Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 95 of 198
Found at i:30474415 original size:115 final size:111
Alignment explanation
Indices: 30474269--30474579 Score: 290
Period size: 115 Copynumber: 2.7 Consensus size: 111
30474259 CCTGAAGAAC
* * *
30474269 TAGTGGCGTTTCTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTGTAAGCACCGCA
1 TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTGAAAGCGCCGCA
* *
30474334 AAATACCTTAACCAAAACGCAGCGTTGGTTCA-ATT-GTATATTAGA-AT
66 AAATACCTTAACCAAAACGCACCGTT--TT-ATATTGGTAGATTA-ATAT
* ** * * ***
30474381 TCGTGGCGTTTTTTTATAAAAAACGCCGCGAAAGAATAGT-ATTAGCGGCGTTTAACAAAAAGCG
1 TAGTGGCG--TTTTTA-AAAAAACGCCGTAAAAGAACA-TAATTAGTGGCGTTT-ATTGAAAGCG
* ** *
30474445 CCGC-AAATATCTTAAGGAAAACGCACCGTTTTATCTTGAGGTAGATTAATAT
61 CCGCAAAATACCTTAACCAAAACGCACCGTTTTATATT--GGTAGATTAATAT
* * *
30474497 TAGTGGCGTTTTTAAAAAAATGCCGTAAAAGAACATAATTAGTGGCGTTTATTTGGATGCGCCGC
1 TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTA-TTGAAAGCGCCGC
*
30474562 AAAACACCTTAACCAAAA
65 AAAATACCTTAACCAAAA
30474580 AGAATAGTAT
Statistics
Matches: 154, Mismatches: 32, Indels: 24
0.73 0.15 0.11
Matches are distributed among these distances:
112 10 0.06
113 41 0.27
114 24 0.16
115 53 0.34
116 26 0.17
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.28
Consensus pattern (111 bp):
TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTGAAAGCGCCGCA
AAATACCTTAACCAAAACGCACCGTTTTATATTGGTAGATTAATAT
Found at i:30474691 original size:167 final size:167
Alignment explanation
Indices: 30474411--30474746 Score: 539
Period size: 167 Copynumber: 2.0 Consensus size: 167
30474401 AAACGCCGCG
30474411 AAAGAATAGTATTAGCGGCGTTTAACAAAAAGCGCCGCAAATATCTTAAGGAAAACGCACCGTTT
1 AAAGAATAGTATTAGCGGCGTTTAACAAAAAGCGCCGCAAATATCTTAAGGAAAACGCACCGTTT
* *
30474476 TATCTTGAGGTAGATTAATATTAGTGGCGTTTTTAAAAAAATGCCGTAAAAGAACATAATTAGTG
66 CATCTTGAGGTAGATTAATATTAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTG
30474541 GCGTTTATTTGGATGCGCCGCAAAACACCTTAACCAA
131 GCGTTTATTTGGATGCGCCGCAAAACACCTTAACCAA
* ** *
30474578 AAAGAATAGTATTAGCGGCGTTT-TCGGTAAAGCGCCGCAAATATCTTAATGAAAACGCACCGTT
1 AAAGAATAGTATTAGCGGCGTTTAAC-AAAAAGCGCCGCAAATATCTTAAGGAAAACGCACCGTT
* * * *
30474642 TCGTCTTGAGGTAGATTAGTATTAGTGGCGTTTTTAGAAAAACGCCGTAAAAGAACATGATTAGT
65 TCATCTTGAGGTAGATTAATATTAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGT
** *
30474707 GGCGTTTATTTTTATGCGCCGCAAAATACCTTAACCAA
130 GGCGTTTATTTGGATGCGCCGCAAAACACCTTAACCAA
30474745 AA
1 AA
30474747 CGCAGCGTTT
Statistics
Matches: 155, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
166 1 0.01
167 154 0.99
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (167 bp):
AAAGAATAGTATTAGCGGCGTTTAACAAAAAGCGCCGCAAATATCTTAAGGAAAACGCACCGTTT
CATCTTGAGGTAGATTAATATTAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTG
GCGTTTATTTGGATGCGCCGCAAAACACCTTAACCAA
Found at i:30474839 original size:74 final size:75
Alignment explanation
Indices: 30474723--30474862 Score: 194
Period size: 74 Copynumber: 1.9 Consensus size: 75
30474713 TATTTTTATG
* * * *
30474723 CGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATTAGA-ATTAGTGGCGT
1 CGCCGCAAAATACCTTAACCAAAACACACCGTTTGGTCTTGAGGTAGATTA-ATATTAGTGGCGT
30474787 TTACGATAAAA
65 TTACGATAAAA
* * *
30474798 CGCCGC-AAATATCTTAGCGAAAACACACCGTTTGGTCTTGAGGTAGATTAATATTAGTGGCGTT
1 CGCCGCAAAATACCTTAACCAAAACACACCGTTTGGTCTTGAGGTAGATTAATATTAGTGGCGTT
30474862 T
66 T
30474863 TTAAAAAAAC
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
73 1 0.02
74 50 0.88
75 6 0.11
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (75 bp):
CGCCGCAAAATACCTTAACCAAAACACACCGTTTGGTCTTGAGGTAGATTAATATTAGTGGCGTT
TACGATAAAA
Found at i:30474872 original size:74 final size:75
Alignment explanation
Indices: 30474723--30474881 Score: 187
Period size: 74 Copynumber: 2.1 Consensus size: 75
30474713 TATTTTTATG
* * * *
30474723 CGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATTAGAATTAGTGGCGTT
1 CGCCGCAAAATACCTTAACCAAAACACACCGTTTGGTCTTGAGGTAGATTAGAATTAGTGGCGTT
* *
30474788 TACGATAAAA
66 TACAAAAAAA
* * *
30474798 CGCCGC-AAATATCTTAGCGAAAACACACCGTTTGGTCTTGAGGTAGATTA-ATATTAGTGGCGT
1 CGCCGCAAAATACCTTAACCAAAACACACCGTTTGGTCTTGAGGTAGATTAGA-ATTAGTGGCGT
**
30474861 TTTTAAAAAAA
65 TTACAAAAAAA
*
30474872 CGCCGTAAAA
1 CGCCGCAAAA
30474882 GAACATAATT
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
73 1 0.01
74 60 0.86
75 9 0.13
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.28
Consensus pattern (75 bp):
CGCCGCAAAATACCTTAACCAAAACACACCGTTTGGTCTTGAGGTAGATTAGAATTAGTGGCGTT
TACAAAAAAA
Found at i:30474916 original size:188 final size:188
Alignment explanation
Indices: 30474588--30474988 Score: 640
Period size: 188 Copynumber: 2.1 Consensus size: 188
30474578 AAAGAATAGT
* * * * *
30474588 ATTAGCGGCGTTTTCGGTAAAGCGCCGCAAATATCTTAATGAAAACGCACCGTTTCGTCTTGAGG
1 ATTAGTGGCGTTTACGGTAAAACGCCGCAAATATCTTAACGAAAACACACCGTTTCGTCTTGAGG
* * *
30474653 TAGATTAGTATTAGTGGCGTTTTTAGAAAAACGCCGTAAAAGAACATGATTAGTGGCGTTTATTT
66 TAGATTAATATTAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTT
** *
30474718 TTATGCGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATTAGA
131 GGAAGCGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATTAGA
* * *
30474776 ATTAGTGGCGTTTACGATAAAACGCCGCAAATATCTTAGCGAAAACACACCGTTTGGTCTTGAGG
1 ATTAGTGGCGTTTACGGTAAAACGCCGCAAATATCTTAACGAAAACACACCGTTTCGTCTTGAGG
30474841 TAGATTAATATTAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTT
66 TAGATTAATATTAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTT
* * *
30474906 GGAAGCGCCGCAAAATGCCTTAACCAAAACGCAGTGTTTGGTTTTGATGTATATTAGA
131 GGAAGCGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATTAGA
*
30474964 ATTAGTGGCGTTTATGGTAAAACGC
1 ATTAGTGGCGTTTACGGTAAAACGC
30474989 TGCTAAAGAA
Statistics
Matches: 194, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
188 194 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (188 bp):
ATTAGTGGCGTTTACGGTAAAACGCCGCAAATATCTTAACGAAAACACACCGTTTCGTCTTGAGG
TAGATTAATATTAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTT
GGAAGCGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATTAGA
Found at i:30475447 original size:12 final size:12
Alignment explanation
Indices: 30475430--30475454 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30475420 NNNNNNNNNG
30475430 GGTTAGGGGTTA
1 GGTTAGGGGTTA
30475442 GGTTAGGGGTTA
1 GGTTAGGGGTTA
30475454 G
1 G
30475455 ATGTTAAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (12 bp):
GGTTAGGGGTTA
Found at i:30475565 original size:7 final size:7
Alignment explanation
Indices: 30475553--30475656 Score: 111
Period size: 7 Copynumber: 14.9 Consensus size: 7
30475543 TAAATAAGTT
30475553 TTAGGGG
1 TTAGGGG
30475560 TTAGGGG
1 TTAGGGG
*
30475567 TTAGAGG
1 TTAGGGG
** *
30475574 CCATGGG
1 TTAGGGG
*
30475581 TTAAGGGT
1 TT-AGGGG
30475589 TTA-GGG
1 TTAGGGG
*
30475595 TTAAGGG
1 TTAGGGG
*
30475602 TTAAGGG
1 TTAGGGG
*
30475609 TTAAGGG
1 TTAGGGG
30475616 TTAGGGG
1 TTAGGGG
*
30475623 TTAAGGG
1 TTAGGGG
30475630 TTAGGGG
1 TTAGGGG
30475637 TTAGGGG
1 TTAGGGG
30475644 TTAGGGG
1 TTAGGGG
30475651 TTAGGG
1 TTAGGG
30475657 ATTGGGTTAT
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
6 5 0.06
7 72 0.88
8 5 0.06
ACGTcount: A:0.20, C:0.02, G:0.49, T:0.29
Consensus pattern (7 bp):
TTAGGGG
Found at i:30475814 original size:95 final size:96
Alignment explanation
Indices: 30475627--30475811 Score: 221
Period size: 95 Copynumber: 1.9 Consensus size: 96
30475617 TAGGGGTTAA
* * * * *
30475627 GGGTTAGGGGTTAGGGGTTAGGGGTTAGGGATTGGGTTATGGTTTAAGGTTTAGATTAATTAGTG
1 GGGTTAGGGGTTAGGGGTTAGGGGTTAGGGATCGGGTTAGGGATTAAGATTTAGATTAATTAGTC
* * * *
30475692 TTTTTTATTTTATATATTAAATAAAGTTTAG
66 TTATTTAATTAACATATTAAATAAAGTTTAG
* * * *
30475723 GGGTTAGTGGTTA-GGGTTATGGGTT-TGGAGTCGGGTTAGGGATTAAGATTTGGATTAATTAGT
1 GGGTTAGGGGTTAGGGGTTAGGGGTTAGGGA-TCGGGTTAGGGATTAAGATTTAGATTAATTAGT
30475786 ACTTATTTAATTAACATATTAAATAA
65 -CTTATTTAATTAACATATTAAATAA
30475812 GTTCTTTATA
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
94 3 0.04
95 39 0.53
96 32 0.43
ACGTcount: A:0.27, C:0.02, G:0.30, T:0.42
Consensus pattern (96 bp):
GGGTTAGGGGTTAGGGGTTAGGGGTTAGGGATCGGGTTAGGGATTAAGATTTAGATTAATTAGTC
TTATTTAATTAACATATTAAATAAAGTTTAG
Found at i:30475901 original size:14 final size:14
Alignment explanation
Indices: 30475882--30475908 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
30475872 GATATGCAAT
30475882 ATATAATAATTTGA
1 ATATAATAATTTGA
30475896 ATATAATAATTTG
1 ATATAATAATTTG
30475909 GAATTGTAAA
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:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (14 bp):
ATATAATAATTTGA
Found at i:30475948 original size:20 final size:20
Alignment explanation
Indices: 30475910--30475950 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
30475900 AATAATTTGG
**
30475910 AATTGTAAAAATTGTAAAAA
1 AATTGTAAAAATTACAAAAA
*
30475930 AATTGTCAAAATTACAAAAA
1 AATTGTAAAAATTACAAAAA
30475950 A
1 A
30475951 TAAAATGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.61, C:0.05, G:0.07, T:0.27
Consensus pattern (20 bp):
AATTGTAAAAATTACAAAAA
Found at i:30475966 original size:18 final size:17
Alignment explanation
Indices: 30475945--30475992 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 17
30475935 TCAAAATTAC
30475945 AAAAAATAAAATGAAAAT
1 AAAAAATAAAATG-AAAT
*
30475963 AAAAAATAAAAAGAAAT
1 AAAAAATAAAATGAAAT
30475980 AAAAAACTAAAAT
1 AAAAAA-TAAAAT
30475993 TTTTATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 10 0.37
18 17 0.63
ACGTcount: A:0.79, C:0.02, G:0.04, T:0.15
Consensus pattern (17 bp):
AAAAAATAAAATGAAAT
Found at i:30476788 original size:198 final size:197
Alignment explanation
Indices: 30476482--30476870 Score: 627
Period size: 198 Copynumber: 2.0 Consensus size: 197
30476472 CAATTTTAAG
*
30476482 AAATTGTTTACGAAAACGGCTCCGTTTTCTTATTATCTTTAGTGGCGCCTTTAGTACACGCCGCA
1 AAATTGTTTACGAAAACGGCTCCGTTTTCTTATTATCTTTAGTGGCGCCTTTAGTAAACGCCGCA
* * * * ** *
30476547 AAATTATTTTAATTTTTATGGAGACGATGCCGTTTTGTCTAAAACGCCATGAGTTTTAGTTTACT
66 AAAATATTTTAATTTTTATGGAGACGATGCCGTTTTCTCTAAAACGCAATGACTTAGAGTTAACT
*
30476612 AATCGGGGAACGACAGCGTTTGATCATATTACTAGTGGCGCTAGTATATAAACGCCGCAAAGTAC
131 AATCGGGAAACGACAGCGTTTGATCATATTACTAGTGGCGCTAGTATATAAACGCCGCAAAGTAC
30476677 AT
196 AT
* * *
30476679 AAATTGTTTAGGAAAACGGCTTCGTTTTCTTATT-TACTTTTAGTGGCGCTTTTAGTAAACGCCG
1 AAATTGTTTACGAAAACGGCTCCGTTTTCTTATTAT-C-TTTAGTGGCGCCTTTAGTAAACGCCG
*
30476743 CAAAAATGTTTTAATTTTTATGGAGACGATGCCGTTTTCTCTAAAACGCAATGACTTAGAGTTAA
64 CAAAAATATTTTAATTTTTATGGAGACGATGCCGTTTTCTCTAAAACGCAATGACTTAGAGTTAA
*
30476808 CTGATCGGGAAACGACAGCGTTTGATCATATTACTAGTGGCGCTAGTATATAAACGCCGCAAA
129 CTAATCGGGAAACGACAGCGTTTGATCATATTACTAGTGGCGCTAGTATATAAACGCCGCAAA
30476871 TGGGTTAATT
Statistics
Matches: 176, Mismatches: 14, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
196 1 0.01
197 33 0.19
198 142 0.81
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (197 bp):
AAATTGTTTACGAAAACGGCTCCGTTTTCTTATTATCTTTAGTGGCGCCTTTAGTAAACGCCGCA
AAAATATTTTAATTTTTATGGAGACGATGCCGTTTTCTCTAAAACGCAATGACTTAGAGTTAACT
AATCGGGAAACGACAGCGTTTGATCATATTACTAGTGGCGCTAGTATATAAACGCCGCAAAGTAC
AT
Found at i:30477397 original size:10 final size:10
Alignment explanation
Indices: 30477382--30477406 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
30477372 TCGAAAATTG
30477382 CAAAATTGTT
1 CAAAATTGTT
30477392 CAAAATTGTT
1 CAAAATTGTT
30477402 CAAAA
1 CAAAA
30477407 CCATGTCGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (10 bp):
CAAAATTGTT
Found at i:30478172 original size:18 final size:19
Alignment explanation
Indices: 30478149--30478192 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
30478139 CAGAAATTTC
*
30478149 TGTTTCTCTAGCA-TGTTA
1 TGTTTCTCTACCATTGTTA
* *
30478167 TGTTTCTGTACCATTTTTA
1 TGTTTCTCTACCATTGTTA
30478186 TGTTTCT
1 TGTTTCT
30478193 TTATTTTCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.14, C:0.16, G:0.14, T:0.57
Consensus pattern (19 bp):
TGTTTCTCTACCATTGTTA
Found at i:30478208 original size:7 final size:7
Alignment explanation
Indices: 30478196--30478275 Score: 106
Period size: 7 Copynumber: 11.3 Consensus size: 7
30478186 TGTTTCTTTA
30478196 TTTTCTG
1 TTTTCTG
30478203 TTTTCTG
1 TTTTCTG
30478210 TTTTCTG
1 TTTTCTG
30478217 TTTTCTG
1 TTTTCTG
**
30478224 CATTCTG
1 TTTTCTG
30478231 TTTTCTG
1 TTTTCTG
*
30478238 TTTTCTA
1 TTTTCTG
*
30478245 TTTTTTG
1 TTTTCTG
30478252 TTTTCTG
1 TTTTCTG
*
30478259 TTTTGCTA
1 TTTT-CTG
30478267 TTTTCTG
1 TTTTCTG
30478274 TT
1 TT
30478276 GAATGAAGTG
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
7 56 0.90
8 6 0.10
ACGTcount: A:0.04, C:0.14, G:0.12, T:0.70
Consensus pattern (7 bp):
TTTTCTG
