTGGAGGTATAGGAATTGGAAGCGGA
48600698 G
1 G
48600699 CTGGCGGTGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.24, C:0.02, G:0.51, T:0.24
Consensus pattern (27 bp):
GGTGGAGGTATAGGAATTGGAAGCGGA
Found at i:48600716 original size:42 final size:42
Alignment explanation
Indices: 48600670--48600782 Score: 163
Period size: 42 Copynumber: 2.7 Consensus size: 42
48600660 TTGGAATTGG
*
48600670 AGGTGGAGGTATAGGAGTTGGAGGCGGAGCTGGCGGTGGAAT
1 AGGTGGAGGTATAGGAGTTGGAGGCGGAGCTGGCGGTGGAAA
*
48600712 AGGTGGAGGCATAGGAGTTGGAGGCGGAGCTGGCGGTGGAAA
1 AGGTGGAGGTATAGGAGTTGGAGGCGGAGCTGGCGGTGGAAA
* ** **
48600754 AAGTGGAGGTCGAGGACATGGAGGCGGAG
1 AGGTGGAGGTATAGGAGTTGGAGGCGGAG
48600783 GTGGAGGAGG
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.24, C:0.09, G:0.52, T:0.15
Consensus pattern (42 bp):
AGGTGGAGGTATAGGAGTTGGAGGCGGAGCTGGCGGTGGAAA
Found at i:48612827 original size:13 final size:14
Alignment explanation
Indices: 48612796--48612828 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
48612786 AATAATTTGA
48612796 AAATATTTTATAATC
1 AAAT-TTTTATAATC
48612811 AAATTTTTATAAT-
1 AAATTTTTATAATC
48612824 AAATT
1 AAATT
48612829 AAATAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 9 0.50
15 4 0.22
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATTTTTATAATC
Found at i:48622800 original size:1 final size:1
Alignment explanation
Indices: 48622789--48622819 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
48622779 TCAACTTTGC
*
48622789 TTTTGTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
48622820 GCAGAGACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:48625202 original size:39 final size:38
Alignment explanation
Indices: 48625130--48625221 Score: 103
Period size: 39 Copynumber: 2.4 Consensus size: 38
48625120 GTAAAGGGAA
* *** *
48625130 AGGGGTGATGGGGAGAGGGAGAGGGTCAGAGTAGGAGG
1 AGGGATGATGGGGAGAGGGAGAAAATCAAAGTAGGAGG
48625168 AGGGATGATAGGGGAGAGGGAGAAAATCAAAGTAGGAGGG
1 AGGGATGAT-GGGGAGAGGGAGAAAATCAAAGTAGGA-GG
* *
48625208 AGAGATGGTGGGGA
1 AGGGATGATGGGGA
48625222 AGAATGAAAG
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
38 8 0.18
39 28 0.62
40 9 0.20
ACGTcount: A:0.33, C:0.02, G:0.54, T:0.11
Consensus pattern (38 bp):
AGGGATGATGGGGAGAGGGAGAAAATCAAAGTAGGAGG
Found at i:48625358 original size:17 final size:16
Alignment explanation
Indices: 48625333--48625374 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
48625323 TCGCCAGTAC
*
48625333 TTCGGCAAACTGTGGAG
1 TTCGCCAAACTG-GGAG
*
48625350 TTCGCCAAAGTGGGAG
1 TTCGCCAAACTGGGAG
48625366 TTCGCCAAA
1 TTCGCCAAA
48625375 AGAGTATTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.21
Consensus pattern (16 bp):
TTCGCCAAACTGGGAG
Found at i:48626652 original size:44 final size:43
Alignment explanation
Indices: 48626587--48626772 Score: 219
Period size: 44 Copynumber: 4.2 Consensus size: 43
48626577 CGAGACAAAT
* *
48626587 TTCTGACAAGTGTGGGCTTGAACATATCTTGTGTTCCTCAGCCA
1 TTCTGATAAGTGT-GGCTTGAACATATCTTGTGTTCCTCAACCA
* * *
48626631 TTTTGATAAGTGTAGGATTGAACATATCTTGTGTTCCTCAACTA
1 TTCTGATAAGTGT-GGCTTGAACATATCTTGTGTTCCTCAACCA
**
48626675 TTCTGATAAGTGTGGTCTTGAACATATCTTGTGTTCCTCAACTG
1 TTCTGATAAGTGTGG-CTTGAACATATCTTGTGTTCCTCAACCA
* * * * *
48626719 TTCTGATAAGTGTGGGTGAGAACATATCTTATGTTCCTCAGCCT
1 TTCTGATAAGTGTGGCT-TGAACATATCTTGTGTTCCTCAACCA
*
48626763 TTCTGGTAAG
1 TTCTGATAAG
48626773 ACAAGTTTGT
Statistics
Matches: 124, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
43 3 0.02
44 121 0.98
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.38
Consensus pattern (43 bp):
TTCTGATAAGTGTGGCTTGAACATATCTTGTGTTCCTCAACCA
Found at i:48626742 original size:88 final size:88
Alignment explanation
Indices: 48626587--48626758 Score: 247
Period size: 88 Copynumber: 2.0 Consensus size: 88
48626577 CGAGACAAAT
* * *
48626587 TTCTGACAAGTGTGGGCTTGAACATATCTTGTGTTCCTCAGCCATTTTGATAAGTGTAGGATTGA
1 TTCTGACAAGTGTGGGCTTGAACATATCTTGTGTTCCTCAACCATTCTGATAAGTGTAGGATAGA
*
48626652 ACATATCTTGTGTTCCTCAACTA
66 ACATATCTTATGTTCCTCAACTA
* * ** *
48626675 TTCTGATAAGTGTGGTCTTGAACATATCTTGTGTTCCTCAACTGTTCTGATAAGTGT-GGGTGAG
1 TTCTGACAAGTGTGGGCTTGAACATATCTTGTGTTCCTCAACCATTCTGATAAGTGTAGGAT-AG
48626739 AACATATCTTATGTTCCTCA
65 AACATATCTTATGTTCCTCA
48626759 GCCTTTCTGG
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
87 3 0.04
88 71 0.96
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.38
Consensus pattern (88 bp):
TTCTGACAAGTGTGGGCTTGAACATATCTTGTGTTCCTCAACCATTCTGATAAGTGTAGGATAGA
ACATATCTTATGTTCCTCAACTA
Found at i:48627452 original size:27 final size:27
Alignment explanation
Indices: 48627414--48627469 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
48627404 ATAATTATAA
48627414 AAATTTTCAAATTTGGTATCGATACCG
1 AAATTTTCAAATTTGGTATCGATACCG
48627441 AAATTTTCAAATTTGGTATCGATACCG
1 AAATTTTCAAATTTGGTATCGATACCG
48627468 AA
1 AA
48627470 TCAATACCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (27 bp):
AAATTTTCAAATTTGGTATCGATACCG
Found at i:48627590 original size:20 final size:21
Alignment explanation
Indices: 48627550--48627591 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
48627540 TAATATATGG
48627550 TATCGATACCTTATTAGAAAA
1 TATCGATACCTTATTAGAAAA
48627571 TATCGATA-CTTAGTTA-AAAA
1 TATCGATACCTTA-TTAGAAAA
48627591 T
1 T
48627592 CAATACAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.36
Consensus pattern (21 bp):
TATCGATACCTTATTAGAAAA
Found at i:48629748 original size:20 final size:19
Alignment explanation
Indices: 48629725--48629766 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
48629715 ATCCTGCCCC
48629725 ATAACCAAATAT-AGACATTA
1 ATAA-CAAATATGAGA-ATTA
*
48629745 ATAACAGATATGAGAATTA
1 ATAACAAATATGAGAATTA
48629764 ATA
1 ATA
48629767 TATCATGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.26
Consensus pattern (19 bp):
ATAACAAATATGAGAATTA
Found at i:48634187 original size:14 final size:14
Alignment explanation
Indices: 48634170--48634199 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
48634160 GCCTCATACA
*
48634170 AACAGTTCGCATAT
1 AACAATTCGCATAT
48634184 AACAATTCGCATAT
1 AACAATTCGCATAT
48634198 AA
1 AA
48634200 ATGGGTTTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (14 bp):
AACAATTCGCATAT
Found at i:48637730 original size:3 final size:3
Alignment explanation
Indices: 48637724--48637749 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
48637714 TTATTATTGT
48637724 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
48637750 TTTATTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:48637757 original size:3 final size:3
Alignment explanation
Indices: 48637751--48637793 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
48637741 ATAATAATAT
48637751 TTA TTA 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 TTA TTA T
48637794 GACGATTTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:48638801 original size:18 final size:18
Alignment explanation
Indices: 48638774--48638810 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
48638764 GTAGGAGTGC
*
48638774 GAAGCTAGTCCTTCGTGA
1 GAAGCAAGTCCTTCGTGA
48638792 GAAGCAAGTCCTTCGTGA
1 GAAGCAAGTCCTTCGTGA
48638810 G
1 G
48638811 GTTTTCACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.24
Consensus pattern (18 bp):
GAAGCAAGTCCTTCGTGA
Found at i:48647643 original size:12 final size:12
Alignment explanation
Indices: 48647626--48647650 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48647616 AAGTTGAGAC
48647626 TATCCCTTCAGA
1 TATCCCTTCAGA
48647638 TATCCCTTCAGA
1 TATCCCTTCAGA
48647650 T
1 T
48647651 TTTGTTGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.32, G:0.08, T:0.36
Consensus pattern (12 bp):
TATCCCTTCAGA
Found at i:48648441 original size:132 final size:132
Alignment explanation
Indices: 48648228--48648790 Score: 841
