Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 123 of 310
Found at i:39511014 original size:27 final size:27
Alignment explanation
Indices: 39510958--39511015 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
39510948 GTGACAGAGT
* * *
39510958 CACCAGATACAGATATTGTGGCAGAGC
1 CACCAGATACAGATAATGTGGCAAACC
39510985 CACCAGA-ATCAGATAATGTGGCAAACC
1 CACCAGATA-CAGATAATGTGGCAAACC
39511012 CACC
1 CACC
39511016 TAACAGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.36, C:0.28, G:0.21, T:0.16
Consensus pattern (27 bp):
CACCAGATACAGATAATGTGGCAAACC
Found at i:39511220 original size:22 final size:22
Alignment explanation
Indices: 39511172--39511230 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
39511162 GTAAATACAT
*
39511172 TTGGCACGAAGCCATAGTCAAG
1 TTGGCACAAAGCCATAGTCAAG
* * * *
39511194 ATGGCACAAAGCCATATTTAGG
1 TTGGCACAAAGCCATAGTCAAG
*
39511216 TTGGCACAGAGCCAT
1 TTGGCACAAAGCCAT
39511231 TAATAACGGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAGTCAAG
Found at i:39511400 original size:27 final size:26
Alignment explanation
Indices: 39511318--39511400 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 26
39511308 TCGATCGGTA
* *
39511318 AACAGATATTGTGACAGAGTCACCAG
1 AACAGATATTGTGGCAGAGCCACCAG
*
39511344 ATAAAGATATTGTGGCAGAGCCACCAG
1 A-ACAGATATTGTGGCAGAGCCACCAG
*
39511371 AACAGATATTTGTGGCATAGCCACCAG
1 AACAGATA-TTGTGGCAGAGCCACCAG
39511398 AAC
1 AAC
39511401 GCTTCCTCCG
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
26 7 0.14
27 43 0.86
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.19
Consensus pattern (26 bp):
AACAGATATTGTGGCAGAGCCACCAG
Found at i:39511615 original size:27 final size:28
Alignment explanation
Indices: 39511553--39511616 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 28
39511543 TAGTCACTTG
*
39511553 CCCACAAGGGCAAAACAGTCATTTAACA
1 CCCACAAGGGCAAAACAGTAATTTAACA
* ** *
39511581 CCC-TAAGGGCAAAATGGTAATTTTAC-
1 CCCACAAGGGCAAAACAGTAATTTAACA
39511607 CCCACAAGGG
1 CCCACAAGGG
39511617 TATCTCGGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
26 3 0.10
27 23 0.79
28 3 0.10
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.17
Consensus pattern (28 bp):
CCCACAAGGGCAAAACAGTAATTTAACA
Found at i:39511626 original size:27 final size:27
Alignment explanation
Indices: 39511596--39511845 Score: 257
Period size: 27 Copynumber: 9.3 Consensus size: 27
39511586 AGGGCAAAAT
* * *
39511596 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
39511623 GGTAATTATACCCTTCAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
39511650 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
39511677 GATAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
39511704 GGTAATTCTATCCTATAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
39511731 AGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
** * *
39511758 GAAAATTCTATCCTATAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
** * *
39511785 AATAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
39511812 AGAAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
39511839 AGTAATT
1 GGTAATT
39511846 TCACAATCAA
Statistics
Matches: 189, Mismatches: 34, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 189 1.00
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:39511662 original size:54 final size:54
Alignment explanation
Indices: 39511599--39511845 Score: 300
Period size: 54 Copynumber: 4.6 Consensus size: 54
39511589 GCAAAATGGT
* * * * * *
39511599 AATTTTACCCCACAAGGGTATCTCGGTAATTATACCCT-TCAGGGGTATTTCGGT
1 AATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTAT-AGGGGTATTTCGGA
* * * *
39511653 ATTTCTACCCTACAAGGGTATTTC-GATAATTCTACCCTACAGGGGTATTTTGGT
1 AATTCTACCCTACAAGGGTATTTCAG-TAATTCTACCCTATAGGGGTATTTCGGA
* * *
39511707 AATTCTATCCTATAAGGGTATTTCAGTAATTCTACCCTATAGGGGTATTTCGAA
1 AATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTATAGGGGTATTTCGGA
* * * *
39511761 AATTCTATCCTATAAGGGTATTTCAATAATTCTACCCTATAGGGGTATTTCAGA
1 AATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTATAGGGGTATTTCGGA
*
39511815 AATTCTACCCTACAGGGGTATTTCAGTAATT
1 AATTCTACCCTACAAGGGTATTTCAGTAATT
39511846 TCACAATCAA
Statistics
Matches: 169, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
53 1 0.01
54 167 0.99
55 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (54 bp):
AATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTATAGGGGTATTTCGGA
Found at i:39511887 original size:27 final size:27
Alignment explanation
Indices: 39511857--39512205 Score: 432
Period size: 27 Copynumber: 12.9 Consensus size: 27
39511847 CACAATCAAT
39511857 GGTAAAACGGTAATTCTGTAAATCGAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
* *
39511884 GGTAAAACGATAATTTTGTAAA-CTGAG
1 GGTAAAACGGTAATTCTGTAAATC-GAG
* * * *
39511911 GGTAAACCAGTAATTCTATAAATCAAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
* **
39511938 GGTAAAACGGTAATTTTACAAATCGAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
*
39511965 GGTAAAACGATAATTCTGTAAATCGAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
*
39511992 GGTAAAATGGTAATTCTGTAAA-CTGAG
1 GGTAAAACGGTAATTCTGTAAATC-GAG
*
39512019 GGTAAAACGGTAATTCTATAAATCGAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
* *
39512046 GGTAAAACGGTAATTCTATAAATTGAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
* * *
39512073 GATAAAACGGTAATTCTGTAAATTGAA
1 GGTAAAACGGTAATTCTGTAAATCGAG
*
39512100 GGTAAAACGGTAATTCTGTAAATTGAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
* * **
39512127 GGTAAAATGGTAATTTTAAAAATCGAG
1 GGTAAAACGGTAATTCTGTAAATCGAG
* * *
39512154 GGTAAAACGGTAATTCTATAAATCAAC
1 GGTAAAACGGTAATTCTGTAAATCGAG
*
39512181 GGTAAAATGGTAATTCTGTAAATCG
1 GGTAAAACGGTAATTCTGTAAATCG
39512206 GGAGTACTTT
Statistics
Matches: 278, Mismatches: 40, Indels: 8
0.85 0.12 0.02
Matches are distributed among these distances:
26 2 0.01
27 274 0.99
28 2 0.01
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (27 bp):
GGTAAAACGGTAATTCTGTAAATCGAG
Found at i:39514265 original size:30 final size:30
Alignment explanation
Indices: 39514231--39514318 Score: 122
Period size: 30 Copynumber: 2.9 Consensus size: 30
39514221 TGAGAATGAG
* *
39514231 AATCAAAATCAGTAACAGAATCAGAATCAA
1 AATCAAAATTAGTAACAGAATCAAAATCAA
*
39514261 AATCAATATTAGTAACAGAATCAAAATCAA
1 AATCAAAATTAGTAACAGAATCAAAATCAA
* *
39514291 AATCAGAATTAGGTGACAGAATCAAAAT
1 AATCAAAATTA-GTAACAGAATCAAAAT
39514319 TAGAATCAGT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 36 0.71
31 15 0.29
ACGTcount: A:0.55, C:0.14, G:0.11, T:0.20
Consensus pattern (30 bp):
AATCAAAATTAGTAACAGAATCAAAATCAA
Found at i:39514313 original size:31 final size:31
Alignment explanation
Indices: 39514241--39514327 Score: 115
Period size: 30 Copynumber: 2.8 Consensus size: 31
39514231 AATCAAAATC
*
39514241 AGTAACAGAATCAGAATCAAAATCA-ATATT
1 AGTAACAGAATCAAAATCAAAATCAGATATT
39514271 AGTAACAGAATCAAAATCAAAATCAGA-ATT
1 AGTAACAGAATCAAAATCAAAATCAGATATT
* * *
39514301 AGGTGACAGAATCAAAATTAGAATCAG
1 A-GTAACAGAATCAAAATCAAAATCAG
39514328 TAACAGAATC
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
30 28 0.55
31 23 0.45
ACGTcount: A:0.53, C:0.13, G:0.14, T:0.21
Consensus pattern (31 bp):
AGTAACAGAATCAAAATCAAAATCAGATATT
Found at i:39514323 original size:25 final size:24
Alignment explanation
Indices: 39514285--39514397 Score: 77
Period size: 25 Copynumber: 4.6 Consensus size: 24
39514275 ACAGAATCAA
* *
39514285 AATCAAAATCAGAATTAGGTGACAG
1 AATCAAAATCAGAATCA-GTAACAG
*
39514310 AATCAAAATTAGAATCAGTAACAG
1 AATCAAAATCAGAATCAGTAACAG
** * *
39514334 AATCAGTATTAGTAA-CAG-AATTAG
1 AATCAAAATCAG-AATCAGTAA-CAG
* *
39514358 AATCAAAATCAGAATTACGTGACAG
1 AATCAAAATCAGAATCA-GTAACAG
* *
39514383 AATCAGAACCAGAAT
1 AATCAAAATCAGAAT
39514398 GTGAATGCAA
Statistics
Matches: 69, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
23 4 0.06
24 31 0.45
25 33 0.48
26 1 0.01
ACGTcount: A:0.50, C:0.13, G:0.16, T:0.21
Consensus pattern (24 bp):
AATCAAAATCAGAATCAGTAACAG
Found at i:39514338 original size:24 final size:24
Alignment explanation
Indices: 39514202--39514372 Score: 91
Period size: 24 Copynumber: 7.1 Consensus size: 24
39514192 AAGAAACATT
** * *
39514202 ATCAGAATTGGAACCAAAATGAGA
1 ATCAGAATCAGAATCAAAATTAGA
* * * *
39514226 ATGAGAATCAAAATCAGTAA-CAGA
1 ATCAGAATCAGAATCA-AAATTAGA
* *
39514250 ATCAGAATCAAAATCAATATTAGTA
1 ATCAGAATCAGAATCAAAATTAG-A
* *
39514275 A-CAGAATCAAAATCAAAATCAGA
1 ATCAGAATCAGAATCAAAATTAGA
* *
39514298 ATTAG-GTGACAGAATCAAAATTAGA
1 ATCAGAAT--CAGAATCAAAATTAGA
**
39514323 ATCAGTAA-CAGAATCAGTATTAGTA
1 ATCAG-AATCAGAATCAAAATTAG-A
* *
39514348 A-CAGAATTAGAATCAAAATCAGA
1 ATCAGAATCAGAATCAAAATTAGA
39514371 AT
1 AT
39514373 TACGTGACAG
Statistics
Matches: 111, Mismatches: 25, Indels: 22
0.70 0.16 0.14
Matches are distributed among these distances:
23 8 0.07
24 79 0.71
25 24 0.22
ACGTcount: A:0.52, C:0.12, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAGAATCAGAATCAAAATTAGA
Found at i:39514338 original size:73 final size:73
Alignment explanation
Indices: 39514247--39514387 Score: 221
Period size: 73 Copynumber: 1.9 Consensus size: 73
39514237 AATCAGTAAC
*
39514247 AGAATCAGAATCAAAATCAATATTAGTAACAGAATCAAAATCAAAATCAGAATTAGGTGACAGAA
1 AGAATCAGAATCAAAATCAATATTAGTAACAGAATCAAAATCAAAATCAGAATTACGTGACAGAA
39514312 TCAAAATT
66 TCAAAATT
* * * *
39514320 AGAATCAGTAA-CAGAATCAGTATTAGTAACAGAATTAGAATCAAAATCAGAATTACGTGACAGA
1 AGAATCAG-AATCAAAATCAATATTAGTAACAGAATCAAAATCAAAATCAGAATTACGTGACAGA
39514384 ATCA
65 ATCA
39514388 GAACCAGAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
73 60 0.97
74 2 0.03
ACGTcount: A:0.51, C:0.13, G:0.14, T:0.22
Consensus pattern (73 bp):
AGAATCAGAATCAAAATCAATATTAGTAACAGAATCAAAATCAAAATCAGAATTACGTGACAGAA
TCAAAATT
Found at i:39514359 original size:6 final size:6
Alignment explanation
Indices: 39514223--39514372 Score: 69
Period size: 6 Copynumber: 24.8 Consensus size: 6
39514213 AACCAAAATG
* * * *
39514223 AGAATG AGAATC AAAATC AGTAA-C AGAATC AGAATC AAAATC A-ATATT
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGA-ATC
* * * * * *
39514271 AGTAA-C AGAATC AAAATC AAAATC AGAATT AG-GTGAC AGAATC AAAATT
1 AG-AATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC
* * * *
39514320 AGAATC AGTAA-C AGAATC AGTATT AGTAA-C AGAATT AGAATC AAAATC
1 AGAATC AG-AATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC
39514368 AGAAT
1 AGAAT
39514373 TACGTGACAG
Statistics
Matches: 107, Mismatches: 24, Indels: 26
0.68 0.15 0.17
Matches are distributed among these distances:
5 10 0.09
6 87 0.81
7 8 0.07
8 2 0.02
ACGTcount: A:0.53, C:0.12, G:0.14, T:0.21
Consensus pattern (6 bp):
AGAATC
Found at i:39514370 original size:18 final size:18
Alignment explanation
Indices: 39514202--39514374 Score: 61
Period size: 18 Copynumber: 9.6 Consensus size: 18
39514192 AAGAAACATT
* *
39514202 ATCAGAATTGGAACCAAA
1 ATCAGAATTAGAATCAAA
* *
39514220 ATGAGAATGAGAATCAAA
1 ATCAGAATTAGAATCAAA
* *
39514238 ATCAGTAA-CAGAATCAGA
1 ATCAG-AATTAGAATCAAA
* * * *
39514256 ATCAAAATCA-ATATTAGTA
1 ATCAGAATTAGA-ATCA-AA
* *
39514275 A-CAGAATCAAAATCAAA
1 ATCAGAATTAGAATCAAA
* *
39514292 ATCAGAATTAG-GTGACAGA
1 ATCAGAATTAGAAT--CAAA
* *
39514311 ATCAAAATTAGAATCAGTA
1 ATCAGAATTAGAATCA-AA
* * * *
39514330 A-CAGAATCAGTATTAGTA
1 ATCAGAATTAGAATCA-AA
39514348 A-CAGAATTAGAATCAAA
1 ATCAGAATTAGAATCAAA
39514365 ATCAGAATTA
1 ATCAGAATTA
39514375 CGTGACAGAA
Statistics
Matches: 116, Mismatches: 28, Indels: 22
0.70 0.17 0.13
Matches are distributed among these distances:
17 8 0.07
18 87 0.75
19 20 0.17
20 1 0.01
ACGTcount: A:0.52, C:0.12, G:0.14, T:0.21
Consensus pattern (18 bp):
ATCAGAATTAGAATCAAA
Found at i:39514397 original size:73 final size:72
Alignment explanation
Indices: 39514237--39514397 Score: 216
Period size: 73 Copynumber: 2.2 Consensus size: 72
39514227 TGAGAATCAA
39514237 AATCAGTAACAGAATCAGAATCAAAATCAATATTAGTAACAGAATCAAAATCAAAATCAGAATTA
1 AATCAG-AACAGAATCAGAATCAAAATCAATATTAGTAACAGAATCAAAATCAAAATCAGAATTA
*
39514302 GGTGACAG
65 CGTGACAG
* * * * * *
39514310 AATCAAAATTAGAATCAGTAA-CAGAATCAGTATTAGTAACAGAATTAGAATCAAAATCAGAATT
1 AATCAGAA-CAGAATCAG-AATCAAAATCAATATTAGTAACAGAATCAAAATCAAAATCAGAATT
39514374 ACGTGACAG
64 ACGTGACAG
39514383 AATCAGAACCAGAAT
1 AATCAGAA-CAGAAT
39514398 GTGAATGCAA
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
72 2 0.03
73 72 0.95
74 2 0.03
ACGTcount: A:0.51, C:0.14, G:0.14, T:0.21
Consensus pattern (72 bp):
AATCAGAACAGAATCAGAATCAAAATCAATATTAGTAACAGAATCAAAATCAAAATCAGAATTAC
GTGACAG
Found at i:39514552 original size:27 final size:27
Alignment explanation
Indices: 39514514--39514579 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
39514504 AGCATGGCTG
*
39514514 CCAGAAT-AGATATCGTGACAGAGTCA
1 CCAGAATCAGATATCGTGACAGAGCCA
* *
39514540 CCAG-ATACAGATATTGTGGCAGAGCCA
1 CCAGAAT-CAGATATCGTGACAGAGCCA
39514567 CCAGAATCAGATA
1 CCAGAATCAGATA
39514580 ATGAGGCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 2 0.06
26 4 0.12
27 26 0.76
28 2 0.06
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (27 bp):
CCAGAATCAGATATCGTGACAGAGCCA
Found at i:39514587 original size:27 final size:27
Alignment explanation
Indices: 39514532--39514587 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
39514522 GATATCGTGA
* * *
39514532 CAGAGTCACCAGATACAGATATTGTGG
1 CAGAGCCACCAGATACAGATAATGAGG
39514559 CAGAGCCACCAGA-ATCAGATAATGAGG
1 CAGAGCCACCAGATA-CAGATAATGAGG
39514586 CA
1 CA
39514588 AACCCACCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 1 0.04
27 24 0.96
ACGTcount: A:0.38, C:0.21, G:0.25, T:0.16
Consensus pattern (27 bp):
CAGAGCCACCAGATACAGATAATGAGG
Found at i:39514594 original size:27 final size:27
Alignment explanation
Indices: 39514538--39514595 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
39514528 GTGACAGAGT
* * * *
39514538 CACCAGATACAGATATTGTGGCAGAGC
1 CACCAGATACAGATAATGAGGCAAACC
39514565 CACCAGA-ATCAGATAATGAGGCAAACC
1 CACCAGATA-CAGATAATGAGGCAAACC
39514592 CACC
1 CACC
39514596 TAATAGAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.38, C:0.28, G:0.21, T:0.14
Consensus pattern (27 bp):
CACCAGATACAGATAATGAGGCAAACC
Found at i:39514800 original size:22 final size:22
Alignment explanation
Indices: 39514752--39514810 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
39514742 GTAAATACGT
*
39514752 TTGGCACGAAGCCATAGTCAAG
1 TTGGCACAAAGCCATAGTCAAG
* * * *
39514774 ATGGCACAAAGCCATATTTAGG
1 TTGGCACAAAGCCATAGTCAAG
*
39514796 TTGGCACAGAGCCAT
1 TTGGCACAAAGCCAT
39514811 TAATAACGGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAGTCAAG
Found at i:39514942 original size:27 final size:28
Alignment explanation
Indices: 39514901--39514980 Score: 94
Period size: 27 Copynumber: 2.9 Consensus size: 28
39514891 ATCGGTCAAC
* *
39514901 AGATATTGTGACAGAGTCACCAGATA-A-
1 AGATATTGTGGCAGAGCCACCAGA-ACAG
39514928 AGATATTGTGGCAGAGCCACCAGAACAG
1 AGATATTGTGGCAGAGCCACCAGAACAG
* *
39514956 AGAT-TTGTGGCATAACCACCAGAAC
1 AGATATTGTGGCAGAGCCACCAGAAC
39514981 GCTTCCTTCG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
26 1 0.02
27 42 0.89
28 4 0.09
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.19
Consensus pattern (28 bp):
AGATATTGTGGCAGAGCCACCAGAACAG
Found at i:39515028 original size:16 final size:16
Alignment explanation
Indices: 39515007--39515037 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39514997 ATCCCAACCC
*
39515007 ATGCAACATGTCATGT
1 ATGCAAAATGTCATGT
39515023 ATGCAAAATGTCATG
1 ATGCAAAATGTCATG
39515038 CCCATATTTG
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:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (16 bp):
ATGCAAAATGTCATGT
Found at i:39515208 original size:27 final size:27
Alignment explanation
Indices: 39515178--39515399 Score: 232
Period size: 27 Copynumber: 8.3 Consensus size: 27
39515168 GGGGAAAAAT
* * * *
39515178 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTATAAGGGTATTTC
*
39515205 GGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTATAAGGGTATTTC
*
39515232 GGTATTTCTACCCTATAAGGGTATTTC
1 GGTAATTCTACCCTATAAGGGTATTTC
* * * *
39515259 GATAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTATAAGGGTATTTC
*
39515286 GGTAATTCTATCCTATAAGGGTATTTC
1 GGTAATTCTACCCTATAAGGGTATTTC
* *
39515313 AGTAATTCTACCCTAT-GGGGTATTTC
1 GGTAATTCTACCCTATAAGGGTATTTC
* * *
39515339 AGAAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTATAAGGGTATTTC
*** * *
39515366 AAAAATTCTACCCTACAGGGGTATTT-
1 GGTAATTCTACCCTATAAGGGTATTTC
39515392 GAGTAATT
1 G-GTAATT
39515400 TCACAATCAA
Statistics
Matches: 167, Mismatches: 26, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
26 24 0.14
27 143 0.86
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTATAAGGGTATTTC
Found at i:39515322 original size:81 final size:81
Alignment explanation
Indices: 39515180--39515399 Score: 264
Period size: 81 Copynumber: 2.7 Consensus size: 81
39515170 GGAAAAATGG
* * * * * * *
39515180 TAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTATAGGGGTATTTCGGTATTTCTACCC
1 TAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTATAAGGGTATTTCAGTAATTCTACCC
39515245 TATAAGGGTATTTC-GA
66 TAT-AGGGTATTTCAGA
* *
39515261 TAATTCTACCCTACAGGGGTATTTTGGTAATTCTATCCTATAAGGGTATTTCAGTAATTCTACCC
1 TAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTATAAGGGTATTTCAGTAATTCTACCC
*
39515326 TATGGGGTATTTCAGA
66 TATAGGGTATTTCAGA
* *** * * *
39515342 -AATTCTACCCTATAGGGGTATTTCAAAAATTCTACCCTACAGGGGTATTTGAGTAATT
1 TAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTATAAGGGTATTTCAGTAATT
39515400 TCACAATCAA
Statistics
Matches: 119, Mismatches: 19, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
80 58 0.49
81 61 0.51
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (81 bp):
TAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTATAAGGGTATTTCAGTAATTCTACCC
TATAGGGTATTTCAGA
Found at i:39515373 original size:107 final size:108
Alignment explanation
Indices: 39515194--39515399 Score: 317