Found at i:30478715 original size:52 final size:51
Alignment explanation
Indices: 30478659--30479222 Score: 147
Period size: 47 Copynumber: 11.2 Consensus size: 51
30478649 TATTTTATCA
30478659 TAACTTATTAATATTAAAAATATATATATGTTAATATTTTTACAATTTAATT
1 TAACTTATTAATATT-AAAATATATATATGTTAATATTTTTACAATTTAATT
* * * *
30478711 TAACTTA-T--TACTAATACATATAT-TGTTCGAATATATTTTTTCAAAATTTATATGT
1 TAACTTATTAATATTAAAATATATATATGTT---A-ATA-TTTTT-ACAATTTA-AT-T
*
30478766 T-AC--ATT-A-CTT-AAATATATATATGTTAATATTTTTACAATTTAATT
1 TAACTTATTAATATTAAAATATATATATGTTAATATTTTTACAATTTAATT
* * * * ***** * *
30478811 TAACTTA-T--TACTAATACATATAT-TGTTCATATAGCCCCGATTCT-ATCC
1 TAACTTATTAATATTAAAATATATATATGTTAATATTTTTACAATT-TAAT-T
* * *
30478859 AAAGTATGTTACATTACTT-AAATATATATATGTTAATATTTTTACAATTTAATT
1 TAACT-TATTA-A-TA-TTAAAATATATATATGTTAATATTTTTACAATTTAATT
* * * *
30478913 TAACTTATTACTAAT-ACATATAT-TGTTCGAATATAAT-TTTTTGA-AATTTATATAT
1 TAACTTATTAATATTAAAATATATAT-AT-G--T-TAATATTTTT-ACAATTTA-AT-T
*
30478968 T-AC--ATT-A-CTT-AAATATATATATGTTAATATTTTTACAATTTAATT
1 TAACTTATTAATATTAAAATATATATATGTTAATATTTTTACAATTTAATT
* ** * *
30479013 TAACTTATT--T-GTAGTACATATAT-TGTTCGAATATATTTTTTCAAAATTTATATGT
1 TAACTTATTAATATTAAAATATATATATGTT---A-ATA-TTTTT-ACAATTTA-AT-T
*
30479068 T-AC--ATT-A-CTT-AAATATATATATGTTAATATTTTTACAATTTAATT
1 TAACTTATTAATATTAAAATATATATATGTTAATATTTTTACAATTTAATT
* * * * *
30479113 TAACTTATTACTAAT-ACATATAT-TGTTCGAATATAAT-TTTTTAAAATTTATATAT
1 TAACTTATTAATATTAAAATATATAT-AT-G--T-TAATATTTTTACAATTTA-AT-T
*
30479168 T-AC--ATT-A-CTT-AAATATATATATGTTAATATTTTTACAATTTAATT
1 TAACTTATTAATATTAAAATATATATATGTTAATATTTTTACAATTTAATT
30479213 TAACTTATTA
1 TAACTTATTA
30479223 CTAATACATA
Statistics
Matches: 371, Mismatches: 69, Indels: 147
0.63 0.12 0.25
Matches are distributed among these distances:
45 8 0.02
46 25 0.07
47 64 0.17
48 48 0.13
49 14 0.04
50 41 0.11
51 13 0.04
52 42 0.11
53 54 0.15
54 39 0.11
55 23 0.06
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.49
Consensus pattern (51 bp):
TAACTTATTAATATTAAAATATATATATGTTAATATTTTTACAATTTAATT
Found at i:30478795 original size:100 final size:100
Alignment explanation
Indices: 30478676--30479287 Score: 995
Period size: 100 Copynumber: 6.1 Consensus size: 100
30478666 TTAATATTAA
30478676 AAATATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGA
1 AAATATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGA
*
30478741 ATAT-ATTTTTTCAAAATTTATATGTTACATTACTT
66 ATATAATTTTTT-AAAATTTATATATTACATTACTT
30478776 AAATATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTC--
1 AAATATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGA
* ** * *
30478839 ATATAGCCCCGATTCTATCCAAA---GTATGTTACATTACTT
66 ATATA------ATT-TTTTAAAATTTATATATTACATTACTT
30478878 AAATATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGA
1 AAATATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGA
*
30478943 ATATAATTTTTTGAAATTTATATATTACATTACTT
66 ATATAATTTTTTAAAATTTATATATTACATTACTT
** *
30478978 AAATATATATATGTTAATATTTTTACAATTTAATTTAACTTATTTGTAGTACATATATTGTTCGA
1 AAATATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGA
*
30479043 ATAT-ATTTTTTCAAAATTTATATGTTACATTACTT
66 ATATAATTTTTT-AAAATTTATATATTACATTACTT
30479078 AAATATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGA
1 AAATATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGA
30479143 ATATAATTTTTTAAAATTTATATATTACATTACTT
66 ATATAATTTTTTAAAATTTATATATTACATTACTT
30479178 AAATATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGA
1 AAATATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGA
30479243 ATATAATTTTTTAAAATTTATATATTACATTACTT
66 ATATAATTTTTTAAAATTTATATATTACATTACTT
30479278 AAATATATAT
1 AAATATATAT
30479288 TTTTAAGTAT
Statistics
Matches: 479, Mismatches: 18, Indels: 30
0.91 0.03 0.06
Matches are distributed among these distances:
97 5 0.01
98 7 0.01
99 7 0.01
100 362 0.76
101 7 0.01
102 78 0.16
104 5 0.01
105 6 0.01
106 2 0.00
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (100 bp):
AAATATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGA
ATATAATTTTTTAAAATTTATATATTACATTACTT
Found at i:30479302 original size:302 final size:297
Alignment explanation
Indices: 30478676--30479287 Score: 1039
Period size: 302 Copynumber: 2.0 Consensus size: 297
30478666 TTAATATTAA
30478676 AAATATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGA
1 AAATATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGA
30478741 ATATATTTTTTCAAAATTTATATGTTACATTACTTAAATATATATATGTTAATATTTTTACAATT
66 ATATATTTTTTCAAAATTTATATGTTACATTACTTAAATATATATATGTTAATATTTTTACAATT
* * *
30478806 TAATTTAACTTATTACTAATACATATATTGTTCATATAGCCCCGATTCTATCCAAAGTATGTTAC
131 TAATTTAACTTATTACTAATACATATATTGTTCATATA----C-ATTCTATCAAAAATATATTAC
30478871 ATTACTTAAATATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATAT
191 ATTACTTAAATATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATAT
*
30478936 TGTTCGAATATAATTTTTTGAAATTTATATATTACATTACTT
256 TGTTCGAATATAATTTTTTAAAATTTATATATTACATTACTT
** *
30478978 AAATATATATATGTTAATATTTTTACAATTTAATTTAACTTATTTGTAGTACATATATTGTTCGA
1 AAATATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGA
30479043 ATATATTTTTTCAAAATTTATATGTTACATTACTTAAATATATATATGTTAATATTTTTACAATT
66 ATATATTTTTTCAAAATTTATATGTTACATTACTTAAATATATATATGTTAATATTTTTACAATT
* *
30479108 TAATTTAACTTATTACTAATACATATATTGTTCGAATATA-ATT-TTTTAAAATTTATATATTAC
131 TAATTTAACTTATTACTAATACATATATTGTTC--ATATACATTCTATCAAAA---ATATATTAC
30479171 ATTACTTAAATATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATAT
191 ATTACTTAAATATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATAT
30479236 TGTTCGAATATAATTTTTTAAAATTTATATATTACATTACTT
256 TGTTCGAATATAATTTTTTAAAATTTATATATTACATTACTT
30479278 AAATATATAT
1 AAATATATAT
30479288 TTTTAAGTAT
Statistics
Matches: 296, Mismatches: 9, Indels: 12
0.93 0.03 0.04
Matches are distributed among these distances:
297 5 0.02
298 3 0.01
300 123 0.42
302 160 0.54
304 5 0.02
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (297 bp):
AAATATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGA
ATATATTTTTTCAAAATTTATATGTTACATTACTTAAATATATATATGTTAATATTTTTACAATT
TAATTTAACTTATTACTAATACATATATTGTTCATATACATTCTATCAAAAATATATTACATTAC
TTAAATATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTC
GAATATAATTTTTTAAAATTTATATATTACATTACTT
Found at i:30479378 original size:15 final size:13
Alignment explanation
Indices: 30479357--30479410 Score: 72
Period size: 13 Copynumber: 4.0 Consensus size: 13
30479347 TTTTACTCTT
30479357 AATATATTACTTGA
1 AATATATTACTT-A
30479371 ATATATATTACTTA
1 A-ATATATTACTTA
*
30479385 AATAAATTACTTA
1 AATATATTACTTA
*
30479398 AATACATTACTTA
1 AATATATTACTTA
30479411 CTAAAATTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
13 23 0.62
14 3 0.08
15 11 0.30
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (13 bp):
AATATATTACTTA
Found at i:30479435 original size:53 final size:53
Alignment explanation
Indices: 30479378--30479513 Score: 191
Period size: 53 Copynumber: 2.6 Consensus size: 53
30479368 TGAATATATA
**
30479378 TTACTTAAATAAATTACTTAAATACATTACTTACTAAAATTTCGTTAAATGTT
1 TTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTCGTTAAATGTT
* ** * * *
30479431 TTACTTAAATATGTTACTCAGTTACATTAATTACTAAAATTTGGTTAAATTTT
1 TTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTCGTTAAATGTT
*
30479484 TTACTTAAATATGTTACTTGAATACATTAC
1 TTACTTAAATATGTTACTTAAATACATTAC
30479514 CCGCTATAAA
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
53 70 1.00
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (53 bp):
TTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTCGTTAAATGTT
Found at i:30479682 original size:9 final size:9
Alignment explanation
Indices: 30479658--30479907 Score: 155
Period size: 9 Copynumber: 28.8 Consensus size: 9
30479648 TATGTACAAG
30479658 AACTTACAT
1 AACTTACAT
* *
30479667 AATTTACAC
1 AACTTACAT
*
30479676 AACTTACTT
1 AACTTACAT
*
30479685 AACCTACAT
1 AACTTACAT
30479694 AACTTACAT
1 AACTTACAT
30479703 AA--TACA-
1 AACTTACAT
30479709 AAGCTTACAT
1 AA-CTTACAT
* *
30479719 AACTAAAAT
1 AACTTACAT
* *
30479728 AGCTTACAC
1 AACTTACAT
30479737 AACTTACAT
1 AACTTACAT
30479746 AACTTACAT
1 AACTTACAT
*
30479755 AACTTACAG
1 AACTTACAT
* *
30479764 AAGTTATAT
1 AACTTACAT
*
30479773 AATACATA-AT
1 -A-ACTTACAT
30479783 AACTTAC--
1 AACTTACAT
30479790 AACTTACAT
1 AACTTACAT
*
30479799 AACATACAT
1 AACTTACAT
* **
30479808 TACTTTGAT
1 AACTTACAT
30479817 AACTTACAT
1 AACTTACAT
*
30479826 AAGTTACAT
1 AACTTACAT
*
30479835 AA--TACAC
1 AACTTACAT
30479842 AAC-TACAT
1 AACTTACAT
** *
30479850 AGTTTACTT
1 AACTTACAT
*
30479859 AA--TACAA
1 AACTTACAT
30479866 AACTTACAT
1 AACTTACAT
*
30479875 AACTTATAT
1 AACTTACAT
*
30479884 -ACGTACAT
1 AACTTACAT
*
30479892 AACCTACAT
1 AACTTACAT
*
30479901 AATTTAC
1 AACTTAC
30479908 TTAATACATA
Statistics
Matches: 180, Mismatches: 47, Indels: 28
0.71 0.18 0.11
Matches are distributed among these distances:
6 2 0.01
7 22 0.12
8 15 0.08
9 133 0.74
10 5 0.03
11 3 0.02
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:30479856 original size:24 final size:24
Alignment explanation
Indices: 30479817--30479875 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 24
30479807 TTACTTTGAT
*
30479817 AACTTACATAAGTTACATAATACAC
1 AACTTACAT-AGTTACATAATACAA
*
30479842 AAC-TACATAGTTTACTTAATACAA
1 AACTTACATAG-TTACATAATACAA
30479866 AACTTACATA
1 AACTTACATA
30479876 ACTTATATAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 2 0.07
24 19 0.63
25 9 0.30
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (24 bp):
AACTTACATAGTTACATAATACAA
Found at i:30485481 original size:66 final size:65
Alignment explanation
Indices: 30485374--30485544 Score: 209
Period size: 66 Copynumber: 2.6 Consensus size: 65
30485364 GAGCAAATTA
* * * *
30485374 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCA
30485438 G
65 G
* *
30485439 CTACAACTGAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCA
30485504 G
65 G
* * ** *
30485505 CAGCAGCTTAAAGCAGATGCGGCAGTAAGAGAAGCAGAGG
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
30485545 CGGCAGCTAG
Statistics
Matches: 91, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
65 2 0.02
66 85 0.93
67 4 0.04
ACGTcount: A:0.40, C:0.19, G:0.28, T:0.13
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:30485539 original size:21 final size:21
Alignment explanation
Indices: 30485515--30485587 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
30485505 CAGCAGCTTA
*
30485515 AAGCAGATGCGGCAG-TAAGAG
1 AAGCAGAGGCGGCAGCT-AGAG
30485536 AAGCAGAGGCGGCAGCTAGAG
1 AAGCAGAGGCGGCAGCTAGAG
* * * * *
30485557 AAGTACAGGCTGCAGCGAGGG
1 AAGCAGAGGCGGCAGCTAGAG
30485578 AAGCAGAGGC
1 AAGCAGAGGC
30485588 TAAAGCGNNN
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
21 42 0.98
22 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.41, T:0.07
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCTAGAG
Found at i:30486101 original size:43 final size:43
Alignment explanation
Indices: 30486054--30486241 Score: 220
Period size: 43 Copynumber: 4.3 Consensus size: 43
30486044 AGGTGTTGGC
*
30486054 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATCATGGT
1 CTTTAGCGGCGTTTTTGGTCAAAGCGCCGCTAAAGATCATGGT
* **
30486097 CTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCATGGT
1 CTTTAGCGGCGTTTTTGGTCAAAGCGCCGCTAAAGATCATGGT
** * *
30486140 CTTTAGCGGCGTTTTTGGGGAAAGCGCTGCTAAAGATTA-GGTT
1 CTTTAGCGGCGTTTTTGGTCAAAGCGCCGCTAAAGATCATGG-T
* * *
30486183 CTTTAGTGGCGTTTTGTGGTCGAAA-CGCCGCTATAGATCAGGGT
1 CTTTAGCGGCGTTTT-TGGTC-AAAGCGCCGCTAAAGATCATGGT
30486227 CTATT-GCGGCGTTTT
1 CT-TTAGCGGCGTTTT
30486242 AGGGGAAAAA
Statistics
Matches: 124, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
42 2 0.02
43 88 0.71
44 27 0.22
45 7 0.06
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.32
Consensus pattern (43 bp):
CTTTAGCGGCGTTTTTGGTCAAAGCGCCGCTAAAGATCATGGT
Found at i:30486326 original size:75 final size:75
Alignment explanation
Indices: 30486175--30486317 Score: 175
Period size: 75 Copynumber: 1.9 Consensus size: 75
30486165 GCTGCTAAAG
* ** * *
30486175 ATTAGGTTCTTTAGTGGCGTTTTGTGGTCGAAACGCCGCTATAGATCAGGGTCTATTGCGGCGTT
1 ATTAGGTTCTTTAGTGGCGTTTTGTAGTCGAAACGCCGCTATAGATCAGGG-CTAAAGCGCCGCT
** *
30486240 TTAGGGGAAAA
65 AAAGGGAAAAA
30486251 ATTAGGTTCTTTAGTGGCG-TTTGTAGTC-AAAGCGCCGCTATAGATCAGGG-TAAAGCGCCGCT
1 ATTAGGTTCTTTAGTGGCGTTTTGTAGTCGAAA-CGCCGCTATAGATCAGGGCTAAAGCGCCGCT
30486313 AAAGG
65 AAAGG
30486318 CCTAAAAAAG
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
73 11 0.19
74 3 0.05
75 26 0.44
76 19 0.32
ACGTcount: A:0.23, C:0.16, G:0.31, T:0.30
Consensus pattern (75 bp):
ATTAGGTTCTTTAGTGGCGTTTTGTAGTCGAAACGCCGCTATAGATCAGGGCTAAAGCGCCGCTA
AAGGGAAAAA
