Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 7 of 153
Found at i:2064259 original size:26 final size:26
Alignment explanation
Indices: 2064243--2064291 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
2064233 TTTCAACATC
2064243 TTAAAAT-T-TTAAAAATTTTAAAAA
1 TTAAAATATATTAAAAATTTTAAAAA
2064267 TTAAAATATATTAAAAATTTGTAAA
1 TTAAAATATATTAAAAATTT-TAAA
2064292 TTTTGTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 7 0.32
25 1 0.05
26 10 0.45
27 4 0.18
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (26 bp):
TTAAAATATATTAAAAATTTTAAAAA
Found at i:2064263 original size:17 final size:17
Alignment explanation
Indices: 2064216--2064265 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
2064206 GTAAAAATGA
*
2064216 TTAAAACATTGTAAAATT
1 TTAAAA-ATTTTAAAATT
* * *
2064234 TTCAACATCTTAAAATT
1 TTAAAAATTTTAAAATT
2064251 TTAAAAATTTTAAAA
1 TTAAAAATTTTAAAA
2064266 ATTAAAATAT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
17 21 0.84
18 4 0.16
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (17 bp):
TTAAAAATTTTAAAATT
Found at i:2064280 original size:17 final size:16
Alignment explanation
Indices: 2064251--2064285 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
2064241 TCTTAAAATT
*
2064251 TTAAAAATTTTAAAAA
1 TTAAAAATATTAAAAA
2064267 TTAAAATATATTAAAAA
1 TTAAAA-ATATTAAAAA
2064284 TT
1 TT
2064286 TGTAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TTAAAAATATTAAAAA
Found at i:2064405 original size:19 final size:19
Alignment explanation
Indices: 2064381--2064419 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2064371 AGCACCAAAA
2064381 TAAAAT-TTATTAAAAATTT
1 TAAAATATT-TTAAAAATTT
*
2064400 TAAAATATTTTAAATATTT
1 TAAAATATTTTAAAAATTT
2064419 T
1 T
2064420 TCCACAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAAAATATTTTAAAAATTT
Found at i:2064766 original size:14 final size:14
Alignment explanation
Indices: 2064747--2064773 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2064737 GTATACTAAC
2064747 ATATTTAATCATTA
1 ATATTTAATCATTA
2064761 ATATTTAATCATT
1 ATATTTAATCATT
2064774 TTATCAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (14 bp):
ATATTTAATCATTA
Found at i:2069536 original size:15 final size:15
Alignment explanation
Indices: 2069516--2069547 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2069506 AACATCGTAC
2069516 TGTGTTTATTATGGT
1 TGTGTTTATTATGGT
2069531 TGTGTTTATTATGGT
1 TGTGTTTATTATGGT
2069546 TG
1 TG
2069548 CAGACATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.28, T:0.59
Consensus pattern (15 bp):
TGTGTTTATTATGGT
Found at i:2070319 original size:69 final size:67
Alignment explanation
Indices: 2070241--2070739 Score: 433
Period size: 66 Copynumber: 7.5 Consensus size: 67
2070231 CCATTATTTT
2070241 AATAATTTCATTCATGAATTTCTAAACAAATATATGAAAAAAAAAACAAGAGAAAACCCTTTTTG
1 AATAATTTCATTCATGAATTTC-AAACAAATATATGAAAAAAAAAACAAGAGAAAACCCTTTTT-
2070306 TAAA
64 TAAA
* * *
2070310 AATAATTTCATTCATGAATTTCAAAGCAAATATGTGAAAGAAAATACAAGAGAAAACCCTCTTTT
1 AATAATTTCATTCATGAATTTCAAA-CAAATATATGAAAAAAAAAACAAGAGAAAACCCT-TTTT
2070375 T---
64 TAAA
* * * *
2070376 AGTAATTTTATTCATGAATTTCAGAACAAAGATATG--AACAAAAACAAGAGAAAACCTTCTTTT
1 AATAATTTCATTCATGAATTTCA-AACAAATATATGAAAAAAAAAACAAGAGAAAACC--CTTTT
*
2070439 TT--T
63 TTAAA
2070442 AATAATTTCATTCATGAATTTCAAAACAAA-ATATG----AAAAAACAAGAGAAAA-CCTTTTCT
1 AATAATTTCATTCATGAATTTC-AAACAAATATATGAAAAAAAAAACAAGAGAAAACCCTTTT-T
2070501 TAAA
64 TAAA
*
2070505 AATAATTTCATTCATGAATCTCAAAGCAAATATATGGAGAGAGAAAAAAA-AGAGAGAAAACCC-
1 AATAATTTCATTCATGAATTTCAAA-CAAATATAT-GA-A-A-AAAAAAACA-AGAGAAAACCCT
2070568 -TTTTAAA
60 TTTTTAAA
* * * *
2070575 AA-AA--GCATTCATGAAATTCATAACAAATATATG----ATAAAACAAGAGAAATCCCTTTTTT
1 AATAATTTCATTCATGAATTTCA-AACAAATATATGAAAAAAAAAACAAGAGAAAACCCTTTTTT
2070633 GAAAAA
65 ---AAA
* * * *
2070639 AAAAAATTCATTCATGAATCTCAAAGCAAATATATGAAGAAAAAAAA-GAGAGAAAACCC--TTT
1 AATAATTTCATTCATGAATTTCAAA-CAAATATATGAA-AAAAAAAACAAGAGAAAACCCTTTTT
2070701 TAAA
64 TAAA
* *
2070705 AA-AA-ATCATTCATGAAATTCAGAACAAATATATGA
1 AATAATTTCATTCATGAATTTCA-AACAAATATATGA
2070740 TAGAACAAGA
Statistics
Matches: 362, Mismatches: 29, Indels: 83
0.76 0.06 0.18
Matches are distributed among these distances:
59 15 0.04
60 6 0.02
61 6 0.02
62 4 0.01
63 40 0.11
64 51 0.14
65 17 0.05
66 65 0.18
67 48 0.13
68 5 0.01
69 60 0.17
70 11 0.03
71 13 0.04
72 19 0.05
73 2 0.01
ACGTcount: A:0.51, C:0.12, G:0.10, T:0.27
Consensus pattern (67 bp):
AATAATTTCATTCATGAATTTCAAACAAATATATGAAAAAAAAAACAAGAGAAAACCCTTTTTTA
AA
Found at i:2070411 original size:135 final size:125
Alignment explanation
Indices: 2070223--2070782 Score: 449
Period size: 131 Copynumber: 4.3 Consensus size: 125
2070213 GAGAGAGAGG
2070223 GAGAAAACCCATTATTTTAATAATTTCATTCATGAATTTCTAAACAAATATATGAAAAAAAAAAC
1 GAGAAAACCC-TT-TTTTAATAATTTCATTCATGAATTTC-AAACAAATATATGAAAAAAAAAAC
* *
2070288 AAGAGAAAACCCTTTTTGTAAAAATAATTTCATTCATGAATTTCAAAGCAAATATGTGAAAGAAA
63 AAGAGAAAACCCTTTTT-T--AAATAATTTCATTCATGAATTTCAAAACAAA-ATATG--A-AAA
2070353 ATACAA
121 A-ACAA
* * * *
2070359 GAGAAAACCCTCTTTTTAGTAATTTTATTCATGAATTTCAGAACAAAGATATG--AACAAAAACA
1 GAGAAAACCCT-TTTTTAATAATTTCATTCATGAATTTCA-AACAAATATATGAAAAAAAAAACA
*
2070422 AGAGAAAACCTTCTTTTTTTAATAATTTCATTCATGAATTTCAAAACAAAATATGAAAAAACAA
64 AGAGAAAACC--CTTTTTTAAATAATTTCATTCATGAATTTCAAAACAAAATATGAAAAAACAA
*
2070486 GAGAAAA-CCTTTTCTTAAAAATAATTTCATTCATGAATCTCAAAGCAAATATATGGAGAGAGAA
1 GAGAAAACCCTTTT-TT---AATAATTTCATTCATGAATTTCAAA-CAAATATAT-GA-A-A-AA
*** * * *
2070550 AAAAA-AGAGAGAAAACCC--TTTTAAA-AAAAGCATTCATGAAATTCATAACAAATATATGATA
57 AAAAACA-AGAGAAAACCCTTTTTTAAATAATTTCATTCATGAATTTCAAAACAAA-ATATGAAA
2070611 AAACAA
120 AAACAA
* * * *
2070617 GAGAAATCCCTTTTTTGAAAAAAAAAAATTCATTCATGAATCTCAAAGCAAATATATGAAGAAAA
1 GAGAAAACCCTTTTTT------AATAATTTCATTCATGAATTTCAAA-CAAATATATGAA-AAAA
* * ** * * * *
2070682 AAAA-GAGAGAAAACCC--TTTTAAAAAAAATCATTCATGAAATTCAGAACAAATATATGATAGA
58 AAAACAAGAGAAAACCCTTTTTTAAATAATTTCATTCATGAATTTCAAAACAAA-ATATGAAAAA
2070744 ACAA
122 ACAA
* * ** *
2070748 GAGAAATCCTTTTTTTTTTAA-ATCATTCATGAATT
1 GAGAAAACCCTTTTTTAATAATTTCATTCATGAATT
2070783 AGCTTTAAAA
Statistics
Matches: 370, Mismatches: 32, Indels: 56
0.81 0.07 0.12
Matches are distributed among these distances:
124 12 0.03
125 5 0.01
126 5 0.01
127 11 0.03
128 6 0.02
129 29 0.08
130 41 0.11
131 92 0.25
132 38 0.10
133 22 0.06
134 40 0.11
135 58 0.16
136 11 0.03
ACGTcount: A:0.49, C:0.12, G:0.10, T:0.29
Consensus pattern (125 bp):
GAGAAAACCCTTTTTTAATAATTTCATTCATGAATTTCAAACAAATATATGAAAAAAAAAACAAG
AGAAAACCCTTTTTTAAATAATTTCATTCATGAATTTCAAAACAAAATATGAAAAAACAA
Found at i:2070441 original size:66 final size:63
Alignment explanation
Indices: 2070223--2070782 Score: 403
Period size: 67 Copynumber: 8.6 Consensus size: 63
2070213 GAGAGAGAGG
*
2070223 GAGAAAACCCATTATTTTAATAATTTCATTCATGAATTTCTAAACAAATATATGAAAAAAAAAAC
1 GAGAAAACCC-TTTTTTTAATAATTTCATTCATGAATTTC-AAACAAATATATG--AAAAAAAAC
2070288 AA
62 AA
* *
2070290 GAGAAAACCCTTTTTGTAAAAATAATTTCATTCATGAATTTCAAAGCAAATATGTGAAAGAAAAT
1 GAGAAAACCCTTTTT-T--TAATAATTTCATTCATGAATTTCAAA-CAAATATATGAAA-AAAA-
2070355 ACAA
60 ACAA
* * * * *
2070359 GAGAAAACCCTCTTTTTAGTAATTTTATTCATGAATTTCAGAACAAAGATATGAACAAAAACAA
1 GAGAAAACCCTTTTTTTAATAATTTCATTCATGAATTTCA-AACAAATATATGAAAAAAAACAA
2070423 GAGAAAACCTTCTTTTTTTAATAATTTCATTCATGAATTTCAAAACAAA-ATATG--AAAAAACA
1 GAGAAAACC--CTTTTTTTAATAATTTCATTCATGAATTTC-AAACAAATATATGAAAAAAAACA
2070485 A
63 A
* *
2070486 GAGAAAA-CCTTTTCTTAAAAATAATTTCATTCATGAATCTCAAAGCAAATATATGGAGAGAGAA
1 GAGAAAACCCTTTT-TT--TAATAATTTCATTCATGAATTTCAAA-CAAATATAT---GA-A-AA
*
2070550 AAAAAAGA
57 AAAACA-A
* *** * *
2070558 GAGAAAACCC---TTTTAAAAAAAGCATTCATGAAATTCATAACAAATATATG--ATAAAACAA
1 GAGAAAACCCTTTTTTTAATAATTTCATTCATGAATTTCA-AACAAATATATGAAAAAAAACAA
* * * * *
2070617 GAGAAATCCCTTTTTTGAAAAAAAAAAATTCATTCATGAATCTCAAAGCAAATATATGAAGAAAA
1 GAGAAAACCCTTTTTT-----TAATAATTTCATTCATGAATTTCAAA-CAAATATATGAA-AAAA
*
2070682 AAAAGA
59 AACA-A
* * ** * * *
2070688 GAGAAAACCC--TTTTAAAAAAAATCATTCATGAAATTCAGAACAAATATATG--ATAGAACAA
1 GAGAAAACCCTTTTTTTAATAATTTCATTCATGAATTTCA-AACAAATATATGAAAAAAAACAA
* ** *
2070748 GAG-AAATCCTTTTTTTTTTAA-ATCATTCATGAATT
1 GAGAAAACCCTTTTTTTAATAATTTCATTCATGAATT
2070783 AGCTTTAAAA
Statistics
Matches: 405, Mismatches: 47, Indels: 89
0.75 0.09 0.16
Matches are distributed among these distances:
59 15 0.04
60 28 0.07
61 13 0.03
62 7 0.02
63 40 0.10
64 49 0.12
65 11 0.03
66 70 0.17
67 73 0.18
68 10 0.02
69 55 0.14
70 7 0.02
71 17 0.04
72 8 0.02
73 2 0.00
ACGTcount: A:0.49, C:0.12, G:0.10, T:0.29
Consensus pattern (63 bp):
GAGAAAACCCTTTTTTTAATAATTTCATTCATGAATTTCAAACAAATATATGAAAAAAAACAA
Found at i:2070643 original size:67 final size:61
Alignment explanation
Indices: 2070568--2070763 Score: 193
Period size: 64 Copynumber: 3.1 Consensus size: 61
2070558 GAGAAAACCC
*
2070568 TTTT-AAAAAAAGCATTCATGAAATTCATAACAAATATATGATAAAACAAGAGAAATCCCTT
1 TTTTAAAAAAAATCATTCATGAAATTCA-AACAAATATATGATAAAACAAGAGAAATCCCTT
* *
2070629 TTTTGAAAAAAAAAAATTCATTCATG-AATCTCAAAGCAAATATATGAAGAAAAAAAAGAGAGAA
1 TTTT----AAAAAAAA-TCATTCATGAAAT-TCAAA-CAAATATAT---GATAAAACA-AGAGAA
*
2070693 AACCC--
55 ATCCCTT
* *
2070698 TTTTAAAAAAAATCATTCATGAAATTCAGAACAAATATATGATAGAACAAGAGAAATCCTTT
1 TTTTAAAAAAAATCATTCATGAAATTCA-AACAAATATATGATAAAACAAGAGAAATCCCTT
2070760 TTTT
1 TTTT
2070764 TTTAAATCAT
Statistics
Matches: 110, Mismatches: 9, Indels: 31
0.73 0.06 0.21
Matches are distributed among these distances:
60 9 0.08
61 10 0.09
62 4 0.04
64 21 0.19
65 13 0.12
66 12 0.11