Period size: 107 Copynumber: 1.9 Consensus size: 108
39515184 TTTACCCCAC
* * * *
39515194 AAGGGTATCTCGGTAATTCTACCCTATAGGGGTATTTCGGTATTTCTACCCTATAAGGGTATTTC
1 AAGGGTATCTCAGTAATTCTACCCTATAGGGGTATTTCAGAAATTCTACCCTATAAGGGTATTTC
* *
39515259 GATAATTCTACCCTACAGGGGTATTTTG-GTAATTCTATCCTAT
66 AAAAATTCTACCCTACAGGGGTA-TTTGAGTAATTCTATCCTAT
* *
39515302 AAGGGTATTTCAGTAATTCTACCCTAT-GGGGTATTTCAGAAATTCTACCCTATAGGGGTATTTC
1 AAGGGTATCTCAGTAATTCTACCCTATAGGGGTATTTCAGAAATTCTACCCTATAAGGGTATTTC
39515366 AAAAATTCTACCCTACAGGGGTATTTGAGTAATT
66 AAAAATTCTACCCTACAGGGGTATTTGAGTAATT
39515400 TCACAATCAA
Statistics
Matches: 89, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
106 4 0.04
107 60 0.67
108 25 0.28
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.36
Consensus pattern (108 bp):
AAGGGTATCTCAGTAATTCTACCCTATAGGGGTATTTCAGAAATTCTACCCTATAAGGGTATTTC
AAAAATTCTACCCTACAGGGGTATTTGAGTAATTCTATCCTAT
Found at i:39515434 original size:27 final size:27
Alignment explanation
Indices: 39515404--39516298 Score: 1106
Period size: 27 Copynumber: 33.2 Consensus size: 27
39515394 GTAATTTCAC
* *
39515404 AATCAAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTATA
* * * *
39515431 AATCAAGGGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTATA
* * * *
39515458 AA-CTAAGGGTAAACCAGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTATA
* ** * * *
39515485 AATCTAGGGTAAAATAGCAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTATA
*
39515512 AATTGAGGGTAAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
*
39515539 AATCGAGGGTAAAACAGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
* *
39515566 AA-CTGAGGGTAAAACGGTAATTTTGTA
1 AATC-GAGGGTAAAACGGTAATTCTATA
*
39515593 AATCGAGGGTAAAACGGTAATTTTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
* *
39515620 AA-CTAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTATA
* *
39515646 AATCGAGGGTAAAACGGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTATA
*
39515673 AATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
**
39515700 AATCGAGGGTAAAACAATAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
*
39515727 AA-CTGAGGGTAAAACGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTATA
* *
39515754 AATCGAGGGTAAAACGGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTATA
*
39515781 AATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
**
39515808 AATCGAGGGTAAAACAATAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
*
39515835 AA-CTGAGGGTAAAACGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTATA
* *
39515862 AATCGAGGGTAAAACGGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTATA
*
39515889 AATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
**
39515916 AATCGAGGGTAAAACAATAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
*
39515943 AA-CTGAGGGTAAAACGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTATA
* *
39515970 AATCGAGGGTAAAACGGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTATA
*
39515997 AATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
**
39516024 AATCGAGGGTAAAACAATAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
*
39516051 AA-CTGAGGGTAAAACGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTATA
*
39516078 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTATA
*
39516105 AA-CTAAGGGTAAAACGGTAATTCTATA
1 AATC-GAGGGTAAAACGGTAATTCTATA
* *
39516132 AATCGAGGGTAAAACGATAATTCTTTA
1 AATCGAGGGTAAAACGGTAATTCTATA
39516159 AA-CTGAGGGTAAAACGGTAATTCTATA
1 AATC-GAGGGTAAAACGGTAATTCTATA
* *
39516186 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTATA
* * * *
39516213 AATTGAGGGAAAAACGGTAATTTTAAA
1 AATCGAGGGTAAAACGGTAATTCTATA
*
39516240 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTATA
* * *
39516267 AATCAAAGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTATA
39516294 AATCG
1 AATCG
39516299 GGAGTACTTT
Statistics
Matches: 752, Mismatches: 99, Indels: 34
0.85 0.11 0.04
Matches are distributed among these distances:
26 31 0.04
27 713 0.95
28 8 0.01
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.27
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTCTATA
Found at i:39516342 original size:108 final size:108
Alignment explanation
Indices: 39515409--39516329 Score: 1298
Period size: 108 Copynumber: 8.5 Consensus size: 108
39515399 TTCACAATCA
* * ** * **
39515409 AGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAACGATAATTTTGTAAA-CTAAGGGTAAACC
1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTACAAATC-GAGGGTAAAAT
* * * * ** * * *
39515473 AGTAATTCTGTAAATCTAGGGTAAAATAGCAATTTTACAAATTG
65 GGTAATTCTATAAATCGAGGGTAAAACAATAATTCTATAAACTG
* * * * *
39515517 AGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACAGTAATTCTATAAA-CTGAGGGTAAAAC
1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTACAAATC-GAGGGTAAAAT
* * ** *
39515581 GGTAATTTTGTAAATCGAGGGTAAAACGGTAATTTTATAAACT-
65 GGTAATTCTATAAATCGAGGGTAAAACAATAATTCTATAAACTG
39515624 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTACAAATCGAGGGTAAAATG
1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTACAAATCGAGGGTAAAATG
39515689 GTAATTCTATAAATCGAGGGTAAAACAATAATTCTATAAACTG
66 GTAATTCTATAAATCGAGGGTAAAACAATAATTCTATAAACTG
39515732 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTACAAATCGAGGGTAAAATG
1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTACAAATCGAGGGTAAAATG
39515797 GTAATTCTATAAATCGAGGGTAAAACAATAATTCTATAAACTG
66 GTAATTCTATAAATCGAGGGTAAAACAATAATTCTATAAACTG
39515840 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTACAAATCGAGGGTAAAATG
1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTACAAATCGAGGGTAAAATG
39515905 GTAATTCTATAAATCGAGGGTAAAACAATAATTCTATAAACTG
66 GTAATTCTATAAATCGAGGGTAAAACAATAATTCTATAAACTG
39515948 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTACAAATCGAGGGTAAAATG
1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTACAAATCGAGGGTAAAATG
39516013 GTAATTCTATAAATCGAGGGTAAAACAATAATTCTATAAACTG
66 GTAATTCTATAAATCGAGGGTAAAACAATAATTCTATAAACTG
* *
39516056 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTA-AACT-AAGGGTAAAA
1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATT-T-TACAAATCGAGGGTAAAA
* * *
39516119 CGGTAATTCTATAAATCGAGGGTAAAACGATAATTCTTTAAACTG
64 TGGTAATTCTATAAATCGAGGGTAAAACAATAATTCTATAAACTG
* ** * * *
39516164 AGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACGGTAATTTTGTAAATTGAGGGAAAAACG
1 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTACAAATCGAGGGTAAAATG
* * ** * *
39516229 GTAATTTTAAAAATCGAGGGTAAAACGGTAATTCTGTAAA-TCA
66 GTAATTCTATAAATCGAGGGTAAAACAATAATTCTATAAACT-G
* **** *
39516272 AAGGTAAAACGGTAATTCTGTAAATCG-GGAGTACTTTGGTAATTTTACAAGTCGAGGG
1 AGGGTAAAACGGTAATTCTGTAAATCGAGG-GTAAAACGGTAATTTTACAAATCGAGGG
39516330 CATTTCAGTA
Statistics
Matches: 754, Mismatches: 51, Indels: 16
0.92 0.06 0.02
Matches are distributed among these distances:
106 1 0.00
107 102 0.14
108 645 0.86
109 4 0.01
110 2 0.00
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.27
Consensus pattern (108 bp):
AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTACAAATCGAGGGTAAAATG
GTAATTCTATAAATCGAGGGTAAAACAATAATTCTATAAACTG
Found at i:39523838 original size:21 final size:20
Alignment explanation
Indices: 39523810--39523848 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
39523800 GCATGTGTTT
*
39523810 TGAAGTTTCTTGATAGATTA
1 TGAAGTTTCTTAATAGATTA
*
39523830 TGAATGTTTGTTAATAGAT
1 TGAA-GTTTCTTAATAGAT
39523849 ATACAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.31, C:0.03, G:0.21, T:0.46
Consensus pattern (20 bp):
TGAAGTTTCTTAATAGATTA
Found at i:39525106 original size:14 final size:14
Alignment explanation
Indices: 39525087--39525136 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
39525077 TGAATGAGTA
39525087 AAACATGAGATAGT
1 AAACATGAGATAGT
* *
39525101 AAACATGCTAG-TTGA
1 AAACATG--AGATAGT
39525116 AAACATGAGATAGT
1 AAACATGAGATAGT
39525130 AAACATG
1 AAACATG
39525137 CTAGTTGTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
13 2 0.07
14 16 0.55
15 9 0.31
16 2 0.07
ACGTcount: A:0.48, C:0.10, G:0.20, T:0.22
Consensus pattern (14 bp):
AAACATGAGATAGT
Found at i:39525128 original size:29 final size:29
Alignment explanation
Indices: 39525086--39525143 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
39525076 TTGAATGAGT
39525086 AAAACATGAGATAGTAAACATGCTAGTTG
1 AAAACATGAGATAGTAAACATGCTAGTTG
39525115 AAAACATGAGATAGTAAACATGCTAGTTG
1 AAAACATGAGATAGTAAACATGCTAGTTG
39525144 TTGGAATTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.10, G:0.21, T:0.24
Consensus pattern (29 bp):
AAAACATGAGATAGTAAACATGCTAGTTG
Found at i:39535396 original size:46 final size:46
Alignment explanation
Indices: 39535339--39535514 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 46
39535329 TATTTGGGCA
39535339 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAGCG
* *** * ** *
39535385 TCCAAACTCGTTGAGTTGAGTCTGAGTTCGAGAGATGTAATTAG-GCA
1 TCCGAACTCGTTGAGTTGAGTCTGAGTTC-ACTTATG-GATGCGAGCG