Found at i:30488389 original size:6 final size:5
Alignment explanation
Indices: 30488367--30488450 Score: 60
Period size: 6 Copynumber: 14.6 Consensus size: 5
30488357 TTTACACCCT
30488367 AATAA AATAA GAATAA AATTAA AATTAA AGATAA AGATAA AGATGAA AATAAA
1 AATAA AATAA -AATAA AA-TAA AA-TAA A-ATAA A-ATAA A-AT-AA AAT-AA
*
30488420 AATAA ATTTAA AATAA AGATAAA AATAA AAT
1 AATAA A-ATAA AATAA A-AT-AA AATAA AAT
30488451 TTATATATCT
Statistics
Matches: 69, Mismatches: 3, Indels: 14
0.80 0.03 0.16
Matches are distributed among these distances:
5 19 0.28
6 43 0.62
7 7 0.10
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (5 bp):
AATAA
Found at i:30488401 original size:12 final size:11
Alignment explanation
Indices: 30488370--30488450 Score: 72
Period size: 12 Copynumber: 6.9 Consensus size: 11
30488360 ACACCCTAAT
30488370 AAAATAAGAATA
1 AAAATAA-AATA
*
30488382 AAATTAAAATTA
1 AAAATAAAA-TA
*
30488394 AAGATAAAGATA
1 AAAATAAA-ATA
*
30488406 AAGATGAAAATA
1 AAAAT-AAAATA
* *
30488418 AAAATAAATTT
1 AAAATAAAATA
30488429 AAAATAAAGATA
1 AAAATAAA-ATA
30488441 AAAATAAAAT
1 AAAATAAAAT
30488451 TTATATATCT
Statistics
Matches: 57, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
11 16 0.28
12 37 0.65
13 4 0.07
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.22
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:30488439 original size:41 final size:42
Alignment explanation
Indices: 30488370--30488448 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
30488360 ACACCCTAAT
* *
30488370 AAAATAAGAATAAAATTAAAATTAAAGATAAAGATAAAGATG
1 AAAATAAAAATAAAATTAAAATTAAAGATAAAAATAAAGATG
*
30488412 AAAATAAAAATAAATTTAAAA-TAAAGATAAAAATAAA
1 AAAATAAAAATAAAATTAAAATTAAAGATAAAAATAAA
30488449 ATTTATATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
41 15 0.44
42 19 0.56
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.22
Consensus pattern (42 bp):
AAAATAAAAATAAAATTAAAATTAAAGATAAAAATAAAGATG
Found at i:30490218 original size:12 final size:12
Alignment explanation
Indices: 30490201--30490225 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30490191 AAAATGGGTT
30490201 GTTCATTTCCAA
1 GTTCATTTCCAA
30490213 GTTCATTTCCAA
1 GTTCATTTCCAA
30490225 G
1 G
30490226 CGTGCATCAT
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:0.24, G:0.12, T:0.40
Consensus pattern (12 bp):
GTTCATTTCCAA
Found at i:30492203 original size:27 final size:27
Alignment explanation
Indices: 30492164--30492471 Score: 305
Period size: 27 Copynumber: 11.4 Consensus size: 27
30492154 CCCCAAAATA
* * *
30492164 GGTAAAATGACCAAAATACCCCCATAT
1 GGTAGAATGACCGAAATACCCCCATAG
* *
30492191 GGTAGAATAACC-ACAATACCCTCATAG
1 GGTAGAATGACCGA-AATACCCCCATAG
*
30492218 GGTAGAATGACCGAAATACCCCCACAG
1 GGTAGAATGACCGAAATACCCCCATAG
* * * *
30492245 GGTAAAATGACTGAAAGACCCTCATAG
1 GGTAGAATGACCGAAATACCCCCATAG
* * *
30492272 AGTAGAATGACTGAAATACCCTCATAG
1 GGTAGAATGACCGAAATACCCCCATAG
* *
30492299 GATAGAATGATCGAAATACCCCCATAG
1 GGTAGAATGACCGAAATACCCCCATAG
* * *
30492326 GATAAAATGACCGAAATA-CCCTATAG
1 GGTAGAATGACCGAAATACCCCCATAG
* * *
30492352 GGTAGAATGATCGAAATAACCCCGTAG
1 GGTAGAATGACCGAAATACCCCCATAG
* * * *
30492379 GGTAAAATAATCGAAATACCCCTATAG
1 GGTAGAATGACCGAAATACCCCCATAG
* *
30492406 GGTAGAATGACTGAAATACCTCCATAG
1 GGTAGAATGACCGAAATACCCCCATAG
* * *
30492433 GGTAAAATCACTGAAATACCCTCCATAG
1 GGTAGAATGACCGAAATACCC-CCATAG
*
30492461 GGTAAAATGAC
1 GGTAGAATGAC
30492472 TATTATACCC
Statistics
Matches: 234, Mismatches: 43, Indels: 7
0.82 0.15 0.02
Matches are distributed among these distances:
26 23 0.10
27 194 0.83
28 17 0.07
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (27 bp):
GGTAGAATGACCGAAATACCCCCATAG
Found at i:30498985 original size:21 final size:22
Alignment explanation
Indices: 30498939--30498985 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
30498929 CATTTTTCTT
*
30498939 TTCTTTTTCACTCTCTCTCAAT
1 TTCTTTTTCACTCTCTCTCAAA
*
30498961 TTCTTTTTCTA-T-TCTTTCAAA
1 TTCTTTTTC-ACTCTCTCTCAAA
30498982 TTCT
1 TTCT
30498986 CCAAAGATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 11 0.50
22 10 0.45
23 1 0.05
ACGTcount: A:0.15, C:0.26, G:0.00, T:0.60
Consensus pattern (22 bp):
TTCTTTTTCACTCTCTCTCAAA
Found at i:30502598 original size:10 final size:10
Alignment explanation
Indices: 30502585--30502611 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
30502575 ATATATGATC
30502585 ATATGTGCTT
1 ATATGTGCTT
30502595 ATATGTGCTT
1 ATATGTGCTT
30502605 ATATGTG
1 ATATGTG
30502612 GTTAATACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.22, C:0.07, G:0.22, T:0.48
Consensus pattern (10 bp):
ATATGTGCTT
Found at i:30504407 original size:41 final size:41
Alignment explanation
Indices: 30504342--30504423 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
30504332 GAGCTTTTCA
*
30504342 GGGCATTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTCT
1 GGGCATTAGCGGCGTTTTTAAAAAAACGCCGCTAATGCTCT
* * *
30504383 GGGCTTTAGCGGCGTTTTTGAAAAAATGCCGCTAATGCTCT
1 GGGCATTAGCGGCGTTTTTAAAAAAACGCCGCTAATGCTCT
30504424 ATTTTTAGTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (41 bp):
GGGCATTAGCGGCGTTTTTAAAAAAACGCCGCTAATGCTCT
Found at i:30504690 original size:29 final size:29
Alignment explanation
Indices: 30504624--30504690 Score: 66
Period size: 30 Copynumber: 2.3 Consensus size: 29
30504614 CATAGAAATA
*
30504624 ATTTGAAATGAAAAACATAAAAAAATATT
1 ATTTAAAATGAAAAACATAAAAAAATATT
* *
30504653 -TGTTAAAAATGAAAAA-ATTAAAATACTATT
1 AT-TT-AAAATGAAAAACA-TAAAAAAATATT
30504683 ATTTAAAA
1 ATTTAAAA
30504691 AAATTTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
28 1 0.03
29 7 0.23
30 22 0.71
31 1 0.03
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.31
Consensus pattern (29 bp):
ATTTAAAATGAAAAACATAAAAAAATATT
Found at i:30504920 original size:7 final size:7
Alignment explanation
Indices: 30504870--30504923 Score: 63
Period size: 7 Copynumber: 7.6 Consensus size: 7
30504860 GTGTTACCAT
*
30504870 TTTAAGG
1 TTTATGG
30504877 TTTATGG
1 TTTATGG
*
30504884 ATTATGGG
1 TTTAT-GG
30504892 TTTATGG
1 TTTATGG
* *
30504899 GTTATGA
1 TTTATGG
30504906 TTTATGG
1 TTTATGG
30504913 TTTATGG
1 TTTATGG
30504920 TTTA
1 TTTA
30504924 AAGACTGGGG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
7 33 0.85
8 6 0.15
ACGTcount: A:0.20, C:0.00, G:0.28, T:0.52
Consensus pattern (7 bp):
TTTATGG
Found at i:30504979 original size:15 final size:16
Alignment explanation
Indices: 30504959--30504996 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
30504949 TTATGTGTTA
30504959 AGGGTTTAT-GGGTTT
1 AGGGTTTATAGGGTTT
*
30504974 ATGGTTT-TAGGGTTT
1 AGGGTTTATAGGGTTT
30504989 AGGGTTTA
1 AGGGTTTA
30504997 GATTAACTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
14 1 0.05
15 18 0.95
ACGTcount: A:0.16, C:0.00, G:0.37, T:0.47
Consensus pattern (16 bp):
AGGGTTTATAGGGTTT
Found at i:30504989 original size:7 final size:7
Alignment explanation
Indices: 30504959--30504997 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
30504949 TTATGTGTTA
30504959 AGGGTTT
1 AGGGTTT
30504966 ATGGGTTT
1 A-GGGTTT
*
30504974 ATGGTTTT
1 A-GGGTTT
30504982 AGGGTTT
1 AGGGTTT
30504989 AGGGTTT
1 AGGGTTT
30504996 AG
1 AG
30504998 ATTAACTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 15 0.52
8 14 0.48
ACGTcount: A:0.15, C:0.00, G:0.38, T:0.46
Consensus pattern (7 bp):
AGGGTTT
Found at i:30508901 original size:87 final size:86
Alignment explanation
Indices: 30508753--30509031 Score: 378
Period size: 86 Copynumber: 3.2 Consensus size: 86
30508743 TCCTTCTACT
* * * *** *
30508753 TTATAAAAGTTGAAAATTTAGTCTGGTTGTTGGTGAGTGCATGAACTTGAATTGTTGATTTTTTT
1 TTATAAAAATTGAAAATTTAGTCTGGTTGTTGGTAAATGCATGAACTTGAACCATTGA-TTTTTG
*
30508818 CTAATTTGTTGCACATAAGTTG
65 CTAATTTGTTGCATATAAGTTG
*
30508840 TTATAAAAATTGAAAATTTAGTCTGGTTGTTGGTAAATGCATGAACTTGAACCATTTATTTTTGC
1 TTATAAAAATTGAAAATTTAGTCTGGTTGTTGGTAAATGCATGAACTTGAACCATTGATTTTTGC
30508905 TAATTTGTTGCATATAAGTTG
66 TAATTTGTTGCATATAAGTTG
* * * * * *
30508926 TTATAAATATTGAAAAATTAGTCTGATTTTTGGTAAATACATGATCTTGAACCATTGATTTTTGC
1 TTATAAAAATTGAAAATTTAGTCTGGTTGTTGGTAAATGCATGAACTTGAACCATTGATTTTTGC
* *
30508991 TAATTTGTTGCATATAAATCG
66 TAATTTGTTGCATATAAGTTG
* *
30509012 TTATAGAAATTGAAGATTTA
1 TTATAAAAATTGAAAATTTA
30509032 TCCCTATTGA
Statistics
Matches: 170, Mismatches: 22, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
86 119 0.70
87 51 0.30
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.43
Consensus pattern (86 bp):
TTATAAAAATTGAAAATTTAGTCTGGTTGTTGGTAAATGCATGAACTTGAACCATTGATTTTTGC
TAATTTGTTGCATATAAGTTG
Found at i:30509047 original size:86 final size:85
Alignment explanation
Indices: 30508753--30509110 Score: 362
Period size: 86 Copynumber: 4.1 Consensus size: 85
30508743 TCCTTCTACT
* * * * *** *
30508753 TTATAAAAGTTGAAAATTTAGTCTGGTTGTTGGTGAGTGCATGAACTTGAATTGTTGATTTTTTT
1 TTATAAAA-TTGAAAATTTAGTCTGATTGTTGGTAAATACATGAACTTGAACCATTGA-TTTTTG
*
30508818 CTAATTTGTTGCACATAAGTTG
64 CTAATTTGTTGCACATAAATTG
* * *
30508840 TTATAAAAATTGAAAATTTAGTCTGGTTGTTGGTAAATGCATGAACTTGAACCATTTATTTTTGC
1 TTAT-AAAATTGAAAATTTAGTCTGATTGTTGGTAAATACATGAACTTGAACCATTGATTTTTGC
* *
30508905 TAATTTGTTGCATATAAGTTG
65 TAATTTGTTGCACATAAATTG
* * *
30508926 TTATAAATATTGAAAAATTAGTCTGATTTTTGGTAAATACATGATCTTGAACCATTGATTTTTGC
1 TTATAAA-ATTGAAAATTTAGTCTGATTGTTGGTAAATACATGAACTTGAACCATTGATTTTTGC
* *
30508991 TAATTTGTTGCATATAAATCG
65 TAATTTGTTGCACATAAATTG
* ** * *
30509012 TTATAGAAATTGAAGATTTA-TCCCT-ATTGACGGTAAATATATGAACTATGAA-TAGTTGATTT
1 TTATA-AAATTGAAAATTTAGT--CTGATTGTTGGTAAATACATGAACT-TGAACCA-TTGATTT
* *
30509074 TTGCTAATTTGTTTCACATAAACTG
61 TTGCTAATTTGTTGCACATAAATTG
* *
30509099 TTGTAAGATTGA
1 TTATAAAATTGA
30509111 TTTGTGTTAA
Statistics
Matches: 234, Mismatches: 30, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
85 4 0.02
86 139 0.59
87 87 0.37
88 4 0.02
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (85 bp):
TTATAAAATTGAAAATTTAGTCTGATTGTTGGTAAATACATGAACTTGAACCATTGATTTTTGCT
AATTTGTTGCACATAAATTG
Found at i:30509076 original size:173 final size:173
Alignment explanation
Indices: 30508753--30509086 Score: 381
Period size: 173 Copynumber: 1.9 Consensus size: 173
30508743 TCCTTCTACT
* * * * * *** *
30508753 TTATAAAAGTTGAAAATTTAGTCTGGTTGTTGGTGAGTGCATGAACTTGAATTGTTGATTTTTTT
1 TTATAAAAGTTGAAAAATTAGTCTGATTGTTGGTAAATACATGAACTTGAACCATTGATTTTTTG
* * * ** *
30508818 CTAATTTGTTGCACATAAGTTGTTATAAAAATTGAAAATTTAGTCTGGTTGTTGGTAAATGCATG
66 CTAATTTGTTGCACATAAATCGTTATAAAAATTGAAAATTTAGTCTGATTGACGGTAAATACATG
*
30508883 AACTTGAACCATTTATTTTTGCTAATTTGTTGCATATAAGTTG
131 AACTTGAACCATTGATTTTTGCTAATTTGTTGCATATAAGTTG
* *
30508926 TTATAAATA-TTGAAAAATTAGTCTGATTTTTGGTAAATACATGATCTTGAACCATTGA-TTTTT
1 TTATAAA-AGTTGAAAAATTAGTCTGATTGTTGGTAAATACATGAACTTGAACCATTGATTTTTT
* * * *
30508989 GCTAATTTGTTGCATATAAATCGTTATAGAAATTGAAGATTTA-TCCCT-ATTGACGGTAAATAT
65 GCTAATTTGTTGCACATAAATCGTTATAAAAATTGAAAATTTAGT--CTGATTGACGGTAAATAC
*
30509052 ATGAACTATGAA-TAGTTGATTTTTGCTAATTTGTT
128 ATGAACT-TGAACCA-TTGATTTTTGCTAATTTGTT
30509087 TCACATAAAC
Statistics
Matches: 133, Mismatches: 23, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
171 1 0.01
172 60 0.45
173 71 0.53
174 1 0.01
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.43
Consensus pattern (173 bp):
TTATAAAAGTTGAAAAATTAGTCTGATTGTTGGTAAATACATGAACTTGAACCATTGATTTTTTG
CTAATTTGTTGCACATAAATCGTTATAAAAATTGAAAATTTAGTCTGATTGACGGTAAATACATG
AACTTGAACCATTGATTTTTGCTAATTTGTTGCATATAAGTTG
Found at i:30509151 original size:40 final size:40
Alignment explanation
Indices: 30509107--30509191 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
30509097 TGTTGTAAGA
* * *
30509107 TTGATTTGTGTTAATTTCTTGCATA-TAAATTATTGAAATG
1 TTGATTTGTGATAATTCCTTACATATTAAA-TATTGAAATG
* *
30509147 TTGATTTTTGATAATTCCTTACATATTAAATATTGAAGTG
1 TTGATTTGTGATAATTCCTTACATATTAAATATTGAAATG
30509187 TTGAT
1 TTGAT
30509192 ATTCAAGCTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 35 0.90
41 4 0.10
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.49
Consensus pattern (40 bp):
TTGATTTGTGATAATTCCTTACATATTAAATATTGAAATG
Found at i:30510398 original size:43 final size:44
Alignment explanation
Indices: 30510350--30510442 Score: 102
Period size: 43 Copynumber: 2.2 Consensus size: 44
30510340 ATAAACACCA
30510350 CTAAAGAACCACACT-TTTAGCAGCGTTTGT-GATAAAAGCGCCG
1 CTAAAGAACCACACTCTTTAGCAGCGTTTGTGGATAAAA-CGCCG
* ** * * *
30510393 CTAAAG-ATCATGCTCTTTAGCAGCGTTTTTGGGTAAAATGCCG
1 CTAAAGAACCACACTCTTTAGCAGCGTTTGTGGATAAAACGCCG
30510436 CTAAAGA
1 CTAAAGA
30510443 TCATGTTTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
42 5 0.12
43 30 0.73
44 6 0.15
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (44 bp):
CTAAAGAACCACACTCTTTAGCAGCGTTTGTGGATAAAACGCCG
Found at i:30510443 original size:43 final size:43