67 20 0.18
69 4 0.04
70 7 0.06
71 10 0.09
ACGTcount: A:0.52, C:0.12, G:0.10, T:0.27
Consensus pattern (61 bp):
TTTTAAAAAAAATCATTCATGAAATTCAAACAAATATATGATAAAACAAGAGAAATCCCTT
Found at i:2076748 original size:16 final size:18
Alignment explanation
Indices: 2076716--2076751 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
2076706 AATATATTGT
2076716 AATATTTGTATTATTTAA
1 AATATTTGTATTATTTAA
2076734 AATATTT-TA-TATTTAA
1 AATATTTGTATTATTTAA
2076750 AA
1 AA
2076752 GACATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 2 0.11
18 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
AATATTTGTATTATTTAA
Found at i:2077138 original size:19 final size:19
Alignment explanation
Indices: 2077097--2077138 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
2077087 ATAAAACTTT
* *
2077097 AATTTTTAATAATTTTTTT
1 AATTTTTAATAATTATTTG
2077116 AATTTTTAAATAA-TATTTG
1 AATTTTT-AATAATTATTTG
2077135 AATT
1 AATT
2077139 GAACCTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
AATTTTTAATAATTATTTG
Found at i:2078402 original size:17 final size:17
Alignment explanation
Indices: 2078380--2078413 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2078370 TATTGGGTTC
2078380 ACCAAAAAGTCTCTTTA
1 ACCAAAAAGTCTCTTTA
* *
2078397 ACCAAATAGTTTCTTTA
1 ACCAAAAAGTCTCTTTA
2078414 CAAGCCTCAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (17 bp):
ACCAAAAAGTCTCTTTA
Found at i:2085421 original size:24 final size:24
Alignment explanation
Indices: 2085393--2085440 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2085383 ATTTGGTGAG
* *
2085393 TTTAAA-TATAATTTACTCTAATTT
1 TTTAAATTA-AATTGACACTAATTT
2085417 TTTAAATTAAATTGACACTAATTT
1 TTTAAATTAAATTGACACTAATTT
2085441 AAAATTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTAAATTAAATTGACACTAATTT
Found at i:2088430 original size:3 final size:3
Alignment explanation
Indices: 2088422--2088447 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2088412 GCCTACTTTT
2088422 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
2088448 TAAGTGTAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:2089069 original size:23 final size:23
Alignment explanation
Indices: 2089039--2089088 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
2089029 TATTCACCAA
2089039 ATAAATAATATTTA-TTATACAAT
1 ATAAATAAT-TTTATTTATACAAT
*
2089062 ATAAATAATTTTATTTATATAAT
1 ATAAATAATTTTATTTATACAAT
2089085 ATAA
1 ATAA
2089089 GTTACGAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
ATAAATAATTTTATTTATACAAT
Found at i:2094373 original size:2 final size:2
Alignment explanation
Indices: 2094368--2094406 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2094358 TATATATATA
2094368 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T- TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2094407 GGTTTCAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:2095012 original size:18 final size:17
Alignment explanation
Indices: 2094989--2095022 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2094979 TCTTTTTTAA
*
2094989 ATAATATTTATATCGATC
1 ATAATATGTAT-TCGATC
2095007 ATAATATGTATTCGAT
1 ATAATATGTATTCGAT
2095023 ATTCACTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (17 bp):
ATAATATGTATTCGATC
Found at i:2095092 original size:67 final size:67
Alignment explanation
Indices: 2094981--2095111 Score: 208
Period size: 67 Copynumber: 2.0 Consensus size: 67
2094971 TTCTTCAATC
* * * * *
2094981 TTTTTTAAATAATATTTATATCGATCATAATATGTATTCGATATTCACTCAAATTCAAGTAACAA
1 TTTTTTAAATAATATTTATATAGAACAGAATATGTATTCAATATTCACTCAAATCCAAGTAACAA
2095046 AT
66 AT
*
2095048 TTTTTTAAATAATATTTATATAGAACAGAATATGTATTCAATATTCACTCAAATCCGAGTAACA
1 TTTTTTAAATAATATTTATATAGAACAGAATATGTATTCAATATTCACTCAAATCCAAGTAACA
2095112 GATTGGGGAT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 58 1.00
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.40
Consensus pattern (67 bp):
TTTTTTAAATAATATTTATATAGAACAGAATATGTATTCAATATTCACTCAAATCCAAGTAACAA
AT
Found at i:2096206 original size:25 final size:25
Alignment explanation
Indices: 2096172--2096220 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
2096162 AAATTTCTTT
* * *
2096172 ATATATTTTTATAATTTTTTTAAAA
1 ATATAATTTTAGAATTTTTATAAAA
*
2096197 ATATAATTTTGGAATTTTTATAAA
1 ATATAATTTTAGAATTTTTATAAA
2096221 TATTTAAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (25 bp):
ATATAATTTTAGAATTTTTATAAAA
Found at i:2096232 original size:18 final size:19
Alignment explanation
Indices: 2096209--2096244 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2096199 ATAATTTTGG
*
2096209 AATTTTTATAAA-TATTTA
1 AATTTTTACAAATTATTTA
2096227 AATTTTTACAAATTATTT
1 AATTTTTACAAATTATTT
2096245 TGAATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
AATTTTTACAAATTATTTA
Found at i:2096735 original size:20 final size:20
Alignment explanation
Indices: 2096710--2096751 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2096700 ATGGGTAAAA
*
2096710 TTTTTACACAAATTCATATT
1 TTTTTACACAAATTAATATT
* *
2096730 TTTTTATACAAGTTAATATT
1 TTTTTACACAAATTAATATT
2096750 TT
1 TT
2096752 GACAATACAA
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:0.33, C:0.10, G:0.02, T:0.55
Consensus pattern (20 bp):
TTTTTACACAAATTAATATT
Found at i:2102366 original size:26 final size:26
Alignment explanation
Indices: 2102335--2102387 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
2102325 CCCATTTTTT
* * * *
2102335 AATAAACATTAAAAAATTGTTTTAAA
1 AATAAAAAATAAAAAAATATTTTAAA
2102361 AATAAAAAATAAAAAAATATTTTAAA
1 AATAAAAAATAAAAAAATATTTTAAA
2102387 A
1 A
2102388 GTATTTTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (26 bp):
AATAAAAAATAAAAAAATATTTTAAA
Found at i:2110980 original size:29 final size:31
Alignment explanation
Indices: 2110930--2110992 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
2110920 TTAAGTTAAT
*
2110930 AAATGATAAAATTATAGTTTAG-CATCCTAA
1 AAATGATAAAATTATAATTTAGTCATCCTAA
* *
2110960 AAATGAT-AAATTTTAATTTAGTCATTCTAA
1 AAATGATAAAATTATAATTTAGTCATCCTAA
2110990 AAA
1 AAA
2110993 ATATAATGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 12 0.41
30 17 0.59
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.37
Consensus pattern (31 bp):
AAATGATAAAATTATAATTTAGTCATCCTAA
Found at i:2113908 original size:18 final size:19
Alignment explanation
Indices: 2113885--2113923 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
2113875 TATTTAATTT
2113885 TAACTAGACT-TGAACAAA
1 TAACTAGACTATGAACAAA
2113903 TAACTAGACTCATGAACAAA
1 TAACTAGACT-ATGAACAAA
2113923 T
1 T
2113924 CTACTTGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.53
20 9 0.47
ACGTcount: A:0.49, C:0.18, G:0.10, T:0.23
Consensus pattern (19 bp):
TAACTAGACTATGAACAAA
Found at i:2129499 original size:44 final size:42
Alignment explanation
Indices: 2129215--2129587 Score: 213
Period size: 44 Copynumber: 8.6 Consensus size: 42
2129205 GTTTATTATA
* * **
2129215 CAGG-TCTTATCTCTCTGAGATTACAGTGGAACAGACCAAAG
1 CAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAG
* *
2129256 AATTTCA-GATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAG
1 -----CAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAG
* * * * * *
2129302 ATAGTAATCCTATCTCCTTGAGATTACAATGGAGCGGATT-AA-
1 -CAG-GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAG
* * * * *
2129344 -AGGATCTTATCTCCCTGA-AGTTACAGTAGAGAAGATCACAT
1 CAGGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAG
** **
2129385 CAGG-TCTTATCTCCCTGAGATTACAGTGGAATAGACCAAAG
1 CAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAG
* * *
2129426 AATTTCGGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAG
1 CA----GGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAG
* **
2129472 CCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAG
1 -CAG-GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAG
** * * *
2129516 ACACTATCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAAATA
1 -CAGGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATT-AAA-G
* * *
2129561 AAGGATCTTATCTCTCTGAGGTTACAG
1 CAGGATCTTATCTCCCTGAGATTACAG
2129588 CAGAGTGGAT
Statistics
Matches: 254, Mismatches: 54, Indels: 40
0.73 0.16 0.11
Matches are distributed among these distances:
38 1 0.00
39 25 0.10
40 3 0.01
41 30 0.12
42 6 0.02
43 31 0.12
44 88 0.35
45 3 0.01
46 66 0.26
47 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (42 bp):
CAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAG
Found at i:2129740 original size:83 final size:83
Alignment explanation
Indices: 2129590--2129746 Score: 188
Period size: 83 Copynumber: 1.9 Consensus size: 83
2129580 GGTTACAGCA
* * * * * * * *
2129590 GAGTGGATCACATCAAGTCTTATCTCCCTAAATAGTAGTGAAGCAGACGAAAGAAACCGATCTTA
1 GAGTAGATCACATCAAGTCTCATCTCCCTAAACAATAGCGAAGCAGACAAAAGAAACCAATCCTA
2129655 TCTCCCTAAGTAGTAGTG
66 TCTCCCTAAGTAGTAGTG
* * * * *
2129673 GAGTAGATCGCATCAAGTCTCATCTCTCTAAGCAATAGCGGAGCAGACAAAAGAAACTAATCCTA
1 GAGTAGATCACATCAAGTCTCATCTCCCTAAACAATAGCGAAGCAGACAAAAGAAACCAATCCTA
*
2129738 TCTCTCTAA
66 TCTCCCTAA
2129747 AGTTGCAGTG
Statistics
Matches: 60, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
83 60 1.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (83 bp):
GAGTAGATCACATCAAGTCTCATCTCCCTAAACAATAGCGAAGCAGACAAAAGAAACCAATCCTA
TCTCCCTAAGTAGTAGTG
Found at i:2131151 original size:3 final size:3
Alignment explanation
Indices: 2131140--2131227 Score: 72
Period size: 3 Copynumber: 29.3 Consensus size: 3
2131130 ATTATTTTGT
* *
2131140 TTA TT- TTA TTA TTA TTA TTA TTA TTTA CTA TTA TTA TCT- TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA T-TA TTA TTA
