Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 124 of 199
Found at i:37600107 original size:49 final size:50
Alignment explanation
Indices: 37600030--37600131 Score: 138
Period size: 49 Copynumber: 2.1 Consensus size: 50
37600020 TCTTATAGAG
* *
37600030 AACATATGGAAAGCATTAAACACTTTATATTCT-TACC-AAAAAGAATTAT
1 AACATATGGAAAGCATTAAACACGTTATATGCTCT-CCAAAAAAGAATTAT
*
37600079 AACATATGGAAAGTATTGAAA-ACGTTATATGCTCTCCAAAAAAGAATTAT
1 AACATATGGAAAGCATT-AAACACGTTATATGCTCTCCAAAAAAGAATTAT
37600129 AAC
1 AAC
37600132 TTCCATGTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
49 28 0.60
50 19 0.40
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.28
Consensus pattern (50 bp):
AACATATGGAAAGCATTAAACACGTTATATGCTCTCCAAAAAAGAATTAT
Found at i:37601348 original size:12 final size:12
Alignment explanation
Indices: 37601331--37601355 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37601321 AAAGCATATG
37601331 TGATTTTAGTTT
1 TGATTTTAGTTT
37601343 TGATTTTAGTTT
1 TGATTTTAGTTT
37601355 T
1 T
37601356 TAGTTTCTAT
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:0.16, T:0.68
Consensus pattern (12 bp):
TGATTTTAGTTT
Found at i:37603572 original size:3 final size:3
Alignment explanation
Indices: 37603557--37603600 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
37603547 TAAACACACT
*
37603557 TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
37603601 TTTGTGGGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:37614305 original size:24 final size:24
Alignment explanation
Indices: 37614270--37614771 Score: 210
Period size: 23 Copynumber: 21.6 Consensus size: 24
37614260 TATATATATA
*
37614270 TATACA-CAAAATTGGACATCATT
1 TATACACCAAAATTGGACAACATT
* * * *
37614293 TACACACCAAAATTTGACAGCATG
1 TATACACCAAAATTGGACAACATT
*
37614317 TATATA-CAAAATTGGACAACATT
1 TATACACCAAAATTGGACAACATT
* * *
37614340 TATTCACCAAAATTAGG-CAGCATA
1 TATACACCAAAATT-GGACAACATT
* * * * *
37614364 TATATA-CTAATTTGGACAGCACT
1 TATACACCAAAATTGGACAACATT
* ** * *
37614387 TATATA-CAAAATTTAACAGCATG
1 TATACACCAAAATTGGACAACATT
** *
37614410 TATA-TGCAAAATTGGACAGCATT
1 TATACACCAAAATTGGACAACATT
* * * * *
37614433 TATTCACAAAAATTGGGCAGCATA
1 TATACACCAAAATTGGACAACATT
* * * *
37614457 CATACACC-AATTTGGACAGCACT
1 TATACACCAAAATTGGACAACATT
* * *
37614480 TATACA-CAAAATTTGACAGCATG
1 TATACACCAAAATTGGACAACATT
** *
37614503 TATA-TGCAAAATTGGACAGCATT
1 TATACACCAAAATTGGACAACATT
* * * **
37614526 TATTCACCAAAATTGGGCAGCACA
1 TATACACCAAAATTGGACAACATT
* * * *
37614550 CATACACC-AATTTGGACAGCACT
1 TATACACCAAAATTGGACAACATT
* * *
37614573 TATACA-CAAAATTTGACAGCATG
1 TATACACCAAAATTGGACAACATT
** *
37614596 TATA-TGCAAAATTGGACAGCATT
1 TATACACCAAAATTGGACAACATT
* * * *
37614619 TATTCACCAAAATTGGGCAGCATA
1 TATACACCAAAATTGGACAACATT
* * * * *
37614643 CATATACC-AATTTGGACAGCACT
1 TATACACCAAAATTGGACAACATT
* *
37614666 TATACA-CAAAATTTGACAACATG
1 TATACACCAAAATTGGACAACATT
**
37614689 TATA-TGCAAAATTGGACAACATT
1 TATACACCAAAATTGGACAACATT
* * * *
37614712 TATTCACCAAAATTGGGCAGCATA
1 TATACACCAAAATTGGACAACATT
* * * * *
37614736 CATATACC-AATTTGGACAGCACT
1 TATACACCAAAATTGGACAACATT
37614759 TATACA-CAAAATT
1 TATACACCAAAATT
37614772 TGATAGCATG
Statistics
Matches: 356, Mismatches: 107, Indels: 32
0.72 0.22 0.06
Matches are distributed among these distances:
22 6 0.02
23 236 0.66
24 112 0.31
25 2 0.01
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (24 bp):
TATACACCAAAATTGGACAACATT
Found at i:37614406 original size:93 final size:93
Alignment explanation
Indices: 37614281--37614806 Score: 881
Period size: 93 Copynumber: 5.6 Consensus size: 93
37614271 ATACACAAAA
* * * * *
37614281 TTGGACATCATTTACACACCAAAATTTGACAGCATGTATATACAAAATTGGACAACATTTATTCA
1 TTGGACAGCACTTATACA-CAAAATTTGACAGCATGTATATGCAAAATTGGACAGCATTTATTCA
* * *
37614346 CCAAAATTAGGCAGCATATATATACTAAT
65 CCAAAATTGGGCAGCATACATATACCAAT
* *
37614375 TTGGACAGCACTTATATACAAAATTTAACAGCATGTATATGCAAAATTGGACAGCATTTATTCAC
1 TTGGACAGCACTTATACACAAAATTTGACAGCATGTATATGCAAAATTGGACAGCATTTATTCAC
* *
37614440 AAAAATTGGGCAGCATACATACACCAAT
66 CAAAATTGGGCAGCATACATATACCAAT
37614468 TTGGACAGCACTTATACACAAAATTTGACAGCATGTATATGCAAAATTGGACAGCATTTATTCAC
1 TTGGACAGCACTTATACACAAAATTTGACAGCATGTATATGCAAAATTGGACAGCATTTATTCAC
* *
37614533 CAAAATTGGGCAGCACACATACACCAAT
66 CAAAATTGGGCAGCATACATATACCAAT
37614561 TTGGACAGCACTTATACACAAAATTTGACAGCATGTATATGCAAAATTGGACAGCATTTATTCAC
1 TTGGACAGCACTTATACACAAAATTTGACAGCATGTATATGCAAAATTGGACAGCATTTATTCAC
37614626 CAAAATTGGGCAGCATACATATACCAAT
66 CAAAATTGGGCAGCATACATATACCAAT
* *
37614654 TTGGACAGCACTTATACACAAAATTTGACAACATGTATATGCAAAATTGGACAACATTTATTCAC
1 TTGGACAGCACTTATACACAAAATTTGACAGCATGTATATGCAAAATTGGACAGCATTTATTCAC
37614719 CAAAATTGGGCAGCATACATATACCAAT
66 CAAAATTGGGCAGCATACATATACCAAT
* *
37614747 TTGGACAGCACTTATACACAAAATTTGATAGCATGTATATGTAAAATTGGACAGCATTTA
1 TTGGACAGCACTTATACACAAAATTTGACAGCATGTATATGCAAAATTGGACAGCATTTA
37614807 AGCATAAAAA
Statistics
Matches: 408, Mismatches: 24, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
93 394 0.97
94 14 0.03
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.28
Consensus pattern (93 bp):
TTGGACAGCACTTATACACAAAATTTGACAGCATGTATATGCAAAATTGGACAGCATTTATTCAC
CAAAATTGGGCAGCATACATATACCAAT
Found at i:37615568 original size:28 final size:28
Alignment explanation
Indices: 37615533--37615685 Score: 216
Period size: 28 Copynumber: 5.5 Consensus size: 28
37615523 TTTAATAAGT
** * *
37615533 TCGCACACTTAGTGCTAAATAATCAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
* *
37615561 TCACACACTTAGTGCTTTACCATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
37615589 TCGCACACTTAGTGCTTTACAATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
*
37615617 TCCCACACTTAGTGCTTTACAATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
* * *
37615645 TTGCACACTTAGTGCTTCACAATTAAAT
1 TCGCACACTTAGTGCTTTACAATTAAAC
37615673 TCGCACACTTAGT
1 TCGCACACTTAGT
37615686 TTCGAAAGTT
Statistics
Matches: 111, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 111 1.00
ACGTcount: A:0.33, C:0.26, G:0.10, T:0.31
Consensus pattern (28 bp):
TCGCACACTTAGTGCTTTACAATTAAAC
Found at i:37620596 original size:46 final size:45
Alignment explanation
Indices: 37620529--37620927 Score: 395
Period size: 46 Copynumber: 9.6 Consensus size: 45
37620519 TTTGAGTACT
* *
37620529 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
37620575 TCTGATCAAGTGAAAAAGTGAT-A-----AG--T-GCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
37620611 TCTGATCAAGAGAGAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
37620657 TCTGATCAAGTGAAAAAGTGAT-A-----A--TTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
37620694 TCTGATCAAGTGAAAAAGTGATAA---GT-GC-TA--T--ACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
37620730 TCTGATCAAGTGAAAAAGTGATAA---GT-GC-TA--T--ACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
37620766 TCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
*
37620812 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
* * *
37620858 TCTGACCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
37620903 TCTGATC-AG-GGACAAGTGATAAGTG
1 TCTGATCAAGTGAAAAAGTGATAAGTG
37620928 ATCATACGTA
Statistics
Matches: 311, Mismatches: 17, Indels: 53
0.82 0.04 0.14
Matches are distributed among these distances:
36 94 0.30
37 37 0.12
38 2 0.01
39 1 0.00
40 6 0.02
41 1 0.00
42 4 0.01
43 13 0.04
44 3 0.01
45 22 0.07
46 128 0.41
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:37620606 original size:36 final size:36
Alignment explanation
Indices: 37620565--37620792 Score: 303
Period size: 36 Copynumber: 6.0 Consensus size: 36
37620555 GGTAGCTTTA
37620565 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
37620601 GCTACACTTATCTGATCAAGAGAGAAAGTGATAAGTGGTAGCTTT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGAT-A-----AG---T
*
37620646 AGCTACACTTATCTGATCAAGTGAAAAAGTGATAATT
1 -GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
37620683 AGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 -GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
*
37620720 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
37620756 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
37620792 G
1 G
37620793 TTAGCCTTAG
Statistics
Matches: 174, Mismatches: 8, Indels: 20
0.86 0.04 0.10
Matches are distributed among these distances:
36 101 0.58
37 38 0.22
40 1 0.01
42 2 0.01
45 2 0.01
46 30 0.17
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:37620632 original size:82 final size:81
Alignment explanation
Indices: 37620529--37620927 Score: 478
Period size: 82 Copynumber: 4.9 Consensus size: 81
37620519 TTTGAGTACT
* *
37620529 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAAGTGAAAAAGT
37620594 GATAAGTGCTACACTTA
65 GATAAGTGCTACACTTA
* *
37620611 TCTGATCAAGAGAGAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAAGTGAAAAAGT
*
37620676 GATAATTAGCTACACTTA
65 GATAAGT-GCTACACTTA
*
37620694 TCTGATCAAGTGAAAAAGTGATAA---GT-GC-TA--T--ACTTATCTGATCAAGTGAAAAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGTGAAAAAGTG
*
37620750 ATAAGTGCTATACTTA
66 ATAAGTGCTACACTTA
* *
37620766 TCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTATCTGATCAAGTGAGAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTTAGCTACACTTATCTGATCAAGTGAAAAAGT
37620831 GATAAGTGGTAGCCTTAGCTACACTTA
65 GAT-A-----AG---T-GCTACACTTA
* * * *
37620858 TCTGACCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATC-AG-GGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGTGAAAAAGTG
37620921 ATAAGTG
66 ATAAGTG
37620928 ATCATACGTA
Statistics
Matches: 280, Mismatches: 16, Indels: 45
0.82 0.05 0.13
Matches are distributed among these distances:
72 32 0.11
73 30 0.11
75 2 0.01
76 1 0.00
77 3 0.01
78 2 0.01
79 3 0.01
80 4 0.01
82 96 0.34
83 35 0.12
88 3 0.01
89 8 0.03
90 2 0.01
91 21 0.08
92 38 0.14
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.29
Consensus pattern (81 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGTGAAAAAGTG
ATAAGTGCTACACTTA
Found at i:37620740 original size:21 final size:20
Alignment explanation
Indices: 37620712--37620777 Score: 52
Period size: 21 Copynumber: 3.5 Consensus size: 20
37620702 AGTGAAAAAG
37620712 TGATAAGTGCTATACTTATC
1 TGATAAGTGCTATACTTATC
* **
37620732 TGATCAAGTG--A-A--AAAG
1 TGAT-AAGTGCTATACTTATC
37620748 TGATAAGTGCTATACTTATC
1 TGATAAGTGCTATACTTATC
37620768 TGATCAAGTG
1 TGAT-AAGTG
37620778 ACAAAGTGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 13
0.63 0.12 0.25
Matches are distributed among these distances:
15 5 0.15
16 5 0.15
17 1 0.03
18 2 0.06
19 1 0.03
20 9 0.27
21 10 0.30
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (20 bp):
TGATAAGTGCTATACTTATC
Found at i:37627312 original size:22 final size:22
Alignment explanation
Indices: 37627284--37627355 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
37627274 AGATAGAGCC
37627284 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
37627306 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