Alignment explanation
Indices: 30510365--30510635 Score: 216
Period size: 43 Copynumber: 6.3 Consensus size: 43
30510355 GAACCACACT
* * *
30510365 TTTAGCAGCGTTTGT-GATAAAAGCGCCGCTAAAGATCATGCTC
1 TTTAGCGGCGTTTGTGGGTAAAA-TGCCGCTAAAGATCATGCTC
* * *
30510408 TTTAGCAGCGTTTTTGGGTAAAATGCCGCTAAAGATCATG-TT
1 TTTAGCGGCGTTTGTGGGTAAAATGCCGCTAAAGATCATGCTC
* * *
30510450 TTATAGCGGCGTTTGTGGGTAAAGTGCCGCTAAAGCTCATGTTC
1 TT-TAGCGGCGTTTGTGGGTAAAATGCCGCTAAAGATCATGCTC
* * * *
30510494 TATAGTGACGTTTGTGGG-AAAA-GCGTCGCTAAA-AGTCATGGTC
1 TTTAGCGGCGTTTGTGGGTAAAATGC--CGCTAAAGA-TCATGCTC
* * * * *
30510537 TATAGTGGCATTTGTGGGAAAAATGCCGCTAAA-AGTCATGATC
1 TTTAGCGGCGTTTGTGGGTAAAATGCCGCTAAAGA-TCATGCTC
* * * *
30510580 TATAGCGGCGTTTGTGAG-AGAATCGCCGCTAAAGGTCATGACT-
1 TTTAGCGGCGTTTGTGGGTAAAAT-GCCGCTAAAGATCATG-CTC
30510623 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
30510636 ATGTCTAAAA
Statistics
Matches: 192, Mismatches: 25, Indels: 22
0.80 0.10 0.09
Matches are distributed among these distances:
41 2 0.01
42 10 0.05
43 165 0.86
44 13 0.07
45 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGTAAAATGCCGCTAAAGATCATGCTC
Found at i:30510608 original size:129 final size:129
Alignment explanation
Indices: 30510373--30510619 Score: 304
Period size: 129 Copynumber: 1.9 Consensus size: 129
30510363 CTTTTAGCAG
* * * * *
30510373 CGTTTGTGATAAAAGCGCCGCTAAAGATCATGCTCTTTAGCAGCGTTTTTGGGTAAAATGCCGCT
1 CGTTTGTGAGAAAAGCGCCGCTAAAGATCATGCTCTATAGCAGCATTTGTGGGAAAAATGCCGCT
* * *
30510438 AAAGATCATGTTTTATAGCGGCGTTTGTGGGTAAAGTGCCGCTAAAGCTCATGTTCTATAGTGA
66 AAAGATCATGATCTATAGCGGCGTTTGTGAGTAAAGTGCCGCTAAAGCTCATGTTCTATAGTGA
* * * **
30510502 CGTTTGTGGGAAAAGCGTCGCTAAA-AGTCATGGTCTATAGTGGCATTTGTGGGAAAAATGCCGC
1 CGTTTGTGAGAAAAGCGCCGCTAAAGA-TCATGCTCTATAGCAGCATTTGTGGGAAAAATGCCGC
*
30510566 TAAA-AGTCATGATCTATAGCGGCGTTTGTGAG-AGAA-TCGCCGCTAAAGGTCATG
65 TAAAGA-TCATGATCTATAGCGGCGTTTGTGAGTA-AAGT-GCCGCTAAAGCTCATG
30510620 ACTTTTAGCG
Statistics
Matches: 100, Mismatches: 14, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
128 4 0.04
129 96 0.96
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.29
Consensus pattern (129 bp):
CGTTTGTGAGAAAAGCGCCGCTAAAGATCATGCTCTATAGCAGCATTTGTGGGAAAAATGCCGCT
AAAGATCATGATCTATAGCGGCGTTTGTGAGTAAAGTGCCGCTAAAGCTCATGTTCTATAGTGA
Found at i:30521223 original size:173 final size:172
Alignment explanation
Indices: 30521044--30521467 Score: 710
Period size: 173 Copynumber: 2.5 Consensus size: 172
30521034 ACTAAGAAAG
30521044 CAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAG
1 CAAGTCTTAT-CTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAG
* *
30521109 TTGTAGTGGAGCAGGTTAAAGTCGATAATCCTATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAA
65 TTGCAGTGGAGCAGGTTAAAGCCGATAATCCTATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAA
30521174 CCTTGGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCAT
130 CCTTGGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCAT
*
30521217 CAAGTCTTATTCTCCTGAAGTGGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAG
1 CAAGTCTTA-TCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAG
30521282 TTGCAGTGGAGCAGGTTAAAGCCGATAATCCTATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAA
65 TTGCAGTGGAGCAGGTTAAAGCCGATAATCCTATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAA
* *
30521347 CCTTGGATCTTATCTCTCTGAAGTTGCAGAGAGTAGATCGCAT
130 CCTTGGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCAT
* *
30521390 CTAGTCTTATCTCCCTGAAGTTGCAGTG-GAGCAGACT-AAG-TAAGCAAATCTTATCTCCCTGA
1 CAAGTCTTATCT-CCTGAAGTTGCAGTGAG-GCAGACTGAAGAT-GGCAAATCTTATCTCCCTGA
*
30521452 AATTGCAGTGGAGCAG
63 AGTTGCAGTGGAGCAG
30521468 ACTGAAGATG
Statistics
Matches: 238, Mismatches: 9, Indels: 9
0.93 0.04 0.04
Matches are distributed among these distances:
171 1 0.00
172 41 0.17
173 195 0.82
174 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (172 bp):
CAAGTCTTATCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGT
TGCAGTGGAGCAGGTTAAAGCCGATAATCCTATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAAC
CTTGGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCAT
Found at i:30521325 original size:217 final size:216
Alignment explanation
Indices: 30520917--30521592 Score: 741
Period size: 217 Copynumber: 3.1 Consensus size: 216
30520907 CAGTAGCCAG
* *
30520917 TAATCCTATCTCTCTGAAGTTGCAGTGGGGTGGATTAAAACCTTGGATCTTATCTCTTTGAAGTT
1 TAATCCTATCTCTCTGAAGTTGCAGTGGAGTGGATTAAAACCTTGGATCTTATCTCTCTGAAGTT
* **
30520982 GCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGAAAGCA
66 GCAGAGAGCAGATCGCATCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGCA
* * * * *
30521046 AGTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGC-A-AATCTTATCTCCCTGA
131 AATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAA-A-GCCGATAATCCTATCTTCCTGA
* * *
30521107 AGTTGTAGTGGAGCAGG-TTAAAGTCGA
191 AGTTGCAGTGGAGC-GGATTAAA-ACCA
30521134 TAATCCTATCT-TCCTGAAGTTGCAGTGGAGTGGATTAAAACCTTGGATCTTATCTCTCTGAAGT
1 TAATCCTATCTCT-CTGAAGTTGCAGTGGAGTGGATTAAAACCTTGGATCTTATCTCTCTGAAGT
* *
30521198 TACAGAGAGCAGATCGCATCAAGTCTTAT-TCTCCTGAAGTGGCAGT-GAGGCAGACTGAAGATG
65 TGCAGAGAGCAGATCGCATCAAGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACTGAAGATG
*
30521261 GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAGCCGATAATCCTATCTTCCTGAAG
128 GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTTCCTGAAG
* *
30521326 TTGCAGTGGAGTGGATTAAAACCT
193 TTGCAGTGGAGCGGATTAAAACCA
* * * * *** * * *
30521350 TGGATCTTATCTCTCTGAAGTTGCAG-AGAGTAGA-TCGCATC-TAG-TCTTATCTCCCTGAAGT
1 T-AATCCTATCTCTCTGAAGTTGCAGTGGAGTGGATTAAAACCTTGGATCTTATCTCTCTGAAGT
* * * * * *
30521411 TGCAGTGGAGCAGACTAAGTAAGCAAATCTTATCTCCCTGAAATTGCAGTGGAGCAGACTGAAGA
65 TGCAG-AGAGCAGA-T-CG-CATCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGA
* * *
30521476 TGACAAATCTTATCTCACTGAAGTTACAGTGGAGCAGATTAAAGCCGATAATCCTATC-TCCTTG
126 TGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTTCC-TG
*
30521540 AAGTTGCAGTGGAGCGGATTAAAACCT
190 AAGTTGCAGTGGAGCGGATTAAAACCA
* *
30521567 TGGATCTTATCTCTCTGAAGTTGCAG
1 T-AATCCTATCTCTCTGAAGTTGCAG
30521593 AGAGCAGATC
Statistics
Matches: 400, Mismatches: 41, Indels: 36
0.84 0.09 0.08
Matches are distributed among these distances:
213 20 0.05
214 9 0.02
215 6 0.01
216 21 0.05
217 303 0.76
218 38 0.09
219 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (216 bp):
TAATCCTATCTCTCTGAAGTTGCAGTGGAGTGGATTAAAACCTTGGATCTTATCTCTCTGAAGTT
GCAGAGAGCAGATCGCATCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGCA
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTTCCTGAAGTTG
CAGTGGAGCGGATTAAAACCA
Found at i:30521419 original size:84 final size:84
Alignment explanation
Indices: 30521140--30521420 Score: 268
Period size: 84 Copynumber: 3.3 Consensus size: 84
30521130 TCGATAATCC
* *
30521140 TATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTACAGAG
1 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAG
*
30521205 AGCAGATCGCATCAAGTCT
66 AGCAGATCGCATCTAGTCT
* * * *
30521224 TAT-TCTCCTGAAGTGGCAGT-GAG-GCAGACTGAAGA---TGGCAAATCTTATCTCCCTGAAGT
1 TATCTC-CCTGAAGTTGCAGTGGAGTG--GA-TTAAAACCTTGG---ATCTTATCTCTCTGAAGT
* ** *** * *
30521283 TGCAGTGGAGCAGGTTAAAGCCGATAATCC
59 TGCAG-AGAGCA-G--ATCGCATCTAGTCT
*
30521313 TATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAG
1 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAG
*
30521378 AGTAGATCGCATCTAGTCT
66 AGCAGATCGCATCTAGTCT
30521397 TATCTCCCTGAAGTTGCAGTGGAG
1 TATCTCCCTGAAGTTGCAGTGGAG
30521421 CAGACTAAGT
Statistics
Matches: 150, Mismatches: 30, Indels: 34
0.70 0.14 0.16
Matches are distributed among these distances:
82 4 0.03
83 4 0.03
84 48 0.32
85 25 0.17
86 6 0.04
87 5 0.03
88 26 0.17
89 24 0.16
90 4 0.03
91 4 0.03
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (84 bp):
TATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAG
AGCAGATCGCATCTAGTCT
Found at i:30521560 original size:44 final size:44
Alignment explanation
Indices: 30521004--30521601 Score: 316
Period size: 44 Copynumber: 13.7 Consensus size: 44
30520994 TCGCATCTAG
* *
30521004 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAAG-C-A-AG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-T--TAAAGCCGATAA
* *
30521048 TCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGC-A-AA
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAA-A-GCCGATAA
* * *
30521093 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGGTTAAAGTCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAA
* * ** * * *
30521137 TCCTATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAACC-TTGGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGAT-AA
* * * *
30521181 TCTTATCTCTCTGAAGTTACAG-AGAGCAGA-T--CG-C-ATCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGAT-AA
* * *
30521220 GTCTTAT-TCTCCTGAAGTGGCAGT-GAGGCAGACTGAAGATGGC-A-AA
1 -TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAA-A-GCCGATAA
*
30521266 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAGCCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAA
* * ** * * *
30521310 TCCTATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAACC-TTGGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGAT-AA
* * * * *** *
30521354 TCTTATCTCTCTGAAGTTGCAG-AGAGTAGA-T--CGCATCTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAA
*
30521394 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAG-C-A-AA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTA--AAGCCGATAA
* * * ** *
30521438 TCTTATCTCCCTGAAATTGCAGTGGAGCAGACTGAAGATGACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGA-TAA
* *
30521483 TCTTATCTCACTGAAGTTACAGTGGAGCAGATTAAAGCCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAA
* * * * * *
30521527 TCCTATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAACC-TTGGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGAT-AA
* *
30521571 TCTTATCTCTCTGAAGTTGCAG-AGAGCAGAT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
30521602 CGCATTTAGT
Statistics
Matches: 426, Mismatches: 89, Indels: 79
0.72 0.15 0.13
Matches are distributed among these distances:
39 5 0.01
40 40 0.09
41 15 0.04
42 9 0.02
43 30 0.07
44 228 0.54
45 86 0.20
46 9 0.02
47 2 0.00
48 2 0.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAA
Found at i:30522993 original size:11 final size:11
Alignment explanation
Indices: 30522977--30523001 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
30522967 TTTTTTTATG
30522977 TTTGTAAGAAT
1 TTTGTAAGAAT
30522988 TTTGTAAGAAT
1 TTTGTAAGAAT
30522999 TTT
1 TTT
30523002 AGCTTTCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (11 bp):
TTTGTAAGAAT
Found at i:30531585 original size:17 final size:17
Alignment explanation
Indices: 30531563--30531597 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
30531553 TCACAATAAT
30531563 TGGAAGGTGCATGCTTA
1 TGGAAGGTGCATGCTTA
30531580 TGGAAGGTGCATGCTTA
1 TGGAAGGTGCATGCTTA
30531597 T
1 T
30531598 TTATAACCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.11, G:0.34, T:0.31
Consensus pattern (17 bp):
TGGAAGGTGCATGCTTA
Found at i:30533042 original size:17 final size:18
Alignment explanation
Indices: 30533022--30533058 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
30533012 CTTCAAAATG
30533022 AAAA-TTACTTCATTTCA
1 AAAATTTACTTCATTTCA
30533039 AAAATTTTACTTCATTTCA
1 AAAA-TTTACTTCATTTCA
30533058 A
1 A
30533059 TTAGCTCCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
19 14 0.78
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.43
Consensus pattern (18 bp):
AAAATTTACTTCATTTCA
Found at i:30542279 original size:51 final size:49
Alignment explanation
Indices: 30542134--30542318 Score: 185
Period size: 51 Copynumber: 3.7 Consensus size: 49
30542124 GAAGTTGCTA
* * *
30542134 GGTCACGTGTGTAGTACTATGTGCAGCCTACTACGTGTACCGGA-ATGAT
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTCTACCGGATA-GAT
* * * * *
30542183 AGGTCGCATGTGTAGTACTATGTGCAGGCTATTATG-CGTGCCGGATAGCTT
1 -GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTC-TACCGGATAG-AT
* * * *
30542234 CGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTCTATCGGATGAAAAT
1 -GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTCTACCGGAT--AGAT
30542286 GGTCACATGTGTAGTACTATGTGCAGGCTACTA
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTA
30542319 TGTGAACTGG
Statistics
Matches: 109, Mismatches: 20, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
50 37 0.34
51 69 0.63
52 2 0.02
53 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTCTACCGGATAGAT
Found at i:30546897 original size:21 final size:21
Alignment explanation
Indices: 30546873--30546921 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