* * * * * *
2131185 TTA TTG TTA GTA TTA TTA CTA CTA TTA TTA TTA CTA TCA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2131228 ATTTATACCT
Statistics
Matches: 67, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
2 3 0.04
3 60 0.90
4 4 0.06
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:2131160 original size:12 final size:12
Alignment explanation
Indices: 2131145--2131227 Score: 85
Period size: 12 Copynumber: 6.6 Consensus size: 12
2131135 TTTGTTTATT
*
2131145 TTATTATTATTA
1 TTATTATTACTA
2131157 TTATTATTTACTA
1 TTATTA-TTACTA
2131170 TTATTATCTTTACTA
1 TTATTA---TTACTA
* *
2131185 TTATTGTTAGTA
1 TTATTATTACTA
*
2131197 TTATTACTACTA
1 TTATTATTACTA
2131209 TTATTATTACTA
1 TTATTATTACTA
*
2131221 TCATTAT
1 TTATTAT
2131228 ATTTATACCT
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
12 37 0.62
13 11 0.18
15 12 0.20
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.59
Consensus pattern (12 bp):
TTATTATTACTA
Found at i:2137513 original size:21 final size:21
Alignment explanation
Indices: 2137472--2137515 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2137462 TTTTAAGAGG
* *
2137472 TTTGAAATTGAATTATAAATT
1 TTTGAAATTAAAATATAAATT
2137493 TTTGAAAGTTAAAATAT-AATT
1 TTTGAAA-TTAAAATATAAATT
2137514 TT
1 TT
2137516 ATCATATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (21 bp):
TTTGAAATTAAAATATAAATT
Found at i:2139841 original size:5 final size:6
Alignment explanation
Indices: 2139814--2139839 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2139804 TTTATTGTTG
2139814 AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
2139840 TATGTGAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:2140549 original size:46 final size:44
Alignment explanation
Indices: 2140462--2140589 Score: 142
Period size: 39 Copynumber: 3.0 Consensus size: 44
2140452 ATTTGTCGGC
* * * *
2140462 TTACTGATTAAGCAC-TTATGTGCCGACTACTGTTACTGTTACT
1 TTACTGATTCAGCACTTTGTGTGTCGAATACTGTTACTGTTACT
*
2140505 AATTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTAC-
1 --TTACTGATTCAGCACTTTGTGTGTCGAATACTGTTACTGTTACT
*
2140550 --A--GATTCAGCACTTTGTGTGTTGAATACTGTTACTGTTACT
1 TTACTGATTCAGCACTTTGTGTGTCGAATACTGTTACTGTTACT
2140590 GCTACCGTTA
Statistics
Matches: 74, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
39 36 0.49
41 1 0.01
45 13 0.18
46 24 0.32
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.41
Consensus pattern (44 bp):
TTACTGATTCAGCACTTTGTGTGTCGAATACTGTTACTGTTACT
Found at i:2140561 original size:39 final size:39
Alignment explanation
Indices: 2140495--2140588 Score: 143
Period size: 39 Copynumber: 2.4 Consensus size: 39
2140485 CGACTACTGT
* * *
2140495 TACTGTTACTAATTACTGATTCGGCACTTTGTGTGTCGAA
1 TACTGTTACT-GTTACAGATTCAGCACTTTGTGTGTCGAA
*
2140535 TACTGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAA
2140574 TACTGTTACTGTTAC
1 TACTGTTACTGTTAC
2140589 TGCTACCGTT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 40 0.80
40 10 0.20
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.41
Consensus pattern (39 bp):
TACTGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAA
Found at i:2140585 original size:6 final size:6
Alignment explanation
Indices: 2140574--2140616 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
2140564 GTGTGTTGAA
* *
2140574 TACTGT TACTGT TACTGC TACCGT TACTGAT TACTGT ATACTG
1 TACTGT TACTGT TACTGT TACTGT TACTG-T TACTGT -TACTG
2140617 GTGTGTTTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
6 20 0.65
7 11 0.35
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (6 bp):
TACTGT
Found at i:2141121 original size:13 final size:15
Alignment explanation
Indices: 2141103--2141134 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2141093 TATATGAAAT
2141103 AATGATT-TT-ATGA
1 AATGATTATTGATGA
2141116 AATGATTATTGATGA
1 AATGATTATTGATGA
2141131 AATG
1 AATG
2141135 CATGAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 2 0.12
15 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (15 bp):
AATGATTATTGATGA
Found at i:2141889 original size:23 final size:23
Alignment explanation
Indices: 2141862--2141907 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
2141852 TCAAAAATAC
*
2141862 TTTTGAAAAATACTTCTGGCAAG
1 TTTTGAAAAACACTTCTGGCAAG
2141885 TTTTGAAAAACACTTCTGGCAAG
1 TTTTGAAAAACACTTCTGGCAAG
2141908 GAGAAGCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (23 bp):
TTTTGAAAAACACTTCTGGCAAG
Found at i:2142095 original size:21 final size:22
Alignment explanation
Indices: 2142070--2142117 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
2142060 TAAATTTTTT
2142070 TTTAAAT-GTTAGT-TATAAATA
1 TTTAAATGGTTA-TATATAAATA
*
2142091 TTT-AATGGTTATATTTAAATA
1 TTTAAATGGTTATATATAAATA
2142112 TTTAAA
1 TTTAAA
2142118 ATATCGTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 4 0.17
21 17 0.74
22 2 0.09
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (22 bp):
TTTAAATGGTTATATATAAATA
Found at i:2161725 original size:16 final size:16
Alignment explanation
Indices: 2161697--2161747 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
2161687 CTAATAATAC
*
2161697 TATTATTTTTATATAT
1 TATTATCTTTATATAT
2161713 TATGTA-CTTTATAT-T
1 TAT-TATCTTTATATAT
*
2161728 ATATTATTTTTATATAT
1 -TATTATCTTTATATAT
2161745 TAT
1 TAT
2161748 ATTTTTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 3 0.10
16 23 0.79
17 3 0.10
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TATTATCTTTATATAT
Found at i:2161837 original size:16 final size:16
Alignment explanation
Indices: 2161806--2161835 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2161796 TGATTATAGA
2161806 AAAAAATTTAATAAAT
1 AAAAAATTTAATAAAT
2161822 AAAAAATTT-ATAAA
1 AAAAAATTTAATAAA
2161836 ATTATTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAAAATTTAATAAAT
Found at i:2169069 original size:378 final size:377
Alignment explanation
Indices: 2168369--2169091 Score: 967
Period size: 378 Copynumber: 1.9 Consensus size: 377
2168359 CATCATCTTC
* * *
2168369 ACAAAGCTTCTCCAAATGATGACTCGTTTCAATTTGTCCGTTAAAGTGTTGACTTTTTTCTCGAA
1 ACAAAGCTTCTCCAAATGAAGACTCGTTTCAATTTGTCCATTAAAGTGTTGACTTTCTTCTCGAA
2168434 CCTCATTAATCGATTCCCTTCTGCCTTCCATTTGTTCTTCAAACCCTTCCGTTCTTCCATCACAA
66 CCTCATTAATCGATTCCCTTCTGCCTTCCATTTGTTCTTCAAACCCTTCCGTTCTTCCATCACAA
*
2168499 GCTCTATCCTGGCCTTTCACTTCAACACTTTGTCTTTCAACTTCACACCGAGTTTCAGATTCTGC
131 GCTCTATCCTGGCCATTCACTTCAACACTTTGTCTTTCAACTTCACACCGAGTTTCAGATTC-GC
** ** * * *
2168564 AGCTTGACCACTGTTTACCCCGTTACAGACATCAAAAGCCTCGACTTCACTCCACTTCCCTTGGA
195 AGCTTGACCACCATTTACCCCACTACAGACATCAAAAGCCTCAACTTCACTCCACTTCCCTCGAA
* * * * * * * *
2168629 CTAAAGTTTGATCTTCCTTCTCAACGCTATTTGAAACGTTCAACCTATGACTCATTTCCTCCTCA
260 CCAAAGCTCGATCTTCCTTCTCAACACAATTTGAAACGTTCAACCCAAGACTCATCTCCTCCTCA
2168694 TT-CTGCAAATCACCATCATCTTCATTATTAACGCATACGATCTCTCCATTCCT
325 TTCCTG-AAATCACCATCATCTTCATTATTAACGCATACGATCTCTCCATTCCT
*
2168747 ACAAAGCTTCTCCAAATGAAGACTCAG-TTCAATTTGTTCATTAAAGTGTTGACTTTCTTCTCGA
1 ACAAAGCTTCTCCAAATGAAGACTC-GTTTCAATTTGTCCATTAAAGTGTTGACTTTCTTCTCGA
* *
2168811 ACCTCATTAATGGATTCCCTTCTGCCTTCCATTTGTTCTTCAAACCCTTCACG-TCTTTCATCAC
65 ACCTCATTAATCGATTCCCTTCTGCCTTCCATTTGTTCTTCAAACCCTTC-CGTTCTTCCATCAC
* *
2168875 AAGCTCTATTCC-GGCCATTCACTTCAACACTTTGTCTTTCAACTTCACATCG-TTTCTCAGATT
129 AAGCTCTA-TCCTGGCCATTCACTTCAACACTTTGTCTTTCAACTTCACACCGAGTT-TCAGATT
** * * ** * *
2168938 C-CAGAACTTGGTCACCATTTACTCCACTCCATCCATTGAAAA-CCTCAACTTCACTCCCCTTCC
192 CGCAG--CTTGACCACCATTTACCCCACTACAGACA-TCAAAAGCCTCAACTTCACTCCACTTCC
* * *
2169001 CTCGAACC-AAGACTCGATCTTCCTTCTCATCACAATTTGAAACTTTCAACCCAAGACTCGTCTC
254 CTCGAACCAAAG-CTCGATCTTCCTTCTCAACACAATTTGAAACGTTCAACCCAAGACTCATCTC
**
2169065 CTCCTTGTTCCTGAAATCACCATCATC
318 CTCCTCATTCCTGAAATCACCATCATC
2169092 CATACAAACC
Statistics
Matches: 299, Mismatches: 37, Indels: 18
0.84 0.10 0.05
Matches are distributed among these distances:
376 3 0.01
377 5 0.02
378 277 0.93
379 14 0.05
ACGTcount: A:0.24, C:0.32, G:0.10, T:0.35
Consensus pattern (377 bp):
ACAAAGCTTCTCCAAATGAAGACTCGTTTCAATTTGTCCATTAAAGTGTTGACTTTCTTCTCGAA
CCTCATTAATCGATTCCCTTCTGCCTTCCATTTGTTCTTCAAACCCTTCCGTTCTTCCATCACAA
GCTCTATCCTGGCCATTCACTTCAACACTTTGTCTTTCAACTTCACACCGAGTTTCAGATTCGCA
GCTTGACCACCATTTACCCCACTACAGACATCAAAAGCCTCAACTTCACTCCACTTCCCTCGAAC
CAAAGCTCGATCTTCCTTCTCAACACAATTTGAAACGTTCAACCCAAGACTCATCTCCTCCTCAT
TCCTGAAATCACCATCATCTTCATTATTAACGCATACGATCTCTCCATTCCT
Found at i:2170017 original size:17 final size:20
Alignment explanation
Indices: 2169996--2170035 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
2169986 TTTTTTAATT
*
2169996 TTTTTTTCC-ATTT-TTTTA
1 TTTTTTCCCAATTTATTTTA
2170014 TTTTTTCCCAATTTATTTTA
1 TTTTTTCCCAATTTATTTTA
2170034 TT
1 TT
2170036 ATAATATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 4 0.21
20 7 0.37
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTTTCCCAATTTATTTTA
Found at i:2170499 original size:19 final size:20
Alignment explanation
Indices: 2170475--2170513 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
2170465 TTTTGTTACG
*
2170475 ATAAATCTAAAAT-TTTAAC
1 ATAAATATAAAATATTTAAC
*
2170494 ATAAATATCAAATATTTAAC
1 ATAAATATAAAATATTTAAC
2170514 GTATATTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAAATATAAAATATTTAAC
Found at i:2178086 original size:10 final size:10
Alignment explanation
Indices: 2178071--2178118 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
2178061 AACTGTCAAA
2178071 ATTTAATATT
1 ATTTAATATT
2178081 ATTTAATATTT
1 ATTTAATA-TT
*
2178092 ATGTAA-ATT
1 ATTTAATATT
2178101 A--TAATATT