** *
37627328 CTCATGTTTCACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
37627350 CTCATG
1 CTCATG
37627356 TTTGAACAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.31
Consensus pattern (22 bp):
CTCATGGCTAACGTACTAAGCT
Found at i:37631332 original size:165 final size:160
Alignment explanation
Indices: 37631055--37631380 Score: 426
Period size: 165 Copynumber: 2.0 Consensus size: 160
37631045 TCAAGTCAAG
** * *
37631055 TCAAGCATATGATTGTCAAATCTCAAAATCTAAAATATCTTCATTGCAAAACTCGCATAATTCTT
1 TCAAGCATACAATTGTCAAATCTCAAAATCTAAAATATCTTCATTGCAAAACTCACATAATTCAT
* *
37631120 ATCTATAATTTTTATAGTCTTAGGAAATAAAGAGATTTGGCCTTTCAAATGAGTAGTGCAGAAAA
66 ATCTATAATTTTTATAGTCATAGGAAATAAAGAGAATTGGCCTTTCAAATGAGTAGTGCAGAAAA
*
37631185 TTTACAGATTCAGATTTTG-AAGCGTTGAAA
131 TTTACACATTCA-ATTTTGTAAGCGTTGAAA
* * *
37631215 TCAAGCATACAATTTTCAAAT-TGCAAATTCTAAGAATATTTTTCATTGCAAAAACTCACATAAT
1 TCAAGCATACAATTGTCAAATCT-CAAAATCTAA-AATA-TCTTCATTGC-AAAACTCACATAAT
* *
37631279 TCATA-CTTATAA-TTTTAGTGAAGTCATATGAAATAAAGAGAATTGGCCTTTCAAATGATTAGT
62 TCATATC-TATAATTTTTA-T--AGTCATAGGAAATAAAGAGAATTGGCCTTTCAAATGAGTAGT
*
37631342 GCAGAAAATTTACACATTCAATTTTGTAAGTGTTGAAA
123 GCAGAAAATTTACACATTCAATTTTGTAAGCGTTGAAA
37631380 T
1 T
37631381 TAAATGAATG
Statistics
Matches: 144, Mismatches: 13, Indels: 13
0.85 0.08 0.08
Matches are distributed among these distances:
159 1 0.01
160 27 0.19
161 4 0.03
162 15 0.10
163 23 0.16
164 6 0.04
165 68 0.47
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (160 bp):
TCAAGCATACAATTGTCAAATCTCAAAATCTAAAATATCTTCATTGCAAAACTCACATAATTCAT
ATCTATAATTTTTATAGTCATAGGAAATAAAGAGAATTGGCCTTTCAAATGAGTAGTGCAGAAAA
TTTACACATTCAATTTTGTAAGCGTTGAAA
Found at i:37632822 original size:7 final size:7
Alignment explanation
Indices: 37632810--37632842 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
37632800 AGAGGGAACC
37632810 AGCAGAG
1 AGCAGAG
37632817 AGCAGAG
1 AGCAGAG
37632824 AGCAGAG
1 AGCAGAG
37632831 AGCAGAG
1 AGCAGAG
37632838 AGCAG
1 AGCAG
37632843 CGTAGCAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.42, T:0.00
Consensus pattern (7 bp):
AGCAGAG
Found at i:37633712 original size:98 final size:96
Alignment explanation
Indices: 37633582--37633772 Score: 296
Period size: 98 Copynumber: 2.0 Consensus size: 96
37633572 CCTTACTTAT
*
37633582 CTAAATATCTTCCTCAAGTAAACTATGAAATATATTGAATAATATCCTTTAAGAAAGTGCACAAA
1 CTAAATATCTTCCTCAAGTAAACTATGAAATATATTGAATAATATCCCTTAA-AAA-TGCACAAA
37633647 AATAATCACAATAATCAAATCAAAATATGCCAA
64 AATAATCACAATAATCAAATCAAAATATGCCAA
*
37633680 CTAAATAT-TCTCCTCATGTAAA-TAATGAAATATATTGAATAATATCCCTTAAAAATGCACAAA
1 CTAAATATCT-TCCTCAAGTAAACT-ATGAAATATATTGAATAATATCCCTTAAAAATGCACAAA
* *
37633743 AATAGTCACAATAATCGAATCAAAATATGC
64 AATAATCACAATAATCAAATCAAAATATGC
37633773 TAACAAAACA
Statistics
Matches: 87, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
96 36 0.41
97 5 0.06
98 46 0.53
ACGTcount: A:0.48, C:0.16, G:0.07, T:0.28
Consensus pattern (96 bp):
CTAAATATCTTCCTCAAGTAAACTATGAAATATATTGAATAATATCCCTTAAAAATGCACAAAAA
TAATCACAATAATCAAATCAAAATATGCCAA
Found at i:37638557 original size:25 final size:25
Alignment explanation
Indices: 37638529--37638584 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
37638519 AAGTATTATG
*
37638529 CAGAGAACATAAATGTGCTAATAAT
1 CAGAGAACACAAATGTGCTAATAAT
* **
37638554 CAGAGAGCACCGATGTGCTAATAAT
1 CAGAGAACACAAATGTGCTAATAAT
37638579 CAGAGA
1 CAGAGA
37638585 GCACGCTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (25 bp):
CAGAGAACACAAATGTGCTAATAAT
Found at i:37638585 original size:25 final size:25
Alignment explanation
Indices: 37638541--37638588 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
37638531 GAGAACATAA
37638541 ATGTGCTAATAATCAGAGAGCACCG
1 ATGTGCTAATAATCAGAGAGCACCG
37638566 ATGTGCTAATAATCAGAGAGCAC
1 ATGTGCTAATAATCAGAGAGCAC
37638589 GCTAAATCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.21
Consensus pattern (25 bp):
ATGTGCTAATAATCAGAGAGCACCG
Found at i:37639614 original size:50 final size:50
Alignment explanation
Indices: 37639490--37639833 Score: 431
Period size: 50 Copynumber: 6.9 Consensus size: 50
37639480 GATAATAACA
* * ** * * *
37639490 TGCCAAAGTCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTGTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * * * ** *
37639539 TGCCAATGCCATATCCCAGATATGGTTTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * **
37639589 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
37639639 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * * *
37639689 TGTCAACGCCATGTCCCAAACATGGTCTAACATGGGACCTTTGATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
37639739 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
37639789 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCAT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT
37639834 AATTTCAATA
Statistics
Matches: 257, Mismatches: 36, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
48 1 0.00
49 37 0.14
50 219 0.85
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:37647010 original size:22 final size:21
Alignment explanation
Indices: 37646967--37647023 Score: 87
Period size: 22 Copynumber: 2.7 Consensus size: 21
37646957 TGTAGTTTTC
*
37646967 TAGGTGAAAAGTTGGATGTGA
1 TAGGTGAAAGGTTGGATGTGA
*
37646988 TAGGTGAAAGGTTAGGATTTGA
1 TAGGTGAAAGGTT-GGATGTGA
37647010 TAGGTGAAAGGTTG
1 TAGGTGAAAGGTTG
37647024 ATAGGTGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
21 13 0.39
22 20 0.61
ACGTcount: A:0.32, C:0.00, G:0.39, T:0.30
Consensus pattern (21 bp):
TAGGTGAAAGGTTGGATGTGA
Found at i:37647350 original size:5 final size:5
Alignment explanation
Indices: 37647340--37647403 Score: 71
Period size: 5 Copynumber: 13.0 Consensus size: 5
37647330 TTTCCCTGCA
*
37647340 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA- ATAAAT -AATT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT AAAAT AAAAT
*
37647389 -AATT AAAATT AAAAT
1 AAAAT AAAA-T AAAAT
37647404 GTGTATTTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
4 7 0.14
5 38 0.76
6 5 0.10
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (5 bp):
AAAAT
Found at i:37656528 original size:38 final size:38
Alignment explanation
Indices: 37656486--37656586 Score: 134
Period size: 38 Copynumber: 2.7 Consensus size: 38
37656476 AGGTATTATT
*
37656486 CAGGCTTAGTG-TCGGTGTTTTTCAGG-TTTAGTGGCTAG
1 CAGGCTTAGTGCT-GGTGTTATTCAGGCTTT-GTGGCTAG
37656524 CAGGCTTAGTGCTGGTGTTATTCAGGCTTTGTGGCTAG
1 CAGGCTTAGTGCTGGTGTTATTCAGGCTTTGTGGCTAG
* * *
37656562 CAAGCTTAATGCTTGTGTTATTCAG
1 CAGGCTTAGTGCTGGTGTTATTCAG
37656587 ACTTAATGTC
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
38 53 0.93
39 4 0.07
ACGTcount: A:0.16, C:0.15, G:0.31, T:0.39
Consensus pattern (38 bp):
CAGGCTTAGTGCTGGTGTTATTCAGGCTTTGTGGCTAG
Found at i:37656591 original size:22 final size:23
Alignment explanation
Indices: 37656566--37656617 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
37656556 GGCTAGCAAG
* *
37656566 CTTAATGCT-TGTGTTATTCAGA
1 CTTAATGCTCGGTGTTAATCAGA
*
37656588 CTTAATG-TCGGTGTTAATCAGG
1 CTTAATGCTCGGTGTTAATCAGA
37656610 CTTAATGC
1 CTTAATGC
37656618 CTAGCAGGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.40
Consensus pattern (23 bp):
CTTAATGCTCGGTGTTAATCAGA
Found at i:37662328 original size:50 final size:50
Alignment explanation
Indices: 37662274--37662401 Score: 141
Period size: 50 Copynumber: 2.6 Consensus size: 50
37662264 ATGAACAAAT
* * * * * *
37662274 GAGTTACTTAATGCAAGAT-TTACTTAAAGATGCACACTTAACTATCATGG
1 GAGTTACATAATGCAAG-TCATAATTAAAGATACAAACTTAACTATCATGA
* * *
37662324 GAGTTACATAATGCATGTCATAATTTAATATACAAACTTAACTATCATGA
1 GAGTTACATAATGCAAGTCATAATTAAAGATACAAACTTAACTATCATGA
* *
37662374 GAGTTACATAATGCATGGCATAATTAAA
1 GAGTTACATAATGCAAGTCATAATTAAA
37662402 TTATAGACTT
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
49 1 0.02
50 65 0.98
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (50 bp):
GAGTTACATAATGCAAGTCATAATTAAAGATACAAACTTAACTATCATGA
Found at i:37667792 original size:50 final size:50
Alignment explanation
Indices: 37667673--37667956 Score: 313
Period size: 50 Copynumber: 5.6 Consensus size: 50
37667663 ACATTTGGGT
* * * *
37667673 GATGAGA--TCCCATGTAAGACTATGTCTGGGACATGGCATTGACATCATTGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C--CGA
*
37667724 GATTATGAGAGGTCCCATGTAAGAACATGTCTGGGACATGGCGTTGGCACCGA
1 G---ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA
* *
37667777 GATGAGAGGTTCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA
* *
37667827 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGACGTTGGCACCAA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA
* * * **
37667877 GATGAGAGGTCCC-TCGTAAGACCATGTTTGGGACATGGCATGGGCACTTA
1 GATGAGAGGTCCCAT-GTAAGACCATGTCTGGGACATGGCGTTGGCACCGA
* ** * *
37667927 TATGAGAATTCTCATGTAAGACCATATCTG
1 GATGAGAGGTCCCATGTAAGACCATGTCTG
37667957 AGATATGACA
Statistics
Matches: 202, Mismatches: 24, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
49 1 0.00
50 156 0.77
51 2 0.01
53 3 0.01
54 6 0.03
55 1 0.00
56 33 0.16
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.24
Consensus pattern (50 bp):
GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA
Found at i:37671242 original size:175 final size:175
Alignment explanation
Indices: 37670950--37671268 Score: 530
Period size: 175 Copynumber: 1.8 Consensus size: 175
37670940 AGGAGTTTGG
* * *
37670950 GAGAGTTTTACGGTTTTTTGGAGAGGATTGTCAGTGAAAACAAAAGAGATTAGAGTAAGCAATGA
1 GAGAGTTTTACGGTTTTTTGGAGAGGATTGTAAGTGAAAACAAAAGAGAATAAAGTAAGCAATGA
* * *
37671015 ATTATTTATAAGAAGGGACCTCAACATCCATGGGTTTTGAAGTCTTTGGTATTAAATGGGTTGGT
66 ATTATTTATAAGAAAGGACCTCAACATCCATGGGTGTTGAAGTCTCTGGTATTAAATGGGTTGGT
*
37671080 TGGGCCTATGAGCAGTAGAAATTTAGAGCTTTTTTTACTAGATGA
131 TGGGCCTACGAGCAGTAGAAATTTAGAGCTTTTTTTACTAGATGA
* *
37671125 GAGAGTTTTAGGGTTTTTTGGAGAGGATTTTAAGTGAAAACAAAAGAGAATAAAGTAAGCAATGA
1 GAGAGTTTTACGGTTTTTTGGAGAGGATTGTAAGTGAAAACAAAAGAGAATAAAGTAAGCAATGA
* *
37671190 GTTATTTATAAGAAAGGACCTGAACATCCATGGGTGTTGAAGTCTCTGGTATTAAATGGGTTGGT
66 ATTATTTATAAGAAAGGACCTCAACATCCATGGGTGTTGAAGTCTCTGGTATTAAATGGGTTGGT
*
37671255 TGGGCTTACGAGCA
131 TGGGCCTACGAGCA
37671269 ATAAATTCAT
Statistics
Matches: 132, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
175 132 1.00
ACGTcount: A:0.32, C:0.09, G:0.27, T:0.32
Consensus pattern (175 bp):
GAGAGTTTTACGGTTTTTTGGAGAGGATTGTAAGTGAAAACAAAAGAGAATAAAGTAAGCAATGA
ATTATTTATAAGAAAGGACCTCAACATCCATGGGTGTTGAAGTCTCTGGTATTAAATGGGTTGGT
TGGGCCTACGAGCAGTAGAAATTTAGAGCTTTTTTTACTAGATGA
Found at i:37671558 original size:194 final size:194
Alignment explanation
Indices: 37671238--37671601 Score: 475
Period size: 194 Copynumber: 1.9 Consensus size: 194
37671228 GAAGTCTCTG
* * ** * *
37671238 GTATTAAATGGGTTGGTTGGGCTTACGAGCAATAAATTCATGATTCAATGTTGATCGGCTAAGCC
1 GTATTAAATGAGTTGGTTGGGCTTAAGAGCAATAAATTCATGAGCCAATATAGATCGGCTAAGCC
* * * ** * *
37671303 TTTATAACCATGGATGTTGAGGTCCTTGGATTTTACTTCATTAGTACTTCTCTTGATAGTTAGGA
66 TTGATAACCATAGATGTTGAGGTCCTTGGATTATACACCATTAGTACTTCTCCTAATAGTTAGGA