30546863 ATGTAATCCA
*
30546873 TATCACTAACTTTATTATTTC
1 TATCAATAACTTTATTATTTC
**
30546894 TATCAATTTCTTTATTATTTC
1 TATCAATAACTTTATTATTTC
30546915 TATCAAT
1 TATCAAT
30546922 TCATTCATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.16, G:0.00, T:0.55
Consensus pattern (21 bp):
TATCAATAACTTTATTATTTC
Found at i:30546922 original size:21 final size:21
Alignment explanation
Indices: 30546882--30546922 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
30546872 ATATCACTAA
30546882 CTTTATTATTTCTATCAATTT
1 CTTTATTATTTCTATCAATTT
30546903 CTTTATTATTTCTATCAATT
1 CTTTATTATTTCTATCAATT
30546923 CATTCATGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.61
Consensus pattern (21 bp):
CTTTATTATTTCTATCAATTT
Found at i:30546934 original size:21 final size:21
Alignment explanation
Indices: 30546889--30546935 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
30546879 TAACTTTATT
* *
30546889 ATTTCTATCAATTTCTTTATT
1 ATTTCTATCAATTTCTTCATG
30546910 ATTTCTATCAA-TTCATTCATG
1 ATTTCTATCAATTTC-TTCATG
30546931 ATTTC
1 ATTTC
30546936 AACAAGCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.26, C:0.17, G:0.02, T:0.55
Consensus pattern (21 bp):
ATTTCTATCAATTTCTTCATG
Found at i:30551637 original size:2 final size:2
Alignment explanation
Indices: 30551630--30551663 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
30551620 CATAATCTAG
30551630 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
30551664 AATTTTTAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30570578 original size:25 final size:26
Alignment explanation
Indices: 30570542--30570594 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
30570532 TGTAAAATGA
30570542 AATGGTTATATGAAATAGATATACGG
1 AATGGTTATATGAAATAGATATACGG
* * *
30570568 AATGG-TATATGAATTAGTTATATGG
1 AATGGTTATATGAAATAGATATACGG
30570593 AA
1 AA
30570595 ACAAATATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.42, C:0.02, G:0.23, T:0.34
Consensus pattern (26 bp):
AATGGTTATATGAAATAGATATACGG
Found at i:30577019 original size:49 final size:49
Alignment explanation
Indices: 30576945--30577079 Score: 216
Period size: 49 Copynumber: 2.8 Consensus size: 49
30576935 GATAATAACA
* * *
30576945 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTGTAC
1 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGATGTTTCCTGTAC
* *
30576994 TGCCAATGCCATATCCTAGATATGGTCTTACATGGGATGTTTCTTGTAC
1 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGATGTTTCCTGTAC
*
30577043 TGCCAATGCCATATCCCAGATATGGTCTTATATGGGA
1 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGA
30577080 GTTCTCATAT
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 79 1.00
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (49 bp):
TGCCAATGCCATATCCCAGATATGGTCTTACATGGGATGTTTCCTGTAC
Found at i:30577118 original size:50 final size:49
Alignment explanation
Indices: 30576945--30577121 Score: 214
Period size: 49 Copynumber: 3.6 Consensus size: 49
30576935 GATAATAACA
* *
30576945 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTGTAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATGTAC
* * * *
30576994 TGCCAATGCCATATCCTAGATATGGTCTTACATGGGATGTTTCTTGTAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATGTAC
* * * * *
30577043 TGCCAATGCCATATCCCAGATATGGTCTTATATGGGA-GTTCTCATATAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATGTT-TCATGTA-C
30577093 TGTCC-ATGCCATGTCCCAGACATGGTCTT
1 TG-CCAATGCCATGTCCCAGACATGGTCTT
30577122 GTGGGGGACC
Statistics
Matches: 113, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
48 3 0.03
49 84 0.74
50 24 0.21
51 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.32
Consensus pattern (49 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATGTAC
Found at i:30577136 original size:50 final size:50
Alignment explanation
Indices: 30576945--30577188 Score: 170
Period size: 49 Copynumber: 4.9 Consensus size: 50
30576935 GATAATAACA
* ** ** * * * *
30576945 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTGTA-C
1 TGCCAATGCCATGTCCCAGACATGGTCTTATGTGGGACCTCTCATATAGG
* * * ** ** * * * *
30576994 TGCCAATGCCATATCCTAGATATGGTCTTACATGGGATGTTTCTTGTA-C
1 TGCCAATGCCATGTCCCAGACATGGTCTTATGTGGGACCTCTCATATAGG
* * * **
30577043 TGCCAATGCCATATCCCAGATATGGTCTTATATGGGAGTTCTCATATAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTATGTGGGACCTCTCATATAGG
* * * *
30577093 TGTCC-ATGCCATGTCCCAGACATGGTCTTGTGGGGGACCTCTCATCTCGG
1 TG-CCAATGCCATGTCCCAGACATGGTCTTATGTGGGACCTCTCATATAGG
* * *
30577143 TGCCAACGCCATGTCCTAGACATGGTCTTACGTGGGACCTCTCATA
1 TGCCAATGCCATGTCCCAGACATGGTCTTATGTGGGACCTCTCATA
30577189 ACCTCAATAA
Statistics
Matches: 164, Mismatches: 28, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
49 87 0.53
50 75 0.46
51 2 0.01
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.30
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTATGTGGGACCTCTCATATAGG
Found at i:30581681 original size:3 final size:3
Alignment explanation
Indices: 30581666--30581740 Score: 141
Period size: 3 Copynumber: 25.0 Consensus size: 3
30581656 TTTAATGCAC
*
30581666 TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
30581714 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
30581741 ATAAAATACA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:30590317 original size:42 final size:42
Alignment explanation
Indices: 30590259--30590382 Score: 159
Period size: 42 Copynumber: 3.0 Consensus size: 42
30590249 ACCAAAAATT
*
30590259 TATTTTAAAAATTAAAAAAAGTATTTTAAAAAAATTTTAAAAA
1 TATTTT-AAAATTAAAAAAAGTATTTTAAAAATATTTTAAAAA
30590302 TATTTTAAAATT-AAAAAA-TATTTTAAAAATATTTT--AAA
1 TATTTTAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAAA
*
30590340 -ATTTAAAAATAATAAAATAAAGTATTTTAAAAATATTTTAAAA
1 TATTTTAAAAT--TAAAA-AAAGTATTTTAAAAATATTTTAAAA
30590383 TTAAAAAAAA
Statistics
Matches: 72, Mismatches: 2, Indels: 13
0.83 0.02 0.15
Matches are distributed among these distances:
37 9 0.12
38 3 0.04
39 1 0.01
40 19 0.26
41 9 0.12
42 23 0.32
43 6 0.08
44 2 0.03
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (42 bp):
TATTTTAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAAA
Found at i:30590326 original size:29 final size:29
Alignment explanation
Indices: 30590284--30590350 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 29
30590274 AAAAAGTATT
30590284 TTAAAAAA-ATTTTAAAAATATTTTAAAA
1 TTAAAAAATATTTTAAAAATATTTTAAAA
30590312 TTAAAAAATATTTTAAAAATATTTTAAAA
1 TTAAAAAATATTTTAAAAATATTTTAAAA
*
30590341 TTTAAAAATA
1 TTAAAAAATA
30590351 ATAAAATAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
28 8 0.22
29 29 0.78
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (29 bp):
TTAAAAAATATTTTAAAAATATTTTAAAA
Found at i:30590350 original size:18 final size:19
Alignment explanation
Indices: 30590259--30590329 Score: 72
Period size: 18 Copynumber: 3.5 Consensus size: 19
30590249 ACCAAAAATT
*
30590259 TATTTTAAAAATTAAAAAAA
1 TATTTT-AAAATTTAAAAAA
*
30590279 GTATTTTAAAAAAATTTTAAAAA
1 -TATTTT---AAAATTTAAAAAA
30590302 TATTTTAAAA-TTAAAAAA
1 TATTTTAAAATTTAAAAAA
30590320 TATTTTAAAA
1 TATTTTAAAA
30590330 ATATTTTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
18 17 0.38
19 4 0.09
21 6 0.13
22 6 0.13
23 12 0.27
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (19 bp):
TATTTTAAAATTTAAAAAA
Found at i:30590378 original size:11 final size:11
Alignment explanation
Indices: 30590274--30590382 Score: 90
Period size: 11 Copynumber: 10.4 Consensus size: 11
30590264 TAAAAATTAA
30590274 AAAAAGTATTTT
1 AAAAA-TATTTT
*
30590286 AAAAAAATTTT
1 AAAAATATTTT
30590297 AAAAATATTTT
1 AAAAATATTTT
*
30590308 --AAA-A-TTA
1 AAAAATATTTT
30590315 AAAAATATTTT
1 AAAAATATTTT
30590326 AAAAATATTTT
1 AAAAATATTTT
30590337 --AAA-A-TTT
1 AAAAATATTTT
* **
30590344 AAAAATAATAA
1 AAAAATATTTT
30590355 AATAAAGTATTTT
1 AA-AAA-TATTTT
30590368 AAAAATATTTT
1 AAAAATATTTT
30590379 AAAA
1 AAAA
30590383 TTAAAAAAAA
Statistics
Matches: 78, Mismatches: 9, Indels: 21
0.72 0.08 0.19
Matches are distributed among these distances:
7 5 0.06
8 2 0.03
9 12 0.15
10 2 0.03
11 41 0.53
12 11 0.14
13 5 0.06
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:30591144 original size:16 final size:17
Alignment explanation
Indices: 30591125--30591156 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
30591115 CCCTTCCCTC
30591125 AAAC-TTTTATTCCCCA
1 AAACTTTTTATTCCCCA
30591141 AAACTTTTTATTCCCC
1 AAACTTTTTATTCCCC
30591157 CCTAAACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.28, C:0.31, G:0.00, T:0.41
Consensus pattern (17 bp):
AAACTTTTTATTCCCCA
Found at i:30599875 original size:42 final size:42
Alignment explanation
Indices: 30599800--30599913 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 42
30599790 TCCTTTGTAT
* * * *
30599800 GTAAGTCAGTGAGTTACACGACCTGGCACACGGGCATCTGGG
1 GTAAATCAGAGAGTTACACGGCCTGGCATACGGGCATCTGGG
* * ** *
30599842 GTAAATTAGAGAGTTACACGGCCTGACATACGGGTGTGTGGG
1 GTAAATCAGAGAGTTACACGGCCTGGCATACGGGCATCTGGG
* *
30599884 GTAACTCAGAGAGTAACACGGCCTGGCATA
1 GTAAATCAGAGAGTTACACGGCCTGGCATA
30599914 TGGACGTGTG
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.27, C:0.20, G:0.32, T:0.20
Consensus pattern (42 bp):
GTAAATCAGAGAGTTACACGGCCTGGCATACGGGCATCTGGG
Found at i:30599923 original size:42 final size:42
Alignment explanation
Indices: 30599838--30599923 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 42
30599828 CACGGGCATC
* * **
30599838 TGGGGTAAATTAGAGAGTTACACGGCCTGACATACGGGTGTG
1 TGGGGTAAATCAGAGAGTAACACGGCCTGACATACGGACGTG
* * *
30599880 TGGGGTAACTCAGAGAGTAACACGGCCTGGCATATGGACGTG
1 TGGGGTAAATCAGAGAGTAACACGGCCTGACATACGGACGTG
30599922 TG
1 TG
30599924 ACCTTACTCA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.26, C:0.16, G:0.36, T:0.22
Consensus pattern (42 bp):
TGGGGTAAATCAGAGAGTAACACGGCCTGACATACGGACGTG
Found at i:30600641 original size:61 final size:62
Alignment explanation
Indices: 30600366--30600648 Score: 310
Period size: 61 Copynumber: 4.6 Consensus size: 62
30600356 GGACAAGAAA
* * * * *
30600366 GCCTTTATGGAAAAAATAT-GGACAAGAAAGCCTTTGTGATGAGTACTGAATGTTAAGGAAC
1 GCCTTTGTGGAAAAACTCTAGGACAGGAAAGCCTTTGTGGTGAGTACTGAATGTTAAGGAAC
* * * *
30600427 GCTTTTGTGGCAAAAA-TCTAGG-CAGGAAAGCCTTTGCGGTGAGTATTGAATGTTAAGGAAT
1 GCCTTTGTGG-AAAAACTCTAGGACAGGAAAGCCTTTGTGGTGAGTACTGAATGTTAAGGAAC
** * * * *
30600488 GTTTTTGTGGAAAACCTCTA-GATAGGAAAGCCTTTGTGGCGAGTACTGAATGTTAAGGAAT
1 GCCTTTGTGGAAAAACTCTAGGACAGGAAAGCCTTTGTGGTGAGTACTGAATGTTAAGGAAC
* *
30600549 GCCTTTGTGGAAAAACTCT-GGACAGGAAAGCCTTTGTGGTGAGTATTAAATGTTAAGGAAC
1 GCCTTTGTGGAAAAACTCTAGGACAGGAAAGCCTTTGTGGTGAGTACTGAATGTTAAGGAAC
* * * *
30600610 ACCTTTATGGAAAAACT-TAGGGA-AGGTAAGCCTATGTGG
1 GCCTTTGTGGAAAAACTCTA-GGACAGGAAAGCCTTTGTGG
30600649 CGAACCTTTG
Statistics
Matches: 189, Mismatches: 26, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
60 6 0.03
61 173 0.92
62 10 0.05
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.28
Consensus pattern (62 bp):
GCCTTTGTGGAAAAACTCTAGGACAGGAAAGCCTTTGTGGTGAGTACTGAATGTTAAGGAAC
Found at i:30603585 original size:25 final size:25
Alignment explanation
Indices: 30603556--30603623 Score: 100
Period size: 25 Copynumber: 2.7 Consensus size: 25
30603546 GATACTCCAC
*
30603556 AGCTCGTGAGAGCATACTGATTTAT
1 AGCTCGTGAGAGCATACCGATTTAT
*
30603581 AGCTCGTAAGAGCATACCGATTTAT
1 AGCTCGTGAGAGCATACCGATTTAT
**
30603606 AGCTTATGAGAGCATACC
1 AGCTCGTGAGAGCATACC
30603624 AATCTACAGC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (25 bp):
AGCTCGTGAGAGCATACCGATTTAT
Found at i:30609583 original size:19 final size:19
Alignment explanation
Indices: 30609549--30609585 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
30609539 ATTTGATCTC
* *
30609549 TTTCCTTTTGTTTTTTTAA
1 TTTCCTTTTATGTTTTTAA
30609568 TTTCCTTTTATGTTTTTA
1 TTTCCTTTTATGTTTTTA
30609586 GGATAGTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.11, G:0.05, T:0.73
Consensus pattern (19 bp):
TTTCCTTTTATGTTTTTAA
Found at i:30621425 original size:20 final size:20
Alignment explanation
Indices: 30621400--30621441 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
30621390 TCAGAGTATT
30621400 TTCTAACTCTTTTAACATGA
1 TTCTAACTCTTTTAACATGA
*
30621420 TTCTAACTTTTTTAACATGA
1 TTCTAACTCTTTTAACATGA
30621440 TT
1 TT
30621442 AGAATGTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.50
Consensus pattern (20 bp):
TTCTAACTCTTTTAACATGA
Found at i:30621466 original size:32 final size:31
Alignment explanation
Indices: 30621424--30621497 Score: 123
Period size: 32 Copynumber: 2.4 Consensus size: 31
30621414 ACATGATTCT
30621424 AACTTT-TTTAACATGATTAGAATGTTTGTA
1 AACTTTCTTTAACATGATTAGAATGTTTGTA
30621454 ATACTTTCTTTAACATGATTAGAATGTTTGTA
1 A-ACTTTCTTTAACATGATTAGAATGTTTGTA
*
30621486 AACTTACTTTAA
1 AACTTTCTTTAA
30621498 AGTTTTATTA