Period size: 132 Copynumber: 4.3 Consensus size: 132
48648218 GAATAGACCA
*
48648228 TTGAAGATTGCAGATCCTGTCTCCCTAAGCAGTAGCGGAG--CA--G-AGACGGCGAATCTTATC
1 TTGAAGATTGCAGATCCTGTCTCCCTAAGCAGTAGCGGAGTAGATCGAAGACGGCGAATCTTATC
*
48648288 TTCCCAAGATAGTGGAGAAGCAGAATTAAGCCATTAGTCTTATCTCCCTGAGCAGCAGTGGAGTA
66 TTCCCAAGATAGTGGAGAAGCAGAATTAAGCCATTAGTCCTATCTCCCTGAGCAGCAGTGGAGTA
48648353 GG
131 GG
*
48648355 TTGAAGATTGCAGATCATGTCTCCCTAAGCAGTAGCGGAGTAGATCGAAGACGGCGAATCTTATC
1 TTGAAGATTGCAGATCCTGTCTCCCTAAGCAGTAGCGGAGTAGATCGAAGACGGCGAATCTTATC
* * * *
48648420 TTCCCAAGATAGTGGAGAAGCAGATTTAAGACATTAGTCCTATCTCCCCGAGCAGCAGTGGAATA
66 TTCCCAAGATAGTGGAGAAGCAGAATTAAGCCATTAGTCCTATCTCCCTGAGCAGCAGTGGAGTA
48648485 GG
131 GG
48648487 TTGAAGATTGCAGATCCTGTCTCCCTAAGCAGTAGCGGAGTAGATCGAAGACGGCGAATCTTATC
1 TTGAAGATTGCAGATCCTGTCTCCCTAAGCAGTAGCGGAGTAGATCGAAGACGGCGAATCTTATC
48648552 TTCCCAAGATAGTGGAGAAGCAG-ATTAAAGCCATTAGTCCTATCTCCCTGAGCAGCAGTGGAGT
66 TTCCCAAGATAGTGGAGAAGCAGAATT-AAGCCATTAGTCCTATCTCCCTGAGCAGCAGTGGAGT
48648616 AGG
130 AGG
* * * * *
48648619 TTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGCGGAGCAGGTCGAGGACGGCAAATCTTATC
1 TTGAAGATTGCAGATCCTGTCTCCCTAAGCAGTAGCGGAGTAGATCGAAGACGGCGAATCTTATC
* * * * *** **
48648684 TTCCTAAGATAGTAGTGAAGCAGATTTAAGCCACCGGTCCTATCTCCCTGAATAGCAGTGGAGTA
66 TTCCCAAGATAGTGGAGAAGCAGAATTAAGCCATTAGTCCTATCTCCCTGAGCAGCAGTGGAGTA
48648749 GG
131 GG
* * ** *
48648751 TTGAAGAATGTAGATATTGTCTCCCTAAGCAGTAGTGGAG
1 TTGAAGATTGCAGATCCTGTCTCCCTAAGCAGTAGCGGAG
48648791 CAAATCATGG
Statistics
Matches: 399, Mismatches: 30, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
127 39 0.10
129 1 0.00
131 3 0.01
132 354 0.89
133 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.24
Consensus pattern (132 bp):
TTGAAGATTGCAGATCCTGTCTCCCTAAGCAGTAGCGGAGTAGATCGAAGACGGCGAATCTTATC
TTCCCAAGATAGTGGAGAAGCAGAATTAAGCCATTAGTCCTATCTCCCTGAGCAGCAGTGGAGTA
GG
Found at i:48648518 original size:44 final size:44
Alignment explanation
Indices: 48648328--48648650 Score: 111
Period size: 44 Copynumber: 7.3 Consensus size: 44
48648318 CCATTAGTCT
* * *
48648328 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCA
1 TATCTCCCTAAGCAGCAGTGGAATAGGTTGAAGATTGCAGATCC
* * * * * * ** *
48648372 TGTCTCCCTAAGCAGTAGCGGAGTAGATCGAAGACGGC-GAATCT
1 TATCTCCCTAAGCAGCAGTGGAATAGGTTGAAGATTGCAG-ATCC
* *
48648416 TATCTTCCC-AAG-A-TAGTGGAGA-AGCAGATTTAAGACATT--AG-TCC
1 TATC-TCCCTAAGCAGCAGTGGA-ATAG--G-TTGAAG--ATTGCAGATCC
**
48648460 TATCTCCCCGAGCAGCAGTGGAATAGGTTGAAGATTGCAGATCC
1 TATCTCCCTAAGCAGCAGTGGAATAGGTTGAAGATTGCAGATCC
* * * * * * ** *
48648504 TGTCTCCCTAAGCAGTAGCGGAGTAGATCGAAGACGGC-GAATCT
1 TATCTCCCTAAGCAGCAGTGGAATAGGTTGAAGATTGCAG-ATCC
* *
48648548 TATCTTCCC-AAG-A-TAGTGGAGA-AGCAGATTAAAGCCATT--AG-TCC
1 TATC-TCCCTAAGCAGCAGTGGA-ATAG--G-TTGAAG--ATTGCAGATCC
* * *
48648592 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCC
1 TATCTCCCTAAGCAGCAGTGGAATAGGTTGAAGATTGCAGATCC
*
48648636 TGTCTCCCTAAGCAG
1 TATCTCCCTAAGCAG
48648651 TAGCGGAGCA
Statistics
Matches: 200, Mismatches: 47, Indels: 64
0.64 0.15 0.21
Matches are distributed among these distances:
41 6 0.03
42 16 0.08
43 26 0.13
44 113 0.56
45 19 0.09
46 18 0.09
47 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.24
Consensus pattern (44 bp):
TATCTCCCTAAGCAGCAGTGGAATAGGTTGAAGATTGCAGATCC
Found at i:48650403 original size:3 final size:3
Alignment explanation
Indices: 48650390--48650429 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
48650380 ATAATAATAA
*
48650390 TAT TAT CAT TAT TAT TAT TAT TAAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT
48650430 ATTTTTATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:48650418 original size:16 final size:16
Alignment explanation
Indices: 48650397--48650428 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
48650387 TAATATTATC
48650397 ATTATTATTATTATTA
1 ATTATTATTATTATTA
48650413 ATTATTATTATTATTA
1 ATTATTATTATTATTA
48650429 TATTTTTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTATTATTATTATTA
Found at i:48650437 original size:8 final size:8
Alignment explanation
Indices: 48650390--48650437 Score: 53
Period size: 9 Copynumber: 5.8 Consensus size: 8
48650380 ATAATAATAA
48650390 TATTATCAT
1 TATTAT-AT
48650399 TATTATTAT
1 TATTA-TAT
48650408 TATTA-AT
1 TATTATAT
48650415 TATTATTAT
1 TATTA-TAT
48650424 TATTATAT
1 TATTATAT
*
48650432 TTTTAT
1 TATTAT
48650438 GACGATTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
7 7 0.20
8 8 0.23
9 19 0.54
10 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (8 bp):
TATTATAT
Found at i:48651744 original size:10 final size:10
Alignment explanation
Indices: 48651713--48651761 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
48651703 AGAAATTTAT
48651713 TTAAAAATTA
1 TTAAAAATTA
48651723 -TAAAGAATTA
1 TTAAA-AATTA
48651733 TTAAAAATTA
1 TTAAAAATTA
*
48651743 TT-AAATTTA
1 TTAAAAATTA
*
48651752 TTAAGAATTA
1 TTAAAAATTA
48651762 ATGAATATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
9 12 0.36
10 17 0.52
11 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:48651754 original size:9 final size:9
Alignment explanation
Indices: 48651689--48651761 Score: 51
Period size: 10 Copynumber: 7.6 Consensus size: 9
48651679 GTTTTTTTTT
48651689 AATTATTAA
1 AATTATTAA
48651698 AA-TA-TAGA
1 AATTATTA-A
48651706 AATTTATTTAAA
1 AA-TTA-TT-AA
*
48651718 AATTATAAA
1 AATTATTAA
48651727 GAATTATTAAA
1 -AATTATT-AA
48651738 AATTATTAA
1 AATTATTAA
*
48651747 ATTTATTAA
1 AATTATTAA
48651756 GAATTA
1 -AATTA
48651762 ATGAATATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 17
0.71 0.06 0.24
Matches are distributed among these distances:
7 2 0.04
8 5 0.10
9 14 0.27
10 20 0.39
11 5 0.10
12 4 0.08
13 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (9 bp):
AATTATTAA
Found at i:48652332 original size:19 final size:19
Alignment explanation
Indices: 48652308--48652346 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
48652298 GTTGCATTTA
*
48652308 ATAATTTTTAATGATTTTT
1 ATAATTTTTAATAATTTTT
48652327 ATAATTTTTAATAATTTTT
1 ATAATTTTTAATAATTTTT
48652346 A
1 A
48652347 AATAATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
ATAATTTTTAATAATTTTT
Found at i:48652343 original size:29 final size:31
Alignment explanation
Indices: 48652304--48652363 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
48652294 GGACGTTGCA
*
48652304 TTTAATAATTTTT-AATGATTTT-TATAATT
1 TTTAATAATTTTTAAATAATTTTCTATAATT
48652333 TTTAATAATTTTTAAATAATTTTCTATAATT
1 TTTAATAATTTTTAAATAATTTTCTATAATT
48652364 ATTTTAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 13 0.46
30 8 0.29
31 7 0.25
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (31 bp):
TTTAATAATTTTTAAATAATTTTCTATAATT
Found at i:48652363 original size:10 final size:10
Alignment explanation
Indices: 48652304--48652355 Score: 79
Period size: 10 Copynumber: 5.2 Consensus size: 10
48652294 GGACGTTGCA
48652304 TTTAATAATT
1 TTTAATAATT
*
48652314 TTTAATGATT
1 TTTAATAATT
48652324 TTT-ATAATT
1 TTTAATAATT
48652333 TTTAATAATT
1 TTTAATAATT
48652343 TTTAAATAATT
1 TTT-AATAATT
48652354 TT
1 TT
48652356 CTATAATTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
9 8 0.21
10 21 0.55
11 9 0.24
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (10 bp):
TTTAATAATT
Found at i:48663615 original size:2 final size:2
Alignment explanation
Indices: 48663610--48663640 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
48663600 AACTCGTGGC
48663610 TA TA 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 TA TA T
48663641 TTTTCTATTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48670870 original size:14 final size:14
Alignment explanation
Indices: 48670851--48670881 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