* * *
37671368 GCACAAATTTCATGGAAATTTTTTATCTCACGAACCTTGAAATTCGTGAGTGTTGAGGTTTTTA
131 GCACAAATTTCATGAAAATTTTATATCTCACAAACCTTGAAATTCGTGAGTGTTGAGGTTTTTA
*
37671432 GTATTAAATGAGTTGGTTGGGCTTATAG-GCAATAAATTCCTGAGCCAATATAGA-CTGGCTGAA
1 GTATTAAATGAGTTGGTTGGGCTTA-AGAGCAATAAATTCATGAGCCAATATAGATC-GGCT-AA
*
37671495 -CCTTGATAACCATAGATGTTGAGGTTCTTAGG-TTATACACCATTAGTACTTCTCCTAATAGTT
63 GCCTTGATAACCATAGATGTTGAGGTCCTT-GGATTATACACCATTAGTACTTCTCCTAATAGTT
* **
37671558 AGGAGCACGAATTTTGTGAAAATTTTATATCTCACAAACCTTGA
127 AGGAGCACAAATTTCATGAAAATTTTATATCTCACAAACCTTGA
37671602 CACCCATAGG
Statistics
Matches: 145, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
193 1 0.01
194 139 0.96
195 5 0.03
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.36
Consensus pattern (194 bp):
GTATTAAATGAGTTGGTTGGGCTTAAGAGCAATAAATTCATGAGCCAATATAGATCGGCTAAGCC
TTGATAACCATAGATGTTGAGGTCCTTGGATTATACACCATTAGTACTTCTCCTAATAGTTAGGA
GCACAAATTTCATGAAAATTTTATATCTCACAAACCTTGAAATTCGTGAGTGTTGAGGTTTTTA
Found at i:37673392 original size:20 final size:19
Alignment explanation
Indices: 37673369--37673427 Score: 84
Period size: 20 Copynumber: 3.1 Consensus size: 19
37673359 AAAAGATTAT
37673369 AAAAAATAATAAATTTTAGA
1 AAAAAATAATAAATTTTA-A
37673389 AAAAAATAATAAATTTTAA
1 AAAAAATAATAAATTTTAA
* *
37673408 TAAAAATAA-AAAATTTAA
1 AAAAAATAATAAATTTTAA
37673426 AA
1 AA
37673428 TTTTTAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
18 9 0.25
19 9 0.25
20 18 0.50
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAAAATAATAAATTTTAA
Found at i:37673467 original size:10 final size:9
Alignment explanation
Indices: 37673452--37673494 Score: 52
Period size: 10 Copynumber: 4.7 Consensus size: 9
37673442 AATTTTTTAT
37673452 AAAAATAGTA
1 AAAAATA-TA
*
37673462 AAAAATAAA
1 AAAAATATA
37673471 AAAAATAT-
1 AAAAATATA
37673479 AAAAATCATA
1 AAAAAT-ATA
37673489 AAAAAT
1 AAAAAT
37673495 TAACAATTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 6 0.21
9 10 0.34
10 13 0.45
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (9 bp):
AAAAATATA
Found at i:37673727 original size:57 final size:57
Alignment explanation
Indices: 37673630--37673758 Score: 142
Period size: 57 Copynumber: 2.2 Consensus size: 57
37673620 GTACGATAAT
37673630 TTTTATAATTTTTTTACGAAATTTATATTTTGTATAATTTTCTTA-TGA-CTTTATAAAA
1 TTTTATAATTTTTTTAC-AAATTTATATTTTGTATAATTTT-TTACT-ATCTTTATAAAA
* * *
37673688 TTTTATAATTTTTTTA-TATTTCTATATATTT-TATAATTTTTTACTATTTTTATAAAA
1 TTTTATAATTTTTTTACAAATT-TATAT-TTTGTATAATTTTTTACTATCTTTATAAAA
37673745 TTTT-TCAATTTTTT
1 TTTTAT-AATTTTTT
37673759 ATAATTTTTA
Statistics
Matches: 63, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
56 8 0.13
57 36 0.57
58 19 0.30
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (57 bp):
TTTTATAATTTTTTTACAAATTTATATTTTGTATAATTTTTTACTATCTTTATAAAA
Found at i:37673735 original size:28 final size:28
Alignment explanation
Indices: 37673662--37673761 Score: 107
Period size: 29 Copynumber: 3.5 Consensus size: 28
37673652 TTATATTTTG
*
37673662 TATAATTTTCTTATGACTT-TATAAAATTT
1 TATAATTTT-TTAT-ATTTCTATAAAATTT
*
37673691 TATAATTTTTTTATATTTCTAT-ATATTT
1 TATAA-TTTTTTATATTTCTATAAAATTT
*
37673719 TATAATTTTTTACTATTTTTATAAAATTT
1 TATAATTTTTTA-TATTTCTATAAAATTT
37673748 T-TCAATTTTTTATA
1 TAT-AATTTTTTATA
37673762 ATTTTTATGG
Statistics
Matches: 62, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
27 7 0.11
28 24 0.39
29 27 0.44
30 4 0.06
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (28 bp):
TATAATTTTTTATATTTCTATAAAATTT
Found at i:37673766 original size:28 final size:28
Alignment explanation
Indices: 37673662--37673766 Score: 108
Period size: 28 Copynumber: 3.7 Consensus size: 28
37673652 TTATATTTTG
* *
37673662 TATAATTTTCTTATGACTTTATAAAATTT
1 TATAATTTT-TTATAATTTTATAAAATTT
*
37673691 TATAATTTTTT-TATATTTCTAT-ATATTT
1 TATAATTTTTTATA-ATTT-TATAAAATTT
*
37673719 TATAATTTTTTACTATTTTTATAAAATTT
1 TATAATTTTTTA-TAATTTTATAAAATTT
37673748 T-TCAATTTTTTATAATTTT
1 TAT-AATTTTTTATAATTTT
37673767 TATGGTTTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
27 1 0.02
28 31 0.48
29 30 0.47
30 2 0.03
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.63
Consensus pattern (28 bp):
TATAATTTTTTATAATTTTATAAAATTT
Found at i:37673785 original size:10 final size:10
Alignment explanation
Indices: 37673688--37673813 Score: 81
Period size: 9 Copynumber: 13.2 Consensus size: 10
37673678 CTTTATAAAA
37673688 TTTTATA-AT
1 TTTTATATAT
*
37673697 TTTTTTATAT
1 TTTTATATAT
*
37673707 TTCTATATA-
1 TTTTATATAT
37673716 TTTTATA-AT
1 TTTTATATAT
37673725 TTTT-TACTAT
1 TTTTATA-TAT
*
37673735 TTTTATAAAAT
1 TTTTAT-ATAT
37673746 TTTTCA-AT-T
1 TTTT-ATATAT
37673755 TTTTATA-AT
1 TTTTATATAT
**
37673764 TTTTAT-GGT
1 TTTTATATAT
37673773 TTTTATATAT
1 TTTTATATAT
* *
37673783 TTTTATAAAA
1 TTTTATATAT
* *
37673793 TTTAATAAAT
1 TTTTATATAT
37673803 TTTTA-ATAT
1 TTTTATATAT
37673812 TT
1 TT
37673814 GAATTTTTTA
Statistics
Matches: 91, Mismatches: 15, Indels: 22
0.71 0.12 0.17
Matches are distributed among these distances:
8 4 0.04
9 41 0.45
10 37 0.41
11 7 0.08
12 2 0.02
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (10 bp):
TTTTATATAT
Found at i:37673810 original size:11 final size:10
Alignment explanation
Indices: 37673679--37673807 Score: 74
Period size: 10 Copynumber: 13.4 Consensus size: 10
37673669 TTCTTATGAC
*
37673679 TTTATAAAAT
1 TTTATAAATT
37673689 TTTAT-AATT
1 TTTATAAATT
* *
37673698 TTTTTATATT
1 TTTATAAATT
* *
37673708 TCTATATA-T
1 TTTATAAATT
37673717 TTTAT-AATT
1 TTTATAAATT
*
37673726 TTT-TACTATT
1 TTTATA-AATT
*
37673736 TTTATAAAAT
1 TTTATAAATT
*
37673746 TTT-TCAATT
1 TTTATAAATT
37673755 TTT-TATAATT
1 TTTATA-AATT
**
37673765 TTTAT-GGTT
1 TTTATAAATT
*
37673774 TTTATATATT
1 TTTATAAATT
*
37673784 TTTATAAAAT
1 TTTATAAATT
*
37673794 TTAATAAATT
1 TTTATAAATT
37673804 TTTA
1 TTTA
37673808 ATATTTGAAT
Statistics
Matches: 89, Mismatches: 22, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
8 2 0.02
9 31 0.35
10 53 0.60
11 3 0.03
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (10 bp):
TTTATAAATT
Found at i:37676569 original size:21 final size:20
Alignment explanation
Indices: 37676535--37676573 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
37676525 TCTTTTAATC
*
37676535 TTTTAAAAGTTATTAAAAGT
1 TTTTAAAAGCTATTAAAAGT
37676555 TTTTAGAAAGCTATTAAAA
1 TTTTA-AAAGCTATTAAAA
37676574 TTGAGTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (20 bp):
TTTTAAAAGCTATTAAAAGT
Found at i:37677838 original size:16 final size:16
Alignment explanation
Indices: 37677813--37677846 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
37677803 CTCTCTCTAC
*
37677813 ACACATGCACACACAT
1 ACACACGCACACACAT
*
37677829 ACACACGCACATACAT
1 ACACACGCACACACAT
37677845 AC
1 AC
37677847 TATGTATATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.38, G:0.06, T:0.12
Consensus pattern (16 bp):
ACACACGCACACACAT
Found at i:37679297 original size:22 final size:22
Alignment explanation
Indices: 37679269--37679326 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
37679259 TTTATTGTTC
37679269 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
*
37679291 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTG
**
37679313 AGCCATGAGAGCTT
1 AAACATGAGAGCTT
37679327 TCTTGCATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:37683919 original size:52 final size:51
Alignment explanation
Indices: 37683863--37683967 Score: 131
Period size: 52 Copynumber: 2.0 Consensus size: 51
37683853 CCTCAAGCCC
*
37683863 TTTTACTTTCC-CCCAAAAAATTGTACTCCCCCCAAACTCTCAAAACTTTTTT
1 TTTTACTTTCCTCCC-AAAAATTGTACTCCCCCCAAAC-CCCAAAACTTTTTT
* * * **
37683915 TTTTACTTTCCTCTCAAAACTTTTACTTTCCCCAAACCCCAAAACTTTTTT
1 TTTTACTTTCCTCCCAAAAATTGTACTCCCCCCAAACCCCAAAACTTTTTT
37683966 TT
1 TT
37683968 CTTTTACTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
51 15 0.33
52 29 0.63
53 2 0.04
ACGTcount: A:0.27, C:0.31, G:0.01, T:0.41
Consensus pattern (51 bp):
TTTTACTTTCCTCCCAAAAATTGTACTCCCCCCAAACCCCAAAACTTTTTT
Found at i:37683982 original size:53 final size:54
Alignment explanation
Indices: 37683892--37684019 Score: 174
Period size: 54 Copynumber: 2.4 Consensus size: 54
37683882 ATTGTACTCC
*
37683892 CCCCAAACTCTCAAAAC--TTTTTTTTTTACTTTCCTCTC-AAAACTTTTACTTT
1 CCCCAAAC-CCCAAAACTTTTTTTTTTTTACTTTCCTCTCTAAAACTTTTACTTT
37683944 CCCCAAACCCCAAAACTTTTTTTTCTTTTACTTT-CTCTCTAAAACTTTTACTTT
1 CCCCAAACCCCAAAACTTTTTTTT-TTTTACTTTCCTCTCTAAAACTTTTACTTT
*
37683998 CCCCAAATGCCGCAAAACTTTT
1 CCCCAAA--CCCCAAAACTTTT
37684020 ACTTTCTCTC
Statistics
Matches: 68, Mismatches: 2, Indels: 8
0.87 0.03 0.10
Matches are distributed among these distances:
51 7 0.10
52 8 0.12
53 11 0.16
54 30 0.44
56 12 0.18
ACGTcount: A:0.26, C:0.30, G:0.02, T:0.42
Consensus pattern (54 bp):
CCCCAAACCCCAAAACTTTTTTTTTTTTACTTTCCTCTCTAAAACTTTTACTTT
Found at i:37684041 original size:27 final size:27
Alignment explanation
Indices: 37683982--37684046 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
37683972 TACTTTCTCT
*
37683982 CTAAAACTTTTACTTTCCCCAAATGCCG
1 CTAAAACTTTTACTTTCCCCAAA-GCCC
*
37684010 C-AAAACTTTTACTTTCTCTCAAA-CCC
1 CTAAAACTTTTACTTTC-CCCAAAGCCC
37684036 CTAAAACTTTT
1 CTAAAACTTTT
37684047 TTTTTCAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
26 3 0.09
27 24 0.73
28 6 0.18
ACGTcount: A:0.31, C:0.31, G:0.03, T:0.35
Consensus pattern (27 bp):
CTAAAACTTTTACTTTCCCCAAAGCCC
Found at i:37684423 original size:19 final size:19
Alignment explanation
Indices: 37684399--37684436 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
37684389 AAGTTAATAA
*
37684399 CAAATTTGATTATGGTGGG
1 CAAATTTGATTACGGTGGG
37684418 CAAATTTGATTACGGTGGG
1 CAAATTTGATTACGGTGGG
37684437 TGGCAGTGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.08, G:0.32, T:0.34
Consensus pattern (19 bp):
CAAATTTGATTACGGTGGG
Found at i:37685347 original size:9 final size:9
Alignment explanation
Indices: 37685330--37685366 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
37685320 TGAGTTTTCG
37685330 AATTCGAAT
1 AATTCGAAT
*
37685339 AACTCGAAT
1 AATTCGAAT
37685348 AATTCGAAT
1 AATTCGAAT
37685357 AATTCGAAT
1 AATTCGAAT
37685366 A
1 A
37685367 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:37697477 original size:29 final size:30
Alignment explanation
Indices: 37697445--37697521 Score: 77
Period size: 31 Copynumber: 2.6 Consensus size: 30
37697435 ATAAACACCA
*
37697445 GTACAAAGTACCTGATAATAA-AGTCATCG
1 GTACAAAGTACCTGATAATAATAATCATCG
* * *
37697474 GTACATAGTACTTGAT-ATAATGTAATCATTG
1 GTACAAAGTACCTGATAATAA--TAATCATCG
*
37697505 GTACACAGTACCTGATA
1 GTACAAAGTACCTGATA
37697522 CTTTAAACTC
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 4 0.11
29 14 0.37
31 20 0.53
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.30
Consensus pattern (30 bp):
GTACAAAGTACCTGATAATAATAATCATCG
Found at i:37698347 original size:26 final size:26
Alignment explanation
Indices: 37698286--37698347 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