*
39535432 TCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAAG-G
1 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCG-AGCG
* *
39535478 CCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGG
39535515 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
45 3 0.03
46 68 0.63
47 34 0.31
48 3 0.03
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAGCG
Found at i:39535494 original size:93 final size:93
Alignment explanation
Indices: 39535335--39535506 Score: 292
Period size: 93 Copynumber: 1.8 Consensus size: 93
39535325 GGGATATTTG
*
39535335 GGCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAGCGTCCAAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAGCGCCCAAACTCGTTGAG
39535400 TTGAGTCTGAGTTCGAGAGATGTAATTA
66 TTGAGTCTGAGTTCGAGAGATGTAATTA
* * *
39535428 GGCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAAG-GCCCGAGCTCGTTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCG-AGCGCCCAAACTCGTTGA
39535492 GTTGAGTCTGAGTTC
65 GTTGAGTCTGAGTTC
39535507 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
93 72 0.97
94 2 0.03
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.30
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAGCGCCCAAACTCGTTGAG
TTGAGTCTGAGTTCGAGAGATGTAATTA
Found at i:39547435 original size:40 final size:40
Alignment explanation
Indices: 39547391--39547493 Score: 145
Period size: 40 Copynumber: 2.5 Consensus size: 40
39547381 CGACAATTTA
* *
39547391 GCTATGTATGGCACTTAATGTGCGACTT-GAGATAGCTTCG
1 GCTATGTATGGCACTTAGTGTGC-AATTCGAGATAGCTTCG
*
39547431 GCTATGTATGGCACTTAGTGTTCAATTCGAGATAGCTTCG
1 GCTATGTATGGCACTTAGTGTGCAATTCGAGATAGCTTCG
*
39547471 GCTATGTATTAGCACTTAGTGTG
1 GCTATGTA-TGGCACTTAGTGTG
39547494 TTAGAATTCG
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
39 3 0.05
40 41 0.73
41 12 0.21
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (40 bp):
GCTATGTATGGCACTTAGTGTGCAATTCGAGATAGCTTCG
Found at i:39557388 original size:27 final size:27
Alignment explanation
Indices: 39557358--39557410 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
39557348 GACCCCAGTT
* *
39557358 TGTAAAATCACTGAAATACCCTTGTAG
1 TGTAAAATCACCGAAATACCCCTGTAG
* *
39557385 TGTAAAATGACCGTAATACCCCTGTA
1 TGTAAAATCACCGAAATACCCCTGTA
39557411 TGGTAGAATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (27 bp):
TGTAAAATCACCGAAATACCCCTGTAG
Found at i:39560177 original size:19 final size:19
Alignment explanation
Indices: 39560153--39560190 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
39560143 TGGGCCACGT
39560153 TGGGCCTAGATGGG-TCGTG
1 TGGGCCTA-ATGGGCTCGTG
39560172 TGGGCCTAATGGGCTCGTG
1 TGGGCCTAATGGGCTCGTG
39560191 GGCCTCACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.11, C:0.18, G:0.45, T:0.26
Consensus pattern (19 bp):
TGGGCCTAATGGGCTCGTG
Found at i:39560193 original size:17 final size:18
Alignment explanation
Indices: 39560153--39560195 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
39560143 TGGGCCACGT
39560153 TGGGCCTAGATGGGTCGTG
1 TGGGCCTAGATGGGTCG-G
39560172 TGGGCCTA-ATGGGCTC-G
1 TGGGCCTAGATGGG-TCGG
39560189 TGGGCCT
1 TGGGCCT
39560196 CACACTGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 8 0.35
18 5 0.22
19 10 0.43
ACGTcount: A:0.09, C:0.21, G:0.44, T:0.26
Consensus pattern (18 bp):
TGGGCCTAGATGGGTCGG
Found at i:39562520 original size:21 final size:21
Alignment explanation
Indices: 39562496--39562549 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
39562486 ACTCCCTTTG
*
39562496 ATGTCGCGACATAAGACTACT
1 ATGTCGTGACATAAGACTACT
39562517 ATGTCGTGACATAAGACTACT
1 ATGTCGTGACATAAGACTACT
39562538 ATGTCGTGACAT
1 ATGTCGTGACAT
39562550 CGACTATGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.28
Consensus pattern (21 bp):
ATGTCGTGACATAAGACTACT
Found at i:39567641 original size:19 final size:19
Alignment explanation
Indices: 39567606--39567643 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
39567596 GTGTGGAGCC
*
39567606 CACGAGCCCATTGGACCCA
1 CACGAGCCCATTCGACCCA
39567625 CACGA-CCCATTTCGACCCA
1 CACGAGCCCA-TTCGACCCA
39567644 ACATGCCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.26, C:0.45, G:0.16, T:0.13
Consensus pattern (19 bp):
CACGAGCCCATTCGACCCA
Found at i:39568634 original size:49 final size:49
Alignment explanation
Indices: 39568546--39569448 Score: 1678
Period size: 49 Copynumber: 18.6 Consensus size: 49
39568536 TATTTGAATA
*
39568546 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
39568593 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATATGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
39568642 AATGTGAAA--GTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
39568689 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
39568738 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
39568787 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
39568836 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
39568885 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
39568934 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
39568983 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
39569032 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
39569081 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
39569130 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
39569179 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
39569228 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
39569277 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
39569326 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * *
39569375 AATGTGAAAGTG--TATATATGTGATAAGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
39569422 GATGTGAAAGTGTATA-A-ATGTGATAAG
1 AATGTGAAAGTGTATATATATGTGATAAG
39569449 TCCCGAAGGG
Statistics
Matches: 840, Mismatches: 10, Indels: 12
0.97 0.01 0.01
Matches are distributed among these distances:
47 109 0.13
48 1 0.00
49 730 0.87
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (49 bp):
AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:39569668 original size:37 final size:37
Alignment explanation
Indices: 39569567--39569668 Score: 177
Period size: 37 Copynumber: 2.8 Consensus size: 37
39569557 CCGAGCTCTA
*
39569567 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
39569604 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
* *
39569641 AAGACCCGATAACTTCGTGTGGAGATTT
1 AAGACCCGATGACTACGTGTGGAGATTT
39569669 CGTCTGAGCT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 62 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (37 bp):
AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
Found at i:39579277 original size:7 final size:7
Alignment explanation
Indices: 39579244--39579332 Score: 67
Period size: 7 Copynumber: 12.9 Consensus size: 7
39579234 ACCCCAAACA
*
39579244 TTAAGAT
1 TTAAGGT
39579251 TTAAGGTT
1 TTAAGG-T
* *
39579259 TTGAGAT
1 TTAAGGT
39579266 TTAAGGT
1 TTAAGGT
39579273 TTAAGGCT
1 TTAAGG-T
*
39579281 TT-TGGT
1 TTAAGGT
39579287 TTAAGGT
1 TTAAGGT
39579294 TT-AGGT
1 TTAAGGT
*
39579300 TTAGGGT
1 TTAAGGT
*
39579307 TTAA-GA
1 TTAAGGT
*
39579313 TTAGGGT
1 TTAAGGT
39579320 TTAAGGT
1 TTAAGGT
*
39579327 TCAAGG
1 TTAAGG
39579333 GTTCGTGGTT
Statistics
Matches: 63, Mismatches: 14, Indels: 10
0.72 0.16 0.11
Matches are distributed among these distances:
6 13 0.21
7 42 0.67
8 8 0.13
ACGTcount: A:0.26, C:0.02, G:0.29, T:0.43
Consensus pattern (7 bp):
TTAAGGT
Found at i:39579302 original size:13 final size:13
Alignment explanation
Indices: 39579269--39579332 Score: 56
Period size: 13 Copynumber: 4.8 Consensus size: 13
39579259 TTGAGATTTA
39579269 AGGTTTAAGGCTTT
1 AGGTTTAAGG-TTT
*
39579283 TGGTTTAAGGTTT
1 AGGTTTAAGGTTT
*
39579296 AGGTTTAGGGTTT
1 AGGTTTAAGGTTT
* * *
39579309 AAGATTAGGGTTT
1 AGGTTTAAGGTTT
*
39579322 AAGGTTCAAGG
1 -AGGTTTAAGG
39579333 GTTCGTGGTT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
13 25 0.62
14 15 0.38
ACGTcount: A:0.23, C:0.03, G:0.33, T:0.41
Consensus pattern (13 bp):
AGGTTTAAGGTTT
Found at i:39579320 original size:20 final size:20
Alignment explanation
Indices: 39579284--39579332 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
39579274 TAAGGCTTTT
* *
39579284 GGTTTAAGGTTTAGGTTTAG
1 GGTTTAAGGATTAGGTTTAA
39579304 GGTTTAA-GATTAGGGTTTAA
1 GGTTTAAGGATTA-GGTTTAA
*
39579324 GGTTCAAGG
1 GGTTTAAGG
39579333 GTTCGTGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 4 0.17
20 19 0.79
21 1 0.04
ACGTcount: A:0.24, C:0.02, G:0.35, T:0.39
Consensus pattern (20 bp):
GGTTTAAGGATTAGGTTTAA
Found at i:39579446 original size:21 final size:20
Alignment explanation
Indices: 39579399--39579447 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
39579389 GGTTTTGGGT
*
39579399 TTGAG-TTTAGGGTTTATGC
1 TTGAGATTTAGGGTTCATGC
39579418 TT-AGGATTTAGGGTTCATGGC
1 TTGA-GATTTAGGGTTCAT-GC
39579439 TTGAGATTT
1 TTGAGATTT
39579448 TAGATTTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 1 0.04