48670841 CTTCTTTTTA
48670851 TTATTCAAAAATGC
1 TTATTCAAAAATGC
48670865 TTATTCAAAAATGC
1 TTATTCAAAAATGC
48670879 TTA
1 TTA
48670882 GTTTTAACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (14 bp):
TTATTCAAAAATGC
Found at i:48671763 original size:23 final size:23
Alignment explanation
Indices: 48671737--48671782 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
48671727 AAAGAATTCA
48671737 ATTTATGTTTAGATTTGATTAAG
1 ATTTATGTTTAGATTTGATTAAG
48671760 ATTTATGTTTAGATTTGATTAAG
1 ATTTATGTTTAGATTTGATTAAG
48671783 CATATGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.52
Consensus pattern (23 bp):
ATTTATGTTTAGATTTGATTAAG
Found at i:48674017 original size:33 final size:36
Alignment explanation
Indices: 48673940--48674015 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
48673930 TCTGTAAGAA
* *
48673940 ATTATTAATAATATTTTTAAATTATAATATATTAAT
1 ATTATTAATAATAGTTTTAAACTATAATATATTAAT
*
48673976 ATTATTAATAATAGTTTTAAACTATAATGTATTAAT
1 ATTATTAATAATAGTTTTAAACTATAATATATTAAT
48674012 ATTA
1 ATTA
48674016 ATATTTATAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (36 bp):
ATTATTAATAATAGTTTTAAACTATAATATATTAAT
Found at i:48675171 original size:16 final size:15
Alignment explanation
Indices: 48675122--48675173 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
48675112 AATTACATAT
* *
48675122 ATTTTTTATCTTTTT
1 ATTTTTCATCTTTTA
* *
48675137 ATTTTTCCATCCTTCA
1 ATTTTT-CATCTTTTA
48675153 ATTTTTCATCATTTTA
1 ATTTTTCATC-TTTTA
48675169 ATTTT
1 ATTTT
48675174 CTTTTCACTC
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
15 10 0.34
16 19 0.66
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.65
Consensus pattern (15 bp):
ATTTTTCATCTTTTA
Found at i:48682591 original size:2 final size:2
Alignment explanation
Indices: 48682584--48682623 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
48682574 AACTTTATTT
48682584 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
48682624 TTTGACCTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:48684046 original size:6 final size:6
Alignment explanation
Indices: 48684035--48684076 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
48684025 GTAGGTTAGT
48684035 TGTAAA TGTAAA TGTAAA TGTAAA TGTAAA TGTAAA TGTAAA
1 TGTAAA TGTAAA TGTAAA TGTAAA TGTAAA TGTAAA TGTAAA
48684077 AATAAAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (6 bp):
TGTAAA
Found at i:48684082 original size:18 final size:18
Alignment explanation
Indices: 48684043--48684082 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
48684033 GTTGTAAATG
**
48684043 TAAATGTAAATGTAAATG
1 TAAATGTAAATGTAAAAA
48684061 TAAATGTAAATGTAAAAA
1 TAAATGTAAATGTAAAAA
48684079 TAAA
1 TAAA
48684083 AATAAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.12, T:0.30
Consensus pattern (18 bp):
TAAATGTAAATGTAAAAA
Found at i:48687730 original size:105 final size:105
Alignment explanation
Indices: 48687557--48688230 Score: 751
Period size: 105 Copynumber: 6.4 Consensus size: 105
48687547 GTCAGTTAAT
* * * * * *
48687557 TGTTTAAGAATTGCGATCTTGAATCAGCTAACTCAAAGAAATTTAGGTTGCGATCTTAAATCAAC
1 TGTTTAGGAGTTGCGATATTAAATCAGCTAACTCAAAGAAATTTAGGTTACGATATTAAATCAAC
* * *
48687622 TAACCTTTATAATTCCAACTGTGAACGTAGGTCAGGGAGC
66 TAACCTTTATAATTCCAGCTGTGAATGTAGGTCAGCGAGC
* * * *
48687662 TGTTTAGGAGTTGCAATATTAAATCAGCTAACTCAAAGAAATTTAGGTTATGATCTTAAATCAGC
1 TGTTTAGGAGTTGCGATATTAAATCAGCTAACTCAAAGAAATTTAGGTTACGATATTAAATCAAC
* * *
48687727 TAACCTTTATAATTCCAGCAGTGAATGTAGGTTAGCGAGT
66 TAACCTTTATAATTCCAGCTGTGAATGTAGGTCAGCGAGC
* * * ** * * *
48687767 TGTTTAAGAGTTGCGATATTAAATCAGCTAACTTAACGAAATTTAGGTTGTGATCTTAAATTAGC
1 TGTTTAGGAGTTGCGATATTAAATCAGCTAACTCAAAGAAATTTAGGTTACGATATTAAATCAAC
* * *** *
48687832 TAACTTTTATAATTCCAGTTGTGAAAACAGGTTAGCGAGC
66 TAACCTTTATAATTCCAGCTGTGAATGTAGGTCAGCGAGC
* * * * *
48687872 TGTTTAGAAGTTGCGATCTTAAA-CTAGCTAACTCAAAGAAAATTGGGTTGCGATATTAAATCAA
1 TGTTTAGGAGTTGCGATATTAAATC-AGCTAACTCAAAGAAATTTAGGTTACGATATTAAATCAA
* * * *
48687936 CTAACTTTTATAATTCCAGTTGTGAACGTAGGTCTGCGAGC
65 CTAACCTTTATAATTCCAGCTGTGAATGTAGGTCAGCGAGC
* * * * * *
48687977 TGTTTAGGAGTTGTGATATTAAATTAGCTAACTCAAAGAAATTTAGGCTATGATATTAAATGAAT
1 TGTTTAGGAGTTGCGATATTAAATCAGCTAACTCAAAGAAATTTAGGTTACGATATTAAATCAAC
* * * *
48688042 TAACCTTTATAATTCCAACTGTAAATATAGGTCAGCAAGC
66 TAACCTTTATAATTCCAGCTGTGAATGTAGGTCAGCGAGC
* * * * * **
48688082 TATTTAGGAGTTGTGATCTTAAATCAACTAACTC--TGAAATTTAGGTTACGATATTAAATCAGG
1 TGTTTAGGAGTTGCGATATTAAATCAGCTAACTCAAAGAAATTTAGGTTACGATATTAAATCAAC
* * *
48688145 TAACCTTTATAATTCTAGTTGTGAATGTAGGTCAGTGAGC
66 TAACCTTTATAATTCCAGCTGTGAATGTAGGTCAGCGAGC
* ** *
48688185 TGTTTAGAAGTTATGATCTTAAATCAGCTAACTCAAAGAAATTTAG
1 TGTTTAGGAGTTGCGATATTAAATCAGCTAACTCAAAGAAATTTAG
48688231 ACATGAAAAT
Statistics
Matches: 481, Mismatches: 84, Indels: 8
0.84 0.15 0.01
Matches are distributed among these distances:
103 86 0.18
104 1 0.00
105 394 0.82
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (105 bp):
TGTTTAGGAGTTGCGATATTAAATCAGCTAACTCAAAGAAATTTAGGTTACGATATTAAATCAAC
TAACCTTTATAATTCCAGCTGTGAATGTAGGTCAGCGAGC
Found at i:48692683 original size:43 final size:42
Alignment explanation
Indices: 48692630--48692736 Score: 135
Period size: 43 Copynumber: 2.5 Consensus size: 42
48692620 CTATAGTTAT
* * *
48692630 ATAAACGGCACTAAGTGTGCGGAACTAAAAT-GATGAGGTTGA
1 ATAAAGGGCACTAAGTGTGCGAAACTAAAATGGA-GAGATTGA
* *
48692672 ATAAAAGGGCACTAAGTGTGCGAAATTAAAATGGAGATATTGA
1 AT-AAAGGGCACTAAGTGTGCGAAACTAAAATGGAGAGATTGA
*
48692715 ATAACGGGCACTAAGTGTGCGA
1 ATAAAGGGCACTAAGTGTGCGA
48692737 TACCGGGAGC
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
42 21 0.37
43 34 0.60
44 2 0.04
ACGTcount: A:0.39, C:0.11, G:0.28, T:0.21
Consensus pattern (42 bp):
ATAAAGGGCACTAAGTGTGCGAAACTAAAATGGAGAGATTGA
Found at i:48703739 original size:20 final size:20
Alignment explanation
Indices: 48703689--48703740 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
48703679 CATATTAGTG
*
48703689 CCCCTGTTTGTACTTCAGTA
1 CCCCTATTTGTACTTCAGTA
* *
48703709 CCCC-AGCTTGTACTTCGGTA
1 CCCCTA-TTTGTACTTCAGTA
48703729 CCCCTATTTGTA
1 CCCCTATTTGTA
48703741 ACAGCCCATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.15, C:0.33, G:0.15, T:0.37
Consensus pattern (20 bp):
CCCCTATTTGTACTTCAGTA
Found at i:48705069 original size:25 final size:25
Alignment explanation
Indices: 48705039--48705132 Score: 86
Period size: 25 Copynumber: 3.8 Consensus size: 25
48705029 GTCCCGACCC
48705039 ACAGCTCGTATGAGCATACTGATTT
1 ACAGCTCGTATGAGCATACTGATTT
* *
48705064 ATAGCTCGTGA-GAGCATATTGATCTT
1 ACAGCTCGT-ATGAGCATACTGAT-TT
* * *
48705090 -CAGCTCG-AGTGAGCATACCGGTTC
1 ACAGCTCGTA-TGAGCATACTGATTT
*
48705114 ACAGCTCATATGAGCATAC
1 ACAGCTCGTATGAGCATAC
48705133 ATGTACATAA
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
23 1 0.02
24 1 0.02
25 49 0.89
26 4 0.07
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (25 bp):
ACAGCTCGTATGAGCATACTGATTT
Found at i:48711526 original size:25 final size:25
Alignment explanation
Indices: 48711500--48711591 Score: 100
Period size: 25 Copynumber: 3.7 Consensus size: 25
48711490 CCCGACCCAT
*
48711500 AGCTCGTATGAGCATACCGATTTAT
1 AGCTCGTATGAGCATACCGATTTAC
* *
48711525 AGCTCATGA-GAGCATATCGATCTT-C
1 AGCTCGT-ATGAGCATACCGAT-TTAC
*
48711550 AGCTCG-AGTGAGCATACCGATTCAC
1 AGCTCGTA-TGAGCATACCGATTTAC
48711575 AGCTCGTATGAGCATAC
1 AGCTCGTATGAGCATAC
48711592 ATGTACATAA
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
23 1 0.02
24 1 0.02
25 49 0.89
26 4 0.07
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (25 bp):
AGCTCGTATGAGCATACCGATTTAC
Found at i:48713265 original size:20 final size:20
Alignment explanation
Indices: 48713225--48713309 Score: 125
Period size: 20 Copynumber: 4.2 Consensus size: 20
48713215 TGTTACACTG