37698276 GACTAAATTG
*
37698286 AAATGAAATAAAAATTATAGGGGCAA
1 AAATGAAATTAAAATTATAGGGGCAA
*
37698312 AAAGGAAATTAAAATTATAGGGGCAA
1 AAATGAAATTAAAATTATAGGGGCAA
*
37698338 AAATGTAATT
1 AAATGAAATT
37698348 TTGCTAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.55, C:0.03, G:0.19, T:0.23
Consensus pattern (26 bp):
AAATGAAATTAAAATTATAGGGGCAA
Found at i:37698645 original size:30 final size:30
Alignment explanation
Indices: 37698611--37698735 Score: 142
Period size: 30 Copynumber: 4.2 Consensus size: 30
37698601 CGACCAATGG
* *
37698611 AAAGGGATAGCTTCGGCTATCGAATTATGA
1 AAAGGGATAGCTTCAGCTATCAAATTATGA
** *
37698641 AAAGGGACGGCTTCAGCTATCAAATTCTGA
1 AAAGGGATAGCTTCAGCTATCAAATTATGA
* * * **
37698671 AAAGTGATGGGTTCAGCTATTGAATTATGA
1 AAAGGGATAGCTTCAGCTATCAAATTATGA
* *
37698701 AAAGGGATAGCTTCGGCTATAAAATTATGA
1 AAAGGGATAGCTTCAGCTATCAAATTATGA
37698731 AAAGG
1 AAAGG
37698736 TATGGTGACA
Statistics
Matches: 78, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 78 1.00
ACGTcount: A:0.36, C:0.12, G:0.26, T:0.26
Consensus pattern (30 bp):
AAAGGGATAGCTTCAGCTATCAAATTATGA
Found at i:37727861 original size:9 final size:9
Alignment explanation
Indices: 37727847--37727931 Score: 109
Period size: 9 Copynumber: 9.4 Consensus size: 9
37727837 TTTGGTTAAA
37727847 AATTAACCG
1 AATTAACCG
*
37727856 AATTAACTG
1 AATTAACCG
*
37727865 AATTACCCG
1 AATTAACCG
37727874 AATTAACCG
1 AATTAACCG
*
37727883 AA-TAACCCT
1 AATTAA-CCG
*
37727892 AATTAATCG
1 AATTAACCG
37727901 AATTAACCG
1 AATTAACCG
*
37727910 AATTACCCG
1 AATTAACCG
37727919 AATTAACCG
1 AATTAACCG
37727928 AATT
1 AATT
37727932 GAATCACTAC
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
8 3 0.05
9 58 0.91
10 3 0.05
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:37729300 original size:29 final size:29
Alignment explanation
Indices: 37729267--37729338 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 29
37729257 ACCAAACAAC
* * *
37729267 CGTGTGACCCACACAACCTACCGCACTGT
1 CGTGTGACCTACACAACCTACCACACGGT
* * *
37729296 CGTGTGATCTACACAGCTTACCACACGGT
1 CGTGTGACCTACACAACCTACCACACGGT
37729325 CGTGTGACCTACAC
1 CGTGTGACCTACAC
37729339 GGTCTACCAC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.24, C:0.36, G:0.19, T:0.21
Consensus pattern (29 bp):
CGTGTGACCTACACAACCTACCACACGGT
Found at i:37729346 original size:29 final size:28
Alignment explanation
Indices: 37729267--37729360 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 28
37729257 ACCAAACAAC
* * * *
37729267 CGTGTGACCCACACAACCTACCGCACTGT
1 CGTGTGACCTACAC-AGCTACCACACGGT
*
37729296 CGTGTGATCTACACAGCTTACCACACGGT
1 CGTGTGACCTACACAGC-TACCACACGGT
* *
37729325 CGTGTGACCTACACGGTCTACCACACGAT
1 CGTGTGACCTACACAG-CTACCACACGGT
*
37729354 CATGTGA
1 CGTGTGA
37729361 TGTCGACAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
28 2 0.04
29 51 0.94
30 1 0.02
ACGTcount: A:0.24, C:0.34, G:0.20, T:0.21
Consensus pattern (28 bp):
CGTGTGACCTACACAGCTACCACACGGT
Found at i:37731917 original size:16 final size:16
Alignment explanation
Indices: 37731896--37731928 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
37731886 AATTTTGAAA
37731896 TATTTTTTAAAATTTT
1 TATTTTTTAAAATTTT
*
37731912 TATTTTTTAATATTTT
1 TATTTTTTAAAATTTT
37731928 T
1 T
37731929 TTAGAATTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TATTTTTTAAAATTTT
Found at i:37732368 original size:16 final size:16
Alignment explanation
Indices: 37732347--37732380 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
37732337 ATAGTTGAAA
37732347 AAATAAATACAAAATT
1 AAATAAATACAAAATT
* *
37732363 AAATAAATTCACAATT
1 AAATAAATACAAAATT
37732379 AA
1 AA
37732381 CACCCAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATAAATACAAAATT
Found at i:37737136 original size:2 final size:2
Alignment explanation
Indices: 37737131--37737155 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
37737121 TATCATACAT
37737131 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
37737156 ATTCATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:37738027 original size:24 final size:25
Alignment explanation
Indices: 37737973--37738031 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
37737963 TTTTTTGATA
*
37737973 AAATATTTTTATTCGATATATATTT
1 AAATATTTTTATTCGATATATATCT
* *
37737998 AGATATTTTTATT--ATGTATTATCT
1 AAATATTTTTATTCGATATA-TATCT
37738022 AAATATTTTT
1 AAATATTTTT
37738032 TATACAGTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 4 0.14
24 13 0.45
25 12 0.41
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (25 bp):
AAATATTTTTATTCGATATATATCT
Found at i:37748019 original size:13 final size:13
Alignment explanation
Indices: 37748003--37748052 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
37747993 ACTTTGATAA
37748003 AATAAAATAAATT
1 AATAAAATAAATT
37748016 AATAAAATAAATTT
1 AATAAAATAAA-TT
***
37748030 AATTTTAT-AATT
1 AATAAAATAAATT
37748042 AATAAAATAAA
1 AATAAAATAAA
37748053 ATAAATTACA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
12 7 0.24
13 15 0.52
14 7 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATAAAATAAATT
Found at i:37755544 original size:15 final size:16
Alignment explanation
Indices: 37755521--37755554 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
37755511 ATTTACAAAA
37755521 TATGTATATATATAAG
1 TATGTATATATATAAG
37755537 TATG-ATATATATAAG
1 TATGTATATATATAAG
37755552 TAT
1 TAT
37755555 ATTTTGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (16 bp):
TATGTATATATATAAG
Found at i:37757069 original size:18 final size:18
Alignment explanation
Indices: 37757046--37757086 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
37757036 TTGTTTTGGT
*
37757046 GCTTCTTTTCTTCAAGTA
1 GCTTCTTTTATTCAAGTA
37757064 GCTTCTTTTATTCAAGTA
1 GCTTCTTTTATTCAAGTA
37757082 GCTTC
1 GCTTC
37757087 ATTCAAATCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.22, G:0.12, T:0.49
Consensus pattern (18 bp):
GCTTCTTTTATTCAAGTA
Found at i:37757423 original size:44 final size:44
Alignment explanation
Indices: 37757246--37757437 Score: 139
Period size: 44 Copynumber: 4.5 Consensus size: 44
37757236 CTACTCTCTG
* *
37757246 CAACTTCAGAGAGATAAGATCTATGGTTTTAATCCGCTCCACTG
1 CAACTTCAGGGAGATAAGATCTATGGTTTTAATCCGCTCCACTA
* * * * * ** * * *
37757290 CAGCTTTAGGGAGGTAGGAT-TA-GATTCTTCTGTCTGCTACACTG
1 CAACTTCAGGGAGATAAGATCTATGGTT-TT-AATCCGCTCCACTA
* * *
37757334 CAACTTCAGGGAGATAAGACTGTATGCG-----ATCTGCT-CTCTA
1 CAACTTCAGGGAGATAAGA-TCTATG-GTTTTAATCCGCTCCACTA
*
37757374 CAACTTCAGAGAGATAAGATCTATGGTTTTAATCCGCTCCACTA
1 CAACTTCAGGGAGATAAGATCTATGGTTTTAATCCGCTCCACTA
*
37757418 CAACTTCGGGGAGATAAGAT
1 CAACTTCAGGGAGATAAGAT
37757438 TAGATTCTTC
Statistics
Matches: 112, Mismatches: 24, Indels: 24
0.70 0.15 0.15
Matches are distributed among these distances:
38 1 0.01
39 5 0.04
40 21 0.19
41 6 0.05
42 3 0.03
43 10 0.09
44 62 0.55
45 1 0.01
46 2 0.02
47 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (44 bp):
CAACTTCAGGGAGATAAGATCTATGGTTTTAATCCGCTCCACTA
Found at i:37757439 original size:128 final size:128
Alignment explanation
Indices: 37757204--37757491 Score: 452
Period size: 128 Copynumber: 2.2 Consensus size: 128
37757194 TCTACTCCAG
* *
37757204 TGCAACTTCAGGGAGATAAGACTGTATACGATCTACTCTCTGCAACTTCAGAGAGATAAGATCTA
1 TGCAACTTCAGGGAGATAAGACTGTATGCGATCTACTCTCTACAACTTCAGAGAGATAAGATCTA
* * * * *
37757269 TGGTTTTAATCCGCTCCACTGCAGCTTTAGGGAGGTAGGATTAGATTCTTCTGTCTGCTAC-AC
66 TGGTTTTAATCCGCTCCACTACAACTTCAGGGAGATAAGATTAGATTCTTCTGTCTGCT-CTAC
*
37757332 TGCAACTTCAGGGAGATAAGACTGTATGCGATCTGCTCTCTACAACTTCAGAGAGATAAGATCTA
1 TGCAACTTCAGGGAGATAAGACTGTATGCGATCTACTCTCTACAACTTCAGAGAGATAAGATCTA
*
37757397 TGGTTTTAATCCGCTCCACTACAACTTCGGGGAGATAAGATTAGATTCTTCTGTCTGCTCTAC
66 TGGTTTTAATCCGCTCCACTACAACTTCAGGGAGATAAGATTAGATTCTTCTGTCTGCTCTAC
* * *
37757460 TGCAACTTCAGGAAGATCATACTGTATGCGAT
1 TGCAACTTCAGGGAGATAAGACTGTATGCGAT
37757492 TTTCGATCTA
Statistics
Matches: 147, Mismatches: 12, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
127 1 0.01
128 146 0.99
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (128 bp):
TGCAACTTCAGGGAGATAAGACTGTATGCGATCTACTCTCTACAACTTCAGAGAGATAAGATCTA
TGGTTTTAATCCGCTCCACTACAACTTCAGGGAGATAAGATTAGATTCTTCTGTCTGCTCTAC
Found at i:37757466 original size:44 final size:44
Alignment explanation
Indices: 37757297--37757476 Score: 133
Period size: 44 Copynumber: 4.2 Consensus size: 44
37757287 CTGCAGCTTT
* * *
37757297 AGGGAGGTAGGATTAGATTCTTCTGTCTGCTAC-ACTGCAACTTC
1 AGGGAGATAAGATTAGATTCTTCTGTCTGCT-CTACTACAACTTC
* * *
37757341 AGGGAGATAAGACT-G--TATGC-GATCTGCTCT-CTACAACTTC
1 AGGGAGATAAGATTAGATTCTTCTG-TCTGCTCTACTACAACTTC
* * ** * *
37757381 AGAGAGATAAGATCTATGGTT-TT-AATCCGCTCCACTACAACTTC
1 AGGGAGATAAGAT-TA-GATTCTTCTGTCTGCTCTACTACAACTTC
* *
37757425 GGGGAGATAAGATTAGATTCTTCTGTCTGCTCTACTGCAACTTC
1 AGGGAGATAAGATTAGATTCTTCTGTCTGCTCTACTACAACTTC
*
37757469 AGGAAGAT
1 AGGGAGAT
37757477 CATACTGTAT
Statistics
Matches: 103, Mismatches: 22, Indels: 22
0.70 0.15 0.15
Matches are distributed among these distances:
40 22 0.21
41 10 0.10
42 3 0.03
43 12 0.12
44 55 0.53
45 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (44 bp):
AGGGAGATAAGATTAGATTCTTCTGTCTGCTCTACTACAACTTC
Found at i:37757605 original size:88 final size:88
Alignment explanation
Indices: 37757493--37758095 Score: 1010
Period size: 88 Copynumber: 6.9 Consensus size: 88
37757483 GTATGCGATT
* * * *
37757493 TTCGATCTATTTCGCTGCTAATACAGGAAGACAAGATCTGATATTTTCAACCTACTCCACTGCTG
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTACTG
*
37757558 CTTA-GGAGGACAAGGCTGAGGTC
66 CTCAGGGA-GACAAGGCTGAGGTC
* *
37757581 TTTGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTACTA
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTACTG
*
37757646 TTCAGGGAGACAAGGCTGAGGTC
66 CTCAGGGAGACAAGGCTGAGGTC
*
37757669 TTTGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTACTG
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTACTG
* * *
37757734 CTCAAGAAGACAAGGCTAAGGTC
66 CTCAGGGAGACAAGGCTGAGGTC
37757757 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTACTG
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTACTG
37757822 CTCAGGGAGACAAGGCTGAGGTC
66 CTCAGGGAGACAAGGCTGAGGTC
* *
37757845 TTCGATCTACTTCGCTGCCAATACATGAAGACAATATCTGCTATTTTCAACCTACTCCACTACTG
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTACTG
* *
37757910 CTCAGAGAGACAATGCTGAGGTC
66 CTCAGGGAGACAAGGCTGAGGTC
37757933 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTACTG
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTACTG
37757998 CTCAGGGAGACAAGGCTGAGGTC
66 CTCAGGGAGACAAGGCTGAGGTC
** * *
37758021 TTCGATCTACTTCATTGCCAATACAAGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGCTG
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTACTG
37758086 CTCAGGGAGA
66 CTCAGGGAGA
37758096 TAGGATTTAT
Statistics
Matches: 485, Mismatches: 29, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
88 482 0.99
89 3 0.01
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (88 bp):
TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTACTG
CTCAGGGAGACAAGGCTGAGGTC
Found at i:37757614 original size:44 final size:44
Alignment explanation
Indices: 37757561--37757878 Score: 153
Period size: 44 Copynumber: 7.2 Consensus size: 44
37757551 ACTGCTGCTT
*
37757561 AGGAGGACAAGGCTGAGGTCTTTGATCTACTTCGCTGCCAATAC
1 AGGAAGACAAGGCTGAGGTCTTTGATCTACTTCGCTGCCAATAC
* *** * * * * * * *
37757605 AGGAAGACAAGATCTGCTAT-TTTCAACCTACTCCACT-ACTATTC
1 AGGAAGACAAG-GCTGAGGTCTTT-GATCTACTTCGCTGCCAATAC
*
37757649 AGGGAGACAAGGCTGAGGTCTTTGATCTACTTCGCTGCCAATAC
1 AGGAAGACAAGGCTGAGGTCTTTGATCTACTTCGCTGCCAATAC
* *** * * * * * ***
37757693 AGGAAGACAAGATCTGCTAT-TTTCAACCTACTCCACTACTGCT-C
1 AGGAAGACAAG-GCTGAGGTCTTT-GATCTACTTCGCTGCCAATAC
* * *
37757737 AAGAAGACAAGGCTAAGGTCTTCGATCTACTTCGCTGCCAATAC
1 AGGAAGACAAGGCTGAGGTCTTTGATCTACTTCGCTGCCAATAC
* *** * * * * * ***
37757781 AGGAAGACAAGATCTGCTAT-TTTCAACCTACTCCACTACTGCT-C
1 AGGAAGACAAG-GCTGAGGTCTTT-GATCTACTTCGCTGCCAATAC
* *
37757825 AGGGAGACAAGGCTGAGGTCTTCGATCTACTTCGCTGCCAATAC
1 AGGAAGACAAGGCTGAGGTCTTTGATCTACTTCGCTGCCAATAC
*
37757869 ATGAAGACAA
1 AGGAAGACAA
37757879 TATCTGCTAT
Statistics
Matches: 179, Mismatches: 83, Indels: 24
0.63 0.29 0.08
Matches are distributed among these distances:
43 42 0.23
44 95 0.53
45 42 0.23
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (44 bp):
AGGAAGACAAGGCTGAGGTCTTTGATCTACTTCGCTGCCAATAC
Found at i:37762852 original size:22 final size:24
Alignment explanation
Indices: 37762824--37762895 Score: 67
Period size: 25 Copynumber: 3.0 Consensus size: 24
37762814 ATGAACAAAT
*
37762824 ATGATTAT-G-AATGAATAAAAGA
1 ATGATTATGGAAAAGAATAAAAGA
37762846 ATGATTATGGAAAAAGAATAAAAGA
1 ATGATTATGG-AAAAGAATAAAAGA
* * * *
37762871 ATAATTACTCGAAAAGGATGAAAGA
1 ATGATTA-TGGAAAAGAATAAAAGA
37762896 CTATTGGCTC
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
22 8 0.20
23 1 0.02
25 30 0.73
26 2 0.05
ACGTcount: A:0.56, C:0.03, G:0.19, T:0.22
Consensus pattern (24 bp):
ATGATTATGGAAAAGAATAAAAGA
Found at i:37762886 original size:25 final size:25
Alignment explanation
Indices: 37762836--37762885 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
37762826 GATTATGAAT
* *
37762836 GAATAAAAGAATGATTATGGAAAAA
1 GAATAAAAGAATAATTATCGAAAAA
37762861 GAATAAAAGAATAATTACTCGAAAA
1 GAATAAAAGAATAATTA-TCGAAAA
37762886 GGATGAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.60, C:0.04, G:0.16, T:0.20
Consensus pattern (25 bp):
GAATAAAAGAATAATTATCGAAAAA
Found at i:37762948 original size:15 final size:15
Alignment explanation
Indices: 37762928--37762957 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
37762918 AAAAGTGTAC
37762928 TTTATTAGAATCATA
1 TTTATTAGAATCATA
37762943 TTTATTAGAATCATA
1 TTTATTAGAATCATA
37762958 ACGTTCAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (15 bp):
TTTATTAGAATCATA
Found at i:37764738 original size:325 final size:326
Alignment explanation
Indices: 37764126--37764767 Score: 1232
Period size: 325 Copynumber: 2.0 Consensus size: 326
37764116 ACATATGTTT
37764126 CGTTCAACACATTCATCAGCGCATTTCGATGCACCTCTGAACTCATGAGCAAAGCTAACACAGAT
1 CGTTCAACACATTCATCAGCGCATTTCGATGCACCTCTGAACTCATGAGCAAAGCTAACACAGAT
37764191 ATACGAGCTGGTTGCTTATTCAGCTGCTCTACAACACTATACTCACTGTGTTTCAAAAATTTCAA
66 ATACGAGCTGGTTGCTTATTCAGCTGCTCTACAACACTATACTCACTGTGTTTCAAAAATTTCAA
*
37764256 GAATTCAGTGGCTTCTTCCTTCTTTATTGGCTCATTAATCAATGGCCTAGATTCAACCATCTTCT
131 GAATTCAGTGGCTTCTTCCTCCTTTATTGGCTCATTAATCAATGGCCTAGATTCAACCATCTTCT
*
37764321 CTTTCTTTTGCTCTGCCGCAAGAAATTTTCCTTTCGCCGATTCTGCTTGGGCATTTATCCAATCG
196 CTTTCTTTTGCTCTGCCGCAAGAAATTTTCCTTCCGCCGATTCTGCTTGGGCATTTATCCAATCG
*
37764386 CAGTGCTTCTCACTACGTGCATAAGAACCTGTCTCTTGGTTTTCTTTTGCAACACTATACTCACT
261 CAGTGCTTCTCACTACATGCATAAGAACCTGTCTCTTGGTTTTCTTTTGCAACACTATACTCACT
37764451 A
326 A
37764452 CGTTCAACACATTCATCAGCGCATTTCGATGCACCTCTGAACTCATGAGCAAAGCTAACACAGAT
1 CGTTCAACACATTCATCAGCGCATTTCGATGCACCTCTGAACTCATGAGCAAAGCTAACACAGAT
37764517 ATACGAGCTGGTTGCTTATTCAGCTGCTCTACAACACTATACTCACTGTGTTTCAAAAATTTCAA
66 ATACGAGCTGGTTGCTTATTCAGCTGCTCTACAACACTATACTCACTGTGTTTCAAAAATTTCAA
*
37764582 GAATTCAGT-GCTTCTTCCTCCTTTATTGGCTCGTTAATCAATGGCCTAGATTCAACCATCTTCT
131 GAATTCAGTGGCTTCTTCCTCCTTTATTGGCTCATTAATCAATGGCCTAGATTCAACCATCTTCT
37764646 CTTTCTTTTGCTCTGCCGCAAGAAATTTTCCTTCCGCCGATTCTGCTTGGGCATTTATCCAATCG
196 CTTTCTTTTGCTCTGCCGCAAGAAATTTTCCTTCCGCCGATTCTGCTTGGGCATTTATCCAATCG
*
37764711 CAGTGCTTCTCATTACATGCATAAGAACCTGTCTCTTGGTTTTCTTTTGCAACACTA
261 CAGTGCTTCTCACTACATGCATAAGAACCTGTCTCTTGGTTTTCTTTTGCAACACTA
37764768 ACCAAAGTTT
Statistics
Matches: 311, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
325 172 0.55
326 139 0.45
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (326 bp):
CGTTCAACACATTCATCAGCGCATTTCGATGCACCTCTGAACTCATGAGCAAAGCTAACACAGAT
ATACGAGCTGGTTGCTTATTCAGCTGCTCTACAACACTATACTCACTGTGTTTCAAAAATTTCAA
GAATTCAGTGGCTTCTTCCTCCTTTATTGGCTCATTAATCAATGGCCTAGATTCAACCATCTTCT
CTTTCTTTTGCTCTGCCGCAAGAAATTTTCCTTCCGCCGATTCTGCTTGGGCATTTATCCAATCG
CAGTGCTTCTCACTACATGCATAAGAACCTGTCTCTTGGTTTTCTTTTGCAACACTATACTCACT
A
Found at i:37770411 original size:15 final size:16
Alignment explanation
Indices: 37770388--37770421 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
37770378 ATTTACAAAA
37770388 TATGTATATATATAAG
1 TATGTATATATATAAG
37770404 TATG-ATATATATAAG
1 TATGTATATATATAAG
37770419 TAT
1 TAT
37770422 ATTTTGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (16 bp):
TATGTATATATATAAG
Found at i:37781995 original size:16 final size:17
Alignment explanation
Indices: 37781976--37782020 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
37781966 CGGGATTTCC
37781976 TTCTTTTTCTCTCC-CT
1 TTCTTTTTCTCTCCTCT
*
37781992 TTCTTTCTC-CTTCCTCT
1 TTCTTTTTCTC-TCCTCT
37782009 TTC-TTTTCTCTC
1 TTCTTTTTCTCTC
37782021 TTTTTCGCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
15 1 0.04
16 17 0.71
17 6 0.25
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (17 bp):
TTCTTTTTCTCTCCTCT
Found at i:37782578 original size:59 final size:61
Alignment explanation
Indices: 37782457--37782578 Score: 167
Period size: 61 Copynumber: 2.0 Consensus size: 61
37782447 AATTTATCGG
* *
37782457 TCTATGGTGATTATGTAAAGAGAAAAGAAAACGTATCCTACGCGCACTGTAGGACGCATTT
1 TCTATGGTGATTATGGAAAGAGAAAAGAAAACGTATCCTACGCGCACTGTAGAACGCATTT
* * * * *
37782518 TCTATGTTGATTTTGGAGAGAGAAAAGAAAATGTATCCTACGC-C-CTGTAGAATGCATTT
1 TCTATGGTGATTATGGAAAGAGAAAAGAAAACGTATCCTACGCGCACTGTAGAACGCATTT
37782577 TC
1 TC
37782579 CAAAAATACG
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 15 0.28
60 1 0.02
61 38 0.70
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.30
Consensus pattern (61 bp):
TCTATGGTGATTATGGAAAGAGAAAAGAAAACGTATCCTACGCGCACTGTAGAACGCATTT
Found at i:37787805 original size:18 final size:18
Alignment explanation
Indices: 37787784--37787819 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
37787774 CTTATTTATA
37787784 GTGTAATATATAAAACTT
1 GTGTAATATATAAAACTT
37787802 GTGTAATATATAAAACTT
1 GTGTAATATATAAAACTT
37787820 AGTAATCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (18 bp):
GTGTAATATATAAAACTT
Found at i:37787832 original size:18 final size:18
Alignment explanation
Indices: 37787786--37787825 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
37787776 TATTTATAGT
*
37787786 GTAATATATAAAACTTGT
1 GTAATATATAAAACTTGA
37787804 GTAATATATAAAACTT-A
1 GTAATATATAAAACTTGA
37787821 GTAAT
1 GTAAT
37787826 CTAATAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.38
Consensus pattern (18 bp):
GTAATATATAAAACTTGA
Found at i:37787982 original size:21 final size:20
Alignment explanation
Indices: 37787948--37787986 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
37787938 ACAATTGATA
* *
37787948 ATAAAAATTTAAAAGAAAAAC
1 ATAAAAA-TCAAAAAAAAAAC
37787969 ATAAAAATCAAAAAAAAA
1 ATAAAAATCAAAAAAAAA
37787987 TTTCTATGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.15
Consensus pattern (20 bp):
ATAAAAATCAAAAAAAAAAC
Found at i:37796180 original size:186 final size:187
Alignment explanation
Indices: 37795863--37796225 Score: 595
Period size: 186 Copynumber: 1.9 Consensus size: 187
37795853 AGAAAAATAA
* *
37795863 ACCGAAAACTAAATTCTATGAAGAAAACTAATAATATCCAAAGCTATCCATAACAAGTGTTAAAT
1 ACCGAAAACTAAATTCTATCAAAAAAACTAATAATATCCAAAGCTATCCATAACAAGTGTTAAAT
* *
37795928 GAGTCTATTTATAGATTTAGGGTTACCGTTATCGTCAACCCTAGGTCTGCTAACGTTCTTGTGTT
66 GAGTCTATTTATAGATTTAGGGTTACCGTTATCCTCAACCCTAGGTCTGCTAACGTTCTCGTGTT
*
37795993 AAACATTTGATTGTGCAGACCAAAACACCCCTAGCTCGTAAGTGTTTCTCATACAGG
131 AAACATTTGACTGTGCAGACCAAAACACCCCTAGCTCGTAAGTGTTTCTCATACAGG
37796050 ACCGAAAACTAAATTCTA-CAAAAAAACTAATAATATCCAAAGCTATCCATAACAAGTGTTAAAT
1 ACCGAAAACTAAATTCTATCAAAAAAACTAATAATATCCAAAGCTATCCATAACAAGTGTTAAAT
* ** * **
37796114 GAGTCTATTTATGGATTTAGGGTTGTCGTTATCCTCAACCCTAGGT-TAGCTGATTTTCTCGTGT
66 GAGTCTATTTATAGATTTAGGGTTACCGTTATCCTCAACCCTAGGTCT-GCTAACGTTCTCGTGT
*
37796178 TAAACATTTGACTGTGCAGACCAAAACAGCCCTAGCTCGTAAGTGTTT
130 TAAACATTTGACTGTGCAGACCAAAACACCCCTAGCTCGTAAGTGTTT
37796226 ATTGTACAAG
Statistics
Matches: 163, Mismatches: 12, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
185 1 0.01
186 144 0.88
187 18 0.11
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.31
Consensus pattern (187 bp):
ACCGAAAACTAAATTCTATCAAAAAAACTAATAATATCCAAAGCTATCCATAACAAGTGTTAAAT
GAGTCTATTTATAGATTTAGGGTTACCGTTATCCTCAACCCTAGGTCTGCTAACGTTCTCGTGTT
AAACATTTGACTGTGCAGACCAAAACACCCCTAGCTCGTAAGTGTTTCTCATACAGG
Found at i:37802764 original size:17 final size:17
Alignment explanation
Indices: 37802733--37802778 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
37802723 TTGTCCCCAT
*
37802733 TGCACTGAC-ATGAAAA
1 TGCAATGACAATGAAAA
*
37802749 TGTAATGACAATGAAAA
1 TGCAATGACAATGAAAA
37802766 TGCAATGACAATG
1 TGCAATGACAATG
37802779 TATACTTATC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 7 0.27
17 19 0.73
ACGTcount: A:0.46, C:0.13, G:0.20, T:0.22
Consensus pattern (17 bp):
TGCAATGACAATGAAAA
Found at i:37806591 original size:394 final size:394
Alignment explanation
Indices: 37805863--37806654 Score: 1323
Period size: 394 Copynumber: 2.0 Consensus size: 394
37805853 GAATAAATAT
* **
37805863 GACTCGTTCCAATGATACTTCATTACATCATGAAGAAATCTTTCTTCTTTATGGCCCTTGATGGG
1 GACTCGTTCCAATGATACTTCACTACATCACAAAGAAATCTTTCTTCTTTATGGCCCTTGATGGG
* **
37805928 AGCTTACCATACACCAAGTAATCAACCAAATCTGCATACCAAGGAGTTACATCGACAATGAATAA
66 AGCTTACCAAACACCAAGTAATCAACCAAATCTGCATACCAAGGAGTTACATCGACAACAAATAA
* *
37805993 CATCTCATCTGGGAATATGTCAACAATTGGAAGTATTTTCCCATCTTCGCTGCCAACTTCCAATC
131 CATCTCATCTGGAAATATGTCAACAACTGGAAGTATTTTCCCATCTTCGCTGCCAACTTCCAATC
* *
37806058 TAGACAAATGATCGGTAACTTGATTCTCTGACCCCTTTTGATCTTTTATCTTGATGCCAAATTCT
196 TAGACAAATGATCGGCAACTTGATTCTCTGACCCCTTTCGATCTTTTATCTTGATGCCAAATTCT
*
37806123 TGCAACAATAATATCCACCGTATCGGTCTTGGTTTGGCATCTATTTTTACAAATAGATATCGCAA
261 TGCAACAATAATATCCACCGTATCGGTCTTGGTTTGGCATCTATTTTTACAAATAGATATCACAA
* * * *
37806188 TGCAAAATGATCAGTGAATACCATAATTTTTGCGCCGACAATATAAGAGTGAAACTTGTCAAACG
326 TGCAAAATGATAACTGAATACCATAATTTTTGCACCGACAAGATAAGAGTGAAACTTGTCAAACG
*
37806253 CAAA