1 ATTTAATATT
2178109 ATTTAATATT
1 ATTTAATATT
2178119 TCTGTAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
7 3 0.09
8 4 0.12
9 3 0.09
10 16 0.48
11 7 0.21
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (10 bp):
ATTTAATATT
Found at i:2178108 original size:28 final size:27
Alignment explanation
Indices: 2178069--2178132 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 27
2178059 TCAACTGTCA
2178069 AAATTTAATATTATTTAATATTTATGT
1 AAATTTAATATTATTTAATATTTATGT
*
2178096 AAATTATAATATTATTTAATATTTCTGT
1 AAATT-TAATATTATTTAATATTTATGT
2178124 AAATTTAAT
1 AAATTTAAT
2178133 TTACTAGGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 9 0.26
28 26 0.74
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (27 bp):
AAATTTAATATTATTTAATATTTATGT
Found at i:2179286 original size:36 final size:36
Alignment explanation
Indices: 2179246--2179331 Score: 118
Period size: 36 Copynumber: 2.4 Consensus size: 36
2179236 AACTTTGGAC
**
2179246 AGTTTGTTCCAGTCAGCGGTGCTGAGAGCTTCGGAT
1 AGTTTGTTCCAGTCAGCGGTGCCAAGAGCTTCGGAT
* * *
2179282 AGTTTGTCCCAGTCGGCGGTGCCAATAGCTTCGGAT
1 AGTTTGTTCCAGTCAGCGGTGCCAAGAGCTTCGGAT
*
2179318 AGTTTGCTCCAGTC
1 AGTTTGTTCCAGTC
2179332 CGAGGGGTCG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.16, C:0.23, G:0.30, T:0.30
Consensus pattern (36 bp):
AGTTTGTTCCAGTCAGCGGTGCCAAGAGCTTCGGAT
Found at i:2184365 original size:21 final size:21
Alignment explanation
Indices: 2184326--2184365 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2184316 TTTTTATTAT
*
2184326 TTTTTTAAGAATTTCAATACA
1 TTTTTTAAGAATTTAAATACA
2184347 TTTTTTAA-AATTTTAAATA
1 TTTTTTAAGAA-TTTAAATA
2184366 TCTTCAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (21 bp):
TTTTTTAAGAATTTAAATACA
Found at i:2184410 original size:17 final size:18
Alignment explanation
Indices: 2184372--2184445 Score: 71
Period size: 18 Copynumber: 4.1 Consensus size: 18
2184362 AATATCTTCA
*
2184372 ATAAATTT-TATTACTCTT
1 ATAAATTTATATTAAT-TT
*
2184390 ATAAATTTTTA-TAATTT
1 ATAAATTTATATTAATTT
2184407 ATAAATTTATATTAATTTT
1 ATAAATTTATATTAA-TTT
* *
2184426 AATAACTTTATATCAATTT
1 -ATAAATTTATATTAATTT
2184445 A
1 A
2184446 GTTTTTTCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
17 12 0.25
18 15 0.31
19 8 0.17
20 13 0.27
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (18 bp):
ATAAATTTATATTAATTT
Found at i:2184435 original size:20 final size:20
Alignment explanation
Indices: 2184390--2184444 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
2184380 TATTACTCTT
*
2184390 ATAAATTTTTAT-AA-TTT-
1 ATAAATTTATATCAATTTTA
*
2184407 ATAAATTTATATTAATTTTA
1 ATAAATTTATATCAATTTTA
*
2184427 ATAACTTTATATCAATTT
1 ATAAATTTATATCAATTT
2184445 AGTTTTTTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 11 0.34
18 2 0.06
19 3 0.09
20 16 0.50
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (20 bp):
ATAAATTTATATCAATTTTA
Found at i:2185184 original size:19 final size:19
Alignment explanation
Indices: 2185143--2185185 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2185133 AAAATAATCG
*
2185143 AAAATCCAACAACAAATTT
1 AAAATCCAACAACAAATTA
*
2185162 AAAATCCAATCAAGAAA-TA
1 AAAATCCAA-CAACAAATTA
2185181 AAAAT
1 AAAAT
2185186 TAAAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.63, C:0.16, G:0.02, T:0.19
Consensus pattern (19 bp):
AAAATCCAACAACAAATTA
Found at i:2185488 original size:16 final size:17
Alignment explanation
Indices: 2185467--2185498 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2185457 ACATTCCTAT
2185467 TAAATT-ATTTTTTAAC
1 TAAATTAATTTTTTAAC
2185483 TAAATTAATTTTTTAA
1 TAAATTAATTTTTTAA
2185499 AATAGTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TAAATTAATTTTTTAAC
Found at i:2188308 original size:31 final size:31
Alignment explanation
Indices: 2188265--2188339 Score: 107
Period size: 31 Copynumber: 2.4 Consensus size: 31
2188255 GAATGGGGCC
*
2188265 TTTTTATTTAAGT-ATTTGAACTATTCAAAAG
1 TTTTTATTTAAGTCA-CTGAACTATTCAAAAG
* *
2188296 TTTTTATCTAAGTCACTGAACTATTCGAAAG
1 TTTTTATTTAAGTCACTGAACTATTCAAAAG
2188327 TTTTTATTTAAGT
1 TTTTTATTTAAGT
2188340 TATTGGGTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 38 0.97
32 1 0.03
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.48
Consensus pattern (31 bp):
TTTTTATTTAAGTCACTGAACTATTCAAAAG
Found at i:2189862 original size:13 final size:13
Alignment explanation
Indices: 2189844--2189868 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2189834 AATAACCCTA
2189844 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
2189857 TTTTTCTTTTTT
1 TTTTTCTTTTTT
2189869 TTTGCAGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:2191296 original size:12 final size:11
Alignment explanation
Indices: 2191277--2191307 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
2191267 TGTATAAAAT
2191277 TTATTTTATTA
1 TTATTTTATTA
2191288 TTAATTTTATTA
1 TT-ATTTTATTA
2191300 TTATTTTA
1 TTATTTTA
2191308 AAGGCATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:2191322 original size:30 final size:30
Alignment explanation
Indices: 2191288--2191347 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
2191278 TATTTTATTA
2191288 TTAATTTTATTATTATTTTAAAGGCATTTG
1 TTAATTTTATTATTATTTTAAAGGCATTTG
* * *
2191318 TTAATTTTGTTATTTTTTTAGAGGCATTTG
1 TTAATTTTATTATTATTTTAAAGGCATTTG
2191348 CTTGTTAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.25, C:0.03, G:0.13, T:0.58
Consensus pattern (30 bp):
TTAATTTTATTATTATTTTAAAGGCATTTG
Found at i:2193939 original size:16 final size:16
Alignment explanation
Indices: 2193918--2193953 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
2193908 TTTTAAACAC
*
2193918 ATTTAAAGAACAAATA
1 ATTTAAAGAAAAAATA
2193934 ATTTAAAGAAAAAATA
1 ATTTAAAGAAAAAATA
2193950 ATTT
1 ATTT
2193954 GCTTTCCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.31
Consensus pattern (16 bp):
ATTTAAAGAAAAAATA
Found at i:2194587 original size:9 final size:9
Alignment explanation
Indices: 2194575--2194605 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2194565 AAATATAAGA
*
2194575 AAAATCATT
1 AAAATTATT
2194584 AAAATTATT
1 AAAATTATT
2194593 AAAATTATT
1 AAAATTATT
2194602 AAAA
1 AAAA
2194606 ACGTATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (9 bp):
AAAATTATT
Found at i:2194944 original size:28 final size:29
Alignment explanation
Indices: 2194895--2194949 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 29
2194885 TCGTTTTTTT
* * *
2194895 ATTATTTAATTTTTTTATATAAATTTAAA
1 ATTATTTAATTATGTTAAATAAATTTAAA
*
2194924 ATTA-TTAATTATGTTAAATAATTTTA
1 ATTATTTAATTATGTTAAATAAATTTA
2194950 TGATAATACT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 18 0.82
29 4 0.18
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (29 bp):
ATTATTTAATTATGTTAAATAAATTTAAA
Found at i:2203719 original size:132 final size:131
Alignment explanation
Indices: 2203482--2203749 Score: 425
Period size: 132 Copynumber: 2.0 Consensus size: 131
2203472 TCAGATCATA
*
2203482 GTTTCTGCTTTTGATTTTATAACTATAAGTTAAATGAAGCTTTCGATGGTTTATTTTATCGTAGT
1 GTTTCTGCTTTTGATTTTATAACTATAAGTTAAATAAAGCTTTCGATGGTTTATTTTATCGTAGT
*
2203547 TTTATATTTCTATATTTTCATGATTCTACAAATGTTTATTAATGGAAGCCAACCAGTATAATTTA
66 ATTATATTTC-ATATTTTCATGATTCTACAAATGTTTATTAATGGAAGCCAACCAGTATAATTTA
2203612 CT
130 CT
*
2203614 GTTTCTGCTTTTGATTTTAATAACTATATGTTAAATAAAGCTTTC-AGTGGTTTATTTTATCGTG
1 GTTTCTGCTTTTGATTTT-ATAACTATAAGTTAAATAAAGCTTTCGA-TGGTTTATTTTATC--G
**
2203678 TAGTATTATATTTC-TA-TTTCATGATTCTACAAATGTTTATTAATGGAAGCTGACCAGTATAAT
62 TAGTATTATATTTCATATTTTCATGATTCTACAAATGTTTATTAATGGAAGCCAACCAGTATAAT
2203741 TTACT
127 TTACT
2203746 GTTT
1 GTTT
2203750 TAATACTCTT
Statistics
Matches: 127, Mismatches: 5, Indels: 8
0.91 0.04 0.06
Matches are distributed among these distances:
132 73 0.57
133 40 0.31
135 14 0.11
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.47
Consensus pattern (131 bp):
GTTTCTGCTTTTGATTTTATAACTATAAGTTAAATAAAGCTTTCGATGGTTTATTTTATCGTAGT
ATTATATTTCATATTTTCATGATTCTACAAATGTTTATTAATGGAAGCCAACCAGTATAATTTAC
T
Found at i:2206536 original size:39 final size:40
Alignment explanation
Indices: 2206452--2206536 Score: 154
Period size: 40 Copynumber: 2.1 Consensus size: 40
2206442 GAAGTTTACA
*
2206452 TTCTGGTATGCAGATTTTGCCTTTACACATTAGGACATAT
1 TTCTAGTATGCAGATTTTGCCTTTACACATTAGGACATAT
2206492 TTCTAGTATGCAGATTTTGCCTTTACACA-TAGGACATAT
1 TTCTAGTATGCAGATTTTGCCTTTACACATTAGGACATAT
2206531 TTCTAG
1 TTCTAG
2206537 CATATACCTA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
39 16 0.36
40 28 0.64
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (40 bp):
TTCTAGTATGCAGATTTTGCCTTTACACATTAGGACATAT
Found at i:2210218 original size:3 final size:3
Alignment explanation
Indices: 2210210--2210258 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
2210200 GATCATTCAC
2210210 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
2210258 T
1 T
2210259 TTGTTTATAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:2234081 original size:69 final size:70
Alignment explanation
Indices: 2233906--2234081 Score: 219
Period size: 71 Copynumber: 2.5 Consensus size: 70
2233896 CTTTCAAAGG
* ** *
2233906 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTAT
*
2233971 TTTTT
66 GTTTT
* ** * *
2233976 CAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTA
1 -AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTA
2234041 TGTTTT
65 TGTTTT
** *
2234047 -AAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
2234082 TTTAATTTTT
Statistics
Matches: 91, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