48713225 TTTGTACTTCGGTACCCCCTA
1 TTTGTACTTCGGTA-CCCCTA
* *
48713246 TTTGTTCTTCGATACCCCTA
1 TTTGTACTTCGGTACCCCTA
*
48713266 ATTGTACTTCGGTACCCCTA
1 TTTGTACTTCGGTACCCCTA
*
48713286 TTTGTACTTCGGTACCCCTG
1 TTTGTACTTCGGTACCCCTA
48713306 TTTG
1 TTTG
48713310 CACATTCGTG
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
20 45 0.79
21 12 0.21
ACGTcount: A:0.14, C:0.29, G:0.15, T:0.41
Consensus pattern (20 bp):
TTTGTACTTCGGTACCCCTA
Found at i:48722209 original size:14 final size:14
Alignment explanation
Indices: 48722180--48722234 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 14
48722170 AATTTAAAAC
*
48722180 ATATACGAATAAAT
1 ATATACAAATAAAT
* *
48722194 ATTTACAAATATAT
1 ATATACAAATAAAT
*
48722208 ATATACAAATACA-
1 ATATACAAATAAAT
*
48722221 ATATACAAGTAAAT
1 ATATACAAATAAAT
48722235 TTACACATGT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
13 11 0.33
14 22 0.67
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.31
Consensus pattern (14 bp):
ATATACAAATAAAT
Found at i:48722485 original size:43 final size:43
Alignment explanation
Indices: 48722424--48722696 Score: 386
Period size: 43 Copynumber: 6.3 Consensus size: 43
48722414 TTATTTGAAA
* *
48722424 AAACGCCGCTAAAGAACATAATCTTTAGCGGCGCTTTACCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTCCCAC
* **
48722467 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTTTCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTCCCAC
*
48722510 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTCCCAC
* * *
48722553 AAACACCGCTAAAGAACATGATCTTTAGCGACGCTTTTTCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTCCCAC
* *
48722596 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAA
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTCCCAC
* * * * *
48722639 AAACGCCACTAAATG-TCAAGTTCTTTAGCGACGCTTTTCCCAC
1 AAACGCCGCTAAA-GAACATGATCTTTAGCGGCGCTTTTCCCAC
48722682 AAACGCCGCTAAAGA
1 AAACGCCGCTAAAGA
48722697 TCATAAAAAA
Statistics
Matches: 206, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
42 1 0.00
43 204 0.99
44 1 0.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTCCCAC
Found at i:48724162 original size:50 final size:50
Alignment explanation
Indices: 48724085--48724211 Score: 209
Period size: 50 Copynumber: 2.5 Consensus size: 50
48724075 GAAAACCAAC
*
48724085 TCCATAACTCACATTTTGCATAGAAGCAGCCTATCATTCCCTTCTCCAGA
1 TCCATAACTCACATTTTGCATATAAGCAGCCTATCATTCCCTTCTCCAGA
*
48724135 TCCATAACTCACATTTTGCATATAAGCAGCCTATCATTCCCTTCTCCAGT
1 TCCATAACTCACATTTTGCATATAAGCAGCCTATCATTCCCTTCTCCAGA
* **
48724185 TCCATAACTCGCATTACGCATATAAGC
1 TCCATAACTCACATTTTGCATATAAGC
48724212 CTGAATCTAG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 72 1.00
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.31
Consensus pattern (50 bp):
TCCATAACTCACATTTTGCATATAAGCAGCCTATCATTCCCTTCTCCAGA
Found at i:48725026 original size:13 final size:13
Alignment explanation
Indices: 48725008--48725033 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
48724998 GCTGAAGCTT
48725008 TGTAAAATGTAAA
1 TGTAAAATGTAAA
48725021 TGTAAAATGTAAA
1 TGTAAAATGTAAA
48725034 AATTTTATAA
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:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTAAAATGTAAA
Found at i:48726294 original size:26 final size:26
Alignment explanation
Indices: 48726257--48726307 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
48726247 ACTTTATGAT
* * *
48726257 TTCATGCGTGTATAAATATAAACCAC
1 TTCATGCATGTAAAAAGATAAACCAC
48726283 TTCATGCATGTAAAAAGATAAACCA
1 TTCATGCATGTAAAAAGATAAACCA
48726308 AACTTCAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.27
Consensus pattern (26 bp):
TTCATGCATGTAAAAAGATAAACCAC
Found at i:48741266 original size:29 final size:29
Alignment explanation
Indices: 48741229--48741308 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 29
48741219 TCAGAGTCTC
* *
48741229 ACCACAAAGGCATTCTTTTAATAAAGATA
1 ACCACAAAGGCATCCTTTTAACAAAGATA
* * *
48741258 ACCATAAAGGTATCCTTTTAACAGAGATA
1 ACCACAAAGGCATCCTTTTAACAAAGATA
* *
48741287 GCCACAAAGGC-TCCATTTAACA
1 ACCACAAAGGCATCCTTTTAACA
48741309 GAGTTAGCCA
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
28 10 0.24
29 32 0.76
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.25
Consensus pattern (29 bp):
ACCACAAAGGCATCCTTTTAACAAAGATA
Found at i:48741311 original size:28 final size:28
Alignment explanation
Indices: 48741234--48741411 Score: 155
Period size: 28 Copynumber: 6.2 Consensus size: 28
48741224 GTCTCACCAC
* * * *
48741234 AAAGGCATTCTTTTAATAAAGATAACCAT
1 AAAGGC-TTCCTTTAACAGAGATAGCCAT
*
48741263 AAAGG-TATCCTTTTAACAGAGATAGCCAC
1 AAAGGCT-TCC-TTTAACAGAGATAGCCAT
*
48741292 AAAGGC-TCCATTTAACAGAGTTAGCCAT
1 AAAGGCTTCC-TTTAACAGAGATAGCCAT
* * * **
48741320 AAATGCTTCCTTTAACAGAAATCGTTAT
1 AAAGGCTTCCTTTAACAGAGATAGCCAT
* * *
48741348 AAAGGCTTTCTTTTAACAGAAACAGCCAT
1 AAAGGC-TTCCTTTAACAGAGATAGCCAT
48741377 AAAGGCTTCCTTTAACA-AGGATAGCCAT
1 AAAGGCTTCCTTTAACAGA-GATAGCCAT
48741405 AAAGGCT
1 AAAGGCT
48741412 CACATTTAGG
Statistics
Matches: 120, Mismatches: 23, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
27 2 0.02
28 68 0.57
29 50 0.42
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (28 bp):
AAAGGCTTCCTTTAACAGAGATAGCCAT
Found at i:48741320 original size:57 final size:55
Alignment explanation
Indices: 48741259--48741419 Score: 153
Period size: 57 Copynumber: 2.8 Consensus size: 55
48741249 ATAAAGATAA
* ***
48741259 CCATAAAGGTATCCTTTTAACAGAGATAGCCACAAAGGCTCCATTTAACAGAGTTAG
1 CCATAAAGGT-TCC-TTTAACAGAGATAGCCATAAAGGCTCCATTTAACAGAAACAG
* * * ** * *
48741316 CCATAAATGCTTCCTTTAACAGAAATCGTTATAAAGGCTTTCTTTTAACAGAAACAG
1 CCATAAA-GGTTCCTTTAACAGAGATAGCCATAAAGGC-TCCATTTAACAGAAACAG
48741373 CCATAAAGGCTTCCTTTAACA-AGGATAGCCATAAAGGCTCACATTTA
1 CCATAAAGG-TTCCTTTAACAGA-GATAGCCATAAAGGCTC-CATTTA
48741420 GGGAAATTGC
Statistics
Matches: 81, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
56 22 0.27
57 57 0.70
58 2 0.02
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (55 bp):
CCATAAAGGTTCCTTTAACAGAGATAGCCATAAAGGCTCCATTTAACAGAAACAG
Found at i:48743900 original size:9 final size:8
Alignment explanation
Indices: 48743884--48743909 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
48743874 TTTTAATTTC
48743884 TATTTTTT
1 TATTTTTT
48743892 TATTTTTT
1 TATTTTTT
48743900 TATTTTTT
1 TATTTTTT
48743908 TA
1 TA
48743910 GAGTAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (8 bp):
TATTTTTT
Found at i:48753315 original size:145 final size:145
Alignment explanation
Indices: 48753052--48753341 Score: 580
Period size: 145 Copynumber: 2.0 Consensus size: 145
48753042 ATCCCTCGAT
48753052 TATTGTGAGAATCGTAACAGAAGAGAGATTGCTCTTTTTGCAGGTGCCTAAGAAGGTAAATGGCG
1 TATTGTGAGAATCGTAACAGAAGAGAGATTGCTCTTTTTGCAGGTGCCTAAGAAGGTAAATGGCG
48753117 ATGCGGACACTCTAGCCAAGGCCGGTAGTTCTGTTGGTCAAGATATTATTTTGATTCTGTAATCC
66 ATGCGGACACTCTAGCCAAGGCCGGTAGTTCTGTTGGTCAAGATATTATTTTGATTCTGTAATCC
48753182 TTTTTTGTTGTCCGA
131 TTTTTTGTTGTCCGA
48753197 TATTGTGAGAATCGTAACAGAAGAGAGATTGCTCTTTTTGCAGGTGCCTAAGAAGGTAAATGGCG
1 TATTGTGAGAATCGTAACAGAAGAGAGATTGCTCTTTTTGCAGGTGCCTAAGAAGGTAAATGGCG
48753262 ATGCGGACACTCTAGCCAAGGCCGGTAGTTCTGTTGGTCAAGATATTATTTTGATTCTGTAATCC
66 ATGCGGACACTCTAGCCAAGGCCGGTAGTTCTGTTGGTCAAGATATTATTTTGATTCTGTAATCC
48753327 TTTTTTGTTGTCCGA
131 TTTTTTGTTGTCCGA
48753342 AACTCATTGT
Statistics
Matches: 145, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
145 145 1.00
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.34
Consensus pattern (145 bp):
TATTGTGAGAATCGTAACAGAAGAGAGATTGCTCTTTTTGCAGGTGCCTAAGAAGGTAAATGGCG
ATGCGGACACTCTAGCCAAGGCCGGTAGTTCTGTTGGTCAAGATATTATTTTGATTCTGTAATCC
TTTTTTGTTGTCCGA
Found at i:48753402 original size:36 final size:36
Alignment explanation