391 AAAA
* *
37806257 GACTCGTTCCAATGATACTTCACTACGTCACAAAGAAATCTTTCTTTTTTATGGCCCTTGATGGG
1 GACTCGTTCCAATGATACTTCACTACATCACAAAGAAATCTTTCTTCTTTATGGCCCTTGATGGG
*
37806322 AGCTTCCCAAACACCAAGTAATCAACCAAATCTGCATACCAAGGAGTTACATCGACAACAAATAA
66 AGCTTACCAAACACCAAGTAATCAACCAAATCTGCATACCAAGGAGTTACATCGACAACAAATAA
* *
37806387 CATCTCATCTGGAAATATGTCGACAACTGGAAGTATTTTTCCATCTTCGCTGCCAACTTCCAATC
131 CATCTCATCTGGAAATATGTCAACAACTGGAAGTATTTTCCCATCTTCGCTGCCAACTTCCAATC
*
37806452 TAGACAAATGATCGGCAACTTGATTCTCTGACCCCTTTCGATCTTTTATCTTGATGTCAAATTCT
196 TAGACAAATGATCGGCAACTTGATTCTCTGACCCCTTTCGATCTTTTATCTTGATGCCAAATTCT
* * *
37806517 TGTAACAATAATATCCACCGTATCGGTCTTGGTTTGGCATCTTTTTTTGCAAATAGATATCACAA
261 TGCAACAATAATATCCACCGTATCGGTCTTGGTTTGGCATCTATTTTTACAAATAGATATCACAA
* * * *
37806582 TGCAAAATGATAACTGAATACCGTAATTTTTTCACTGACAAGATAAGAGTGAAACTTGTCAAAGG
326 TGCAAAATGATAACTGAATACCATAATTTTTGCACCGACAAGATAAGAGTGAAACTTGTCAAACG
37806647 AAAA
391 AAAA
37806651 GACT
1 GACT
37806655 ACAACCAACA
Statistics
Matches: 369, Mismatches: 29, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
394 369 1.00
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (394 bp):
GACTCGTTCCAATGATACTTCACTACATCACAAAGAAATCTTTCTTCTTTATGGCCCTTGATGGG
AGCTTACCAAACACCAAGTAATCAACCAAATCTGCATACCAAGGAGTTACATCGACAACAAATAA
CATCTCATCTGGAAATATGTCAACAACTGGAAGTATTTTCCCATCTTCGCTGCCAACTTCCAATC
TAGACAAATGATCGGCAACTTGATTCTCTGACCCCTTTCGATCTTTTATCTTGATGCCAAATTCT
TGCAACAATAATATCCACCGTATCGGTCTTGGTTTGGCATCTATTTTTACAAATAGATATCACAA
TGCAAAATGATAACTGAATACCATAATTTTTGCACCGACAAGATAAGAGTGAAACTTGTCAAACG
AAAA
Found at i:37815711 original size:37 final size:38
Alignment explanation
Indices: 37815647--37815734 Score: 135
Period size: 37 Copynumber: 2.4 Consensus size: 38
37815637 GTGCTGAGGT
* *
37815647 GTGTTATCGGTCGGGTTTAGCTCTTATGAGTGTTTGGC
1 GTGTTATCGGTTGGGTTTAGCTCTTATGAGCGTTTGGC
*
37815685 GTGTTATTGGTTGGG-TTAGCTCTTATGAGCGTTTGGC
1 GTGTTATCGGTTGGGTTTAGCTCTTATGAGCGTTTGGC
37815722 GTGTT-TCGGTTGG
1 GTGTTATCGGTTGG
37815735 ACTACTAGTG
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 7 0.15
37 26 0.57
38 13 0.28
ACGTcount: A:0.09, C:0.11, G:0.36, T:0.43
Consensus pattern (38 bp):
GTGTTATCGGTTGGGTTTAGCTCTTATGAGCGTTTGGC
Found at i:37825880 original size:26 final size:26
Alignment explanation
Indices: 37825833--37825892 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
37825823 AGCCATATCG
*
37825833 GGAAGCTC-TGAAGAGCCATTAATCA
1 GGAAGCTCATAAAGAGCCATTAATCA
** *
37825858 GGAAGCTCATAAAGAGCTTTTAATCG
1 GGAAGCTCATAAAGAGCCATTAATCA
37825884 GGAAGCTCA
1 GGAAGCTCA
37825893 CGGAAAGCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 8 0.27
26 22 0.73
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (26 bp):
GGAAGCTCATAAAGAGCCATTAATCA
Found at i:37834273 original size:31 final size:31
Alignment explanation
Indices: 37834224--37834786 Score: 272
Period size: 31 Copynumber: 18.4 Consensus size: 31
37834214 AAATCATTTT
* * * *
37834224 AGCAATATATATTCATATACGAACCAAATTT
1 AGCAATGTATATCCATATACGAATCAAATTC
* *
37834255 GGCAATGTATATCTATATA-GAAATC-AATTC
1 AGCAATGTATATCCATATACG-AATCAAATTC
* * *
37834285 AGCAATGTACAACCATATACGAATCAAGTTC
1 AGCAATGTATATCCATATACGAATCAAATTC
* * * * *
37834316 GGTAATGTATAAT-CATATACAAATTAAATTT
1 AGCAATGTAT-ATCCATATACGAATCAAATTC
* *
37834347 AGCAATGTATAACCATATACGAA-CCAATTC
1 AGCAATGTATATCCATATACGAATCAAATTC
*
37834377 AGCAACT-TATATCCATAAAC-AATTC-AATTCC
1 AGCAA-TGTATATCCATATACGAA-TCAAATT-C
* * * * * *
37834408 AACAATGTATAACCATGTACAAATTAATTTC
1 AGCAATGTATATCCATATACGAATCAAATTC
* *
37834439 AGCAATATATAAT-CATATACAAATC-AATTC
1 AGCAATGTAT-ATCCATATACGAATCAAATTC
* * *
37834469 AACAACT-TATATCCATATA-AAATTCAATTTC
1 AGCAA-TGTATATCCATATACGAA-TCAAATTC
* * * * *
37834500 AACAATGTATAACCATATACAAATTAATTTC
1 AGCAATGTATATCCATATACGAATCAAATTC
* * *
37834531 AGCAATGTACAACCATATATGAATC-AATTC
1 AGCAATGTATATCCATATACGAATCAAATTC
* *
37834561 GGCAACT-TATATCCATATAC-AATTCAATTTC
1 AGCAA-TGTATATCCATATACGAA-TCAAATTC
* * * * *
37834592 AACAATGTATAACCATGTAC-ACATTAATTTC
1 AGCAATGTATATCCATATACGA-ATCAAATTC
* *
37834623 AGCAATGTATAAT-CATATCCAAATC-AATTC
1 AGCAATGTAT-ATCCATATACGAATCAAATTC
* * *
37834653 GGCAACT-TATATCCATAAAC-AATTCAATTTC
1 AGCAA-TGTATATCCATATACGAA-TCAAATTC
* * * * *
37834684 AACAATGTATAACCATATACAAATTAATTTC
1 AGCAATGTATATCCATATACGAATCAAATTC
* * *
37834715 AGCAATGTAAAAT-CATATACAAAT-TAATTC
1 AGCAATGT-ATATCCATATACGAATCAAATTC
* * * *
37834745 GGCAACT-TATATCCATATGCAAATCAATTTC
1 AGCAA-TGTATATCCATATACGAATCAAATTC
37834776 -GACAATGTATA
1 AG-CAATGTATA
37834787 ACTATAAACA
Statistics
Matches: 409, Mismatches: 85, Indels: 76
0.72 0.15 0.13
Matches are distributed among these distances:
29 16 0.04
30 131 0.32
31 245 0.60
32 17 0.04
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (31 bp):
AGCAATGTATATCCATATACGAATCAAATTC
Found at i:37834323 original size:61 final size:60
Alignment explanation
Indices: 37834237--37834788 Score: 397
Period size: 61 Copynumber: 9.0 Consensus size: 60
37834227 AATATATATT
* ** * * * *
37834237 CATATACGAACCAAATTTGGCAATGTATATCTATATAGAAATCAATTCAGCAATGTACAAC
1 CATATACGAATC-AATTCAGCAATGTATATCCATATACAAATCAATTCAACAATGTATAAC
* * * * *
37834298 CATATACGAATCAAGTTCGGTAATGTATAAT-CATATACAAATTAAATTTAGCAATGTATAAC
1 CATATACGAATCAA-TTCAGCAATGTAT-ATCCATATACAAA-TCAATTCAACAATGTATAAC
* * *
37834360 CATATACGAACCAATTCAGCAACT-TATATCCATAAACAATTCAATTCCAACAATGTATAAC
1 CATATACGAATCAATTCAGCAA-TGTATATCCATATACAAATCAATT-CAACAATGTATAAC
* * * * *
37834421 CATGTACAAATTAATTTCAGCAATATATAAT-CATATACAAATCAATTCAACAACT-TATATC
1 CATATACGAATCAA-TTCAGCAATGTAT-ATCCATATACAAATCAATTCAACAA-TGTATAAC
* * * * * *
37834482 CATATA-AAATTCAATTTCAACAATGTATAACCATATACAAATTAATTTCAGCAATGTACAAC
1 CATATACGAA-TCAA-TTCAGCAATGTATATCCATATACAAATCAA-TTCAACAATGTATAAC
* * *
37834544 CATATATGAATCAATTCGGCAACT-TATATCCATATACAATTCAATTTCAACAATGTATAAC
1 CATATACGAATCAATTCAGCAA-TGTATATCCATATACAAATCAA-TTCAACAATGTATAAC
* * * ** *
37834605 CATGTAC-ACATTAATTTCAGCAATGTATAAT-CATATCCAAATCAATTCGGCAACT-TATATC
1 CATATACGA-ATCAA-TTCAGCAATGTAT-ATCCATATACAAATCAATTCAACAA-TGTATAAC
* * * * * * *
37834666 CATAAAC-AATTCAATTTCAACAATGTATAACCATATACAAATTAATTTCAGCAATGTAAAAT
1 CATATACGAA-TCAA-TTCAGCAATGTATATCCATATACAAATCAA-TTCAACAATGTATAAC
* * * * *
37834728 CATATACAAATTAATTCGGCAACT-TATATCCATATGCAAATCAATTTCGACAATGTATAAC
1 CATATACGAATCAATTCAGCAA-TGTATATCCATATACAAATCAA-TTCAACAATGTATAAC
37834789 TATAAACAAT
Statistics
Matches: 393, Mismatches: 71, Indels: 54
0.76 0.14 0.10
Matches are distributed among these distances:
60 16 0.04
61 245 0.62
62 124 0.32
63 8 0.02
ACGTcount: A:0.43, C:0.19, G:0.07, T:0.31
Consensus pattern (60 bp):
CATATACGAATCAATTCAGCAATGTATATCCATATACAAATCAATTCAACAATGTATAAC
Found at i:37834393 original size:92 final size:92
Alignment explanation
Indices: 37834256--37834797 Score: 694
Period size: 92 Copynumber: 5.9 Consensus size: 92
37834246 ACCAAATTTG
* * * * * * ***
37834256 GCAATGTATATCTATATAGAAATCAATTCAGCAA-TGTACAACCATATACGAA-TCAAGTTCGGT
1 GCAATGTATAACCATATACAAATCAATTCAGCAACT-TATATCCATATAC-AATTCAATTTCAAC
*
37834319 AATGTATAATCATATACAAATTAAATTT-A
64 AATGTATAACCATATACAAATT-AATTTCA
* * * *
37834348 GCAATGTATAACCATATACGAACCAATTCAGCAACTTATATCCATAAACAATTCAATTCCAACAA
1 GCAATGTATAACCATATACAAATCAATTCAGCAACTTATATCCATATACAATTCAATTTCAACAA
*
37834413 TGTATAACCATGTACAAATTAATTTCA
66 TGTATAACCATATACAAATTAATTTCA
* * * *
37834440 GCAATATATAATCATATACAAATCAATTCAACAACTTATATCCATATAAAATTCAATTTCAACAA
1 GCAATGTATAACCATATACAAATCAATTCAGCAACTTATATCCATATACAATTCAATTTCAACAA
37834505 TGTATAACCATATACAAATTAATTTCA
66 TGTATAACCATATACAAATTAATTTCA
* ** *
37834532 GCAATGTACAACCATATATGAATCAATTCGGCAACTTATATCCATATACAATTCAATTTCAACAA
1 GCAATGTATAACCATATACAAATCAATTCAGCAACTTATATCCATATACAATTCAATTTCAACAA
* *
37834597 TGTATAACCATGTACACATTAATTTCA
66 TGTATAACCATATACAAATTAATTTCA
* * * *
37834624 GCAATGTATAATCATATCCAAATCAATTCGGCAACTTATATCCATAAACAATTCAATTTCAACAA
1 GCAATGTATAACCATATACAAATCAATTCAGCAACTTATATCCATATACAATTCAATTTCAACAA
37834689 TGTATAACCATATACAAATTAATTTCA
66 TGTATAACCATATACAAATTAATTTCA
* * * * * * *
37834716 GCAATGTAAAATCATATACAAATTAATTCGGCAACTTATATCCATATGCAAATCAATTTCGACAA
1 GCAATGTATAACCATATACAAATCAATTCAGCAACTTATATCCATATACAATTCAATTTCAACAA
* *
37834781 TGTATAACTATAAACAA
66 TGTATAACCATATACAA
37834798 TTCGGCAATA
Statistics
Matches: 396, Mismatches: 51, Indels: 6
0.87 0.11 0.01
Matches are distributed among these distances:
91 7 0.02
92 388 0.98
93 1 0.00
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (92 bp):
GCAATGTATAACCATATACAAATCAATTCAGCAACTTATATCCATATACAATTCAATTTCAACAA
TGTATAACCATATACAAATTAATTTCA
Found at i:37834850 original size:30 final size:30
Alignment explanation
Indices: 37834816--37834878 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
37834806 TATATAAAAC
* *
37834816 AATCAAATTCAGCAACGTATATCTATAATT
1 AATCAAATTCAGAAACATATATCTATAATT
*
37834846 AATCAAATTCGGAAACATATATCTATAATT
1 AATCAAATTCAGAAACATATATCTATAATT
37834876 AAT
1 AAT
37834879 TACATTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.33
Consensus pattern (30 bp):
AATCAAATTCAGAAACATATATCTATAATT
Found at i:37837612 original size:25 final size:25
Alignment explanation
Indices: 37837578--37837708 Score: 118
Period size: 25 Copynumber: 4.6 Consensus size: 25
37837568 TATAATTATT
37837578 TTATATTAAAATATTTTATTTTAAA
1 TTATATTAAAATATTTTATTTTAAA
37837603 TTATATTAAAATATTTTTTAGTTTTATATTAAA
1 TTATATTAAAATA--TTTTA----T-T-TTAAA
37837636 TTATATTAAAATATTTTATTTTAAA
1 TTATATTAAAATATTTTATTTTAAA
*
37837661 TTATACTTTGAAATAAAATATTTTATGTTAAA
1 TTATA---T----TAAAATATTTTATTTTAAA
37837693 TTATATTAAAATATTT
1 TTATATTAAAATATTT
37837709 CAAATATTTT
Statistics
Matches: 90, Mismatches: 1, Indels: 30
0.74 0.01 0.25
Matches are distributed among these distances:
25 33 0.37
26 1 0.01
27 6 0.07
28 1 0.01
29 1 0.01
31 6 0.07
32 24 0.27
33 18 0.20
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (25 bp):
TTATATTAAAATATTTTATTTTAAA
Found at i:37837641 original size:58 final size:56
Alignment explanation
Indices: 37837578--37837708 Score: 174
Period size: 58 Copynumber: 2.3 Consensus size: 56
37837568 TATAATTATT
***
37837578 TTATATTAAAATATTTTATTTTAAATTATA-TTAAAATATTTTTTAGTTTTATATTAAA
1 TTATATTAAAATATTTTATTTTAAATTATACTTAAAATA--AAATA-TTTTATATTAAA
* *
37837636 TTATATTAAAATATTTTATTTTAAATTATACTTTGAAATAAAATATTTTATGTTAAA
1 TTATATTAAAATATTTTATTTTAAATTATAC-TTAAAATAAAATATTTTATATTAAA
37837693 TTATATTAAAATATTT
1 TTATATTAAAATATTT
37837709 CAAATATTTT
Statistics
Matches: 66, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
57 27 0.41
58 32 0.48
60 7 0.11
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (56 bp):
TTATATTAAAATATTTTATTTTAAATTATACTTAAAATAAAATATTTTATATTAAA
Found at i:37844137 original size:15 final size:15
Alignment explanation
Indices: 37844117--37844145 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
37844107 TTAATTAATG
37844117 ATGATGTCATCGCAA
1 ATGATGTCATCGCAA
37844132 ATGATGTCATCGCA
1 ATGATGTCATCGCA
37844146 TGTCGATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (15 bp):