69 31 0.34
71 60 0.66
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (70 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTAT
GTTTT
Found at i:2234213 original size:75 final size:74
Alignment explanation
Indices: 2234099--2234437 Score: 450
Period size: 72 Copynumber: 4.5 Consensus size: 74
2234089 TTTGTTTTTC
*
2234099 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
2234164 GTTGTTAAAA
66 GTT-TTAAAA
**
2234174 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
*
2234239 GTTTT--CA
66 GTTTTAAAA
* * ** * * *
2234246 AAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
2234311 GTTTTCAAAAA
66 GTTTT--AAAA
* * * *
2234322 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGCATC-GGTTCACATGCTGAGGTATTTTCAATT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTAATTTCAATT
2234386 TCTGTTTTTAAAA
63 TCTG-TTTTAAAA
*
2234399 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
2234438 ATTACACACT
Statistics
Matches: 236, Mismatches: 19, Indels: 15
0.87 0.07 0.06
Matches are distributed among these distances:
72 66 0.28
74 2 0.01
75 66 0.28
76 34 0.14
77 39 0.17
78 25 0.11
79 4 0.02
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Consensus pattern (74 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
GTTTTAAAA
Found at i:2234884 original size:88 final size:88
Alignment explanation
Indices: 2234658--2234905 Score: 313
Period size: 88 Copynumber: 2.8 Consensus size: 88
2234648 GTGTTTAATT
*
2234658 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACGCCGAGGTATTTTCAATTAAGC-
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACA--CCGAGGTATTTTCAATT--TCT
*
2234722 CTTTT-AATTTATGTTTTTCAAAAAAAA
62 GTTTTCAATTTATGTTTTT-AAAAAAAA
* *
2234749 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACCGAGGTATTTTCCATTTCTGTTT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACCGAGGTATTTTCAATTTCTGTTT
* *
2234814 TCATTATTATGTTTTT-GAAAAAA
66 TCAAT-TTATGTTTTTAAAAAAAA
** * ** *
2234837 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACCGAGGTATTTTCAATTTCTGTTT
2234902 TCAA
66 TCAA
2234906 AATTCAACTC
Statistics
Matches: 139, Mismatches: 15, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
87 1 0.01
88 70 0.50
89 18 0.13
90 10 0.07
91 40 0.29
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (88 bp):
TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACCGAGGTATTTTCAATTTCTGTTT
TCAATTTATGTTTTTAAAAAAAA
Found at i:2234954 original size:72 final size:73
Alignment explanation
Indices: 2234832--2235162 Score: 542
Period size: 73 Copynumber: 4.5 Consensus size: 73
2234822 ATGTTTTTGA
* *
2234832 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTC
2234897 TG-TTTTC
66 TGCTTTTC
*
2234904 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTC
2234969 TGCTTTTC
66 TGCTTTTC
*
2234977 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTC
2235042 TGCTTTTC
66 TGCTTTTC
* *
2235050 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTC
*
2235115 TG-TTGTC
66 TGCTTTTC
*
2235122 AAAAAAATCAACTCATATTGCGA-AAAGTGAGTTGAGCCTCA
1 --AAAATTCAACTCATATTGCGAGAAA-TGAGTTGAGCCTCA
2235163 GTTCACATGT
Statistics
Matches: 247, Mismatches: 8, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
72 68 0.28
73 145 0.59
74 34 0.14
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (73 bp):
AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTC
TGCTTTTC
Found at i:2240939 original size:35 final size:35
Alignment explanation
Indices: 2240893--2240962 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
2240883 TAGCAGCTGC
*
2240893 TCTTTTCCTCTCCAAATGTTCAAACAAGCTTCCAT
1 TCTTTCCCTCTCCAAATGTTCAAACAAGCTTCCAT
2240928 TCTTTCCCTCTCCAAATGTTCAAACAAGCTTCCAT
1 TCTTTCCCTCTCCAAATGTTCAAACAAGCTTCCAT
2240963 CATAAACAGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.26, C:0.33, G:0.06, T:0.36
Consensus pattern (35 bp):
TCTTTCCCTCTCCAAATGTTCAAACAAGCTTCCAT
Found at i:2245880 original size:28 final size:29
Alignment explanation
Indices: 2245815--2245882 Score: 70
Period size: 27 Copynumber: 2.4 Consensus size: 29
2245805 AATAAACACC
*
2245815 AAAAAAT-TATTTTAAAAAATAAAATATT
1 AAAAAATATATTTTAAAAAATAAAAAATT
*** *
2245843 TTTAAA-ATATTTT-AAAATTAAAAAATT
1 AAAAAATATATTTTAAAAAATAAAAAATT
2245870 AAAAAATATATTT
1 AAAAAATATATTT
2245883 ATTATATTTA
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
27 15 0.50
28 15 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (29 bp):
AAAAAATATATTTTAAAAAATAAAAAATT
Found at i:2245985 original size:54 final size:53
Alignment explanation
Indices: 2245903--2246011 Score: 191
Period size: 54 Copynumber: 2.0 Consensus size: 53
2245893 GGCCGGGTCG
*
2245903 GGCCAAAACCAGGCCAATAATGTGGTGTCCGAGGCCCGGGCCGGTCTTCTAAAC
1 GGCCAAAACCAGGCCAATAATGTGGTGTCCGAGGCCC-GGCCCGTCTTCTAAAC
*
2245957 GGCCAAAACCAGGCCAATAATGTGGTGTCCGAGGCCCGGCCCGTTTTCTAAAC
1 GGCCAAAACCAGGCCAATAATGTGGTGTCCGAGGCCCGGCCCGTCTTCTAAAC
2246010 GG
1 GG
2246012 GCCTCATTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
53 16 0.30
54 37 0.70
ACGTcount: A:0.24, C:0.29, G:0.29, T:0.17
Consensus pattern (53 bp):
GGCCAAAACCAGGCCAATAATGTGGTGTCCGAGGCCCGGCCCGTCTTCTAAAC
Found at i:2246823 original size:13 final size:12
Alignment explanation
Indices: 2246787--2246823 Score: 56
Period size: 13 Copynumber: 2.9 Consensus size: 12
2246777 TAATTATGTC
2246787 AAAATTTAAATA
1 AAAATTTAAATA
2246799 AAAATTTAAAATA
1 AAAATTT-AAATA
2246812 AAAATTATAAAT
1 AAAATT-TAAAT
2246824 TATTAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.30
13 15 0.65
14 1 0.04
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATTTAAATA
Found at i:2250717 original size:15 final size:15
Alignment explanation
Indices: 2250688--2250731 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
2250678 TGTCCAAAAA
*
2250688 TATTTAATTTTTATT
1 TATTTAATTTATATT
*
2250703 TATTTAATTGATATT
1 TATTTAATTTATATT
*
2250718 T-TTGAATTTATATT
1 TATTTAATTTATATT
2250732 CCGTCTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (15 bp):
TATTTAATTTATATT
Found at i:2257723 original size:46 final size:45
Alignment explanation
Indices: 2257656--2257853 Score: 229
Period size: 46 Copynumber: 4.6 Consensus size: 45
2257646 TTTGAGTACT
*
2257656 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
2257702 TCTGATCAAGTGAAAAAGTGATAA---GT-GC-TA--T--ACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* * *
2257738 TATGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
* *
2257784 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
2257829 TCTGATC-AG-GGACAAGTGATAAGTG
1 TCTGATCAAGTGAAAAAGTGATAAGTG
2257854 ATCATATGTA
Statistics
Matches: 131, Mismatches: 11, Indels: 23
0.79 0.07 0.14
Matches are distributed among these distances:
36 27 0.21
38 1 0.01
39 1 0.01
40 3 0.02
41 1 0.01
42 4 0.03
43 15 0.11
44 3 0.02
45 20 0.15
46 56 0.43
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:2257738 original size:36 final size:36
Alignment explanation
Indices: 2257692--2257764 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
2257682 GGTAGCTTTA
*
2257692 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATATGATCAAGTGAAAAAGTGATAAGT
* *
2257728 GCTATACTTATATGATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATATGATCAAGTGAAAAAGTGATAAGT
2257764 G
1 G
2257765 TTAGCCTTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (36 bp):
GCTACACTTATATGATCAAGTGAAAAAGTGATAAGT
Found at i:2257752 original size:82 final size:82
Alignment explanation
Indices: 2257658--2257810 Score: 279
Period size: 82 Copynumber: 1.9 Consensus size: 82
2257648 TGAGTACTTC
*
2257658 TGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGA
1 TGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGTGA
2257723 TAAGTGCTATACTTATA
66 TAAGTGCTATACTTATA
* *
2257740 TGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTATCTGATCAAGTGAGAAAGTGA
1 TGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGTGA
2257805 TAAGTG
66 TAAGTG
2257811 GTAGCCTAGC
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 68 1.00
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29
Consensus pattern (82 bp):
TGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGTGA
TAAGTGCTATACTTATA
Found at i:2259658 original size:29 final size:29
Alignment explanation
Indices: 2259624--2259718 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 29
2259614 ACAAAATTGA
*
2259624 ATAGTTGAATGACCATGTTATAATTTTTC
1 ATAGTTGAATGACCATATTATAATTTTTC
* ** * ** *
2259653 ATAGTTGAGTGA-CATAAAAGAAAGTTACTA
1 ATAGTTGAATGACCATATTA-TAA-TTTTTC
* *
2259683 ATAGTCGAATGACCATTTTATAATTTTTC
1 ATAGTTGAATGACCATATTATAATTTTTC
2259712 ATAGTTG
1 ATAGTTG
2259719 GGATGACAAA
Statistics
Matches: 45, Mismatches: 18, Indels: 6
0.65 0.26 0.09
Matches are distributed among these distances:
28 4 0.09
29 22 0.49
30 15 0.33
31 4 0.09
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (29 bp):
ATAGTTGAATGACCATATTATAATTTTTC
Found at i:2264014 original size:16 final size:16
Alignment explanation
Indices: 2263993--2264023 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2263983 GTCTAAATTT
*
2263993 TCACCAACATACAATG
1 TCACCAACACACAATG
2264009 TCACCAACACACAAT
1 TCACCAACACACAAT
2264024 TGTTGCTGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.35, G:0.03, T:0.16
Consensus pattern (16 bp):
TCACCAACACACAATG
Found at i:2265991 original size:12 final size:12
Alignment explanation
Indices: 2265974--2266002 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
2265964 ATAAGATATA
2265974 TTATTATCGTAT
1 TTATTATCGTAT
2265986 TTATTATCGTAT
1 TTATTATCGTAT