Indices: 48753355--48753444 Score: 162
Period size: 36 Copynumber: 2.5 Consensus size: 36
48753345 TCATTGTTTT
48753355 GTGCATGAGGGACTGTTTCGCTACTTTGGTAGTTGG
1 GTGCATGAGGGACTGTTTCGCTACTTTGGTAGTTGG
48753391 GTGCATGAGGGACTGTTTCGCTACTTTGGTAGTTGG
1 GTGCATGAGGGACTGTTTCGCTACTTTGGTAGTTGG
* *
48753427 GTGCATGAAGAACTGTTT
1 GTGCATGAGGGACTGTTT
48753445 TACTATTTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.17, C:0.13, G:0.34, T:0.36
Consensus pattern (36 bp):
GTGCATGAGGGACTGTTTCGCTACTTTGGTAGTTGG
Found at i:48757110 original size:19 final size:21
Alignment explanation
Indices: 48757088--48757130 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
48757078 ATAATTTCAA
48757088 AAATA-AC-AATATATTTTTT
1 AAATAGACTAATATATTTTTT
**
48757107 AAATAGACTCCTATATTTTTT
1 AAATAGACTAATATATTTTTT
48757128 AAA
1 AAA
48757131 AACTTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 2 0.10
21 13 0.65
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (21 bp):
AAATAGACTAATATATTTTTT
Found at i:48760359 original size:12 final size:12
Alignment explanation
Indices: 48760342--48760366 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48760332 GGCTATGTTT
48760342 ATTTTTTTTTCA
1 ATTTTTTTTTCA
48760354 ATTTTTTTTTCA
1 ATTTTTTTTTCA
48760366 A
1 A
48760367 AGTTGACAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (12 bp):
ATTTTTTTTTCA
Found at i:48765336 original size:24 final size:24
Alignment explanation
Indices: 48765307--48765359 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
48765297 ATTAGTAAGT
* * *
48765307 TAAATAAACTATGCTAGTAAATGC
1 TAAATAAACTATACTAATAAATAC
* *
48765331 TAAATATATTATACTAATAAATAC
1 TAAATAAACTATACTAATAAATAC
48765355 TAAAT
1 TAAAT
48765360 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (24 bp):
TAAATAAACTATACTAATAAATAC
Found at i:48765562 original size:29 final size:27
Alignment explanation
Indices: 48765530--48765585 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 27
48765520 TATATATATA
*
48765530 TATATATATATATATAACACAGTTTGTGC
1 TATATATAAATATAT-A-ACAGTTTGTGC
48765559 TATATATAAATATATAACAGTTTGTGC
1 TATATATAAATATATAACAGTTTGTGC
48765586 AGGTTTGGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 11 0.42
28 1 0.04
29 14 0.54
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (27 bp):
TATATATAAATATATAACAGTTTGTGC
Found at i:48765564 original size:2 final size:2
Alignment explanation
Indices: 48765511--48765545 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
48765501 AAACAAACTT
48765511 TA TA TA -A 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
48765546 ACACAGTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:48768915 original size:18 final size:18
Alignment explanation
Indices: 48768876--48768917 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
48768866 ATTCCAAATT
*
48768876 TTTTATAATTATTAAGTA
1 TTTTATAATTATTAAGAA
*
48768894 TTTTA-AATTATTTAGAA
1 TTTTATAATTATTAAGAA
48768911 GTTTTAT
1 -TTTTAT
48768918 GTTAACAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (18 bp):
TTTTATAATTATTAAGAA
Found at i:48769369 original size:18 final size:18
Alignment explanation
Indices: 48769330--48769370 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
48769320 TTAATCTTTG
*
48769330 ATTTA-TTATTTTATTTT
1 ATTTATTTATTTTATTGT
48769347 ATTTATTTATTTTAATTGT
1 ATTTATTTATTTT-ATTGT
48769366 -TTTAT
1 ATTTAT
48769371 CTGACTTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 5 0.24
18 12 0.57
19 4 0.19
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (18 bp):
ATTTATTTATTTTATTGT
Found at i:48778179 original size:18 final size:18
Alignment explanation
Indices: 48778152--48778194 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
48778142 GCTCATAAGG
*
48778152 TTATATAATGACATTTAA
1 TTATAGAATGACATTTAA
*
48778170 TTATAGAATGCCATTTAA
1 TTATAGAATGACATTTAA
48778188 TTATAGA
1 TTATAGA
48778195 GTAATTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (18 bp):
TTATAGAATGACATTTAA
Found at i:48778707 original size:16 final size:16
Alignment explanation
Indices: 48778686--48778722 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
48778676 AGTTTTGTAA
48778686 AAGAATTTTACGGTTC
1 AAGAATTTTACGGTTC
48778702 AAGAATTTTACGGTTC
1 AAGAATTTTACGGTTC
48778718 AAGAA
1 AAGAA
48778723 AATTTTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (16 bp):
AAGAATTTTACGGTTC
Found at i:48780863 original size:16 final size:16
Alignment explanation
Indices: 48780842--48780873 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
48780832 ATTATTGAGA
48780842 GGTGTGTTTTCTTTGT
1 GGTGTGTTTTCTTTGT
48780858 GGTGTGTTTTCTTTGT
1 GGTGTGTTTTCTTTGT
48780874 TCGTAGAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.06, G:0.31, T:0.62
Consensus pattern (16 bp):
GGTGTGTTTTCTTTGT
Found at i:48785328 original size:2 final size:2
Alignment explanation
Indices: 48785321--48785367 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
48785311 TAAATAAATA
48785321 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48785363 AT AT A
1 AT AT A
48785368 NNNNNNNNNN
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48788308 original size:7 final size:7
Alignment explanation
Indices: 48788296--48788321 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
48788286 TCTCTTGATA
48788296 AATTATT
1 AATTATT
48788303 AATTATT
1 AATTATT
48788310 AATTATT
1 AATTATT
48788317 AATTA
1 AATTA
48788322 ATCTATAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
AATTATT
Found at i:48788585 original size:21 final size:21
Alignment explanation
Indices: 48788569--48788648 Score: 58
Period size: 21 Copynumber: 3.7 Consensus size: 21
48788559 AGATAATTTT
48788569 TAAATATAATAATATAATTGA
1 TAAATATAATAATATAATTGA
* *
48788590 TAAA-AGT-AT-AGATAATCGTGT
1 TAAATA-TAATAATATAAT--TGA
* *
48788611 TAAGTATAATAATATATATTTA
1 TAAATATAATAATATA-ATTGA
48788633 TAAATATATATAATAT
1 TAAATATA-ATAATAT
48788649 TACTTCACTA
Statistics
Matches: 44, Mismatches: 7, Indels: 14
0.68 0.11 0.22
Matches are distributed among these distances:
19 6 0.14
20 3 0.07
21 11 0.25
22 11 0.25
23 11 0.25
24 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.07, T:0.40
Consensus pattern (21 bp):
TAAATATAATAATATAATTGA
Found at i:48788586 original size:40 final size:41
Alignment explanation
Indices: 48788558--48788636 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 41
48788548 TATCAAGATT
* *
48788558 TAGATAAT-TTTTAAATATAATAATATAATTGATAAAAGTA
1 TAGATAATCTGTTAAATATAATAATATAATTTATAAAAGTA
*
48788598 TAGATAATCGTGTTAAGTATAATAATATATATTTATAAA
1 TAGATAATC-TGTTAAATATAATAATATA-ATTTATAAA
48788637 TATATATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 8 0.24
42 17 0.52
43 8 0.24
ACGTcount: A:0.49, C:0.01, G:0.09, T:0.41
Consensus pattern (41 bp):
TAGATAATCTGTTAAATATAATAATATAATTTATAAAAGTA
Found at i:48789323 original size:16 final size:17
Alignment explanation
Indices: 48789297--48789331 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
48789287 TACGTACTTC
48789297 ATAATTATATTAATAAT
1 ATAATTATATTAATAAT
*
48789314 ATAA-TATATTTATAAT
1 ATAATTATATTAATAAT
48789330 AT
1 AT
48789332 TTCAAGTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATAATTATATTAATAAT
Found at i:48789872 original size:22 final size:22
Alignment explanation
Indices: 48789832--48789873 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
48789822 TTCTCTTAAA
* **
48789832 CTCTCAATTTCCTTTCAAAATC
1 CTCTCAATTTCATACCAAAATC
48789854 CTCTCAATTTCATACCAAAA
1 CTCTCAATTTCATACCAAAA
48789874 ATCTTTCAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.31, G:0.00, T:0.36
Consensus pattern (22 bp):
CTCTCAATTTCATACCAAAATC
Found at i:48789960 original size:31 final size:31
Alignment explanation
Indices: 48789916--48789982 Score: 100