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
30 1 0.02
31 15 0.37
32 25 0.61
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (31 bp):
AACTTTCTTTAACATGATTAGAATGTTTGTA
Found at i:30625951 original size:47 final size:47
Alignment explanation
Indices: 30625882--30625975 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
30625872 AATTGGGTTT
30625882 AATCTTTCTTTTCTTTAATTTAATTTAAAGATGTTTGCTATGAGTTC
1 AATCTTTCTTTTCTTTAATTTAATTTAAAGATGTTTGCTATGAGTTC
30625929 AATCTTTCTTTTCTTTAATTTAATTTAAAGATGTTTGCTATGAGTTC
1 AATCTTTCTTTTCTTTAATTTAATTTAAAGATGTTTGCTATGAGTTC
30625976 CCTGTTCTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.53
Consensus pattern (47 bp):
AATCTTTCTTTTCTTTAATTTAATTTAAAGATGTTTGCTATGAGTTC
Found at i:30627881 original size:15 final size:16
Alignment explanation
Indices: 30627861--30627901 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
30627851 GAATACACAT
30627861 GAATTTATATATAT-A
1 GAATTTATATATATAA
*
30627876 GAATTTAGAT-TATAA
1 GAATTTATATATATAA
*
30627891 AAATTTATATA
1 GAATTTATATA
30627902 AACAAAATAC
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (16 bp):
GAATTTATATATATAA
Found at i:30627949 original size:2 final size:2
Alignment explanation
Indices: 30627942--30627975 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
30627932 GAGTATAGAA
30627942 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30627976 AAGATGACGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30629858 original size:84 final size:85
Alignment explanation
Indices: 30629769--30630056 Score: 252
Period size: 84 Copynumber: 3.4 Consensus size: 85
30629759 TTGGCTTTAA
** * *
30629769 TCTGCTCCACTAAAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTACCT-CAACTTCAGGAG
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGCAATCTTCAGTCTACCTGCAACTTCAGAAG
30629833 GATAAGACTTGCTTACTTAG
66 GATAAGACTTGCTTACTTAG
* * * * *
30629853 TCTGCTTCACTGTAACTTCAGGGAGATAAGACTAGATGCGATCTGC--TCT--CTGCAAATTCA-
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGA-T--TTGCAATCTTCAGTCTACCTGCAACTTCAG
** *
30629913 AAGAGATAAGATCCAAAG-TT--TTAA
63 AAG-GATAAGA--C-TTGCTTACTTAG
* * * *
30629937 TCCGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTAATCTTCAGTCTACCTCACTGCAACTTCA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGCAATCTTCAGTCTA---C-CTGCAACTTCA
30630002 GAAGGATAAGACTTGCTTACTTAG
62 GAAGGATAAGACTTGCTTACTTAG
* *
30630026 TATGCTCCACTGTAGCTTCAGGGAGATAAGA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGA
30630057 CTAGATGGGA
Statistics
Matches: 156, Mismatches: 28, Indels: 35
0.71 0.13 0.16
Matches are distributed among these distances:
81 7 0.04
83 8 0.05
84 72 0.46
85 4 0.03
86 4 0.03
87 12 0.08
89 46 0.29
90 3 0.02
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (85 bp):
TCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGCAATCTTCAGTCTACCTGCAACTTCAGAAG
GATAAGACTTGCTTACTTAG
Found at i:30630050 original size:173 final size:168
Alignment explanation
Indices: 30629764--30630142 Score: 542
Period size: 173 Copynumber: 2.2 Consensus size: 168
30629754 AATTATTGGC
* ** *
30629764 TTTAATCTGCTCCACTAAAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTACCTCAACTTCA
1 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATTTGCAATCTTCAGTCTACCTCAACTTCA
* * *
30629829 GGAGGATAAGACTTGCTTACTTAGTCTGCTTCACTGTAACTTCAGGGAGATAAGACTAGATGCGA
66 GAAGGATAAGACTTGCTTACTTAGTATGCTCCACTGTAACTTCAGGGAGATAAGACTAGATGCGA
* *
30629894 TCTGCTCTCTGCAAATTCAAAGAGATAAGATCCAAAGT
131 TCTACTCTATGCAAATTCAAAGAGATAAGATCCAAAGT
* *
30629932 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTAATCTTCAGTCTACCTCACTGCAA
1 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATTTGCAATCTTCAGTCTA---C-CT-CAA
*
30629997 CTTCAGAAGGATAAGACTTGCTTACTTAGTATGCTCCACTGTAGCTTCAGGGAGATAAGACTAGA
61 CTTCAGAAGGATAAGACTTGCTTACTTAGTATGCTCCACTGTAACTTCAGGGAGATAAGACTAGA
* * * * *
30630062 TGGGATCTACTCTATGCAACTTCAGAGATATAAGATCCAAGGT
126 TGCGATCTACTCTATGCAAATTCAAAGAGATAAGATCCAAAGT
* *
30630105 TTTAATCCGCTCCACTGCAACTTCAAGGAGATAGGATT
1 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATT
30630143 ATCGGCTTTA
Statistics
Matches: 186, Mismatches: 20, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
168 48 0.26
171 1 0.01
172 2 0.01
173 135 0.73
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (168 bp):
TTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATTTGCAATCTTCAGTCTACCTCAACTTCA
GAAGGATAAGACTTGCTTACTTAGTATGCTCCACTGTAACTTCAGGGAGATAAGACTAGATGCGA
TCTACTCTATGCAAATTCAAAGAGATAAGATCCAAAGT
Found at i:30630118 original size:84 final size:84
Alignment explanation
Indices: 30629860--30630137 Score: 242
Period size: 84 Copynumber: 3.2 Consensus size: 84
30629850 TAGTCTGCTT
* * * * *
30629860 CACTGTAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAAATTCAAAGAGATAAGAT
1 CACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTACTCTATGCAACTTCAGAGAGATAAGAT
*
30629925 CCAAAGTTTTAATCCGCTC
66 CCAAGGTTTTAATCCGCTC
** * *
30629944 CACTGCAACTTCAGGGAGATAAGGTTTGTAAT-CTTCAGTCTAC-CTCACTGCAACTTCAGA-AG
1 CACTGCAACTTCAGGGAGATAAGACTAG--ATGC--GA-TCTACTCT-A-TGCAACTTCAGAGA-
** * * **
30630006 GATAAGA--CTTGCTTACTTAGTATGCTC
58 GATAAGATCCAAGGTT--TTAATCCGCTC
* * * *
30630033 CACTGTAGCTTCAGGGAGATAAGACTAGATGGGATCTACTCTATGCAACTTCAGAGATATAAGAT
1 CACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTACTCTATGCAACTTCAGAGAGATAAGAT
30630098 CCAAGGTTTTAATCCGCTC
66 CCAAGGTTTTAATCCGCTC
*
30630117 CACTGCAACTTCAAGGAGATA
1 CACTGCAACTTCAGGGAGATA
30630138 GGATTATCGG
Statistics
Matches: 146, Mismatches: 33, Indels: 30
0.70 0.16 0.14
Matches are distributed among these distances:
84 68 0.47
85 8 0.05
86 9 0.06
87 8 0.05
88 5 0.03
89 48 0.33
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (84 bp):
CACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTACTCTATGCAACTTCAGAGAGATAAGAT
CCAAGGTTTTAATCCGCTC
Found at i:30630167 original size:217 final size:217
Alignment explanation
Indices: 30629932--30630361 Score: 666
Period size: 217 Copynumber: 2.0 Consensus size: 217
30629922 GATCCAAAGT
*
30629932 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTAATCTTCAGTCTACCTCACTGCAA
1 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGGTTTGCAATCTTCAGTCTACCTCACTGCAA
* * *
30629997 CTTCA-GAAGGATAAGACTTGCTTACTTAGTATGCTCCACTGTAGCTTCAGGGAGATAAGACTAG
66 CTTCATG-AGGATAAAACTTGCTTACTTAGTATGCTCCACTGCAACTTCAGGGAGATAAGACTAG
** * * *
30630061 ATGGGATCTACTCTATGCAACTTCAGAGATATAAGATCCAAGGTTTTAATCCGCTCCACTGCAAC
130 ATGAAATCTACTATATGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCGCTACACTGCAAC
30630126 TTCAAGGAGATAGGATTATCGGC
195 TTCAAGGAGATAGGATTATCGGC
* *
30630149 TTTAA-CCTGCTCCACTGCAACTTTAGGGAGATAAGGTTTGCAATCTTCAGTCTGCCTCACTGCA
1 TTTAATCC-GCTCCACTGCAACTTCAGGGAGATAAGGTTTGCAATCTTCAGTCTACCTCACTGCA
* *
30630213 ACTTCATGAGGATAAAACTTGCTTACTTAGTTTGCTCCCCTGCAACTTCAGGGAGATAAGACTAG
65 ACTTCATGAGGATAAAACTTGCTTACTTAGTATGCTCCACTGCAACTTCAGGGAGATAAGACTAG
* * * *
30630278 ATGAAATCTGCTATCTGTAACTTCAGAGAGATAAGATCCAATGTTTTAATCCGCTACACTGCAAC
130 ATGAAATCTACTATATGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCGCTACACTGCAAC
*
30630343 TTCAGGGAGATAGGATTAT
195 TTCAAGGAGATAGGATTAT
30630362 TGGCCATGGA
Statistics
Matches: 193, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
216 2 0.01
217 190 0.98
218 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (217 bp):
TTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGGTTTGCAATCTTCAGTCTACCTCACTGCAA
CTTCATGAGGATAAAACTTGCTTACTTAGTATGCTCCACTGCAACTTCAGGGAGATAAGACTAGA
TGAAATCTACTATATGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCGCTACACTGCAACT
TCAAGGAGATAGGATTATCGGC
Found at i:30638516 original size:24 final size:24
Alignment explanation
Indices: 30638478--30638542 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 24
30638468 AATCTTCTCA
* *
30638478 AACTGCTTATTCATTTGCTGTT-G
1 AACTGCTTCTGCATTTGCTGTTGG
* *
30638501 AAGCTGCTTCTGCATTTCCTTTTGG
1 AA-CTGCTTCTGCATTTGCTGTTGG
30638526 AACTG-TTCTAGCATTTG
1 AACTGCTTCT-GCATTTG
30638543 GTCCATGTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
23 6 0.18
24 25 0.74
25 3 0.09
ACGTcount: A:0.17, C:0.20, G:0.18, T:0.45
Consensus pattern (24 bp):
AACTGCTTCTGCATTTGCTGTTGG
Found at i:30642289 original size:17 final size:17
Alignment explanation
Indices: 30642269--30642303 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
30642259 AATGGCATAG
30642269 AAATAATAT-AAACAAAT
1 AAATAA-ATGAAACAAAT
30642286 AAATAAATGAAACAAAT
1 AAATAAATGAAACAAAT
30642303 A
1 A
30642304 TACATAAGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.20
Consensus pattern (17 bp):
AAATAAATGAAACAAAT
Found at i:30642478 original size:15 final size:16
Alignment explanation
Indices: 30642458--30642498 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
30642448 GAATACACAT
30642458 GAATTTATATATAT-A
1 GAATTTATATATATAA
*
30642473 GAATTTAGAT-TATAA
1 GAATTTATATATATAA
*
30642488 AAATTTATATA
1 GAATTTATATA
30642499 AACAAAATAC
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (16 bp):
GAATTTATATATATAA
Found at i:30642546 original size:2 final size:2
Alignment explanation
Indices: 30642539--30642569 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
30642529 GAGTATAGAA
30642539 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30642570 AATTATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30651069 original size:17 final size:15
Alignment explanation
Indices: 30651055--30651106 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
30651045 CTTCTTCTTC
30651055 TTTTTTTATTTTTCTT
1 TTTTTTTATTTTT-TT
*
30651071 TTCTTTTTATTTTTAT
1 TT-TTTTTATTTTTTT
*
30651087 TTTTCTTATTTTTTT
1 TTTTTTTATTTTTTT
30651102 CTTTT
1 -TTTT
30651107 ATAACATTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 11 0.35
16 9 0.29
17 11 0.35
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTTTATTTTTTT
Found at i:30651083 original size:23 final size:24
Alignment explanation
Indices: 30651033--30651106 Score: 89
Period size: 23 Copynumber: 3.1 Consensus size: 24
30651023 TTTGTACTTA
* *
30651033 TTTATTTTTCTTCTTCTTCTTCTTTT
1 TTTATTTTTCTTATTCTT-TT-TATT
30651059 TTTATTTTTCTT-TTCTTTTTATT
1 TTTATTTTTCTTATTCTTTTTATT
*
30651082 TTTATTTTTCTTATT-TTTTTCTT
1 TTTATTTTTCTTATTCTTTTTATT
30651105 TT
1 TT
30651107 ATAACATTAG
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
23 24 0.53
24 4 0.09
25 5 0.11
26 12 0.27
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (24 bp):
TTTATTTTTCTTATTCTTTTTATT
Found at i:30651106 original size:6 final size:6
Alignment explanation
Indices: 30651037--30651106 Score: 54
Period size: 6 Copynumber: 11.7 Consensus size: 6
30651027 TACTTATTTA
* * * * *
30651037 TTTTTC TTCTTC TTCTTC TTTTT- TTATTTT TCTTTTC TTTTTA TTTTTA
1 TTTTTC TTTTTC TTTTTC TTTTTC TT-TTTC T-TTTTC TTTTTC TTTTTC
*
30651086 TTTTTC TTATT- TTTTTC TTTT
1 TTTTTC TTTTTC TTTTTC TTTT
30651107 ATAACATTAG
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
5 6 0.11
6 41 0.77
7 5 0.09
8 1 0.02
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:30654227 original size:37 final size:40
Alignment explanation
Indices: 30654172--30654262 Score: 125
Period size: 37 Copynumber: 2.3 Consensus size: 40
30654162 ATTTTATATA
30654172 TATTCTAATTTCAAAAACG-TTT-TAC-TTTTGTAAATGT
1 TATTCTAATTTCAAAAACGTTTTCTACTTTTTGTAAATGT
*
30654209 TATTTTAATTTCAAAAACGTTTTCTACTTTTTGTAAATGT
1 TATTCTAATTTCAAAAACGTTTTCTACTTTTTGTAAATGT
30654249 ATAATTCTATATTT
1 -T-ATTCTA-ATTT
30654263 TATTATAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
37 18 0.39
38 3 0.07
39 3 0.07
40 12 0.26
41 1 0.02
42 5 0.11
43 4 0.09
ACGTcount: A:0.32, C:0.10, G:0.07, T:0.52
Consensus pattern (40 bp):
TATTCTAATTTCAAAAACGTTTTCTACTTTTTGTAAATGT
Found at i:30654308 original size:2 final size:2
Alignment explanation
Indices: 30654301--30654330 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
30654291 CAAATGTATG
30654301 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
30654331 AATCTACATA
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):
TA
Found at i:30660920 original size:50 final size:50
Alignment explanation
Indices: 30660794--30661140 Score: 232
Period size: 50 Copynumber: 6.9 Consensus size: 50
30660784 TAGATTTTAC
* ** * **
30660794 TTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTATGACGGCAGATCTGGT
1 TTCCTTAGCAGTGCAGTGGAACAGATTGAAGCCACAACGGCGGATCTTAT
* * * * ** * * *
30660844 TTCCCT-GATATTGCAATTAAAAAGATTGAAGCCACAATGGCGGATCTTAC
1 TTCCTTAG-CAGTGCAGTGGAACAGATTGAAGCCACAACGGCGGATCTTAT
* * * **
30660894 TTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCAGATCTGGT
1 TTCCTTAGCAGTGCAGTGGAACAGATTGAAGCCACAACGGCGGATCTTAT
* * * * ** * * *
30660944 TTCCCT-GATATTGCAATTAAAAAGATTGAAGCCACAACGGTGGATCTTAC