2265998 TTATT
1 TTATT
2266003 TTTAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (12 bp):
TTATTATCGTAT
Found at i:2267878 original size:24 final size:24
Alignment explanation
Indices: 2267851--2267912 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 24
2267841 ATTCCTTTGT
2267851 TTTTTTTTCTCTTGA-TTTTAATGA
1 TTTTTTTTCT-TTGATTTTTAATGA
** *
2267875 TTTTTTAGCTTTGATTTTTGATGA
1 TTTTTTTTCTTTGATTTTTAATGA
*
2267899 TTTCTTTTGCTTTG
1 TTT-TTTTTCTTTG
2267913 GGGTTTAGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 4 0.12
24 19 0.59
25 9 0.28
ACGTcount: A:0.13, C:0.08, G:0.13, T:0.66
Consensus pattern (24 bp):
TTTTTTTTCTTTGATTTTTAATGA
Found at i:2279790 original size:37 final size:37
Alignment explanation
Indices: 2279739--2279870 Score: 151
Period size: 37 Copynumber: 3.5 Consensus size: 37
2279729 ATGTATGTAA
*
2279739 TTTTCAAAAATTTAAAATTTACTACTTATATTTCTAT
1 TTTTTAAAAATTTAAAATTTACTACTTATATTTCTAT
* * * * *
2279776 TTTTTAAAATTTTAAAA-TTA-AAATCATATATCTAT
1 TTTTTAAAAATTTAAAATTTACTACTTATATTTCTAT
2279811 GTAATTTTCAAAAATTTAAAATTTACTACTTATATTTCTAT
1 -T--TTTT-AAAAATTTAAAATTTACTACTTATATTTCTAT
*
2279852 TTTTTAAAATTTTAAAATT
1 TTTTTAAAAATTTAAAATT
2279871 AAAATTCAAT
Statistics
Matches: 77, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
35 11 0.14
36 4 0.05
37 28 0.36
38 8 0.10
39 11 0.14
40 4 0.05
41 11 0.14
ACGTcount: A:0.41, C:0.08, G:0.01, T:0.51
Consensus pattern (37 bp):
TTTTTAAAAATTTAAAATTTACTACTTATATTTCTAT
Found at i:2279849 original size:76 final size:76
Alignment explanation
Indices: 2279723--2279875 Score: 297
Period size: 76 Copynumber: 2.0 Consensus size: 76
2279713 TTGAAATTTG
*
2279723 TCATATATGTATGTAATTTTCAAAAATTTAAAATTTACTACTTATATTTCTATTTTTTAAAATTT
1 TCATATATCTATGTAATTTTCAAAAATTTAAAATTTACTACTTATATTTCTATTTTTTAAAATTT
2279788 TAAAATTAAAA
66 TAAAATTAAAA
2279799 TCATATATCTATGTAATTTTCAAAAATTTAAAATTTACTACTTATATTTCTATTTTTTAAAATTT
1 TCATATATCTATGTAATTTTCAAAAATTTAAAATTTACTACTTATATTTCTATTTTTTAAAATTT
2279864 TAAAATTAAAA
66 TAAAATTAAAA
2279875 T
1 T
2279876 TCAATTATTA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (76 bp):
TCATATATCTATGTAATTTTCAAAAATTTAAAATTTACTACTTATATTTCTATTTTTTAAAATTT
TAAAATTAAAA
Found at i:2280353 original size:29 final size:29
Alignment explanation
Indices: 2280321--2280376 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
2280311 AATGATTTTT
* *
2280321 TTTAATAATACATGTACTAAATTGATCCA
1 TTTAATAATACAAGGACTAAATTGATCCA
*
2280350 TTTAATAATACAAGGACTAATTTGATC
1 TTTAATAATACAAGGACTAAATTGATC
2280377 AGGTCCTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (29 bp):
TTTAATAATACAAGGACTAAATTGATCCA
Found at i:2282348 original size:171 final size:170
Alignment explanation
Indices: 2282002--2282396 Score: 458
Period size: 171 Copynumber: 2.3 Consensus size: 170
2281992 TTTCTGCTGG
* * *
2282002 TACTTTTTACAAACACATTGACTACATTCCATTTTTGTATCTAATTCAAAATAACAACCTAAACA
1 TACTTTTTACAAACACATTGACTACATTGCATATTTGCA-CTAATTCAAAATAACAACCTAAACA
* * *
2282067 AAAGACTGACGGGTTCTTCACATACATCCAAGAGATAAAATTCATGAAACGGGCATGACAAAAAT
65 AAAGACTGAAGGGTTCTTAACATACATCCAAGAGATAAAATTCATAAAACGGGCATGACAAAAAT
* * *
2282132 TGAGATTTTACACGTAAAATAATAGAACCACTGTCTGTTAA
130 TGACATTTTACACGTAAAATAATAGAACCACTGTCCGTCAA
* * * *
2282173 TACTTTTAACAAACACATTGACTACATTGCATATCTGCACATAATTCAAAATAACGAGCTAAACA
1 TACTTTTTACAAACACATTGACTACATTGCATATTTGCAC-TAATTCAAAATAACAACCTAAACA
* * * * * *
2282238 AATA-ACT-AAGGGCTTCTTAACATACATTCAAGAGATCAAATTCATAAAATGGGTATTAGAGAA
65 AA-AGACTGAAGGG-TTCTTAACATACATCCAAGAGATAAAATTCATAAAACGGGCATGACA-AA
** * *
2282301 AA-TGACATTTTATGCGT-AAATGCATAGCAA-CACTTTCCGTCAA
127 AATTGACATTTTACACGTAAAAT-AATAG-AACCACTGTCCGTCAA
2282344 TACTTTTTTACAAACACATTGACTACATTGCATATTTGCACCTAATTCTAAAA
1 TAC-TTTTTACAAACACATTGACTACATTGCATATTTGCA-CTAATTC-AAAA
2282397 CAAATAACTA
Statistics
Matches: 190, Mismatches: 25, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
170 9 0.05
171 129 0.68
172 47 0.25
173 5 0.03
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.30
Consensus pattern (170 bp):
TACTTTTTACAAACACATTGACTACATTGCATATTTGCACTAATTCAAAATAACAACCTAAACAA
AAGACTGAAGGGTTCTTAACATACATCCAAGAGATAAAATTCATAAAACGGGCATGACAAAAATT
GACATTTTACACGTAAAATAATAGAACCACTGTCCGTCAA
Found at i:2288487 original size:2 final size:2
Alignment explanation
Indices: 2288480--2288508 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2288470 CTTTAACATT
2288480 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2288509 AATCAATCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2292483 original size:29 final size:30
Alignment explanation
Indices: 2292417--2292483 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 30
2292407 TTTATGTGTT
* *
2292417 ATTTA-ATTTAAATTTTTTGTATTTTTATA
1 ATTTATATTTTAATTTTTTGTAGTTTTATA
*
2292446 A-TAAT-TTTTAATTTTTTGTAGTTTTA-A
1 ATTTATATTTTAATTTTTTGTAGTTTTATA
2292473 ATTTATATTTT
1 ATTTATATTTT
2292484 TTTTATATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
27 2 0.06
28 24 0.77
29 5 0.16
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (30 bp):
ATTTATATTTTAATTTTTTGTAGTTTTATA
Found at i:2294320 original size:31 final size:31
Alignment explanation
Indices: 2294285--2294356 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
2294275 TTTGATGAAT
2294285 TTTGACTTAAGCAACTAATTATCTGATTTAA
1 TTTGACTTAAGCAACTAATTATCTGATTTAA
* *
2294316 TTTGACTTAAGTAACTAATTATTTGATTTAA
1 TTTGACTTAAGCAACTAATTATCTGATTTAA
2294347 TTTGACTTAA
1 TTTGACTTAA
2294357 TTATTCACTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.46
Consensus pattern (31 bp):
TTTGACTTAAGCAACTAATTATCTGATTTAA
Found at i:2302484 original size:33 final size:33
Alignment explanation
Indices: 2302445--2302512 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
2302435 TCAAAGAATA
*
2302445 ATCAATCTTTTATATGGTTGATGGTATAATCAG
1 ATCAATCTTTTATATGGTTGATGGTATAATAAG
2302478 ATCAATCTTTTATATGGTTGATGGTATAATAAG
1 ATCAATCTTTTATATGGTTGATGGTATAATAAG
2302511 AT
1 AT
2302513 TGTGACACAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.43
Consensus pattern (33 bp):
ATCAATCTTTTATATGGTTGATGGTATAATAAG
Found at i:2303944 original size:22 final size:22
Alignment explanation
Indices: 2303918--2304019 Score: 75
Period size: 22 Copynumber: 4.5 Consensus size: 22
2303908 CAGATTAATT
2303918 GTTTAATTTAAAATATTTTAAA
1 GTTTAATTTAAAATATTTTAAA
* * *
2303940 GTTTAATATAAAATTTGGTATTTAA
1 GTTTAATTTAAAATAT--T-TTAAA
*
2303965 --TTAATATAATAATGAATTTTAAAA
1 GTTTAATTTAA-AAT--ATTTT-AAA
*
2303989 ATTTAA-TTAAAATATTTTAAA
1 GTTTAATTTAAAATATTTTAAA
2304010 GTTTAATTTA
1 GTTTAATTTA
2304020 GACCAAGGGC
Statistics
Matches: 63, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
21 8 0.13
22 22 0.35
23 11 0.17
24 10 0.16
25 7 0.11
26 5 0.08
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (22 bp):
GTTTAATTTAAAATATTTTAAA
Found at i:2307059 original size:30 final size:30
Alignment explanation
Indices: 2307025--2307088 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
2307015 TTTGGACTTG
** *
2307025 TTGATTCTTTTTAATAGTACAGGGACTAAA
1 TTGATTCCATTTAATAATACAGGGACTAAA
* *
2307055 TTGA-TCCATTTAATAATAGAGGGACTAAT
1 TTGATTCCATTTAATAATACAGGGACTAAA
2307084 TTGAT
1 TTGAT
2307089 CCAGTCACTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.39
Consensus pattern (30 bp):
TTGATTCCATTTAATAATACAGGGACTAAA
Found at i:2307066 original size:29 final size:29
Alignment explanation
Indices: 2307034--2307109 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
2307024 GTTGATTCTT
*
2307034 TTTAATAGTACAGGGACTAAATTGATCCA
1 TTTAATAATACAGGGACTAAATTGATCCA
* *
2307063 TTTAATAATAGAGGGACTAATTTGATCCA
1 TTTAATAATACAGGGACTAAATTGATCCA
* *
2307092 GTCACTATAATACAGGGA
1 TTTA--ATAATACAGGGA
2307110 TTTCCCAGAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 28 0.72
31 11 0.28
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.30
Consensus pattern (29 bp):
TTTAATAATACAGGGACTAAATTGATCCA
Found at i:2310854 original size:31 final size:28
Alignment explanation
Indices: 2310810--2310869 Score: 66
Period size: 28 Copynumber: 2.0 Consensus size: 28
2310800 TTACAAAATT
2310810 ATCACTAAACTATTCAAAAGTTTTTATTTAA
1 ATCACTAAACTATT---AAGTTTTTATTTAA
* * *
2310841 ATCACTGAGCTATTAAGTTTTTTTTTAA
1 ATCACTAAACTATTAAGTTTTTATTTAA
2310869 A
1 A
2310870 AAGGAAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 14 0.54
31 12 0.46
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.45
Consensus pattern (28 bp):
ATCACTAAACTATTAAGTTTTTATTTAA
Found at i:2319707 original size:21 final size:21
Alignment explanation
Indices: 2319665--2319714 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
2319655 TAAATAAGTG
*
2319665 TAATAATAGCACCAATAATAA
1 TAATAATAGCAACAATAATAA
* * *
2319686 TAATAATAGTAACAGTACTAA
1 TAATAATAGCAACAATAATAA
*
2319707 TAACAATA
1 TAATAATA
2319715 ATAATGATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.26
Consensus pattern (21 bp):
TAATAATAGCAACAATAATAA
Found at i:2321630 original size:30 final size:29
Alignment explanation
Indices: 2321596--2321652 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
2321586 ACCAATTATA
*
2321596 ATTAAATT-CTAAAATTTGAAAAATAAAAAG
1 ATTAAATTCCTAAAA-GT-AAAAATAAAAAG
2321626 ATTAAATTCCTAAAAGTAAAAATAAAA
1 ATTAAATTCCTAAAAGTAAAAATAAAA
2321653 TAACTAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 10 0.40
30 9 0.36
31 6 0.24
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.28
Consensus pattern (29 bp):
ATTAAATTCCTAAAAGTAAAAATAAAAAG
Found at i:2321762 original size:29 final size:28
Alignment explanation