Period size: 32 Copynumber: 2.2 Consensus size: 31
48789906 CCTCAATTTC
*
48789916 ATTTTTTTTAATAATTTCAAA-TTTTTTTAT
1 ATTTTTTTAAATAATTTCAAATTTTTTTTAT
*
48789946 ATTTTTTTAAAATAATTTTAAATTTTTTTTAT
1 ATTTTTTT-AAATAATTTCAAATTTTTTTTAT
48789978 ATTTT
1 ATTTT
48789983 CATCAATGGC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 8 0.24
31 11 0.33
32 14 0.42
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.67
Consensus pattern (31 bp):
ATTTTTTTAAATAATTTCAAATTTTTTTTAT
Found at i:48792347 original size:29 final size:29
Alignment explanation
Indices: 48792305--48792844 Score: 893
Period size: 29 Copynumber: 18.7 Consensus size: 29
48792295 ATAAAAATCG
* *
48792305 TAATTAAAAACCCTAACCCTACCCTAATT
1 TAATTAAAAACCCTAACCTTAACCTAATT
*
48792334 TAATTAAAAACCCTAATCTTAACCTAATT
1 TAATTAAAAACCCTAACCTTAACCTAATT
*
48792363 TAATTAAAAACCCTAACTTTAACCTAATT
1 TAATTAAAAACCCTAACCTTAACCTAATT
48792392 TAATTAAAAACCCTAACCTTAACCTAATT
1 TAATTAAAAACCCTAACCTTAACCTAATT
*
48792421 TAATTAAAAACCCTAACCTTAGCCTAATT
1 TAATTAAAAACCCTAACCTTAACCTAATT
48792450 TAATTAAAAA-CCTAACCTTAACCTAATT
1 TAATTAAAAACCCTAACCTTAACCTAATT
*
48792478 TAATTAAAAACCCTAACATTAACCTAATT
1 TAATTAAAAACCCTAACCTTAACCTAATT
48792507 TAATTAAAAACCCTAACCTTAACCTAATT
1 TAATTAAAAACCCTAACCTTAACCTAATT
* *
48792536 TAATTAAAAACCCTAACCCTACCCTAATT
1 TAATTAAAAACCCTAACCTTAACCTAATT
* *
48792565 TAATTAAAAACCCTAACCCTACCCTAATT
1 TAATTAAAAACCCTAACCTTAACCTAATT
*
48792594 TAATTAAAAACCCTAACCTTAGCCTAATT
1 TAATTAAAAACCCTAACCTTAACCTAATT
48792623 TAATTAAAAACCCTAACCTTAACCTAATT
1 TAATTAAAAACCCTAACCTTAACCTAATT
*
48792652 TAATTAAAAACCCTAACATTAACCTAATT
1 TAATTAAAAACCCTAACCTTAACCTAATT
*
48792681 TAATTAAAAACTCTAACCTTAACCTAATT
1 TAATTAAAAACCCTAACCTTAACCTAATT
* * *
48792710 TAATTAAAAACCTTAACCCTACCCTAATT
1 TAATTAAAAACCCTAACCTTAACCTAATT
*
48792739 TAATTAAAAACCCTAACCTTACCCTAATT
1 TAATTAAAAACCCTAACCTTAACCTAATT
*
48792768 TAATTAAAAACCCTAACATTAACCTAATT
1 TAATTAAAAACCCTAACCTTAACCTAATT
* *
48792797 TAATTTAAAACCCTAACATTAACCTAATT
1 TAATTAAAAACCCTAACCTTAACCTAATT
48792826 TAATTAAAAACCCTAACCT
1 TAATTAAAAACCCTAACCT
48792845 AATTTATTTA
Statistics
Matches: 481, Mismatches: 29, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
28 27 0.06
29 454 0.94
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.31
Consensus pattern (29 bp):
TAATTAAAAACCCTAACCTTAACCTAATT
Found at i:48792926 original size:56 final size:56
Alignment explanation
Indices: 48792866--48792990 Score: 198
Period size: 56 Copynumber: 2.2 Consensus size: 56
48792856 AAACCATAAC
* * * *
48792866 ATAATTTTACCTAATTTGAT-AATCTTACTAACCATTAACACAATTTTTTGGGCTTA
1 ATAATTTTACATAATTTGATAAAT-TTACTAACCATTAACAAAAGTTATTGGGCTTA
48792922 ATAATTTTACATAATTTGATAAATTTACTAACCATTAACAAAAGTTATTGGGCTTA
1 ATAATTTTACATAATTTGATAAATTTACTAACCATTAACAAAAGTTATTGGGCTTA
48792978 ATAATTTTACATA
1 ATAATTTTACATA
48792991 GTTTTTACAT
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
56 61 0.95
57 3 0.05
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (56 bp):
ATAATTTTACATAATTTGATAAATTTACTAACCATTAACAAAAGTTATTGGGCTTA
Found at i:48797548 original size:47 final size:47
Alignment explanation
Indices: 48797479--48797589 Score: 177
Period size: 47 Copynumber: 2.4 Consensus size: 47
48797469 GGTTTAACCA
* * * * *
48797479 CATATCTGTTCTAGTAGTTTGACTGCAATTATGGTGGCTCGACCACT
1 CATATCTATTCTGGCAGCTTGACTGCAATTATGGTGGCTCGACCACC
48797526 CATATCTATTCTGGCAGCTTGACTGCAATTATGGTGGCTCGACCACC
1 CATATCTATTCTGGCAGCTTGACTGCAATTATGGTGGCTCGACCACC
48797573 CATATCTATTCTGGCAG
1 CATATCTATTCTGGCAG
48797590 TTTATTTGCG
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 59 1.00
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (47 bp):
CATATCTATTCTGGCAGCTTGACTGCAATTATGGTGGCTCGACCACC
Found at i:48803225 original size:42 final size:42
Alignment explanation
Indices: 48803179--48803302 Score: 140
Period size: 42 Copynumber: 3.0 Consensus size: 42
48803169 CTGTATGAGC
* * *
48803179 TACACGAGCAAAGTCATGAGCGTGTGTCCAGGCCGTGTAAGA
1 TACACGAGCAAAGACATGGGTGTGTGTCCAGGCCGTGTAAGA
* * * * *
48803221 TACACGAGCAACGACATGGGTGTATGCCCAGGCCGTGTGAGC
1 TACACGAGCAAAGACATGGGTGTGTGTCCAGGCCGTGTAAGA
* * * *
48803263 CACACGGGCAAAGGCATGGGTGTGTGTCCAGGACGTGTAA
1 TACACGAGCAAAGACATGGGTGTGTGTCCAGGCCGTGTAA
48803303 CTCATTGTTT
Statistics
Matches: 66, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.26, C:0.23, G:0.34, T:0.18
Consensus pattern (42 bp):
TACACGAGCAAAGACATGGGTGTGTGTCCAGGCCGTGTAAGA
Found at i:48804322 original size:20 final size:20
Alignment explanation
Indices: 48804277--48804349 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
48804267 GCTTTATCCC
48804277 GTTCTGTTCTATTCAGCA-T-T
1 GTTCTGTTCTATTC--CATTCT
*
48804297 GCTCTGTTCTATTCCATTCT
1 GTTCTGTTCTATTCCATTCT
** * *
48804317 GTTCTGTTCTGCTCTATTCG
1 GTTCTGTTCTATTCCATTCT
*
48804337 GTTTTGTTCTATT
1 GTTCTGTTCTATT
48804350 TGAATTGTGT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
18 2 0.05
19 1 0.02
20 39 0.93
ACGTcount: A:0.10, C:0.22, G:0.15, T:0.53
Consensus pattern (20 bp):
GTTCTGTTCTATTCCATTCT
Found at i:48805155 original size:21 final size:23
Alignment explanation
Indices: 48805131--48805188 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
48805121 CTAGTGTATC
*
48805131 AATAATTTTTT-CAA-TAATTGT
1 AATAATTTTTTAAAAGTAATTGT
*
48805152 AATATTTTTTTAAAAGTAATTGT
1 AATAATTTTTTAAAAGTAATTGT
48805175 AAT-ATTATTTTAAA
1 AATAATT-TTTTAAA
48805189 TCTAAGACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 10 0.32
22 4 0.13
23 17 0.55
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (23 bp):
AATAATTTTTTAAAAGTAATTGT
Found at i:48805171 original size:23 final size:23
Alignment explanation
Indices: 48805145--48805188 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
48805135 ATTTTTTCAA
*
48805145 TAATTGTAATATTTTTTTAAAAG
1 TAATTGTAATATTATTTTAAAAG
48805168 TAATTGTAATATTATTTTAAA
1 TAATTGTAATATTATTTTAAA
48805189 TCTAAGACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (23 bp):
TAATTGTAATATTATTTTAAAAG
Found at i:48805271 original size:3 final size:3
Alignment explanation
Indices: 48805263--48805306 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
48805253 AGTACTAACC
48805263 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
48805307 AGAAAATCTA
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:48809059 original size:15 final size:15
Alignment explanation
Indices: 48809018--48809060 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
48809008 AAGTATATAT
48809018 TTAAGTGTTGAAAAAA
1 TTAAGTGTT-AAAAAA
* * *
48809034 ATAAATATTAAAAAA
1 TTAAGTGTTAAAAAA
48809049 TTAAGTGTTAAA
1 TTAAGTGTTAAA
48809061 TTTAAGTTAT
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.33
Consensus pattern (15 bp):
TTAAGTGTTAAAAAA
Found at i:48812021 original size:14 final size:14
Alignment explanation
Indices: 48811988--48812020 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
48811978 CAATACTTAA
*
48811988 ATTTTTAATACTTC
1 ATTTTTAACACTTC
48812002 ATTTTTAACACTT-
1 ATTTTTAACACTTC
48812015 ATTTTT
1 ATTTTT
48812021 TTTTAGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (14 bp):
ATTTTTAACACTTC
Found at i:48812308 original size:21 final size:21
Alignment explanation
Indices: 48812283--48812323 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
48812273 ATGATTAAAC
48812283 TGAAATTATGTTTAA-ATTAAT
1 TGAAA-TATGTTTAAGATTAAT
*
48812304 TGAAATCTGTTTAAGATTAA
1 TGAAATATGTTTAAGATTAA
48812324 AATTAGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.44
Consensus pattern (21 bp):
TGAAATATGTTTAAGATTAAT
Found at i:48813198 original size:13 final size:13
Alignment explanation
Indices: 48813180--48813216 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
48813170 AGAACGAAAC
48813180 AGAGAAGAAAAAG
1 AGAGAAGAAAAAG
48813193 AGAGAAAGAAAAAG