19 3 0.12
20 11 0.44
21 9 0.36
22 1 0.04
ACGTcount: A:0.18, C:0.06, G:0.31, T:0.45
Consensus pattern (20 bp):
TTGAGATTTAGGGTTCATGC
Found at i:39579508 original size:26 final size:27
Alignment explanation
Indices: 39579451--39579521 Score: 76
Period size: 26 Copynumber: 2.7 Consensus size: 27
39579441 GAGATTTTAG
*
39579451 ATTTATGATTTT-GGGTTTATGGTTATT
1 ATTT-TGATTTTAGGGTTTATGCTTATT
*
39579478 GTTTTGATTTTAGGGTTTATGCTT-TT
1 ATTTTGATTTTAGGGTTTATGCTTATT
*
39579504 ATTTT-TTGTTTAGGGTTT
1 ATTTTGAT-TTTAGGGTTT
39579522 GAGATTCTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
25 1 0.03
26 23 0.61
27 14 0.37
ACGTcount: A:0.14, C:0.01, G:0.23, T:0.62
Consensus pattern (27 bp):
ATTTTGATTTTAGGGTTTATGCTTATT
Found at i:39580261 original size:29 final size:27
Alignment explanation
Indices: 39580222--39580286 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 27
39580212 ATACATATTT
*
39580222 AATTATTTATATTTTAGTCA-TATAATA
1 AATTATTTATAATTTA-TCATTATAATA
*
39580249 AATTATTACTATAATTTATCATTTTAATA
1 AATTATT--TATAATTTATCATTATAATA
39580278 AATTATTTA
1 AATTATTTA
39580287 ATATTTCAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 9 0.27
28 3 0.09
29 21 0.64
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.52
Consensus pattern (27 bp):
AATTATTTATAATTTATCATTATAATA
Found at i:39584898 original size:19 final size:21
Alignment explanation
Indices: 39584862--39584903 Score: 70
Period size: 19 Copynumber: 2.1 Consensus size: 21
39584852 TAACTACTTG
39584862 AAGATTAATGTATAATTAATT
1 AAGATTAATGTATAATTAATT
39584883 AAGATTAA-GT-TAATTAATT
1 AAGATTAATGTATAATTAATT
39584902 AA
1 AA
39584904 TTTTAACTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 11 0.52
20 2 0.10
21 8 0.38
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (21 bp):
AAGATTAATGTATAATTAATT
Found at i:39585195 original size:22 final size:20
Alignment explanation
Indices: 39585155--39585195 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
39585145 CATTGTTAAG
*
39585155 AAATTGATGAATTAGGTTTC
1 AAATTGATGAATTAAGTTTC
39585175 AAATTGATAGAAATTAAGTTT
1 AAATTGAT-G-AATTAAGTTT
39585196 ACATTATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.41, C:0.02, G:0.17, T:0.39
Consensus pattern (20 bp):
AAATTGATGAATTAAGTTTC
Found at i:39588622 original size:17 final size:17
Alignment explanation
Indices: 39588600--39588673 Score: 68
Period size: 17 Copynumber: 4.5 Consensus size: 17
39588590 ATTTTAATAG
39588600 TTTAATATTAAATTTAA
1 TTTAATATTAAATTTAA
39588617 TTTAATACTT--ATCTTAA
1 TTTAATA-TTAAAT-TTAA
**
39588634 --TAATATTTTA-TTAA
1 TTTAATATTAAATTTAA
39588648 TTTAATATTAAATTTAA
1 TTTAATATTAAATTTAA
*
39588665 TCTAATATT
1 TTTAATATT
39588674 TATCTTGATA
Statistics
Matches: 47, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
14 6 0.13
15 5 0.11
16 11 0.23
17 23 0.49
18 2 0.04
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTAATATTAAATTTAA
Found at i:39588641 original size:48 final size:48
Alignment explanation
Indices: 39588583--39588704 Score: 149
Period size: 48 Copynumber: 2.5 Consensus size: 48
39588573 TTTCAAAAAA
* * *
39588583 TAATATTATTTTAATAGTTTAATATTAAATTTAATTTAATACTTATCT
1 TAATAATATTTTAATAATTTAATATTAAATTTAATCTAATACTTATCT
* *
39588631 TAATAATATTTTATTAATTTAATATTAAATTTAATCTAATATTTATCT
1 TAATAATATTTTAATAATTTAATATTAAATTTAATCTAATACTTATCT
* *
39588679 TGAT-ATA-TTAAATTAAATTTAATATT
1 TAATAATATTTTAA-T-AATTTAATATT
39588705 TAAGTGATTA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
46 3 0.05
47 4 0.06
48 57 0.89
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (48 bp):
TAATAATATTTTAATAATTTAATATTAAATTTAATCTAATACTTATCT
Found at i:39588656 original size:11 final size:11
Alignment explanation
Indices: 39588583--39588665 Score: 50
Period size: 12 Copynumber: 7.4 Consensus size: 11
39588573 TTTCAAAAAA
*
39588583 TAATATTATTT
1 TAATATTAATT
39588594 TAATAGTTTAATAT
1 TAATA--TTAAT-T
39588608 TAA-ATTTAATT
1 TAATA-TTAATT
39588619 TAATACTT-ATCT
1 TAATA-TTAAT-T
*
39588631 TAATAAT-ATT
1 TAATATTAATT
39588641 T--TATTAATT
1 TAATATTAATT
39588650 TAATATTAAATT
1 TAATATT-AATT
39588662 TAAT
1 TAAT
39588666 CTAATATTTA
Statistics
Matches: 59, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
8 3 0.05
9 4 0.07
10 2 0.03
11 18 0.31
12 23 0.39
13 5 0.08
14 4 0.07
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.54
Consensus pattern (11 bp):
TAATATTAATT
Found at i:39588665 original size:31 final size:32
Alignment explanation
Indices: 39588613--39588702 Score: 80
Period size: 31 Copynumber: 2.7 Consensus size: 32
39588603 AATATTAAAT
39588613 TTAATTTAATACTT--ATCTTAATAATATTT-TA
1 TTAATTTAATA-TTAAAT-TTAATAATATTTATA
*
39588644 TTAATTTAATATTAAATTTAATCTAATATTTATC
1 TTAATTTAATATTAAATTTAA--TAATATTTATA
39588678 TTGATATATTAA-ATTAAATTTAATA
1 TT-A-AT-TTAATATTAAATTTAATA
39588703 TTTAAGTGAT
Statistics
Matches: 50, Mismatches: 1, Indels: 13
0.78 0.02 0.20
Matches are distributed among these distances:
30 2 0.04
31 15 0.30
32 2 0.04
33 8 0.16
34 5 0.10
35 1 0.02
36 13 0.26
37 4 0.08
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (32 bp):
TTAATTTAATATTAAATTTAATAATATTTATA
Found at i:39588703 original size:31 final size:31
Alignment explanation
Indices: 39588652--39588766 Score: 121
Period size: 31 Copynumber: 3.8 Consensus size: 31
39588642 TATTAATTTA
*
39588652 ATATTAAATTTAATCTAATATTTATCTTGAT
1 ATATTAAATTAAATCTAATATTTATCTTGAT
* **
39588683 ATATTAAATTAAATTTAATATTTA-AGTGAT
1 ATATTAAATTAAATCTAATATTTATCTTGAT
*
39588713 -TAAGTTTAATT--ATCTAATATTTATCTTGAT
1 AT-A-TTAAATTAAATCTAATATTTATCTTGAT
* *
39588743 AAATTAAATTAAATTTAATATTTA
1 ATATTAAATTAAATCTAATATTTA
39588767 AGTGATTAAG
Statistics
Matches: 67, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
29 18 0.27
30 10 0.15
31 39 0.58
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (31 bp):
ATATTAAATTAAATCTAATATTTATCTTGAT
Found at i:39588715 original size:21 final size:19
Alignment explanation
Indices: 39588647--39588782 Score: 68
Period size: 21 Copynumber: 7.0 Consensus size: 19
39588637 TATTTTATTA
39588647 ATTTAATATTAAATTT-A-
1 ATTTAATATTAAATTTAAT
* * *
39588664 ATCTAATATT-TATCTTGAT
1 ATTTAATATTAAAT-TTAAT
39588683 ATATTAA-ATTAAATTTAAT
1 AT-TTAATATTAAATTTAAT
*
39588702 ATTTAAGTGATTAAGTTTAATT
1 ATTTAA-T-ATTAAATTTAA-T
* * *
39588724 ATCTAATATT-TATCTTGAT
1 ATTTAATATTAAAT-TTAAT
*
39588743 AAATTAA-ATTAAATTTAAT
1 -ATTTAATATTAAATTTAAT
*
39588762 ATTTAAGTGATTAAGTTTAAT
1 ATTTAA-T-ATTAAATTTAAT
39588783 TATAGTTGAA
Statistics
Matches: 88, Mismatches: 16, Indels: 26
0.68 0.12 0.20
Matches are distributed among these distances:
16 2 0.02
17 11 0.12
18 10 0.11
19 20 0.23
20 17 0.19
21 22 0.25
22 6 0.07
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (19 bp):
ATTTAATATTAAATTTAAT
Found at i:39588729 original size:60 final size:60
Alignment explanation
Indices: 39588664--39588785 Score: 235
Period size: 60 Copynumber: 2.0 Consensus size: 60
39588654 ATTAAATTTA
*
39588664 ATCTAATATTTATCTTGATATATTAAATTAAATTTAATATTTAAGTGATTAAGTTTAATT
1 ATCTAATATTTATCTTGATAAATTAAATTAAATTTAATATTTAAGTGATTAAGTTTAATT
39588724 ATCTAATATTTATCTTGATAAATTAAATTAAATTTAATATTTAAGTGATTAAGTTTAATT
1 ATCTAATATTTATCTTGATAAATTAAATTAAATTTAATATTTAAGTGATTAAGTTTAATT
39588784 AT
1 AT
39588786 AGTTGAACTC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (60 bp):
ATCTAATATTTATCTTGATAAATTAAATTAAATTTAATATTTAAGTGATTAAGTTTAATT
Found at i:39588784 original size:31 final size:31
Alignment explanation
Indices: 39588689--39588784 Score: 117
Period size: 31 Copynumber: 3.2 Consensus size: 31
39588679 TGATATATTA
39588689 AATTAAATTTAATATTTAAGTGATTAAGTTT
1 AATTAAATTTAATATTTAAGTGATTAAGTTT
* ** * *
39588720 AATT--ATCTAATATTTATCTTGA-TAAATTA
1 AATTAAATTTAATATTTA-AGTGATTAAGTTT
39588749 AATTAAATTTAATATTTAAGTGATTAAGTTT
1 AATTAAATTTAATATTTAAGTGATTAAGTTT
39588780 AATTA
1 AATTA
39588785 TAGTTGAACT
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
29 20 0.39
30 6 0.12
31 25 0.49
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (31 bp):
AATTAAATTTAATATTTAAGTGATTAAGTTT
Found at i:39590261 original size:37 final size:37
Alignment explanation
Indices: 39590217--39590308 Score: 175
Period size: 37 Copynumber: 2.5 Consensus size: 37
39590207 CACTTGTCCC
39590217 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
1 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
*
39590254 TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
1 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
39590291 TGATCAGATAAGTGTAGC
1 TGATCAGATAAGTGTAGC
39590309 TAAAGCTATC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.37
Consensus pattern (37 bp):
TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
Found at i:39590339 original size:46 final size:46
Alignment explanation
Indices: 39590272--39590540 Score: 331
Period size: 46 Copynumber: 5.6 Consensus size: 46
39590262 TAAGTGTAGC
** **
39590272 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