1 TTCCTTAG-CAGTGCAGTGGAACAGATTGAAGCCACAACGGCGGATCTTAT
* * * **
30660994 TTCCTTAGCAGTGCAGTGGAACAGATTAAAGCTACAATGGCGGATCTGGT
1 TTCCTTAGCAGTGCAGTGGAACAGATTGAAGCCACAACGGCGGATCTTAT
* * * * ** * *
30661044 TTCCCT-GATATTGCAATTAAAAAGACTGAAGCCACAACGGCGGATCTTAT
1 TTCCTTAG-CAGTGCAGTGGAACAGATTGAAGCCACAACGGCGGATCTTAT
* * * *
30661094 TTCCTTAGCAGTGCAGTGGAACAGATTAAAGCTACGACGGCAGATCT
1 TTCCTTAGCAGTGCAGTGGAACAGATTGAAGCCACAACGGCGGATCT
30661141 GGTTTCCCCG
Statistics
Matches: 209, Mismatches: 82, Indels: 12
0.69 0.27 0.04
Matches are distributed among these distances:
49 3 0.01
50 203 0.97
51 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (50 bp):
TTCCTTAGCAGTGCAGTGGAACAGATTGAAGCCACAACGGCGGATCTTAT
Found at i:30661174 original size:100 final size:100
Alignment explanation
Indices: 30660790--30661148 Score: 628
Period size: 100 Copynumber: 3.6 Consensus size: 100
30660780 ACCATAGATT
* *
30660790 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTATGACGGCAGATCTGGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTAAAGCTACGACGGCAGATCTGGTTTCCCTGATAT
*
30660855 TGCAATTAAAAAGATTGAAGCCACAATGGCGGATC
66 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
*
30660890 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCAGATCTGGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTAAAGCTACGACGGCAGATCTGGTTTCCCTGATAT
*
30660955 TGCAATTAAAAAGATTGAAGCCACAACGGTGGATC
66 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
* * *
30660990 TTACTTCCTTAGCAGTGCAGTGGAACAGATTAAAGCTACAATGGCGGATCTGGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTAAAGCTACGACGGCAGATCTGGTTTCCCTGATAT
*
30661055 TGCAATTAAAAAGACTGAAGCCACAACGGCGGATC
66 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
*
30661090 TTATTTCCTTAGCAGTGCAGTGGAACAGATTAAAGCTACGACGGCAGATCTGGTTTCCC
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTAAAGCTACGACGGCAGATCTGGTTTCCC
30661149 CGACATTGTA
Statistics
Matches: 246, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 246 1.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (100 bp):
TTACTTCCTTAGCAGTGCAGTGGAACAGATTAAAGCTACGACGGCAGATCTGGTTTCCCTGATAT
TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
Found at i:30661405 original size:132 final size:132
Alignment explanation
Indices: 30661222--30661708 Score: 742
Period size: 132 Copynumber: 3.7 Consensus size: 132
30661212 ATTAAAATCG
*
30661222 CAGATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGT
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGT
*
30661287 TACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAAGAT
66 TACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGAT
30661352 TT
131 TT
** * * *
30661354 CAGATCTTGCCTCCCTAAGCAGTAGTGGAACAGATCGAAGATGGTGGATTTTACCTCCCTGAAGT
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGT
* * * *
30661419 TGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCTTGGACAGCAGTGAAATAGATTGAAGAT
66 TACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGAT
30661484 TT
131 TT
* * * * * * *
30661486 CAGAACTTGTCTCCCTAAGCAGTAGTGGGGCAGATCAAAGATGATGAATTTTACCTCTCTGTGGT
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGT
* *
30661551 TACAGTGGAGTACATTGAAGCCAGTAATTCTA-TCTCCCTAGGCAGCAGTGGAATAGATTAAAGA
66 TACAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCCCTGGGCAGCAGTGGAATAGATTGAAGA
*
30661615 TTA
130 TTT
* *
30661618 CAGATCTTATCTCCCTAAGAAATAGTGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGT
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGT
*
30661683 TACAGTGGAGTACGTTGAAGCCAGTA
66 TACAGTGGAGTACATTGAAGCCAGTA
30661709 TTCCTATCTC
Statistics
Matches: 316, Mismatches: 38, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
131 1 0.00
132 315 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (132 bp):
CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGT
TACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGAT
TT
Found at i:30663391 original size:37 final size:39
Alignment explanation
Indices: 30663336--30663426 Score: 123
Period size: 37 Copynumber: 2.3 Consensus size: 39
30663326 ATTTTATATA
30663336 TATTCTAATTTCAAAAACGTTTT-AC-TTTTGTAAATGT
1 TATTCTAATTTCAAAAACGTTTTCACTTTTTGTAAATGT
*
30663373 TATTTTAATTTCAAAAACGTTTTCCACTTTTTGTAAATGT
1 TATTCTAATTTCAAAAACGTTTT-CACTTTTTGTAAATGT
30663413 ATAATTCTATATTT
1 -T-ATTCTA-ATTT
30663427 TATTATAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
37 22 0.48
39 2 0.04
40 12 0.26
41 1 0.02
42 5 0.11
43 4 0.09
ACGTcount: A:0.32, C:0.11, G:0.07, T:0.51
Consensus pattern (39 bp):
TATTCTAATTTCAAAAACGTTTTCACTTTTTGTAAATGT
Found at i:30663528 original size:2 final size:2
Alignment explanation
Indices: 30663516--30663549 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
30663506 TTCACCTTAC
*
30663516 AT AT CT 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
30663550 TATTCTACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30672405 original size:17 final size:17
Alignment explanation
Indices: 30672358--30672399 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
30672348 GAAATGAGCC
* * *
30672358 CACACGCCCATATGGTT
1 CACACGGCCATGTGGTG
30672375 CACACGGCCATGTGGTG
1 CACACGGCCATGTGGTG
30672392 CACACGGC
1 CACACGGC
30672400 AGTGTGACGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.21, C:0.36, G:0.26, T:0.17
Consensus pattern (17 bp):
CACACGGCCATGTGGTG
Found at i:30674670 original size:7 final size:7
Alignment explanation
Indices: 30674652--30674686 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
30674642 GTTTTGATGA
30674652 TTATAA-
1 TTATAAT
30674658 TTATAAT
1 TTATAAT
30674665 TTATAAT
1 TTATAAT
30674672 TTATAAT
1 TTATAAT
30674679 TTATAAT
1 TTATAAT
30674686 T
1 T
30674687 ATTAGTTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 6 0.21
7 22 0.79
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TTATAAT
Found at i:30677249 original size:19 final size:19
Alignment explanation
Indices: 30677225--30677286 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
30677215 TTTAAAGTTA
30677225 TATTTTAAATATTTTATTT
1 TATTTTAAATATTTTATTT
** *
30677244 TATTTT-AATCA--CGAATT
1 TATTTTAAAT-ATTTTATTT
30677261 T-TTTTAAATATTTTATTT
1 TATTTTAAATATTTTATTT
30677279 TATTTTAA
1 TATTTTAA
30677287 TCACGAATGT
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
16 5 0.16
17 7 0.22
18 7 0.22
19 13 0.41
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (19 bp):
TATTTTAAATATTTTATTT
Found at i:30677271 original size:35 final size:35
Alignment explanation
Indices: 30677227--30677320 Score: 156
Period size: 35 Copynumber: 2.7 Consensus size: 35
30677217 TAAAGTTATA
*
30677227 TTTTAAATATTTTATTTTATTTTAATCACGAATTT
1 TTTTAAATATTTTATTTTATTTTAATCACGAATGT
30677262 TTTTAAATATTTTATTTTATTTTAATCACGAATGT
1 TTTTAAATATTTTATTTTATTTTAATCACGAATGT
30677297 TTTTAAATA-TTTACTTTT-TTTTAA
1 TTTTAAATATTTTA-TTTTATTTTAA
30677321 AGTTCAAATT
Statistics
Matches: 57, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
34 10 0.18
35 47 0.82
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (35 bp):
TTTTAAATATTTTATTTTATTTTAATCACGAATGT
Found at i:30677348 original size:9 final size:9
Alignment explanation
Indices: 30677327--30677383 Score: 66
Period size: 9 Copynumber: 6.7 Consensus size: 9
30677317 TTAAAGTTCA
30677327 AATTT-CAT
1 AATTTACAT
*
30677335 AATTTACGT
1 AATTTACAT
30677344 AATTTACAT
1 AATTTACAT
*
30677353 AACTTACAT
1 AATTTACAT
30677362 AA-TT-CAT
1 AATTTACAT
*
30677369 AACTTACAT
1 AATTTACAT
30677378 AATTTA
1 AATTTA
30677384 AATTTATAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
7 5 0.12
8 9 0.21
9 28 0.67
ACGTcount: A:0.42, C:0.14, G:0.02, T:0.42
Consensus pattern (9 bp):
AATTTACAT
Found at i:30677371 original size:16 final size:16
Alignment explanation
Indices: 30677330--30677381 Score: 68
Period size: 16 Copynumber: 3.1 Consensus size: 16
30677320 AAGTTCAAAT
* *
30677330 TTCATAATTTACGTAA
1 TTCATAACTTACATAA
30677346 TTTACATAACTTACATAA
1 -TT-CATAACTTACATAA
30677364 TTCATAACTTACATAA
1 TTCATAACTTACATAA
30677380 TT
1 TT
30677382 TAAATTTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
16 16 0.50
17 4 0.12
18 12 0.38
ACGTcount: A:0.40, C:0.15, G:0.02, T:0.42
Consensus pattern (16 bp):
TTCATAACTTACATAA
Found at i:30677448 original size:19 final size:19
Alignment explanation
Indices: 30677426--30677462 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
30677416 TATAGTTTTA
30677426 ATATATATATTTAAAATTT
1 ATATATATATTTAAAATTT
*
30677445 ATATATATTTTTAAAATT
1 ATATATATATTTAAAATT
30677463 GATACATTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATATATATATTTAAAATTT
Found at i:30677514 original size:23 final size:22
Alignment explanation
Indices: 30677464--30677527 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
30677454 TTTAAAATTG
30677464 ATACATTACATAACTTACATAAC
1 ATACA-TACATAACTTACATAAC
*
30677487 CTACATACATAAACTTACAT---
1 ATACATACAT-AACTTACATAAC
*
30677507 ATA-ATACATAACTTATATAAC
1 ATACATACATAACTTACATAAC
30677528 TTAAATTTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
18 8 0.24
19 6 0.18
20 2 0.06
22 5 0.15
23 13 0.38
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.31
Consensus pattern (22 bp):
ATACATACATAACTTACATAAC
Found at i:30677612 original size:12 final size:12
Alignment explanation
Indices: 30677588--30677628 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
30677578 CACAACTTAC
*
30677588 ATAACCAACATA
1 ATAACCTACATA
* *
30677600 ATGACTTACATA
1 ATAACCTACATA
30677612 ATAACCTACATA
1 ATAACCTACATA
30677624 ATAAC
1 ATAAC
30677629 TGACATTATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.51, C:0.22, G:0.02, T:0.24
Consensus pattern (12 bp):
ATAACCTACATA
Found at i:30677622 original size:24 final size:24
Alignment explanation
Indices: 30677588--30677646 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
30677578 CACAACTTAC
* * *
30677588 ATAACCAACATAATGACTTACATA
1 ATAACCTACATAATAACTGACATA
*
30677612 ATAACCTACATAATAACTGACATT
1 ATAACCTACATAATAACTGACATA
30677636 ATAA--TACATAA
1 ATAACCTACATAA
30677647 CATACATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 7 0.23
24 24 0.77
ACGTcount: A:0.51, C:0.19, G:0.03, T:0.27
Consensus pattern (24 bp):
ATAACCTACATAATAACTGACATA
Found at i:30677634 original size:12 final size:11
Alignment explanation
Indices: 30677595--30677646 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 11
30677585 TACATAACCA
*
30677595 ACATAATGACTT
1 ACATAATAAC-T
30677607 ACATAATAACCT
1 ACATAATAA-CT
30677619 ACATAATAACT
1 ACATAATAACT
*
30677630 GACATTATAA-T
1 -ACATAATAACT
30677641 ACATAA
1 ACATAA
30677647 CATACATAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
10 5 0.14
11 3 0.09
12 26 0.74
13 1 0.03
ACGTcount: A:0.50, C:0.17, G:0.04, T:0.29
Consensus pattern (11 bp):
ACATAATAACT
Found at i:30677674 original size:34 final size:34
Alignment explanation
Indices: 30677636--30677942 Score: 144
Period size: 34 Copynumber: 9.4 Consensus size: 34
30677626 AACTGACATT
*
30677636 ATAATACATAACATACATAAATTAAATAAGTTAC
1 ATAATACATAACATACATAAATTAAATAACTTAC
* * * *
30677670 ATAATACACAA-AAACAAAAACTTACATAACTTAC
1 ATAATACATAACATACATAAA-TTAAATAACTTAC
* *
30677704 ATAATATC-TTACATA-ATAACTT--AT-A--TA-
1 ATAATA-CATAACATACATAAATTAAATAACTTAC
* * *
30677731 ATAATACATACCCTACATAAATTAAATAAGTTAC
1 ATAATACATAACATACATAAATTAAATAACTTAC
* * * *
30677765 ATAATACACAA-AAACAAAAACTTACATAACTTAC
1 ATAATACATAACATACATAAA-TTAAATAACTTAC
** **
30677799 ATAATACATAAC-TACATAACCTACTTAA--TAC
1 ATAATACATAACATACATAAATTAAATAACTTAC
* * * *
30677830 ATAACTTGCATAACTTACAT-AA-TACACAACTTAC
1 ATAA--TACATAACATACATAAATTAAATAACTTAC
* * * * *
30677864 ATATGTAAAT-A-ATACACAATTTACATAACTTAC
1 ATA-ATACATAACATACATAAATTAAATAACTTAC
* * * * *
30677897 ATAATACACAACTTACATAACTTACATAACCTAC
1 ATAATACATAACATACATAAATTAAATAACTTAC
*
30677931 TTAATACATAAC
1 ATAATACATAAC
30677943 TTGCATAACT
Statistics
Matches: 203, Mismatches: 47, Indels: 46
0.69 0.16 0.16
Matches are distributed among these distances:
26 1 0.00
27 10 0.05
28 8 0.04
30 3 0.01
31 14 0.07
32 10 0.05
33 49 0.24
34 105 0.52
35 3 0.01
ACGTcount: A:0.51, C:0.19, G:0.01, T:0.29
Consensus pattern (34 bp):
ATAATACATAACATACATAAATTAAATAACTTAC
Found at i:30677702 original size:95 final size:95
Alignment explanation
Indices: 30677603--30677804 Score: 341
Period size: 95 Copynumber: 2.1 Consensus size: 95
30677593 CAACATAATG
*
30677603 ACTTACATAATAACCTACATAATAACTGACATTATAATACATAACATACATAAATTAAATAAGTT
1 ACTTACATAATAACCTACATAATAACTGACATAATAATACATAACATACATAAATTAAATAAGTT
30677668 ACATAATACACAAAAACAAAAACTTACATA
66 ACATAATACACAAAAACAAAAACTTACATA
* * * * * *
30677698 ACTTACATAATATCTTACATAATAACTTATATAATAATACATACCCTACATAAATTAAATAAGTT
1 ACTTACATAATAACCTACATAATAACTGACATAATAATACATAACATACATAAATTAAATAAGTT