1 AGAG-AAGAAAAAG
48813207 -GAGAA-AAAAA
1 AGAGAAGAAAAA
48813217 ATTAGGGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 5 0.22
12 2 0.09
13 7 0.30
14 9 0.39
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (13 bp):
AGAGAAGAAAAAG
Found at i:48813203 original size:14 final size:14
Alignment explanation
Indices: 48813180--48813217 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
48813170 AGAACGAAAC
48813180 AGAG-AAGAAAAAG
1 AGAGAAAGAAAAAG
48813193 AGAGAAAGAAAAAG
1 AGAGAAAGAAAAAG
48813207 -GAGAAA-AAAAA
1 AGAGAAAGAAAAA
48813218 TTAGGGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.21
13 10 0.42
14 9 0.38
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (14 bp):
AGAGAAAGAAAAAG
Found at i:48815479 original size:2 final size:2
Alignment explanation
Indices: 48815472--48815519 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
48815462 CTTCATATTC
*
48815472 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48815514 AT AT AT
1 AT AT AT
48815520 CATTCAAGAC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48817859 original size:7 final size:7
Alignment explanation
Indices: 48817847--48817875 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
48817837 TTGCTCTCTG
48817847 TTTCTTT
1 TTTCTTT
48817854 TTTCTTT
1 TTTCTTT
48817861 TTTCTTT
1 TTTCTTT
48817868 TTT-TTT
1 TTTCTTT
48817874 TT
1 TT
48817876 GTTTCTTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.23
7 17 0.77
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (7 bp):
TTTCTTT
Found at i:48817872 original size:16 final size:16
Alignment explanation
Indices: 48817845--48817883 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
48817835 GTTTGCTCTC
*
48817845 TGTTTC-TTTTTTCTT
1 TGTTTCTTTTTTTTTT
48817860 T-TTTCTTTTTTTTTT
1 TGTTTCTTTTTTTTTT
48817875 TGTTTCTTT
1 TGTTTCTTT
48817884 CCTTTCTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 4 0.19
15 10 0.48
16 7 0.33
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (16 bp):
TGTTTCTTTTTTTTTT
Found at i:48825040 original size:24 final size:24
Alignment explanation
Indices: 48825013--48825069 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
48825003 AAACCTAATT
48825013 CTAATCAAA-GTCAAATATATTATG
1 CTAAT-AAATGTCAAATATATTATG
* *
48825037 CTAATAAATGTTAAATATATTATA
1 CTAATAAATGTCAAATATATTATG
*
48825061 CTCATAAAT
1 CTAATAAAT
48825070 ACTAAATCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 3 0.10
24 26 0.90
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (24 bp):
CTAATAAATGTCAAATATATTATG
Found at i:48825075 original size:24 final size:24
Alignment explanation
Indices: 48825025--48825076 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
48825015 AATCAAAGTC
* **
48825025 AAATATATTATGCTAATAAATGTT
1 AAATATATTATACTAATAAATACT
*
48825049 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
48825073 AAAT
1 AAAT
48825077 CTTTTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:48829343 original size:24 final size:24
Alignment explanation
Indices: 48829316--48829391 Score: 107
Period size: 24 Copynumber: 3.2 Consensus size: 24
48829306 AATCAAAGTC
48829316 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* *
48829340 AAATATATTATGCAAATAAAGGCT
1 AAATATATTATGCTAATAAATGCT
* * *
48829364 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATGCT
48829388 AAAT
1 AAAT
48829392 CTTTTCGAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.34
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:48834304 original size:2 final size:2
Alignment explanation
Indices: 48834297--48834331 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
48834287 CATACGGTGT
48834297 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
48834332 ATATTAGAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:48838631 original size:21 final size:21
Alignment explanation
Indices: 48838605--48838690 Score: 72
Period size: 21 Copynumber: 4.1 Consensus size: 21
48838595 TATGTACACG
*
48838605 AAAATAATAATTACAATATTA
1 AAAATAATAATTACAATAATA
*
48838626 AAAATAATACATAACAATAATA
1 AAAATAATA-ATTACAATAATA
*
48838648 AACAAGT-ATAA-TATAATAATA
1 AA-AA-TAATAATTACAATAATA
* *
48838669 AATA-AATAATTA-AATAGTA
1 AAAATAATAATTACAATAATA
48838688 AAA
1 AAA
48838691 TAGTTCAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
19 12 0.23
20 3 0.06
21 19 0.36
22 13 0.25
23 5 0.09
24 1 0.02
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (21 bp):
AAAATAATAATTACAATAATA
Found at i:48846822 original size:21 final size:20
Alignment explanation
Indices: 48846797--48846836 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
48846787 GATGTCTTCA
48846797 ATTCTATCATTGGTTGGCTTG
1 ATTCTATCA-TGGTTGGCTTG
* *
48846818 ATTCTTTCATGTTTGGCTT
1 ATTCTATCATGGTTGGCTT
48846837 TAGAGTCCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.12, C:0.15, G:0.20, T:0.53
Consensus pattern (20 bp):
ATTCTATCATGGTTGGCTTG
Found at i:48850826 original size:12 final size:12
Alignment explanation
Indices: 48850809--48850834 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
48850799 ATCGAATGAG
48850809 TATGCTTTCCTT
1 TATGCTTTCCTT
48850821 TATGCTTTCCTT
1 TATGCTTTCCTT
48850833 TA
1 TA
48850835 GTATTATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.12, C:0.23, G:0.08, T:0.58
Consensus pattern (12 bp):
TATGCTTTCCTT
Found at i:48859276 original size:29 final size:29
Alignment explanation
Indices: 48859199--48859292 Score: 127
Period size: 29 Copynumber: 3.2 Consensus size: 29
48859189 ACCGTGTATC
* * *
48859199 ACACATGGTCTGTCACAC-GACTATGTGTA
1 ACACATGGTCTGTCACACGGTC-GTGTGTG
*
48859228 ACACATGGTTTGTCACACGGTCGTGTGTG
1 ACACATGGTCTGTCACACGGTCGTGTGTG
*
48859257 ACACATGGTCTGTCACACGGTTGTGTGTG
1 ACACATGGTCTGTCACACGGTCGTGTGTG
48859286 ACACATG
1 ACACATG
48859293 ACCTACCACA
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
29 56 0.97
30 2 0.03
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (29 bp):
ACACATGGTCTGTCACACGGTCGTGTGTG
Found at i:48859302 original size:29 final size:29
Alignment explanation
Indices: 48859241--48859302 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
48859231 CATGGTTTGT
** **
48859241 CACACGGTCGTGTGTGACACATGGTCTGT
1 CACACGGTCGTGTGTGACACATGACCTAC
*
48859270 CACACGGTTGTGTGTGACACATGACCTAC
1 CACACGGTCGTGTGTGACACATGACCTAC
48859299 CACA
1 CACA
48859303 TGGCCCTACA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.23, C:0.27, G:0.26, T:0.24
Consensus pattern (29 bp):
CACACGGTCGTGTGTGACACATGACCTAC
Found at i:48862722 original size:11 final size:11
Alignment explanation
Indices: 48862704--48862746 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
48862694 GAACAAACAA
48862704 AAAG-AAAAAG
1 AAAGAAAAAAG
*
48862714 AACGAAAAAAG
1 AAAGAAAAAAG
*
48862725 AAGGAAAAAGAG
1 AAAGAAAAA-AG
48862737 AAAGAAAAAA
1 AAAGAAAAAA
48862747 ACAAATCAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 3 0.11
11 15 0.54
12 10 0.36
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAG
Found at i:48862857 original size:9 final size:9
Alignment explanation
Indices: 48862843--48862881 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
48862833 GCAGTTTTTT
48862843 TAATAAAAA
1 TAATAAAAA
*
48862852 TAATAATAA
1 TAATAAAAA
48862861 TAA-AAGAAA
1 TAATAA-AAA
48862870 TAATAAAAA
1 TAATAAAAA
48862879 TAA
1 TAA
48862882 AAATACTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
8 2 0.08
9 22 0.85
10 2 0.08
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (9 bp):
TAATAAAAA
Found at i:48862863 original size:15 final size:15
Alignment explanation
Indices: 48862843--48862886 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 15
48862833 GCAGTTTTTT
48862843 TAATAAAAATAATAA
1 TAATAAAAATAATAA
48862858 TAATAAAAGAAATAATAA
1 TAAT--AA-AAATAATAA
*