39590318 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
39590364 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
39590416 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
39590462 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
39590514 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
39590541 AGTACTCAAA
Statistics
Matches: 198, Mismatches: 13, Indels: 24
0.84 0.06 0.10
Matches are distributed among these distances:
46 111 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:39590391 original size:52 final size:52
Alignment explanation
Indices: 39590315--39590534 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
39590305 TAGCTAAAGC
* *
39590315 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
39590368 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
39590420 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
39590466 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
39590518 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
39590535 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:39590437 original size:98 final size:98
Alignment explanation
Indices: 39590289--39590540 Score: 450
Period size: 98 Copynumber: 2.6 Consensus size: 98
39590279 CACTTTGTTT
*
39590289 CTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAG
1 CTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAG
*
39590354 CCGAAGCTATCACTTATCACTTTTCACTTGTCA
66 CCGAAGCTATCACTTATCACTTTCCACTTGTCA
**
39590387 CTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAG
*
39590452 CCGAAGCTATTACTTATCACTTTCCACTTGTCA
66 CCGAAGCTATCACTTATCACTTTCCACTTGTCA
*
39590485 CTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGA
1 CTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTTGATCAGA
39590541 AGTACTCAAA
Statistics
Matches: 146, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 146 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (98 bp):
CTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAG
CCGAAGCTATCACTTATCACTTTCCACTTGTCA
Found at i:39606183 original size:16 final size:15
Alignment explanation
Indices: 39606156--39606189 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
39606146 ATAACTAGTA
39606156 TATAATTATATTAAT
1 TATAATTATATTAAT
39606171 TATAATATATATTAAT
1 TATAAT-TATATTAAT
39606187 TAT
1 TAT
39606190 TATCAACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATAATTATATTAAT
Found at i:39608125 original size:41 final size:40
Alignment explanation
Indices: 39608080--39608160 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 40
39608070 TCAATAAGAA
39608080 CCGCTCGTACGAAAATATACAATGACCCATTTATTTTTGT
1 CCGCTCGTACGAAAATATACAATGACCCATTTATTTTTGT
* *
39608120 NCCGCTCTTACGAAAATATTCAATGACCCATTTATTTTTGT
1 -CCGCTCGTACGAAAATATACAATGACCCATTTATTTTTGT
39608161 GCCTGAGTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.37
Consensus pattern (40 bp):
CCGCTCGTACGAAAATATACAATGACCCATTTATTTTTGT
Found at i:39615124 original size:27 final size:27
Alignment explanation
Indices: 39615063--39615124 Score: 65
Period size: 27 Copynumber: 2.2 Consensus size: 27
39615053 TTCAAGCAAT
39615063 TAATAAAAATTATTTGTAAAATTAATGA
1 TAAT-AAAATTATTTGTAAAATTAATGA
*
39615091 TACATAAAA-TATTTTTAAAACTTAAAT-A
1 TA-ATAAAATTATTTGTAAAA-TT-AATGA
39615119 TAATAA
1 TAATAA
39615125 TAAATGATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
27 14 0.47
28 11 0.37
29 5 0.17
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (27 bp):
TAATAAAATTATTTGTAAAATTAATGA
Found at i:39620320 original size:16 final size:15
Alignment explanation
Indices: 39620299--39620362 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 15
39620289 AATCAAAAGT
39620299 ATTTTTAAAATATTTA
1 ATTTTTAAAAT-TTTA
* *
39620315 ATTTTTAATATTTTT
1 ATTTTTAAAATTTTA
*
39620330 ATTTTT-GAA-TTTA
1 ATTTTTAAAATTTTA
*
39620343 A-ATTTAAAATTTTTA
1 ATTTTTAAAA-TTTTA
39620358 ATTTT
1 ATTTT
39620363 AATAAACCTA
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
12 3 0.08
13 6 0.17
14 1 0.03
15 14 0.39
16 12 0.33
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (15 bp):
ATTTTTAAAATTTTA
Found at i:39620333 original size:15 final size:16
Alignment explanation
Indices: 39620298--39620335 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
39620288 AAATCAAAAG
39620298 TATTTTTAAAATATTT
1 TATTTTTAAAATATTT
* *
39620314 AATTTTTAATAT-TTT
1 TATTTTTAAAATATTT
39620329 TATTTTT
1 TATTTTT
39620336 GAATTTAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTTTTAAAATATTT
Found at i:39631340 original size:29 final size:29
Alignment explanation
Indices: 39631308--39631363 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
39631298 AAAGGCCAGT
39631308 TTTTTTCAA-AATTTACCGAAATGGGCCGG
1 TTTTTT-AATAATTTACCGAAATGGGCCGG
* *
39631337 TTTTTTAATTATTTACCGGAATGGGCC
1 TTTTTTAATAATTTACCGAAATGGGCC
39631364 ATTTTCCGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (29 bp):
TTTTTTAATAATTTACCGAAATGGGCCGG
Found at i:39631342 original size:30 final size:29
Alignment explanation
Indices: 39631301--39631368 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
39631291 AACCAAAAAA
39631301 GGCCAGTTTTTTTCAA-AATTTACCGAAATG
1 GGCCAG-TTTTTT-AATAATTTACCGAAATG
* * *
39631331 GGCCGGTTTTTTAATTATTTACCGGAATG
1 GGCCAGTTTTTTAATAATTTACCGAAATG
39631360 GGCCA-TTTT
1 GGCCAGTTTT
39631369 CCGCGAAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 6 0.18
29 22 0.67
30 5 0.15
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.40
Consensus pattern (29 bp):
GGCCAGTTTTTTAATAATTTACCGAAATG
Found at i:39633015 original size:3 final size:3
Alignment explanation
Indices: 39633009--39633039 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
39632999 CTTAATAACA
*
39633009 AAG AAG AAG AAG AAG ATG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
39633040 GACTATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:39634408 original size:6 final size:6
Alignment explanation
Indices: 39634397--39634440 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
39634387 ATGAAACTTC
* * *
39634397 TCCATT TCCATT TCCAAT TCCAAT TCCAAT TCCATT TCCATT TC
1 TCCATT TCCATT TCCATT TCCATT TCCATT TCCATT TCCATT TC
39634441 TTATTGCCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.23, C:0.34, G:0.00, T:0.43
Consensus pattern (6 bp):
TCCATT
Found at i:39638672 original size:20 final size:20
Alignment explanation
Indices: 39638647--39638685 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
39638637 GAGTTCATAC
39638647 AGAGGCACCGAAGTGCAAAT
1 AGAGGCACCGAAGTGCAAAT
*
39638667 AGAGGCACTGAAGTGCAAA
1 AGAGGCACCGAAGTGCAAA
39638686 CAAATACATT
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:0.41, C:0.18, G:0.31, T:0.10
Consensus pattern (20 bp):
AGAGGCACCGAAGTGCAAAT
Found at i:39644353 original size:100 final size:103
Alignment explanation
Indices: 39644238--39644467 Score: 261
Period size: 100 Copynumber: 2.2 Consensus size: 103
39644228 CAATGTCATA
* * ** *
39644238 TCCCAGATATGGTCTTACATGGGAGTTCTCATATTGGTGCCTATGCCATGTCCCAGACAT-AGTC
1 TCCCAGACATGGTCTTACATGGGACTTCTCATATCAGTGCCAATGCCATGTCCCAGACATGA-TC
**
39644302 TTATGGGGGACCTCTC-ATCTC-GG-TGCCAACACCATG
65 TTACAGGGGACCTCTCAATCTCAGGATGCCAACACCATG
* * * *
39644338 TCCCAGACATGGTCTTACATAGGACTTCTCGTCTCAGTGTCAATGCCATGTCCCAGACATGATCT
1 TCCCAGACATGGTCTTACATGGGACTTCTCATATCAGTGCCAATGCCATGTCCCAGACATGATCT
* **
39644403 TACATGGGACCTCTCATGATCTCAAGGATGCCAATGCCATG
66 TACAGGGGACCTCTCA--ATCTC-AGGATGCCAACACCATG
*
39644444 TCCCAGACATGATCTTACATGGGA
1 TCCCAGACATGGTCTTACATGGGA
39644468 TCTCTTTACC
Statistics
Matches: 107, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
100 66 0.62
101 1 0.01
103 5 0.05
105 2 0.02
106 33 0.31
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.28
Consensus pattern (103 bp):
TCCCAGACATGGTCTTACATGGGACTTCTCATATCAGTGCCAATGCCATGTCCCAGACATGATCT
TACAGGGGACCTCTCAATCTCAGGATGCCAACACCATG
Found at i:39644439 original size:56 final size:52
Alignment explanation
Indices: 39644225--39644472 Score: 231
Period size: 50 Copynumber: 4.8 Consensus size: 52
39644215 TTTCTTGTAC
* * * * ** * *
39644225 TGCCAATGTCATATCCCAGATATGGTCTTACATGGGAGTTCTC-ATAT-TGG
1 TGCCAATGCCATGTCCCAGACATGATCTTACATGGGACCTCTCGATCTCAGG
* ***
39644275 TGCCTATGCCATGTCCCAGACAT-AGTCTTATGGGGGACCTCTC-ATCTC-GG
1 TGCCAATGCCATGTCCCAGACATGA-TCTTACATGGGACCTCTCGATCTCAGG
** * * *
39644325 TGCCAACACCATGTCCCAGACATGGTCTTACATAGGACTTCTCG-TCTCA-G
1 TGCCAATGCCATGTCCCAGACATGATCTTACATGGGACCTCTCGATCTCAGG
*
39644375 TGTCAATGCCATGTCCCAGACATGATCTTACATGGGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGATCTTACATGGGACCTCTC--GATCTC-AGG
*
39644430 ATGCCAATGCCATGTCCCAGACATGATCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGATCTTACATGGGACCTCT
39644473 TTACCCAAAT
Statistics
Matches: 159, Mismatches: 28, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
50 112 0.70
52 1 0.01
53 4 0.03
54 1 0.01
55 1 0.01
56 40 0.25
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (52 bp):