Indices: 2321730--2321795 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 28
2321720 TCAATTATGT
2321730 TTAAATTTTAAAAAATAAAAATAAAAGGA
1 TTAAATTTT-AAAAATAAAAATAAAAGGA
* *
2321759 TTAAATTCCTAAAAATAAAAATAAAATGA
1 TTAAATT-TTAAAAATAAAAATAAAAGGA
*
2321788 CTAAATTT
1 TTAAATTT
2321796 CAAATGTGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 31 0.97
30 1 0.03
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.30
Consensus pattern (28 bp):
TTAAATTTTAAAAATAAAAATAAAAGGA
Found at i:2321805 original size:132 final size:132
Alignment explanation
Indices: 2321449--2321809 Score: 501
Period size: 133 Copynumber: 2.7 Consensus size: 132
2321439 TAGTAGAAAA
* * *
2321449 AGTTACCAATTATATTTAAAATTTGAAATTTGAAAAATATAAAGATTAAATTCCTAAAAATCAAA
1 AGTTACCAATTATATTTAAATTTTAAAATTTGAAAAATA-AAAGATTAAATTCCTAAAAATAAAA
* * * * * *
2321514 ATAGAATGACTAAATTTCAAACGTGTGAAGATGTCGAACCAATAAATTTAGCAGAGAAATTTAGC
65 ATAAAATGACTAAATTTCAAATGTGTGAAGATGTCAAACAAACAAATTTAGCAGAAAAATTTAGC
*
2321579 TGG
130 TAG
* * *
2321582 AGTTACCAATTATAATTAAATTCTAAAATTTGAAAAATAAAAAGATTAAATTCCTAAAAGTAAAA
1 AGTTACCAATTATATTTAAATTTTAAAATTTGAAAAAT-AAAAGATTAAATTCCTAAAAATAAAA
* *
2321647 ATAAAATAACTAAATTTCAAATGTGTGAATATGTCAAACAAACAAATTTAGCAGAAAAATTTAG-
65 ATAAAATGACTAAATTTCAAATGTGTGAAGATGTCAAACAAACAAATTTAGCAGAAAAATTTAGC
2321711 TCAG
130 T-AG
* * **
2321715 AGTTATCAATTATGTTTAAATTTTAAAAAAT-AAAAATAAAAGGATTAAATTCCTAAAAATAAAA
1 AGTTACCAATTATATTTAAATTTTAAAATTTGAAAAATAAAA-GATTAAATTCCTAAAAATAAAA
2321779 ATAAAATGACTAAATTTCAAATGTGTGAAGA
65 ATAAAATGACTAAATTTCAAATGTGTGAAGA
2321810 GTAATAGATT
Statistics
Matches: 201, Mismatches: 24, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
131 4 0.02
132 57 0.28
133 139 0.69
134 1 0.00
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (132 bp):
AGTTACCAATTATATTTAAATTTTAAAATTTGAAAAATAAAAGATTAAATTCCTAAAAATAAAAA
TAAAATGACTAAATTTCAAATGTGTGAAGATGTCAAACAAACAAATTTAGCAGAAAAATTTAGCT
AG
Found at i:2322032 original size:90 final size:88
Alignment explanation
Indices: 2321888--2322249 Score: 352
Period size: 90 Copynumber: 4.0 Consensus size: 88
2321878 CATAAAAAGT
* ** * * *
2321888 CCTCAATTTTTTCAAAAAAAAATTAATTAAG-TCTAGATTTTTTTTTACACTTAATTAGATACTT
1 CCTCAAATTTTTC--AAAAAAAGCAATTAAGCTCT-GCTTTTTTTTTACACTCAATTAGGTACTT
** * *
2321952 AAATTTTCAAAATGTATCAAGAAGGC
63 AAATTTTCAAAATACATCAAAAAGAC
* * * * *
2321978 CCTCAAGATTTTTCAAAAAAAGTAATTAAGCTCATGCTTTTTTTTTCCATTTAATTGGGTACTTA
1 CCTCAA-ATTTTTCAAAAAAAGCAATTAAGCTC-TGCTTTTTTTTTACACTCAATTAGGTACTTA
* *
2322043 AACTTTCAAAATATATCAAAAAGAC
64 AATTTTCAAAATACATCAAAAAGAC
* * * *
2322068 CCTCAAAATTTTTCAAAAAAAGCAATTAAGCCCCTACTTTTTTTTTACATTCAATTGGGTACTTG
1 CCTC-AAATTTTTCAAAAAAAGCAATTAAG-CTCTGCTTTTTTTTTACACTCAATTAGGTACTT-
**
2322133 AGCTTTT-AAAATACATCAAAAAGAC
63 AAATTTTCAAAATACATCAAAAAGAC
* * *
2322158 CCTCAAATTTTTTCAAAAAAAGCAATTAAGCCTCT-CATTTTTTTAACACTCAATTAGGTACTTC
1 CCTCAAA-TTTTTCAAAAAAAGCAATTAAG-CTCTGCTTTTTTTTTACACTCAATTAGGTACTTA
* * *
2322222 AATTGTCAAAATGCATCAAAAAAAC
64 AATTTTCAAAATACATCAAAAAGAC
2322247 CCT
1 CCT
2322250 TTGATCGATA
Statistics
Matches: 233, Mismatches: 31, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
88 3 0.01
89 61 0.26
90 154 0.66
91 15 0.06
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (88 bp):
CCTCAAATTTTTCAAAAAAAGCAATTAAGCTCTGCTTTTTTTTTACACTCAATTAGGTACTTAAA
TTTTCAAAATACATCAAAAAGAC
Found at i:2336000 original size:29 final size:28
Alignment explanation
Indices: 2335917--2336000 Score: 64
Period size: 29 Copynumber: 2.9 Consensus size: 28
2335907 ATTAACCGTT
2335917 AGACTCAAATTTTGAAATTTGA-AAAGTAAA
1 AGACT-AAATTTT-AAATTT-ACAAAGTAAA
* ** *
2335947 ATGACTAAATTTTTAA-GAACAAAAGTATAG
1 A-GACTAAATTTTAAATTTAC-AAAGTA-AA
2335977 AGACTAAATTTTAAATTTACAAAG
1 AGACTAAATTTTAAATTTACAAAG
2336001 AATGCAAAGA
Statistics
Matches: 42, Mismatches: 7, Indels: 11
0.70 0.12 0.18
Matches are distributed among these distances:
27 1 0.02
29 25 0.60
30 12 0.29
31 4 0.10
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (28 bp):
AGACTAAATTTTAAATTTACAAAGTAAA
Found at i:2355150 original size:17 final size:17
Alignment explanation
Indices: 2355130--2355167 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2355120 AAAAGAATTC
2355130 GAAAAAAAAATCGAAAA
1 GAAAAAAAAATCGAAAA
*
2355147 GAAAAAAAAATTGAAAA
1 GAAAAAAAAATCGAAAA
2355164 -AAAA
1 GAAAA
2355168 TTGTATACGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.79, C:0.03, G:0.11, T:0.08
Consensus pattern (17 bp):
GAAAAAAAAATCGAAAA
Found at i:2356521 original size:22 final size:22
Alignment explanation
Indices: 2356490--2356534 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2356480 TAAAGAGAAA
* *
2356490 AGGTACGTTCTGTTCTTTCCCT
1 AGGTAAGTTCTGATCTTTCCCT
2356512 AGGTAAGTTCTGATCTTTCCCT
1 AGGTAAGTTCTGATCTTTCCCT
2356534 A
1 A
2356535 ATACTTCTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.42
Consensus pattern (22 bp):
AGGTAAGTTCTGATCTTTCCCT
Found at i:2363214 original size:66 final size:65
Alignment explanation
Indices: 2363108--2363239 Score: 228
Period size: 66 Copynumber: 2.0 Consensus size: 65
2363098 TTCTTTTTCC
* *
2363108 TGCTGAATTTAGTGGTTTACTTGGTAAACAGTTTGAATTTTGATTGATTGATGATGAAGCTACAG
1 TGCTGAATTTAGTGGTTTACTTGGTAAACAGTTTGAATTTTGATTAATTGATGATGAAACTACAG
*
2363173 NTGCTGAATTTAGTGGTTTGCTTGGTAAACAGTTTGAATTTTGATTAATTGATGATGAAACTACA
1 -TGCTGAATTTAGTGGTTTACTTGGTAAACAGTTTGAATTTTGATTAATTGATGATGAAACTACA
2363238 G
65 G
2363239 T
1 T
2363240 TTCAGTCTTC
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
65 1 0.02
66 62 0.98
ACGTcount: A:0.28, C:0.08, G:0.23, T:0.40
Consensus pattern (65 bp):
TGCTGAATTTAGTGGTTTACTTGGTAAACAGTTTGAATTTTGATTAATTGATGATGAAACTACAG
Found at i:2370750 original size:3 final size:3
Alignment explanation
Indices: 2370744--2370771 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2370734 AGAAAAAAAT
2370744 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
2370772 GTGATTGTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2382587 original size:21 final size:20
Alignment explanation
Indices: 2382543--2382587 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
2382533 CATTTAATTT
* *
2382543 TTTATTTTTTATTAAATGAA
1 TTTATTTTTTATCAAATCAA
*
2382563 TTTATATTTTTATCAAATCAC
1 TTTAT-TTTTTATCAAATCAA
2382584 TTTA
1 TTTA
2382588 AAATAAATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (20 bp):
TTTATTTTTTATCAAATCAA
Found at i:2397013 original size:19 final size:18
Alignment explanation
Indices: 2396972--2397016 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
2396962 TATATATTGA
2396972 ATTTT-AATTCTTTTAAT
1 ATTTTAAATTCTTTTAAT
*
2396989 -TTTTAAATTTTTTTATAT
1 ATTTTAAATTCTTTTA-AT
2397007 ATTTTAAATT
1 ATTTTAAATT
2397017 ATTTGTTGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 4 0.17
17 9 0.38
18 2 0.08
19 9 0.38
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTAAATTCTTTTAAT
Found at i:2403298 original size:24 final size:25
Alignment explanation
Indices: 2403253--2403303 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
2403243 ATTAAGTCCG
* **
2403253 AATTTTCCTATGTAAAGTTTGTTTT
1 AATTTTCCTATCTAAAAATTGTTTT
2403278 AATTTTCCTA-CTAAAAATTGTTTT
1 AATTTTCCTATCTAAAAATTGTTTT
2403302 AA
1 AA
2403304 ATATTAATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (25 bp):
AATTTTCCTATCTAAAAATTGTTTT
Found at i:2408830 original size:130 final size:128
Alignment explanation
Indices: 2408591--2409182 Score: 535
Period size: 130 Copynumber: 4.6 Consensus size: 128
2408581 TTAAAAGAAT
* * * * * **
2408591 TTAAATTTGATTGCATAAGTTTGAGGCAACCTGAATCAAGTGATTAATGAATTTACTAAATGAGT
1 TTAAATTTGATTGCGTAAGTTTGAGACAACCTGAATCGAGTGATTGATAAATTTACTAAAAAAGT
* ** ** * * * *
2408656 GATTACACGTTCATACCAAATTCTAAAATAATTTGAATACTTTTTCAATTAAAGTAACCTAAAG
66 GACTACGTGTTCATATTAAATCCTAAGAGAATTTGAATATTTTTTCAATTAAAGTAA-CTAAAG
* ** *
2408720 TTATAATTTGATTGCGTAAGTTTGAGGCAACCCCAAACGAGTGATTGATAAATTTACTAAAAAAG
1 TTA-AATTTGATTGCGTAAGTTTGAGACAACCTGAATCGAGTGATTGATAAATTTACTAAAAAAG
* * * * **
2408785 TGACTACGTGTTGATATTAAGTCTTAAGAGAATTTGAATATTTTTTCAATTAGAGTAACTTGAG
65 TGACTACGTGTTCATATTAAATCCTAAGAGAATTTGAATATTTTTTCAATTAAAGTAACTAAAG
*
2408849 ATTAAAATTTGGTTGCGTAAGTTTGAGACAACCTGAATCGAGTGATGATAGATAAATTTACTAAA
1 -TT-AAATTTGATTGCGTAAGTTTGAGACAACCTGAATCGAGTGAT--T-GATAAATTTACTAAA
* * * * * * *
2408914 AGACTGACTATGTGTTCATATTAAATCCTAAGAGGATTTAAATACTTTTTT-AGTTAGAGTAATC
61 AAAGTGACTACGTGTTCATATTAAATCCTAAGAGAATTTGAATA-TTTTTTCAATTAAAGTAA-C
**
2408978 TATCG
124 TAAAG
* * * * * *
2408983 TTAAATTTTGATTGCGTAAATTTGAGATAACCTGAATTGAGGGATCGATAAATTTATTAAAAAA-
1 TTAAA-TTTGATTGCGTAAGTTTGAGACAACCTGAATCGAGTGATTGATAAATTTACTAAAAAAG
* * * *
2409047 AGACTACGTGTTCATATTAAATCCTAAGAGAATTTGAATATTTTTTCAATTGAAGTGACATAAGG
65 TGACTACGTGTTCATATTAAATCCTAAGAGAATTTGAATATTTTTTCAATTAAAGTAAC-TAAAG
* * * ** * * * * *
2409112 TTAAAACTAGGTTATGTAAATTTGAGGCAACCTGAATCAAGGGATTGATAAGA-TTACT-AAAAG
1 TT-AAATTTGATTGCGTAAGTTTGAGACAACCTGAATCGAGTGATTGATAA-ATTTACTAAAAAA
2409175 GTGACTAC
64 GTGACTAC
2409183 ATTTATATCA
Statistics
Matches: 377, Mismatches: 72, Indels: 28
0.79 0.15 0.06
Matches are distributed among these distances:
128 11 0.03
129 100 0.27
130 155 0.41
131 1 0.00
132 4 0.01
133 97 0.26
134 9 0.02
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (128 bp):
TTAAATTTGATTGCGTAAGTTTGAGACAACCTGAATCGAGTGATTGATAAATTTACTAAAAAAGT
GACTACGTGTTCATATTAAATCCTAAGAGAATTTGAATATTTTTTCAATTAAAGTAACTAAAG
Found at i:2410608 original size:9 final size:9
Alignment explanation
Indices: 2410594--2410629 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
2410584 TGATTCGGTG