30677763 ACATAATACACAAAAACAAAAACTTACATA
66 ACATAATACACAAAAACAAAAACTTACATA
30677793 ACTTACATAATA
1 ACTTACATAATA
30677805 CATAACTACA
Statistics
Matches: 100, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
95 100 1.00
ACGTcount: A:0.53, C:0.17, G:0.01, T:0.28
Consensus pattern (95 bp):
ACTTACATAATAACCTACATAATAACTGACATAATAATACATAACATACATAAATTAAATAAGTT
ACATAATACACAAAAACAAAAACTTACATA
Found at i:30677716 original size:12 final size:12
Alignment explanation
Indices: 30677695--30677734 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
30677685 AAAAACTTAC
30677695 ATAACTTACATA
1 ATAACTTACATA
*
30677707 ATATCTTACATA
1 ATAACTTACATA
*
30677719 ATAACTTATATA
1 ATAACTTACATA
30677731 ATAA
1 ATAA
30677735 TACATACCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:30677926 original size:9 final size:9
Alignment explanation
Indices: 30677783--30678126 Score: 258
Period size: 9 Copynumber: 41.2 Consensus size: 9
30677773 CAAAAACAAA
30677783 AACTTACAT
1 AACTTACAT
30677792 AACTTACAT
1 AACTTACAT
30677801 AA--TACAT
1 AACTTACAT
30677808 AAC-TACAT
1 AACTTACAT
* *
30677816 AACCTACTT
1 AACTTACAT
30677825 AA--TACAT
1 AACTTACAT
*
30677832 AACTTGCAT
1 AACTTACAT
30677841 AACTTACAT
1 AACTTACAT
*
30677850 AA--TACAC
1 AACTTACAT
30677857 AACTTACAT
1 AACTTACAT
*
30677866 -A-TGTAAAT
1 AACT-TACAT
*
30677874 AA--TACAC
1 AACTTACAT
*
30677881 AATTTACAT
1 AACTTACAT
30677890 AACTTACAT
1 AACTTACAT
*
30677899 AA--TACAC
1 AACTTACAT
30677906 AACTTACAT
1 AACTTACAT
30677915 AACTTACAT
1 AACTTACAT
* *
30677924 AACCTACTT
1 AACTTACAT
30677933 AA--TACAT
1 AACTTACAT
*
30677940 AACTTGCAT
1 AACTTACAT
*
30677949 AACTTGCAT
1 AACTTACAT
*
30677958 AA--TACAC
1 AACTTACAT
30677965 AACTTACAT
1 AACTTACAT
** *
30677974 -GTTTAAAT
1 AACTTACAT
*
30677982 AA--TACAC
1 AACTTACAT
*
30677989 AATTTACAT
1 AACTTACAT
30677998 AACTTACAT
1 AACTTACAT
*
30678007 AA--TACAC
1 AACTTACAT
30678014 AACTTACAT
1 AACTTACAT
30678023 AACTTACAT
1 AACTTACAT
30678032 AA--TACAT
1 AACTTACAT
30678039 AACTTACAT
1 AACTTACAT
* *
30678048 AACCTACTT
1 AACTTACAT
*
30678057 AA--GACAT
1 AACTTACAT
*
30678064 AACTTGCAT
1 AACTTACAT
30678073 AACTTACAT
1 AACTTACAT
*
30678082 AA--TACAC
1 AACTTACAT
*
30678089 AACTTACAC
1 AACTTACAT
30678098 AACTTACAT
1 AACTTACAT
30678107 AACTTACAT
1 AACTTACAT
30678116 AACTTACAT
1 AACTTACAT
30678125 AA
1 AA
30678127 TGTATAACTT
Statistics
Matches: 269, Mismatches: 39, Indels: 54
0.74 0.11 0.15
Matches are distributed among these distances:
7 71 0.26
8 18 0.07
9 180 0.67
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.30
Consensus pattern (9 bp):
AACTTACAT
Found at i:30677938 original size:25 final size:25
Alignment explanation
Indices: 30677787--30678126 Score: 265
Period size: 25 Copynumber: 13.6 Consensus size: 25
30677777 AACAAAAACT
30677787 TACATAACTTACATAA--TACATAA
1 TACATAACTTACATAACTTACATAA
* *
30677810 CTACATAACCTACTTAA--TACATAA
1 -TACATAACTTACATAACTTACATAA
* *
30677834 CTTGCATAACTTACATAA--TACACAA
1 --TACATAACTTACATAACTTACATAA
* *
30677859 CTTACAT-A-TGTAAATAA--TACACAA
1 --TACATAACT-TACATAACTTACATAA
*
30677883 TTTACATAACTTACATAA--TACACAA
1 --TACATAACTTACATAACTTACATAA
* *
30677908 CTTACATAACTTACATAACCTACTTAA
1 --TACATAACTTACATAACTTACATAA
* *
30677935 TACATAACTTGCATAACTTGCATAA
1 TACATAACTTACATAACTTACATAA
* ** *
30677960 TACACAACTTACAT-GTTTAAATAA
1 TACATAACTTACATAACTTACATAA
* *
30677984 TACACAATTTACATAACTTACATAA
1 TACATAACTTACATAACTTACATAA
*
30678009 TACACAACTTACATAACTTACATAA
1 TACATAACTTACATAACTTACATAA
* *
30678034 TACATAACTTACATAACCTACTTAA
1 TACATAACTTACATAACTTACATAA
* *
30678059 GACATAACTTGCATAACTTACATAA
1 TACATAACTTACATAACTTACATAA
* *
30678084 TACACAACTTACACAACTTACATAA
1 TACATAACTTACATAACTTACATAA
30678109 CTTACATAACTTACATAA
1 --TACATAACTTACATAA
30678127 TGTATAACTT
Statistics
Matches: 265, Mismatches: 42, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
23 1 0.00
24 60 0.23
25 184 0.69
26 1 0.00
27 19 0.07
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.30
Consensus pattern (25 bp):
TACATAACTTACATAACTTACATAA
Found at i:30677953 original size:108 final size:108
Alignment explanation
Indices: 30677803--30678033 Score: 428
Period size: 108 Copynumber: 2.1 Consensus size: 108
30677793 ACTTACATAA
30677803 TACATAAC-TACATAACCTACTTAATACATAACTTGCATAACTTACATAATACACAACTTACATA
1 TACATAACTTACATAACCTACTTAATACATAACTTGCATAACTTACATAATACACAACTTACATA
30677867 TGTAAATAATACACAATTTACATAACTTACATAATACACAACT
66 TGTAAATAATACACAATTTACATAACTTACATAATACACAACT
* *
30677910 TACATAACTTACATAACCTACTTAATACATAACTTGCATAACTTGCATAATACACAACTTACATG
1 TACATAACTTACATAACCTACTTAATACATAACTTGCATAACTTACATAATACACAACTTACATA
*
30677975 TTTAAATAATACACAATTTACATAACTTACATAATACACAACT
66 TGTAAATAATACACAATTTACATAACTTACATAATACACAACT
30678018 TACATAACTTACATAA
1 TACATAACTTACATAA
30678034 TACATAACTT
Statistics
Matches: 120, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
107 8 0.07
108 112 0.93
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.31
Consensus pattern (108 bp):
TACATAACTTACATAACCTACTTAATACATAACTTGCATAACTTACATAATACACAACTTACATA
TGTAAATAATACACAATTTACATAACTTACATAATACACAACT
Found at i:30678077 original size:108 final size:104
Alignment explanation
Indices: 30677786--30678117 Score: 342
Period size: 108 Copynumber: 3.2 Consensus size: 104
30677776 AAACAAAAAC
* * * *
30677786 TTACATAACTTACATAATACATAAC-TACATAACCTACTTAATACATAACTTGCAT-A--ACTT-
1 TTACATAACTTACATAATACACAACTTACATAACTTACATAATACATAACTTACATAACTACTTA
*
30677846 --ACATAATACACAACTTACATATGTAAATAATACACAAT
66 AGACATAATACACAACTTACAT-TATAAATAATACACAAT
* *
30677884 TTACATAACTTACATAATACACAACTTACATAACTTACATAACCTACTTAA--TACATAACTTGC
1 TTACATAACTTACATAATACACAACTTACATAACTTACATAA--TACATAACTTACATAAC-TAC
* *
30677947 ATAACTTG-CATAATACACAACTTACATGTTTAAATAATACACAAT
63 TTAA---GACATAATACACAACTTACAT-TATAAATAATACACAAT
30677992 TTACATAACTTACATAATACACAACTTACATAACTTACATAATACATAACTTACATAACCTACTT
1 TTACATAACTTACATAATACACAACTTACATAACTTACATAATACATAACTTACATAA-CTACTT
* * * * * *
30678057 AAGACATAACTTGCATAACTTACATAATACACAACTTACACAAC
65 AAGACATAA--TACACAACTTACATTATAAATAA--TACACAAT
30678101 TTACATAACTTACATAA
1 TTACATAACTTACATAA
30678118 CTTACATAAT
Statistics
Matches: 194, Mismatches: 19, Indels: 31
0.80 0.08 0.13
Matches are distributed among these distances:
98 24 0.12
99 18 0.09
100 1 0.01
101 6 0.03
103 2 0.01
105 1 0.01
106 11 0.06
107 5 0.03
108 101 0.52
109 25 0.13
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.30
Consensus pattern (104 bp):
TTACATAACTTACATAATACACAACTTACATAACTTACATAATACATAACTTACATAACTACTTA
AGACATAATACACAACTTACATTATAAATAATACACAAT
Found at i:30678136 original size:34 final size:33
Alignment explanation
Indices: 30677901--30678137 Score: 100
Period size: 34 Copynumber: 7.1 Consensus size: 33
30677891 ACTTACATAA
* *
30677901 TACACAACTTACATAACTTACATAACCTACTTAA--
1 TACATAACTTACATAACTTACATAA-TTA--TAACT
* * * *
30677935 TACATAACTTGCATAACTTGCATAATACACAACT
1 TACATAACTTACATAACTTACATAAT-TATAACT
** * *
30677969 TACAT-GTTTAAATAA--TACACAATTTACATAACT
1 TACATAACTTACATAACTTACATAA-TT--ATAACT
*
30678002 TACATAA--TACACAACTTACATAACTTACATAA--
1 TACATAACTTACATAACTTACATAA-TT--ATAACT
* * **
30678034 TACATAACTTACATAACCTACTTAAGACATAACT
1 TACATAACTTACATAACTTACATAA-TTATAACT
* * *
30678068 TGCATAACTTACATAA--TACACAACTTACACAACT
1 TACATAACTTACATAACTTACATAA-TT--ATAACT
30678102 TACATAACTTACATAACTTACATAATGTATAACT
1 TACATAACTTACATAACTTACATAAT-TATAACT
30678136 TA
1 TA
30678138 TTCCTAAATC
Statistics
Matches: 150, Mismatches: 35, Indels: 36
0.68 0.16 0.16
Matches are distributed among these distances:
31 5 0.03
32 24 0.16
33 16 0.11
34 97 0.65
35 1 0.01
36 7 0.05
ACGTcount: A:0.45, C:0.22, G:0.03, T:0.31
Consensus pattern (33 bp):
TACATAACTTACATAACTTACATAATTATAACT
Found at i:30683638 original size:21 final size:21
Alignment explanation
Indices: 30683599--30683666 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
30683589 CAACTTAAAA
* *
30683599 CAGAGGCGGCAGCGAGGGAAG
1 CAGAGGCTGCAGCAAGGGAAG
* *
30683620 CAGCGGCTGTAGCAAGGGAAG
1 CAGAGGCTGCAGCAAGGGAAG
* *
30683641 CAGAGGCTGCAGCGAGAGAAG
1 CAGAGGCTGCAGCAAGGGAAG
30683662 CAGAG
1 CAGAG
30683667 CAGAGCAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.31, C:0.19, G:0.46, T:0.04
Consensus pattern (21 bp):
CAGAGGCTGCAGCAAGGGAAG
Found at i:30689675 original size:43 final size:43
Alignment explanation
Indices: 30689624--30689778 Score: 212
Period size: 43 Copynumber: 3.7 Consensus size: 43
30689614 TTTAAAAGCT
30689624 ACTAAAGGTCATGATCTTTAGCGGCGTTTGTGATAAAAGCGCC
1 ACTAAAGGTCATGATCTTTAGCGGCGTTTGTGATAAAAGCGCC
30689667 ACTAAAGGTCAT-ATCCTTTAGCGGCGTTTGTGATAAAAGCG--
1 ACTAAAGGTCATGAT-CTTTAGCGGCGTTTGTGATAAAAGCGCC
*
30689708 -CTAAAGGTCATGATCTTTAGCGGCGTTTGTAGGT-AAAGCGCC
1 ACTAAAGGTCATGATCTTTAGCGGCGTTTGT-GATAAAAGCGCC
* * * *
30689750 GCTAAAGATCATGTTCTATAGCGGCGTTT
1 ACTAAAGGTCATGATCTTTAGCGGCGTTT
30689779 TTCACATAAA
Statistics
Matches: 102, Mismatches: 4, Indels: 12
0.86 0.03 0.10
Matches are distributed among these distances:
40 33 0.32
41 4 0.04
42 2 0.02
43 63 0.62
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (43 bp):
ACTAAAGGTCATGATCTTTAGCGGCGTTTGTGATAAAAGCGCC
Found at i:30689772 original size:83 final size:84
Alignment explanation
Indices: 30689616--30689778 Score: 240
Period size: 83 Copynumber: 2.0 Consensus size: 84
30689606 TAAATGTTTT
*
30689616 TAAAAGCTACTAAAGGTCATGATCTTTAGCGGCGTTTGTGATAAAAGCGCCACTAAAGGTCATAT
1 TAAAAGCTACTAAAGGTCATGATCTTTAGCGGCGTTTGTGATAAAAGCGCCACTAAAGATCATAT
*
30689681 CCTTTAGCGGCGTTTGTGA
66 CCTATAGCGGCGTTTGTGA
* * * *
30689700 TAAAAGC-GCTAAAGGTCATGATCTTTAGCGGCGTTTGTAGGT-AAAGCGCCGCTAAAGATCATG
1 TAAAAGCTACTAAAGGTCATGATCTTTAGCGGCGTTTGT-GATAAAAGCGCCACTAAAGATCATA
*
30689763 TTCTATAGCGGCGTTT
65 TCCTATAGCGGCGTTT
30689779 TTCACATAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
83 62 0.87
84 9 0.13
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (84 bp):
TAAAAGCTACTAAAGGTCATGATCTTTAGCGGCGTTTGTGATAAAAGCGCCACTAAAGATCATAT
CCTATAGCGGCGTTTGTGA
Found at i:30692958 original size:39 final size:39
Alignment explanation
Indices: 30692908--30693069 Score: 224
Period size: 39 Copynumber: 4.2 Consensus size: 39
30692898 ATAATAAATA
*
30692908 TTTTT-ATTTTTTTAATTTTAAAATACTTTTAAAATACT
1 TTTTTAATTTTTTTAATTTTAAAATTCTTTTAAAATACT
30692946 CTTTTTAATTTTTTTAAATTTTAAAA-TCTTTTTAAAATACT
1 -TTTTTAATTTTTTT-AATTTTAAAATTC-TTTTAAAATACT
* *
30692987 TTTTTAATTTTTTTAATTTTTAAATTTTTTTAAAATACT
1 TTTTTAATTTTTTTAATTTTAAAATTCTTTTAAAATACT
* *
30693026 TTTTTAA-TTTTTTAATTTTAAATTTTTTTTAAAATA-T
1 TTTTTAATTTTTTTAATTTTAAAATTCTTTTAAAATACT
30693063 TTTTTAA
1 TTTTTAA
30693070 AATTTTTGTT
Statistics
Matches: 114, Mismatches: 5, Indels: 10
0.88 0.04 0.08
Matches are distributed among these distances:
37 8 0.07
38 27 0.24
39 33 0.29
40 24 0.21
41 22 0.19
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.64
Consensus pattern (39 bp):
TTTTTAATTTTTTTAATTTTAAAATTCTTTTAAAATACT
Found at i:30692977 original size:40 final size:38
Alignment explanation
Indices: 30692908--30693069 Score: 213
Period size: 40 Copynumber: 4.2 Consensus size: 38
30692898 ATAATAAATA
30692908 TTTTT-ATTTTTTTAATTTTAAAATACTTTTAAAATACT
1 TTTTTAATTTTTTTAATTTTAAAAT-CTTTTAAAATACT
30692946 CTTTTTAATTTTTTTAAATTTTAAAATCTTTTTAAAATACT
1 -TTTTTAATTTTTTT-AATTTTAAAATC-TTTTAAAATACT
* *
30692987 TTTTTAATTTTTTTAATTTTTAAATTTTTTTAAAATACT
1 TTTTTAATTTTTTTAA-TTTTAAAATCTTTTAAAATACT
* *
30693026 TTTTTAA-TTTTTTAATTTTAAATTTTTTTTAAAATA-T
1 TTTTTAATTTTTTTAATTTTAAA-ATCTTTTAAAATACT
30693063 TTTTTAA
1 TTTTTAA
30693070 AATTTTTGTT
Statistics
Matches: 116, Mismatches: 2, Indels: 12
0.89 0.02 0.09
Matches are distributed among these distances:
37 15 0.13
38 21 0.18
39 26 0.22
40 31 0.27
41 23 0.20
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.64
Consensus pattern (38 bp):
TTTTTAATTTTTTTAATTTTAAAATCTTTTAAAATACT
Found at i:30693074 original size:39 final size:39
Alignment explanation
Indices: 30692915--30693076 Score: 220
Period size: 38 Copynumber: 4.2 Consensus size: 39
30692905 ATATTTTTAT
** *
30692915 TTTTTTAATTTTAAAATACTTTTAAAATACTCTTTTTAAT
1 TTTTTTAATTTTAAAATTTTTTTAAAATACT-TTTTTAAA
* *
30692955 TTTTTTAAATTTTAAAATCTTTTTAAAATACTTTTTTAAT
1 TTTTTT-AATTTTAAAATTTTTTTAAAATACTTTTTTAAA
*
30692995 TTTTTTAATTTTTAAATTTTTTTAAAATACTTTTTT-AA
1 TTTTTTAATTTTAAAATTTTTTTAAAATACTTTTTTAAA
*
30693033 TTTTTTAATTTTAAATTTTTTTTAAAATA-TTTTTTAAA
1 TTTTTTAATTTTAAAATTTTTTTAAAATACTTTTTTAAA
*
30693071 ATTTTT
1 TTTTTT
30693077 GTTTTAATTT
Statistics
Matches: 112, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
37 6 0.05
38 35 0.31
39 28 0.25
40 20 0.18
41 23 0.21
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (39 bp):
TTTTTTAATTTTAAAATTTTTTTAAAATACTTTTTTAAA
Done.