TGCCAATGCCATGTCCCAGACATGATCTTACATGGGACCTCTCGATCTCAGG
Found at i:39651788 original size:102 final size:102
Alignment explanation
Indices: 39651674--39651878 Score: 401
Period size: 102 Copynumber: 2.0 Consensus size: 102
39651664 TTGAAAGTCC
*
39651674 TTCCCATTTTTTTCTTATGAAAATTGTGTTAGATTTTCTTTAAGTGTGCACACTGTGCTAGTCCA
1 TTCCCATTTTTTTCTTATGAAAATTGTGTTAGATTTTCTCTAAGTGTGCACACTGTGCTAGTCCA
39651739 GCTTCATGTCCATTTTCTGGGTTGGATCATATATCAG
66 GCTTCATGTCCATTTTCTGGGTTGGATCATATATCAG
39651776 TTCCCATTTTTTTCTTATGAAAATTGTGTTAGATTTTCTCTAAGTGTGCACACTGTGCTAGTCCA
1 TTCCCATTTTTTTCTTATGAAAATTGTGTTAGATTTTCTCTAAGTGTGCACACTGTGCTAGTCCA
39651841 GCTTCATGTCCATTTTCTGGGTTGGATCATATATCAG
66 GCTTCATGTCCATTTTCTGGGTTGGATCATATATCAG
39651878 T
1 T
39651879 GAGGCTAAAT
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 102 1.00
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.44
Consensus pattern (102 bp):
TTCCCATTTTTTTCTTATGAAAATTGTGTTAGATTTTCTCTAAGTGTGCACACTGTGCTAGTCCA
GCTTCATGTCCATTTTCTGGGTTGGATCATATATCAG
Found at i:39660903 original size:50 final size:50
Alignment explanation
Indices: 39660792--39660989 Score: 279
Period size: 50 Copynumber: 3.8 Consensus size: 50
39660782 ATTTGGGTAA
* *
39660792 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC--GAG---ATG
*
39660848 AGAGGTCCCATGTAAGGCCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
*
39660898 AGAGGTCCCATGTAAGACCATGTCTGGGATATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** *
39660948 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
39660990 TGTTATGATG
Statistics
Matches: 133, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
50 89 0.67
53 3 0.02
55 2 0.02
56 39 0.29
ACGTcount: A:0.24, C:0.22, G:0.32, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:39666070 original size:19 final size:19
Alignment explanation
Indices: 39666046--39666083 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
39666036 AGAAACATGT
*
39666046 GGCTCATGTGTTGGAGAAA
1 GGCTCATGTATTGGAGAAA
39666065 GGCTCATGTATTGGAGAAA
1 GGCTCATGTATTGGAGAAA
39666084 TGCACTATAG
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:0.29, C:0.11, G:0.34, T:0.26
Consensus pattern (19 bp):
GGCTCATGTATTGGAGAAA
Found at i:39668126 original size:31 final size:29
Alignment explanation
Indices: 39668057--39668130 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
39668047 ACAAAATAAT
**
39668057 AACATAAGTGACTAAAACGTAACATTTCA
1 AACATAAGTGACTAAAACGTAACAAGTCA
*
39668086 AACATAAGTGACTAAAATGTAACCTAAGTCA
1 AACATAAGTGACTAAAACGTAA-C-AAGTCA
*
39668117 AACAAAAGTGACTA
1 AACATAAGTGACTA
39668131 TTTTTGTAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 21 0.54
30 1 0.03
31 17 0.44
ACGTcount: A:0.50, C:0.16, G:0.12, T:0.22
Consensus pattern (29 bp):
AACATAAGTGACTAAAACGTAACAAGTCA
Found at i:39678933 original size:30 final size:33
Alignment explanation
Indices: 39678899--39678969 Score: 94
Period size: 34 Copynumber: 2.2 Consensus size: 33
39678889 TATGGAATAT
*
39678899 TATCTTTTAGG-A-ATATCTA-AATATATTGTA
1 TATCTTTTAGGTATATATCTAGAATATATTATA
*
39678929 TATCTTTTAGGTATATATTTAGGAATATATTATA
1 TATCTTTTAGGTATATATCTA-GAATATATTATA
39678963 TATCTTT
1 TATCTTT
39678970 GGCTTAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 11 0.31
31 1 0.03
32 6 0.17
34 17 0.49
ACGTcount: A:0.34, C:0.06, G:0.10, T:0.51
Consensus pattern (33 bp):
TATCTTTTAGGTATATATCTAGAATATATTATA
Found at i:39682729 original size:73 final size:73
Alignment explanation
Indices: 39682642--39682973 Score: 646
Period size: 73 Copynumber: 4.5 Consensus size: 73
39682632 ACAACTTGAC
39682642 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
39682707 CACTAACA
66 CACTAACA
39682715 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
39682780 CACTAACA
66 CACTAACA
39682788 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
39682853 CACTAACA
66 CACTAACA
39682861 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
39682926 CACTAACA
66 CACTAACA
* *
39682934 AACTTTGTTGGAATACAACTAAGTTACATCATTACATCCA
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCA
39682974 AATAATAATA
Statistics
Matches: 257, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 257 1.00
ACGTcount: A:0.41, C:0.25, G:0.06, T:0.28
Consensus pattern (73 bp):
AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
CACTAACA
Found at i:39687329 original size:3 final size:3
Alignment explanation
Indices: 39687321--39687349 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
39687311 ATTACATCCA
39687321 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
39687350 AACATGTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:39691898 original size:72 final size:73
Alignment explanation
Indices: 39691781--39691921 Score: 230
Period size: 72 Copynumber: 1.9 Consensus size: 73
39691771 AAGAACAAAC
* * *
39691781 CTTTAGTGGCGCTCCTCGCAAAAAAGCCGCTAAAAACATAACCTTT-AAAAAATTATTTTAATCA
1 CTTTAGCGGCGCTCCTCACAAAAAAGCCACTAAAAACATAACCTTTAAAAAAATTATTTTAATCA
39691845 AATAATAT
66 AATAATAT
* *
39691853 CTTTAGCGGCGCTTCTCACAAAAACGCCACTAAAAACATAACCTTTAAAAAAATTATTTTAATCA
1 CTTTAGCGGCGCTCCTCACAAAAAAGCCACTAAAAACATAACCTTTAAAAAAATTATTTTAATCA
39691918 AATA
66 AATA
39691922 TTTTATTTTA
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
72 41 0.65
73 22 0.35
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.28
Consensus pattern (73 bp):
CTTTAGCGGCGCTCCTCACAAAAAAGCCACTAAAAACATAACCTTTAAAAAAATTATTTTAATCA
AATAATAT
Found at i:39695686 original size:21 final size:21
Alignment explanation
Indices: 39695660--39695709 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
39695650 GGTGGTGGTA
* *
39695660 AGATTAGTTACTGTAGCGGTG
1 AGATTAGATACTGTAGCAGTG
39695681 AGATTAGATACTGTAGCAGTG
1 AGATTAGATACTGTAGCAGTG
39695702 AGATTAGA
1 AGATTAGA
39695710 AACAGCGGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (21 bp):
AGATTAGATACTGTAGCAGTG
Found at i:39698663 original size:6 final size:6
Alignment explanation
Indices: 39698652--39698701 Score: 82
Period size: 6 Copynumber: 8.2 Consensus size: 6
39698642 TTTGCAATCC
*
39698652 AAGGGG AAGGGG AAAGGG AAGGGG AAGGGG AAGGGG AAGGGG AAAGGGG
1 AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG -AAGGGG
39698701 A
1 A
39698702 GAAGAAGGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
6 35 0.85
7 6 0.15
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (6 bp):
AAGGGG
Found at i:39698708 original size:18 final size:17
Alignment explanation
Indices: 39698652--39698709 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 17
39698642 TTTGCAATCC
39698652 AAGGGGAAGGGGA-AAGGG
1 AAGGGGAAGGGGAGAA--G
**
39698670 AAGGGGAAGGGGAAGGGG
1 AAGGGGAAGGGG-AGAAG
39698688 AAGGGGAAAGGGGAGAAG
1 AAGGGG-AAGGGGAGAAG
39698706 AAGG
1 AAGG
39698710 TAACAGACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 26 0.79
19 7 0.21
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (17 bp):
AAGGGGAAGGGGAGAAG
Found at i:39704524 original size:32 final size:32
Alignment explanation
Indices: 39704483--39704555 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
39704473 TAGAGTATAA
*
39704483 CTTAAAAAAACCATGAAAAGTGAGGATATTCC
1 CTTAAAAAAACCATAAAAAGTGAGGATATTCC
39704515 CTTAAAAAAACCATAAAAAGTGAGGATATTCC
1 CTTAAAAAAACCATAAAAAGTGAGGATATTCC
39704547 CTTAAAAAA
1 CTTAAAAAA
39704556 TTATTCGAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.51, C:0.15, G:0.12, T:0.22
Consensus pattern (32 bp):
CTTAAAAAAACCATAAAAAGTGAGGATATTCC
Found at i:39714914 original size:18 final size:18
Alignment explanation
Indices: 39714880--39714930 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
39714870 TAGGGTGTGC
39714880 AAAATTCGGTTAAAACCGAA
1 AAAATTCGGTT--AACCGAA
*
39714900 AAAATTCGGTTAACCGAC
1 AAAATTCGGTTAACCGAA
**
39714918 CGAATTCGGTTAA
1 AAAATTCGGTTAA
39714931 TCAGTCGGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 17 0.61
20 11 0.39
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.24
Consensus pattern (18 bp):
AAAATTCGGTTAACCGAA
Found at i:39715137 original size:13 final size:13
Alignment explanation
Indices: 39715119--39715145 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39715109 CCTCCAGGCT
39715119 CTAAGCCCAAGAA
1 CTAAGCCCAAGAA
39715132 CTAAGCCCAAGAA
1 CTAAGCCCAAGAA
39715145 C
1 C
39715146 AATTCATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.33, G:0.15, T:0.07
Consensus pattern (13 bp):
CTAAGCCCAAGAA
Found at i:39715160 original size:7 final size:7
Alignment explanation
Indices: 39715148--39715206 Score: 73
Period size: 7 Copynumber: 8.3 Consensus size: 7
39715138 CCAAGAACAA
39715148 TTCATGT
1 TTCATGT
39715155 TTCATGT
1 TTCATGT
39715162 TTCATGT
1 TTCATGT
*
39715169 TTCACGAT
1 TTCATG-T
39715177 TTCATGT
1 TTCATGT
**
39715184 TTCATAC
1 TTCATGT
*
39715191 TGCATGT
1 TTCATGT
39715198 TTCATGT
1 TTCATGT
39715205 TT
1 TT
39715207 TCTTCTGTAC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
7 37 0.86
8 6 0.14
ACGTcount: A:0.17, C:0.17, G:0.14, T:0.53
Consensus pattern (7 bp):