2410594 CAGCAGCAA
1 CAGCAGCAA
2410603 CAGCAGCAA
1 CAGCAGCAA
* *
2410612 CAACAGCAG
1 CAGCAGCAA
2410621 CAGCAGCAA
1 CAGCAGCAA
2410630 ATAGCGTCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.44, C:0.33, G:0.22, T:0.00
Consensus pattern (9 bp):
CAGCAGCAA
Found at i:2410610 original size:12 final size:12
Alignment explanation
Indices: 2410593--2410625 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
2410583 ATGATTCGGT
2410593 GCAGCAGCAACA
1 GCAGCAGCAACA
*
2410605 GCAGCAACAACA
1 GCAGCAGCAACA
2410617 GCAGCAGCA
1 GCAGCAGCA
2410626 GCAAATAGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.42, C:0.33, G:0.24, T:0.00
Consensus pattern (12 bp):
GCAGCAGCAACA
Found at i:2416636 original size:34 final size:34
Alignment explanation
Indices: 2416595--2416661 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
2416585 TAATAATCAC
* *
2416595 TTATCATACTGCTGTTTGTAATGATGTTATTTCG
1 TTATCATACTGCTATATGTAATGATGTTATTTCG
*
2416629 TTATCATACTGCTATATGTAATGGTGTTATTTC
1 TTATCATACTGCTATATGTAATGATGTTATTTC
2416662 ATTGGCTGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.49
Consensus pattern (34 bp):
TTATCATACTGCTATATGTAATGATGTTATTTCG
Found at i:2420021 original size:3 final size:3
Alignment explanation
Indices: 2420013--2420048 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2420003 TTTTAATTCT
2420013 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA
1 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA
2420049 TTATTATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CTA
Found at i:2421732 original size:34 final size:33
Alignment explanation
Indices: 2421689--2421755 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 33
2421679 GACACTGCTA
2421689 CATGAAAGATGTTTATCTTTTTATTGCTGAACC
1 CATGAAAGATGTTTATCTTTTTATTGCTGAACC
2421722 NCATGAAAGATGTTTATCTTTTTATTGCTGAACC
1 -CATGAAAGATGTTTATCTTTTTATTGCTGAACC
2421756 GGGCAATACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (33 bp):
CATGAAAGATGTTTATCTTTTTATTGCTGAACC
Found at i:2448495 original size:22 final size:22
Alignment explanation
Indices: 2448432--2448511 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 22
2448422 AAAGAACACT
* **
2448432 ATAACAACAAAACAACAGCAGT
1 ATAACAACAAAACAGCAGCAAA
* * ** *
2448454 ATAATAACAATATGGTAGCAAA
1 ATAACAACAAAACAGCAGCAAA
2448476 ATAACAACAAAACAGCAGCAAA
1 ATAACAACAAAACAGCAGCAAA
* *
2448498 ACAACAACGAAACA
1 ATAACAACAAAACA
2448512 ACATGAAAAC
Statistics
Matches: 43, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.60, C:0.20, G:0.10, T:0.10
Consensus pattern (22 bp):
ATAACAACAAAACAGCAGCAAA
Found at i:2448520 original size:22 final size:22
Alignment explanation
Indices: 2448470--2448524 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
2448460 ACAATATGGT
* *
2448470 AGCAAAATAACAACAAAACAGC
1 AGCAAAACAACAACAAAACAAC
*
2448492 AGCAAAACAACAACGAAACAAC
1 AGCAAAACAACAACAAAACAAC
2448514 ATG-AAAACAAC
1 A-GCAAAACAAC
2448525 TAATTCGGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 28 0.97
23 1 0.03
ACGTcount: A:0.64, C:0.24, G:0.09, T:0.04
Consensus pattern (22 bp):
AGCAAAACAACAACAAAACAAC
Found at i:2450597 original size:18 final size:18
Alignment explanation
Indices: 2450576--2450610 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2450566 TAAACTTGTA
*
2450576 ATATCTGAGCTGAAGAAT
1 ATATCTGAACTGAAGAAT
2450594 ATATCTGAACTGAAGAA
1 ATATCTGAACTGAAGAA
2450611 CTTCTATAGA
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:0.43, C:0.11, G:0.20, T:0.26
Consensus pattern (18 bp):
ATATCTGAACTGAAGAAT
Found at i:2456706 original size:22 final size:20
Alignment explanation
Indices: 2456681--2456724 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
2456671 CTTTAACCAA
2456681 AAATAATATATATTAAAGATAT
1 AAATAATAT-TA-TAAAGATAT
* *
2456703 AAATACTATTATAAGGATAT
1 AAATAATATTATAAAGATAT
2456723 AA
1 AA
2456725 TTTATTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 10 0.50
21 2 0.10
22 8 0.40
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (20 bp):
AAATAATATTATAAAGATAT
Found at i:2460690 original size:40 final size:40
Alignment explanation
Indices: 2460641--2460719 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
2460631 AACTTTTGGG
* *
2460641 ATTTTCGCATGATTTTCTTACGAGTGCCGTGGGATGGGAC
1 ATTTTCGCATGATTTTCTTACAAGTGCCATGGGATGGGAC
2460681 ATTTTCGCATGATTTTCTTACAAGTGCCATGGGATGGGA
1 ATTTTCGCATGATTTTCTTACAAGTGCCATGGGATGGGA
2460720 GTGTAGCTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.20, C:0.16, G:0.28, T:0.35
Consensus pattern (40 bp):
ATTTTCGCATGATTTTCTTACAAGTGCCATGGGATGGGAC
Found at i:2470376 original size:28 final size:28
Alignment explanation
Indices: 2470345--2470404 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
2470335 AAAAAGCATT
2470345 TTTTTTTAA-ATTTACCGAAATAGGCCA
1 TTTTTTTAATATTTACCGAAATAGGCCA
* * *
2470372 CTTTTTTAATTATTTACCGGAATGGGCCA
1 TTTTTTTAA-TATTTACCGAAATAGGCCA
2470401 TTTT
1 TTTT
2470405 CCGCGAAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 8 0.30
29 19 0.70
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (28 bp):
TTTTTTTAATATTTACCGAAATAGGCCA
Found at i:2471475 original size:51 final size:51
Alignment explanation
Indices: 2471420--2471555 Score: 148
Period size: 51 Copynumber: 2.7 Consensus size: 51
2471410 TGGAAACATG
*
2471420 ATCTTA-AAGGATATGATATTATAATCTTAGAGATCTTAGATATGATATGGA
1 ATCTTAGAA-GATATGATATTATAATCTTAGAGATCTTAGATAAGATATGGA
* * * ** * * ** *
2471471 ATCTTATAAGATATTATTTTATAAGATTACATATCTTATCTAAGATATGTA
1 ATCTTAGAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGGA
*
2471522 ATCTTAGAAGATATGATATTATATTCTTAGAGAT
1 ATCTTAGAAGATATGATATTATAATCTTAGAGAT
2471556 TTGATGGTAG
Statistics
Matches: 66, Mismatches: 18, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
51 64 0.97
52 2 0.03
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.41
Consensus pattern (51 bp):
ATCTTAGAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGGA
Found at i:2476748 original size:93 final size:93
Alignment explanation
Indices: 2476630--2476813 Score: 343
Period size: 93 Copynumber: 2.0 Consensus size: 93
2476620 TCTAATCTCC
2476630 CCTCCAAAGAATATCAATGGCAAGAAGAAGGTTGAAGATGGCTCCCACAATCAAAAGATTGTTAA
1 CCTCCAAAGAATATCAATGGCAAGAAGAAGGTTGAAGATGGCTCCCACAATC-AAAGATTGTTAA
2476695 AACAGCTTCTAAAGAAAACTCAAGAGACT
65 AACAGCTTCTAAAGAAAACTCAAGAGACT
*
2476724 CCTCCAAA-AATATCAATGGTAAGAAGAAGGTTGAAGATGGCTCCCACAATCAAAGATTGTTAAA
1 CCTCCAAAGAATATCAATGGCAAGAAGAAGGTTGAAGATGGCTCCCACAATCAAAGATTGTTAAA
2476788 ACAGCTTCTAAAGAAAACTCAAGAGA
66 ACAGCTTCTAAAGAAAACTCAAGAGA
2476814 GAATTCTTGA
Statistics
Matches: 89, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
92 39 0.44
93 42 0.47
94 8 0.09
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.20
Consensus pattern (93 bp):
CCTCCAAAGAATATCAATGGCAAGAAGAAGGTTGAAGATGGCTCCCACAATCAAAGATTGTTAAA
ACAGCTTCTAAAGAAAACTCAAGAGACT
Found at i:2486968 original size:21 final size:21
Alignment explanation
Indices: 2486942--2486986 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2486932 TTAAGATGAA
*
2486942 TATTTATATTTATGATAATAT
1 TATTTATATTTATAATAATAT
* *
2486963 TATTTATCTTTATAATAATTT
1 TATTTATATTTATAATAATAT
2486984 TAT
1 TAT
2486987 ACATAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
TATTTATATTTATAATAATAT
Found at i:2491191 original size:2 final size:2
Alignment explanation
Indices: 2491184--2491230 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
2491174 GCAAGTGCAC
*
2491184 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2491226 AG AG A
1 AG AG A
2491231 AGCAAGACAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2499344 original size:24 final size:24
Alignment explanation
Indices: 2499308--2499354 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2499298 TATAAAATGT
*
2499308 ATGTAATATATAAATACATAAAAA
1 ATGTAATACATAAATACATAAAAA
* *
2499332 ATGTACTACATAAATACGTAAAA
1 ATGTAATACATAAATACATAAAA
2499355 GTAAAGGTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.57, C:0.09, G:0.06, T:0.28
Consensus pattern (24 bp):
ATGTAATACATAAATACATAAAAA
Found at i:2516486 original size:44 final size:44
Alignment explanation
Indices: 2516438--2516548 Score: 213
Period size: 44 Copynumber: 2.5 Consensus size: 44
2516428 CTTACGTATG
2516438 ATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCT
1 ATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCT
2516482 ATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCT
1 ATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCT
*
2516526 ATTACTTATCACTTGTCACTGAT
1 ATCACTTATCACTTGTCACTGAT
2516549 TAGAAGTACT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
44 66 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (44 bp):
ATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCT
Found at i:2522745 original size:58 final size:58
Alignment explanation
Indices: 2522615--2522751 Score: 154
Period size: 58 Copynumber: 2.4 Consensus size: 58
2522605 TATTATTATT
* *
2522615 AAATTTTAATA-AGATTATTATTAAAAATAATTTAATAAAAATAATAATTAATTTAACC
1 AAATTTTAATATA-ATTATTATTAAAAATAATTTAATAAAAATAATAATTAATCTAACA
* * * * * *
2522673 ATATTTTAACATAATAATTATTAAATATAATTTAATAGAAA-AAT-ATATAATCTAATA
1 AAATTTTAATATAATTATTATTAAAAATAATTTAATAAAAATAATAAT-TAATCTAACA
2522730 AAATTCTTAATATAATTATTAT
1 AAATT-TTAATATAATTATTAT
2522752 ATGAATTTAC
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
56 2 0.03
57 14 0.22
58 48 0.74
59 1 0.02
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (58 bp):
AAATTTTAATATAATTATTATTAAAAATAATTTAATAAAAATAATAATTAATCTAACA
Done.