48862876 AAATAAAAATA
1 TAATAAAAATA
48862887 CTATCCCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
15 9 0.36
16 2 0.08
17 2 0.08
18 12 0.48
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (15 bp):
TAATAAAAATAATAA
Found at i:48862872 original size:18 final size:18
Alignment explanation
Indices: 48862849--48862883 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
48862839 TTTTTAATAA
*
48862849 AAATAATAATAATAAAAG
1 AAATAATAAAAATAAAAG
48862867 AAATAATAAAAATAAAA
1 AAATAATAAAAATAAAA
48862884 ATACTATCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (18 bp):
AAATAATAAAAATAAAAG
Found at i:48863542 original size:13 final size:13
Alignment explanation
Indices: 48863524--48863554 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
48863514 TTTTTTTTCC
48863524 ATTATCAATGTCT
1 ATTATCAATGTCT
48863537 ATTATCAATGTCT
1 ATTATCAATGTCT
48863550 ATTAT
1 ATTAT
48863555 AAAAGTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.13, G:0.06, T:0.48
Consensus pattern (13 bp):
ATTATCAATGTCT
Found at i:48871056 original size:27 final size:27
Alignment explanation
Indices: 48871014--48871069 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
48871004 GAGCTCAATC
48871014 ACAATACTATAATGGAATGACTTCGTG
1 ACAATACTATAATGGAATGACTTCGTG
* *
48871041 ACAATACTATAGTGGAATGACTTTGTG
1 ACAATACTATAATGGAATGACTTCGTG
48871068 AC
1 AC
48871070 TAAGTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (27 bp):
ACAATACTATAATGGAATGACTTCGTG
Found at i:48871305 original size:27 final size:27
Alignment explanation
Indices: 48871267--48871322 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
48871257 GGGCTCAATC
**
48871267 ACAATACTATAGTGGAATGGTTTCGTG
1 ACAATACTATAGTGGAATGACTTCGTG
48871294 ACAATACTATAGTGGAATGACTTCGTG
1 ACAATACTATAGTGGAATGACTTCGTG
48871321 AC
1 AC
48871323 TAAGTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.30
Consensus pattern (27 bp):
ACAATACTATAGTGGAATGACTTCGTG
Found at i:48871374 original size:253 final size:252
Alignment explanation
Indices: 48870927--48871435 Score: 928
Period size: 253 Copynumber: 2.0 Consensus size: 252
48870917 AGGACATCCT
48870927 ATGAGGGTAACACATTTATGACAAGGCCATTGACGAGCACTTACTGAGTAAATTTCACAATGGTA
1 ATGAGGGTAACACATTTATGACAAGGCCATTGACGAGCACTTACTGAGTAAATTTCACAATGGTA
48870992 GATTATTAGGGAGAGCTCAATCACAATACTATAATGGAATGACTTCGTGACAATACTATAGTGGA
66 GATTATTAGGGAGAGCTCAATCACAATACTATAATGGAATGACTTCGTGACAATACTATAGTGGA
*
48871057 ATGACTTTGTGACTAAGTAAGTTTATAATTAATAGGTGAAAAGCTAGAACTTAATTATAAATTAT
131 ATGACTTCGTGACTAAGTAAGTTTATAATTAATAGGTGAAAAGCTAGAACTTAATTATAAATTAT
*
48871122 TTGAACTCTAATTATATATGTTCAATCGGTCCTTCCGTTAGCTGATTGATACCATAA
196 TTGAACTCTAATTATATATGTCCAATCGGTCCTTCCGTTAGCTGATTGATACCATAA
*
48871179 ATGAGGGTAACACATTTATGACAAGGCCATTGGACGAGCACTTACTGAGTAACTTTCACAATGGT
1 ATGAGGGTAACACATTTATGACAAGGCCATT-GACGAGCACTTACTGAGTAAATTTCACAATGGT
* * **
48871244 AGATTATTAGGGAGGGCTCAATCACAATACTATAGTGGAATGGTTTCGTGACAATACTATAGTGG
65 AGATTATTAGGGAGAGCTCAATCACAATACTATAATGGAATGACTTCGTGACAATACTATAGTGG
*
48871309 AATGACTTCGTGACTAAGTAAGTTTATAATTAATAGGTGAAAAGCTGGAACTTAATTATAAATTA
130 AATGACTTCGTGACTAAGTAAGTTTATAATTAATAGGTGAAAAGCTAGAACTTAATTATAAATTA
*
48871374 TTTGAACTCTAATTATATATGTCCAATCGGTCCTTTCGTTAGCTGATTGATACCATAA
195 TTTGAACTCTAATTATATATGTCCAATCGGTCCTTCCGTTAGCTGATTGATACCATAA
48871432 ATGA
1 ATGA
48871436 ATTATAAATG
Statistics
Matches: 247, Mismatches: 9, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
252 31 0.13
253 216 0.87
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (252 bp):
ATGAGGGTAACACATTTATGACAAGGCCATTGACGAGCACTTACTGAGTAAATTTCACAATGGTA
GATTATTAGGGAGAGCTCAATCACAATACTATAATGGAATGACTTCGTGACAATACTATAGTGGA
ATGACTTCGTGACTAAGTAAGTTTATAATTAATAGGTGAAAAGCTAGAACTTAATTATAAATTAT
TTGAACTCTAATTATATATGTCCAATCGGTCCTTCCGTTAGCTGATTGATACCATAA
Found at i:48871444 original size:11 final size:11
Alignment explanation
Indices: 48871428--48871458 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
48871418 GATTGATACC
48871428 ATAAATGAATT
1 ATAAATGAATT
48871439 ATAAATGAA-T
1 ATAAATGAATT
48871449 ATAAATGAAT
1 ATAAATGAAT
48871459 GGAAATGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.32
Consensus pattern (11 bp):
ATAAATGAATT
Found at i:48871739 original size:16 final size:18
Alignment explanation
Indices: 48871713--48871745 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
48871703 TTGAATTGGG
48871713 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
48871730 TTGA-AAAATTAATTTA
1 TTGAGAAAATTAATTTA
48871746 GTTAACTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:48873177 original size:19 final size:20
Alignment explanation
Indices: 48873137--48873179 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
48873127 TCATTAAATA
*
48873137 AAAAGTATCTAAAAATTACT
1 AAAAGTAGCTAAAAATTACT
*
48873157 AAAAGTAGCTTAAAA-TACT
1 AAAAGTAGCTAAAAATTACT
48873176 AAAA
1 AAAA
48873180 TATGAAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.58, C:0.09, G:0.07, T:0.26
Consensus pattern (20 bp):
AAAAGTAGCTAAAAATTACT
Found at i:48875038 original size:241 final size:241
Alignment explanation
Indices: 48874611--48875053 Score: 706
Period size: 241 Copynumber: 1.8 Consensus size: 241
48874601 GGTCTTTATA
* *
48874611 TTTGTGATATAAGCATTCAACTATATTTCTTTTTCATGGATTAGATCGTATGGGTGGTATAGTCC
1 TTTGTGATATAAGCATTCAACTATATTCCTTTTTCATGGATTAGATCGTATGGGTGGTAGAGTCC
* *
48874676 CTAATATTCCTTTACTCTTGCCATGATATCTCTTTGCAAACTATTTAAGGGAGTGTAATGGTGGA
66 CTAATATTCCTTTACTCTTACCAAGATATCTCTTTGCAAACTATTTAAGGGAGTGTAATGGTGGA
* * * * * **
48874741 TAGCATTGGCGATATTCTCTTTAGGTGTTTCAGTTGTCAACAATTTTGACGCCTTATCACAGTTT
131 CAGCATGGGCGATACTCTCTTTAAGTGTTTCAGTTATCAACAATTTTGACGCCTTATCACAGCCT
48874806 TATTATTTAAGGGATTGTAATGGTGGATAGCTTGGGCGATACTCTC
196 TATTATTTAAGGGATTGTAATGGTGGATAGCTTGGGCGATACTCTC
*
48874852 TTTGTGATATAAGCATTCAACTATATTCCTTTTTCATGGATTGGATCGTATGGGTGGTAGAGTCC
1 TTTGTGATATAAGCATTCAACTATATTCCTTTTTCATGGATTAGATCGTATGGGTGGTAGAGTCC
* *
48874917 CTAATATTCCTTTACTCTTACTAAGATATCTCTTTGCAAAGTATTTAAGGGAGTGTAATGGTGGA
66 CTAATATTCCTTTACTCTTACCAAGATATCTCTTTGCAAACTATTTAAGGGAGTGTAATGGTGGA
* ** * * *
48874982 CAGCATGGGCGATACTCTTTTTAAGTGTTTTGGTTATCGATAATTTTGATGCCTTATCACAGCCT
131 CAGCATGGGCGATACTCTCTTTAAGTGTTTCAGTTATCAACAATTTTGACGCCTTATCACAGCCT
48875047 TATTATT
196 TATTATT
48875054 CATCCTTTTG
Statistics
Matches: 182, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
241 182 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.40
Consensus pattern (241 bp):
TTTGTGATATAAGCATTCAACTATATTCCTTTTTCATGGATTAGATCGTATGGGTGGTAGAGTCC
CTAATATTCCTTTACTCTTACCAAGATATCTCTTTGCAAACTATTTAAGGGAGTGTAATGGTGGA
CAGCATGGGCGATACTCTCTTTAAGTGTTTCAGTTATCAACAATTTTGACGCCTTATCACAGCCT
TATTATTTAAGGGATTGTAATGGTGGATAGCTTGGGCGATACTCTC
Found at i:48876050 original size:2 final size:2
Alignment explanation
Indices: 48876043--48876071 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
48876033 AAATGTATGC
48876043 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
48876072 AAATTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48876483 original size:5 final size:5
Alignment explanation
Indices: 48876473--48876497 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
48876463 ATGAATACCC
48876473 TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT
48876498 ATCCATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:48883881 original size:16 final size:15
Alignment explanation
Indices: 48883860--48883889 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
48883850 GCAAAAAAAT
48883860 TTGGCCCGGGCCCGGC
1 TTGGCCC-GGCCCGGC
48883876 TTGGCCCGGCCCGG
1 TTGGCCCGGCCCGG
48883890 ATATAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.00, C:0.43, G:0.43, T:0.13
Consensus pattern (15 bp):
TTGGCCCGGCCCGGC
Done.