ATGATGTCATCGCAA
Found at i:37851698 original size:66 final size:65
Alignment explanation
Indices: 37851558--37851736 Score: 182
Period size: 66 Copynumber: 2.7 Consensus size: 65
37851548 GAAAAATCAA
** * * *
37851558 ATACCG-GATCTTTCCAAGCTCTTGAACGAGATATCAGGTCTTCTCATTCCCAAGCTCCTAAACG
1 ATACCGAG-TCTTTCCAAGCTCTTGAATAAGATATCAGGTCTTCTCA-ACCCAAGATCCTAAACA
*
37851622 CG
64 AG
* * * *
37851624 ATACCGAGTCTTTCCAAGCTCTTGAATTAGATATCAGGTTTTCTCAACCTCAAGATCCTGAATAA
1 ATACCGAGTCTTTCCAAGCTCTTGAATAAGATATCAGGTCTTCTCAACC-CAAGATCCTAAACAA
37851689 G
65 G
** * *
37851690 ATTTCGAGT-TTTCCCAAGCTCCTGAATAAGATATCGGGTCTTCTCAA
1 ATACCGAGTCTTT-CCAAGCTCTTGAATAAGATATCAGGTCTTCTCAA
37851737 GTTTCTGAAC
Statistics
Matches: 95, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
65 5 0.05
66 89 0.94
67 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (65 bp):
ATACCGAGTCTTTCCAAGCTCTTGAATAAGATATCAGGTCTTCTCAACCCAAGATCCTAAACAAG
Found at i:37851745 original size:30 final size:30
Alignment explanation
Indices: 37851672--37851737 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
37851662 TTTTCTCAAC
* *
37851672 CTCAAGATCCTGAATAAGATTTCGAGTTTT
1 CTCAAGATCCTGAATAAGATATCGAGTCTT
* * *
37851702 CCCAAGCTCCTGAATAAGATATCGGGTCTT
1 CTCAAGATCCTGAATAAGATATCGAGTCTT
37851732 CTCAAG
1 CTCAAG
37851738 TTTCTGAACA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (30 bp):
CTCAAGATCCTGAATAAGATATCGAGTCTT
Found at i:37855713 original size:31 final size:31
Alignment explanation
Indices: 37855669--37855737 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
37855659 TTTCAATTTA
*
37855669 GTCACTAAAGTTTTAGATCATTTCTATTTCG
1 GTCACTCAAGTTTTAGATCATTTCTATTTCG
* * * *
37855700 GTCACTCACGTTTTAGATCGTTTTTATTTTG
1 GTCACTCAAGTTTTAGATCATTTCTATTTCG
37855731 GTCACTC
1 GTCACTC
37855738 TCTGTTAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.46
Consensus pattern (31 bp):
GTCACTCAAGTTTTAGATCATTTCTATTTCG
Found at i:37856145 original size:23 final size:23
Alignment explanation
Indices: 37856120--37856163 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
37856110 ACTTTTTATA
*
37856120 AAAATATTTAAAAA-TTTAAAAG
1 AAAATATATAAAAATTTTAAAAG
37856142 AAAATATATAAAAATTTTAAAA
1 AAAATATATAAAAATTTTAAAA
37856164 ATAAAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (23 bp):
AAAATATATAAAAATTTTAAAAG
Found at i:37856173 original size:29 final size:29
Alignment explanation
Indices: 37856115--37856181 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 29
37856105 AATGTACTTT
37856115 TTATAAAAATATTTAAAAATTTAAAAGAAAA
1 TTATAAAAATATTTAAAAA-TTAAAAG-AAA
37856146 TATATAAAAAT-TTTAAAAA-TAAAAGAAA
1 T-TATAAAAATATTTAAAAATTAAAAGAAA
37856174 TTATAAAA
1 TTATAAAA
37856182 TATAAAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
27 7 0.20
28 4 0.11
29 6 0.17
31 9 0.26
32 9 0.26
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (29 bp):
TTATAAAAATATTTAAAAATTAAAAGAAA
Found at i:37856188 original size:19 final size:18
Alignment explanation
Indices: 37856142--37856189 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
37856132 AATTTAAAAG
* *
37856142 AAAATATATAAAAATTTT
1 AAAATATAAAAAAATTAT
37856160 AAAA-ATAAAAGAAATTAT
1 AAAATATAAAA-AAATTAT
37856178 AAAATATAAAAA
1 AAAATATAAAAA
37856190 TAGATGTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 5 0.19
18 15 0.58
19 6 0.23
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (18 bp):
AAAATATAAAAAAATTAT
Found at i:37856428 original size:12 final size:12
Alignment explanation
Indices: 37856411--37856437 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
37856401 TTTTTTTCCC
37856411 ATATTTAGGGAA
1 ATATTTAGGGAA
37856423 ATATTTAGGGAA
1 ATATTTAGGGAA
37856435 ATA
1 ATA
37856438 GGCAGGACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (12 bp):
ATATTTAGGGAA
Found at i:37856775 original size:49 final size:49
Alignment explanation
Indices: 37856719--37856813 Score: 136
Period size: 49 Copynumber: 1.9 Consensus size: 49
37856709 TTGCAACTCA
**
37856719 GGCTCTCAATTCAAGGTGGTTATACGGTCATGGGTTGAAGTATAACTAG
1 GGCTCTCAATTCAAGGTGGTTATACGGTCACAGGTTGAAGTATAACTAG
* ** *
37856768 GGCTCTCAATTGAAGGTGGTTATGTGGTCACAGGTTGGAGTATAAC
1 GGCTCTCAATTCAAGGTGGTTATACGGTCACAGGTTGAAGTATAAC
37856814 ACGGGCCCCC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.25, C:0.14, G:0.31, T:0.31
Consensus pattern (49 bp):
GGCTCTCAATTCAAGGTGGTTATACGGTCACAGGTTGAAGTATAACTAG
Found at i:37870760 original size:9 final size:9
Alignment explanation
Indices: 37870746--37870790 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
37870736 AACTAAATAC
37870746 TTGAGAGAA
1 TTGAGAGAA
37870755 TTGAGAG-A
1 TTGAGAGAA
37870763 TT-AGATGAA
1 TTGAGA-GAA
*
37870772 TTGAAAGAA
1 TTGAGAGAA
37870781 TTGAGAGAA
1 TTGAGAGAA
37870790 T
1 T
37870791 AGGATTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
7 3 0.10
8 4 0.13
9 22 0.71
10 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.29, T:0.27
Consensus pattern (9 bp):
TTGAGAGAA
Found at i:37871652 original size:31 final size:31
Alignment explanation
Indices: 37871584--37871643 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
37871574 ATTTAACGAA
*
37871584 GAGTTACCAAAATAGAAACGATCTAAAACAT
1 GAGTGACCAAAATAGAAACGATCTAAAACAT
* *
37871615 GAGTGACCAAAATATAAATGATCTAAAAC
1 GAGTGACCAAAATAGAAACGATCTAAAAC
37871644 GCTAGTGACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.52, C:0.15, G:0.13, T:0.20
Consensus pattern (31 bp):
GAGTGACCAAAATAGAAACGATCTAAAACAT
Found at i:37872596 original size:30 final size:30
Alignment explanation
Indices: 37872554--37872612 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
37872544 AGGGGGGATA
37872554 GGAGGAGAGTAAAAGGT-TTGGAGGGAAAGTG
1 GGAGGAGAGTAAAA-GTATTGG-GGGAAAGTG
37872585 GGAGG-GAGTAAAAGTATTGGGGGAAAGT
1 GGAGGAGAGTAAAAGTATTGGGGGAAAGT
37872613 AAAAATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 10 0.37
30 12 0.44
31 5 0.19
ACGTcount: A:0.36, C:0.00, G:0.47, T:0.17
Consensus pattern (30 bp):
GGAGGAGAGTAAAAGTATTGGGGGAAAGTG
Found at i:37872849 original size:44 final size:44
Alignment explanation
Indices: 37872799--37872887 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
37872789 ATTTTACTCA
37872799 CCTTTAATGAATATTTCTCACCTCACTGTAACCCAAAATATTCG
1 CCTTTAATGAATATTTCTCACCTCACTGTAACCCAAAATATTCG
37872843 CCTTTAATGAATATTTCTCACCTCACTGTAACCCAAAATATTCG
1 CCTTTAATGAATATTTCTCACCTCACTGTAACCCAAAATATTCG
37872887 C
1 C
37872888 TGGAGTTAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (44 bp):
CCTTTAATGAATATTTCTCACCTCACTGTAACCCAAAATATTCG
Found at i:37875938 original size:26 final size:27
Alignment explanation
Indices: 37875895--37875949 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
37875885 TTTTAAAATT
** *
37875895 TTTTTAAAATACTTTTTTTATTTTTTA
1 TTTTTAAAATACAGTTTTTAGTTTTTA
*
37875922 TTTTTAAAATA-AGTTTTTGGTTTTTA
1 TTTTTAAAATACAGTTTTTAGTTTTTA
37875948 TT
1 TT
37875950 AAAAAATGGG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.67
Consensus pattern (27 bp):
TTTTTAAAATACAGTTTTTAGTTTTTA
Found at i:37875945 original size:27 final size:27
Alignment explanation
Indices: 37875895--37875946 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
37875885 TTTTAAAATT
** *
37875895 TTTTTAAAATACTTTTTTTATTTTTTA
1 TTTTTAAAATAAGTTTTTGATTTTTTA
*
37875922 TTTTTAAAATAAGTTTTTGGTTTTT
1 TTTTTAAAATAAGTTTTTGATTTTT
37875947 ATTAAAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.67
Consensus pattern (27 bp):
TTTTTAAAATAAGTTTTTGATTTTTTA
Found at i:37885396 original size:24 final size:25
Alignment explanation
Indices: 37885345--37885396 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
37885335 TGCCAATCCT
*
37885345 AATTATATTCTATAAATTAAAATAA
1 AATTATATCCTATAAATTAAAATAA
* *
37885370 AATTATATCCTA-AATTTATAATAA
1 AATTATATCCTATAAATTAAAATAA
37885394 AAT
1 AAT
37885397 AAAATAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (25 bp):
AATTATATCCTATAAATTAAAATAA
Found at i:37893019 original size:11 final size:11
Alignment explanation
Indices: 37893005--37893029 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
37892995 GTGAATAAAT
37893005 TGTGAAATTGA
1 TGTGAAATTGA
37893016 TGTGAAATTGA
1 TGTGAAATTGA
37893027 TGT
1 TGT
37893030 AATAATAGAT
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:0.28, T:0.40
Consensus pattern (11 bp):
TGTGAAATTGA
Found at i:37899053 original size:20 final size:20
Alignment explanation
Indices: 37899028--37899066 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
37899018 GGATTAAATT
*
37899028 AGAAAAATTTGGAAAATTTA
1 AGAAAAATTTAGAAAATTTA
37899048 AGAAAAATTTAGAAAATTT
1 AGAAAAATTTAGAAAATTT
37899067 GAACTGTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (20 bp):
AGAAAAATTTAGAAAATTTA
Found at i:37906119 original size:68 final size:67
Alignment explanation
Indices: 37906047--37906187 Score: 155
Period size: 68 Copynumber: 2.1 Consensus size: 67
37906037 TGACTAGTGT
**
37906047 TACAAAATAATA-ATAAAACATCAAGTTTG-T-TTTACTAATCAAATGTTAGATTTTGTTACAAC
1 TACAAAATAATACA-AAAA-AT-AA-TTTGATATTTACTAATCAAATGTTAGATTTAATTACAAC
37906109 AATTAA
62 AATTAA
* **
37906115 TAC-AATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTAATTACAACAA
1 TACAAAATAATACAAAAAATAATTTGAT--ATTTACTAATCAAATGTTAGATTTAATTACAACAA
37906179 TTAA
64 TTAA
37906183 TACAA
1 TACAA
37906188 TTAACAATTA
Statistics
Matches: 62, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
64 4 0.06
65 3 0.05
66 2 0.03
67 9 0.15
68 43 0.69
69 1 0.02
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.37
Consensus pattern (67 bp):
TACAAAATAATACAAAAAATAATTTGATATTTACTAATCAAATGTTAGATTTAATTACAACAATT
AA
Found at i:37906121 original size:9 final size:9
Alignment explanation
Indices: 37906107--37906134 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
37906097 TTTTGTTACA
37906107 ACAATTAAT
1 ACAATTAAT
37906116 ACAATTAAT
1 ACAATTAAT
37906125 ACAATTAAT
1 ACAATTAAT
37906134 A
1 A
37906135 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:37906188 original size:68 final size:66
Alignment explanation
Indices: 37906077--37906218 Score: 239
Period size: 68 Copynumber: 2.1 Consensus size: 66
37906067 TCAAGTTTGT
**
37906077 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTAATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
37906142 AAA
64 AAA
37906145 TTTACTAATCAAATGTTAGATTTAATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
1 TTTACTAATCAAATGTTAGATTTAATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
*
37906210 T
66 A
37906211 TTTACTAA
1 TTTACTAA
37906219 CAATTAATTT
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
66 27 0.38
67 1 0.01
68 43 0.61
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (66 bp):
TTTACTAATCAAATGTTAGATTTAATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
A
Found at i:37906228 original size:16 final size:16
Alignment explanation
Indices: 37906207--37906248 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
37906197 AATAATTTGA
*
37906207 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
37906223 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
37906239 TAGTTTTAAT
1 TAATTTTAAT
37906249 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:37906232 original size:22 final size:22
Alignment explanation
Indices: 37906222--37906282 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
37906212 TTACTAACAA
* * *
37906222 TTAATTTTAATAACAATTAGTT
1 TTAATTTTAATAAAAAATAATT
*
37906244 TTAATTTTATTAAAAAATAATT
1 TTAATTTTAATAAAAAATAATT
*
37906266 TTAATTTTAATTAAAAA
1 TTAATTTTAATAAAAAA
37906283 CGGGCCGGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TTAATTTTAATAAAAAATAATT
Found at i:37907995 original size:20 final size:20
Alignment explanation
Indices: 37907946--37908017 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
37907936 GTATGTCCAT
* *
37907946 TATGTATATTATTGA-TTGTG
1 TATGTATATTAGT-ATTTATG
*
37907966 TATGTCTATTAGTATGTTATG
1 TATGTATATTAGTAT-TTATG
*
37907987 TA-GTATATTACTATTTATG
1 TATGTATATTAGTATTTATG
*
37908006 TATGTATGTTAG
1 TATGTATATTAG
37908018 GTTTATTATT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
19 8 0.19
20 28 0.67
21 6 0.14
ACGTcount: A:0.26, C:0.03, G:0.18, T:0.53
Consensus pattern (20 bp):
TATGTATATTAGTATTTATG
Found at i:37916728 original size:32 final size:32
Alignment explanation
Indices: 37916686--37916746 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
37916676 TTTTTTGAAA
37916686 AATAATTATAACTATTTAAAT-AAT-ATTATTTG
1 AATAATTATAA-TA-TTAAATGAATAATTATTTG
*
37916718 AATAGTTATAATATTAAATGAATAATTAT
1 AATAATTATAATATTAAATGAATAATTAT
37916747 GTGTTTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 6 0.23
31 5 0.19
32 15 0.58
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (32 bp):
AATAATTATAATATTAAATGAATAATTATTTG
Found at i:37916739 original size:20 final size:20
Alignment explanation
Indices: 37916705--37916746 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
37916695 AACTATTTAA
** *
37916705 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
37916725 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
37916745 AT
1 AT
37916747 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:37921744 original size:14 final size:14
Alignment explanation
Indices: 37921725--37921769 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
37921715 GAATTTTTTT
37921725 TATTTTTTTCTTAG
1 TATTTTTTTCTTAG
* *
37921739 TATTTTTTGGCATTAA
1 TATTTTTT-TC-TTAG
37921755 TATTTTTTTCTTAG
1 TATTTTTTTCTTAG
37921769 T
1 T
37921770 TAGTATTTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 2 0.08
16 11 0.44
ACGTcount: A:0.18, C:0.07, G:0.09, T:0.67
Consensus pattern (14 bp):
TATTTTTTTCTTAG
Found at i:37922855 original size:114 final size:113
Alignment explanation
Indices: 37922651--37922883 Score: 414
Period size: 114 Copynumber: 2.1 Consensus size: 113
37922641 AATACTCAAG
*
37922651 TATTG-AGGAGTATTGTTAGGCATAAAGCTTCAAATTAAGTTTGGGGGTGGTAAAACCCGTTAGT
1 TATTGAAGGAGTATTGTTAGGAATAAAGCTTCAAATTAAGTTTGGGGGTGGTAAAACCCGTTAGT
* *
37922715 AGGAAGGATGTACCTTGAAAGGATCCAAGACAAAGTTGGGGTTAAGAT
66 AGGAAGGATGTACCTCGAAAGGATCCAAGACAAAGTTAGGGTTAAGAT
*
37922763 TATTGAAGGAGTATTGTTGGGAATAAAGCTTCAAATTAAGTTTGGGGGGTGGTAAAACCCGTTAG
1 TATTGAAGGAGTATTGTTAGGAATAAAGCTTCAAATTAAGTTT-GGGGGTGGTAAAACCCGTTAG
37922828 TAGGAAGGATGTACCTCGAAAGGATCCAAGACAAAGTTAGGGTTAAGAT
65 TAGGAAGGATGTACCTCGAAAGGATCCAAGACAAAGTTAGGGTTAAGAT
37922877 TATTGAA
1 TATTGAA
37922884 CCTAAAAAAT
Statistics
Matches: 115, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
112 5 0.04
113 35 0.30
114 75 0.65
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.27
Consensus pattern (113 bp):
TATTGAAGGAGTATTGTTAGGAATAAAGCTTCAAATTAAGTTTGGGGGTGGTAAAACCCGTTAGT
AGGAAGGATGTACCTCGAAAGGATCCAAGACAAAGTTAGGGTTAAGAT
Found at i:37928032 original size:18 final size:18
Alignment explanation
Indices: 37927993--37928034 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
37927983 CATCATCACC
*
37927993 GCCATCTCCTTCAACATA
1 GCCAACTCCTTCAACATA
*
37928011 GCCAACTCCTCTCACCAT-
1 GCCAACTCCT-TCAACATA
37928029 GCCAAC
1 GCCAAC
37928035 CTTTTCAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.26, C:0.45, G:0.07, T:0.21
Consensus pattern (18 bp):
GCCAACTCCTTCAACATA
Found at i:37928948 original size:74 final size:74
Alignment explanation
Indices: 37928856--37929006 Score: 284
Period size: 74 Copynumber: 2.0 Consensus size: 74
37928846 CTGTTCTCTT
37928856 TCAATAACATCTTATTTTGAAGCATTATTTCATTGAGCGTGCATCCTTGTTCTATTGCAGTTGAA
1 TCAATAACATCTTATTTTGAAGCATTATTTCATTGAGCGTGCATCCTTGTTCTATTGCAGTTGAA
37928921 TCCGTCCTG
66 TCCGTCCTG
**
37928930 TCAATAACATCTTATTTTGAAGCATTATTTCATTGATTGTGCATCCTTGTTCTATTGCAGTTGAA
1 TCAATAACATCTTATTTTGAAGCATTATTTCATTGAGCGTGCATCCTTGTTCTATTGCAGTTGAA
37928995 TCCGTCCTG
66 TCCGTCCTG
37929004 TCA
1 TCA
37929007 CTATTACGTT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.42
Consensus pattern (74 bp):
TCAATAACATCTTATTTTGAAGCATTATTTCATTGAGCGTGCATCCTTGTTCTATTGCAGTTGAA
TCCGTCCTG
Found at i:37929089 original size:35 final size:34
Alignment explanation
Indices: 37929042--37929152 Score: 107
Period size: 35 Copynumber: 3.0 Consensus size: 34
37929032 AAATCACATC
37929042 TTAAACCGATCTTAAACCCAAATTGTAACAAAATG
1 TTAAACC-ATCTTAAACCCAAATTGTAACAAAATG
*
37929077 TTAAATCCATCTTAAACCCAAATT-TCAACAAAAAAAATC
1 TTAAA-CCATCTTAAACCCAAATTGT-AAC----AAAATG
* *
37929116 TAAGAACACATCTTAAACCCAAATTGCAACAAAATG
1 TTA-AAC-CATCTTAAACCCAAATTGTAACAAAATG
37929152 T
1 T
37929153 CAAAACACAT
Statistics
Matches: 63, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
34 1 0.02
35 24 0.38
36 8 0.13
39 8 0.13
40 22 0.35
ACGTcount: A:0.49, C:0.22, G:0.05, T:0.24
Consensus pattern (34 bp):
TTAAACCATCTTAAACCCAAATTGTAACAAAATG
Found at i:37929373 original size:16 final size:16
Alignment explanation
Indices: 37929352--37929386 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
37929342 GTGTAGACAT
37929352 GAAAGAGAT-GGAAAAC
1 GAAAGAGATAGG-AAAC
37929368 GAAAGAGATAGGAAAC
1 GAAAGAGATAGGAAAC
37929384 GAA
1 GAA
37929387 GAAGTGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.57, C:0.06, G:0.31, T:0.06
Consensus pattern (16 bp):
GAAAGAGATAGGAAAC
Found at i:37929540 original size:48 final size:50
Alignment explanation
Indices: 37929441--37929544 Score: 142
Period size: 51 Copynumber: 2.1 Consensus size: 50
37929431 AAATAAAATA
*
37929441 GATGTCAGAGAAAATGAAAGAAAAAGAGGCTGGAATGAAAAATGTTGAAGAC
1 GATGTCAGAGAAAATGAAAGAAAAAGAGGCAGG-A-GAAAAATGTTGAAGAC
*
37929493 GATG-CAGAGAAAATGAAAGAGAAAGTA-GCAGG-GAAAAATGTTGAAGAC
1 GATGTCAGAGAAAATGAAAGAAAAAG-AGGCAGGAGAAAAATGTTGAAGAC
37929541 GATG
1 GATG
37929545 GTGAATAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
48 20 0.41
51 24 0.49
52 5 0.10
ACGTcount: A:0.49, C:0.06, G:0.31, T:0.14
Consensus pattern (50 bp):
GATGTCAGAGAAAATGAAAGAAAAAGAGGCAGGAGAAAAATGTTGAAGAC
Found at i:37942372 original size:3 final size:3
Alignment explanation
Indices: 37942364--37942400 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
37942354 ATTATAGTAC
* *
37942364 TTA TTA TTA TCA TTA TGA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
37942401 ATTTAATTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:37944796 original size:49 final size:49
Alignment explanation
Indices: 37944724--37944821 Score: 169
Period size: 49 Copynumber: 2.0 Consensus size: 49
37944714 CGCCTTACAC
* *
37944724 ACATAAAGCTCATTGATGAGACTTTATAGATGTAGTATCAAAATACAGA
1 ACATAAAGCTCACTGATGAGACTTCATAGATGTAGTATCAAAATACAGA
*
37944773 ACATAAAGCTCACTGATGAGACTTCATATATGTAGTATCAAAATACAGA
1 ACATAAAGCTCACTGATGAGACTTCATAGATGTAGTATCAAAATACAGA
37944822 TTTAATAACA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (49 bp):
ACATAAAGCTCACTGATGAGACTTCATAGATGTAGTATCAAAATACAGA
Found at i:37947758 original size:12 final size:12
Alignment explanation
Indices: 37947741--37947774 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
37947731 TAGGTTTCCA
37947741 AAAATAGAAATG
1 AAAATAGAAATG
*
37947753 AAAATAAAAATG
1 AAAATAGAAATG
*
37947765 AAAATGGAAA
1 AAAATAGAAA
37947775 CTTGCAATCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (12 bp):
AAAATAGAAATG
Found at i:37947956 original size:25 final size:25
Alignment explanation
Indices: 37947918--37947970 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
37947908 ATTTTTTTTG
*
37947918 AAATTTTATCAGGGGTAAACTCGTC
1 AAATTTTATCAGGGGTAAAATCGTC
*
37947943 AAATTTTA-CTAGGGGTAAAATTGTC
1 AAATTTTATC-AGGGGTAAAATCGTC
37947968 AAA
1 AAA
37947971 CAAATTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 24 0.96
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (25 bp):
AAATTTTATCAGGGGTAAAATCGTC
Found at i:37953934 original size:17 final size:15
Alignment explanation
Indices: 37953902--37953930 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
37953892 AATTATAAGT
37953902 TTTTTGTAAATTTTA
1 TTTTTGTAAATTTTA
37953917 TTTTTGTAAATTTT
1 TTTTTGTAAATTTT
37953931 TTATAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (15 bp):
TTTTTGTAAATTTTA
Found at i:37966283 original size:36 final size:36
Alignment explanation
Indices: 37966243--37966315 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
37966233 TTAAGTTTGT
37966243 AACTTTTTAACCCTCTACTACGTAGGATTAATTATA
1 AACTTTTTAACCCTCTACTACGTAGGATTAATTATA
*
37966279 AACTTTTTAACCCTCTACTACTTAGGATTAATTATA
1 AACTTTTTAACCCTCTACTACGTAGGATTAATTATA
37966315 A
1 A
37966316 CTCCTGATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.40
Consensus pattern (36 bp):
AACTTTTTAACCCTCTACTACGTAGGATTAATTATA
Found at i:37973960 original size:18 final size:18
Alignment explanation
Indices: 37973937--37973971 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
37973927 CAAGAACAGG
37973937 AAGCATCAAAATAGTTTC
1 AAGCATCAAAATAGTTTC
*
37973955 AAGCATGAAAATAGTTT
1 AAGCATCAAAATAGTTT
37973972 GACACATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (18 bp):
AAGCATCAAAATAGTTTC
Found at i:37984236 original size:50 final size:51
Alignment explanation
Indices: 37984120--37984356 Score: 214
Period size: 50 Copynumber: 4.6 Consensus size: 51
37984110 AATATAACAC
* * * ** * * *
37984120 GCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTT-TCCTTTA-CT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTTCTCATCTAGGT
* * * *
37984169 GCCAATGCCATATCCCAGATATGGTCTTACATGGGA-GTTCTCATATAGGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTTCTCATCTAGGT
* * *
37984219 GCCAATGCCATGTCCCAGACATGGTCTTAC-GGAGGACC-ACTCATCTCGGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATG-GGACCTTCTCATCTAGGT
* * * *
37984269 GCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCGTAATCTCAATGAT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCT-TC-TCATCT--A-GGT
37984325 GCCAATGCCATGTCCCAGACATGGTCTTACAT
1 GCCAATGCCATGTCCCAGACATGGTCTTACAT
37984357 AGGATCTCTT
Statistics
Matches: 154, Mismatches: 23, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
48 3 0.02
49 37 0.24
50 74 0.48
51 1 0.01
52 1 0.01
53 5 0.03
56 33 0.21
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (51 bp):
GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTTCTCATCTAGGT
Done.