TTCATGT
Found at i:39715496 original size:37 final size:37
Alignment explanation
Indices: 39715453--39715558 Score: 158
Period size: 37 Copynumber: 2.9 Consensus size: 37
39715443 TGTGTTAAAG
*
39715453 ACTTATGTAATGTTTTTAATTATTTAGTGATTCAAAA
1 ACTTATGTAATGTTTTTAATTATATAGTGATTCAAAA
* * * *
39715490 ATTTATGTAATGTTTTTAGTTATGTAGTGATTCAAAG
1 ACTTATGTAATGTTTTTAATTATATAGTGATTCAAAA
*
39715527 ACTTATGTAATTTTTTTAATTATATAGTGATT
1 ACTTATGTAATGTTTTTAATTATATAGTGATT
39715559 TAAATCGGTT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.32, C:0.04, G:0.13, T:0.51
Consensus pattern (37 bp):
ACTTATGTAATGTTTTTAATTATATAGTGATTCAAAA
Found at i:39715577 original size:9 final size:9
Alignment explanation
Indices: 39715558--39715650 Score: 143
Period size: 9 Copynumber: 10.4 Consensus size: 9
39715548 ATATAGTGAT
39715558 TTAAATCGG
1 TTAAATCGG
* *
39715567 TTAAGTTGG
1 TTAAATCGG
39715576 TTAAATCGG
1 TTAAATCGG
39715585 TTAAATCGG
1 TTAAATCGG
39715594 TTAAATCGG
1 TTAAATCGG
39715603 TTAAATCGG
1 TTAAATCGG
*
39715612 TTAAGTCGG
1 TTAAATCGG
39715621 TT-AATCGG
1 TTAAATCGG
*
39715629 TTAAATAGG
1 TTAAATCGG
39715638 TTAAATCGG
1 TTAAATCGG
39715647 TTAA
1 TTAA
39715651 TTTTTAACCA
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
8 7 0.09
9 68 0.91
ACGTcount: A:0.32, C:0.09, G:0.24, T:0.35
Consensus pattern (9 bp):
TTAAATCGG
Found at i:39715827 original size:12 final size:12
Alignment explanation
Indices: 39715810--39715834 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39715800 AACTAATTCG
39715810 GGTCGGTTAACC
1 GGTCGGTTAACC
39715822 GGTCGGTTAACC
1 GGTCGGTTAACC
39715834 G
1 G
39715835 AATGCACACC
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:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:39724977 original size:2 final size:2
Alignment explanation
Indices: 39724935--39724964 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
39724925 CTGTTGGCAA
39724935 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
39724965 CATGTGAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39730146 original size:18 final size:18
Alignment explanation
Indices: 39730123--39730160 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
39730113 GATAATAAAG
39730123 AATGTAGAATAAA-ATTAA
1 AATGTAGAA-AAATATTAA
*
39730141 AATGTATAAAAATATTAA
1 AATGTAGAAAAATATTAA
39730159 AA
1 AA
39730161 CAAAAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (18 bp):
AATGTAGAAAAATATTAA
Found at i:39730381 original size:18 final size:18
Alignment explanation
Indices: 39730358--39730402 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
39730348 AATAAACCAC
39730358 AACTTACAAGTCTAACAA
1 AACTTACAAGTCTAACAA
39730376 AACTTACAAGTCTAACAA
1 AACTTACAAGTCTAACAA
*
39730394 AATTTACAA
1 AACTTACAA
39730403 ACCCTATCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.51, C:0.20, G:0.04, T:0.24
Consensus pattern (18 bp):
AACTTACAAGTCTAACAA
Found at i:39730656 original size:29 final size:28
Alignment explanation
Indices: 39730609--39730710 Score: 75
Period size: 29 Copynumber: 3.7 Consensus size: 28
39730599 TATGCTATTC
* *
39730609 TATACATTAACTTTGAATTTGGGTAATTT
1 TATACATAAAATTTGAATTT-GGTAATTT
* **
39730638 TATACATAAAATTTTAATTT-G--ATCC
1 TATACATAAAATTTGAATTTGGTAATTT
* * * *
39730663 AATTCATGAACTTTGAATTTGTGTAATTT
1 TATACATAAAATTTGAATTTG-GTAATTT
*
39730692 TATACATAAAATTTTAATT
1 TATACATAAAATTTGAATT
39730711 AATTTGATCC
Statistics
Matches: 52, Mismatches: 17, Indels: 8
0.68 0.22 0.10
Matches are distributed among these distances:
25 17 0.33
27 2 0.04
29 33 0.63
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.47
Consensus pattern (28 bp):
TATACATAAAATTTGAATTTGGTAATTT
Found at i:39730879 original size:31 final size:30
Alignment explanation
Indices: 39730844--39730929 Score: 82
Period size: 31 Copynumber: 2.8 Consensus size: 30
39730834 ATTAAAAGTG
*
39730844 TATAATTGAATCAAAATTAAAGTTTCATATA
1 TATAATTGAA-CAAAATTAAAGTTTCACATA
* ** * *
39730875 TATAATTGAACCACAACCAAATTTTCACATG
1 TATAATTGAA-CAAAATTAAAGTTTCACATA
* *
39730906 TATAATTGTACCAAATTAAAGTTT
1 TATAATTGAACAAAATTAAAGTTT
39730930 AAGTATAAAA
Statistics
Matches: 42, Mismatches: 13, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
30 9 0.21
31 33 0.79
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (30 bp):
TATAATTGAACAAAATTAAAGTTTCACATA
Found at i:39738620 original size:254 final size:254
Alignment explanation
Indices: 39738171--39738672 Score: 977
Period size: 254 Copynumber: 2.0 Consensus size: 254
39738161 TTGACCTCAC
39738171 AGTCCAGATTGGTTCAGGCCTAATGTGTTCGCGGATAGGCCATACCAATTTTGGGTTAATTTCTA
1 AGTCCAGATTGGTTCAGGCCTAATGTGTTCGCGGATAGGCCATACCAATTTTGGGTTAATTTCTA
*
39738236 CCTAAATGACTTATTAGGGTTGTCAAGCCTAAGGTTTAAGTTCTTCCTCTCCCAAACAGTTGATC
66 CCTAAATGACTTATTAAGGTTGTCAAGCCTAAGGTTTAAGTTCTTCCTCTCCCAAACAGTTGATC
39738301 CATTAAGAAAACCCTACATAACAATTAATAAATCACACATCCACTCATAATCCACCATAAAAGGA
131 CATTAAGAAAACCCTACATAACAATTAATAAATCACACATCCACTCATAATCCACCATAAAAGGA
39738366 TTAGTTCCTTATGGATCTCATGAACACAATAATCTTGATAATAAATGTAAGAAAGGATT
196 TTAGTTCCTTATGGATCTCATGAACACAATAATCTTGATAATAAATGTAAGAAAGGATT
39738425 AGTCCAGATTGGTTCAGGCCTAATGTGTTCGCGGATAGGCCATACCAATTTTGGGTTAATTTCTA
1 AGTCCAGATTGGTTCAGGCCTAATGTGTTCGCGGATAGGCCATACCAATTTTGGGTTAATTTCTA
39738490 CCTAAATGACTTATTAAGGTTGTCAAGCCTAAGGTTTAAGTTCTTCCTCTCCCAAACAGTTGATC
66 CCTAAATGACTTATTAAGGTTGTCAAGCCTAAGGTTTAAGTTCTTCCTCTCCCAAACAGTTGATC
* *
39738555 CATTAAGAATACCCTACATAGCAATTAATAAATCACACATCCACTCATAATCCACCATAAAAGGA
131 CATTAAGAAAACCCTACATAACAATTAATAAATCACACATCCACTCATAATCCACCATAAAAGGA
39738620 TTAGTTCCTTATGGATCTCATGAACACAATAATCTTGATAATAAATGTAAGAA
196 TTAGTTCCTTATGGATCTCATGAACACAATAATCTTGATAATAAATGTAAGAA
39738673 TAAATAATAA
Statistics
Matches: 245, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
254 245 1.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.30
Consensus pattern (254 bp):
AGTCCAGATTGGTTCAGGCCTAATGTGTTCGCGGATAGGCCATACCAATTTTGGGTTAATTTCTA
CCTAAATGACTTATTAAGGTTGTCAAGCCTAAGGTTTAAGTTCTTCCTCTCCCAAACAGTTGATC
CATTAAGAAAACCCTACATAACAATTAATAAATCACACATCCACTCATAATCCACCATAAAAGGA
TTAGTTCCTTATGGATCTCATGAACACAATAATCTTGATAATAAATGTAAGAAAGGATT
Found at i:39743105 original size:98 final size:99
Alignment explanation
Indices: 39742936--39743168 Score: 369
Period size: 98 Copynumber: 2.3 Consensus size: 99
39742926 TTTACATTTG
* * *
39742936 TAGTGCCATAACCCAGTTGTGGTCTTATCATCAGAATGTCATAGCCTAGCTATGGTCTTACATAT
1 TAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTATGGTCTTACATAT
*
39743001 AAACACTGCC-ATCTAACCATGGTCTTACGTTCA
66 AAACACTGCCAATCCAACCATGGTCTTACGTTCA
* * *
39743034 TAGTGTCATAACCCAGTTATGGTCTTATCATGAGAATGCCATGGCCCAGCTATGGTCTTACATAT
1 TAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTATGGTCTTACATAT
39743099 AAACACTGCCATGATCCAACCATGGTCTTACGTTCA
66 AAACACTGCCA--ATCCAACCATGGTCTTACGTTCA
39743135 TAGTGCCATAACCCAGTTATGGTCTTATCCATCA
1 TAGTGCCATAACCCAGTTATGGTCTTAT-CATCA
39743169 ATTCATCATT
Statistics
Matches: 122, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
98 69 0.57
101 49 0.40
102 4 0.03
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (99 bp):
TAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTATGGTCTTACATAT
AAACACTGCCAATCCAACCATGGTCTTACGTTCA
Found at i:39743157 original size:33 final size:33
Alignment explanation
Indices: 39743019--39743161 Score: 103
Period size: 33 Copynumber: 4.3 Consensus size: 33
39743009 CCATCTAACC
* *
39743019 ATGGTCTTACGTTCATAGTGTCATAACCCAGTT
1 ATGGTCTTACGTTCATAGTGCCATAACCCAGCT
**
39743052 ATGGTCTTA---TCATGAGAATGCCATGGCCCAGCT
1 ATGGTCTTACGTTCAT-AG--TGCCATAACCCAGCT
* * * * * * * *
39743085 ATGGTCTTACATATAAACACTGCCATGATCCAACC
1 ATGGTCTTACGT-T-CATAGTGCCATAACCCAGCT
*
39743120 ATGGTCTTACGTTCATAGTGCCATAACCCAGTT
1 ATGGTCTTACGTTCATAGTGCCATAACCCAGCT
39743153 ATGGTCTTA
1 ATGGTCTTA
39743162 TCCATCAATT
Statistics
Matches: 82, Mismatches: 20, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
30 4 0.05
31 2 0.02
33 50 0.61
34 1 0.01
35 22 0.27
37 2 0.02
38 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (33 bp):
ATGGTCTTACGTTCATAGTGCCATAACCCAGCT
Found at i:39745583 original size:43 final size:43
Alignment explanation
Indices: 39745535--39745623 Score: 117
Period size: 43 Copynumber: 2.1 Consensus size: 43
39745525 CTTATGTCAA
* *
39745535 TTGTTAGAGTATATTATACTTATATCT-CAAAGGTATTATTTTC
1 TTGTTAGAATATATTATACTTATAT-TACAAAGGTATTATTCTC
* * *
39745578 TTGTTAGAATATGTTGTACTTATATTATAAAGGTATTATTCTC
1 TTGTTAGAATATATTATACTTATATTACAAAGGTATTATTCTC
39745621 TTG
1 TTG
39745624 GTATCATCTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 1 0.03
43 39 0.98
ACGTcount: A:0.29, C:0.08, G:0.13, T:0.49
Consensus pattern (43 bp):
TTGTTAGAATATATTATACTTATATTACAAAGGTATTATTCTC
Found at i:39746193 original size:19 final size:20
Alignment explanation
Indices: 39746156--39746209 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
39746146 ACAAAAACTA
*
39746156 TAAAAATTTAAAATAATTT-
1 TAAAAATTCAAAATAATTTG
39746175 TCAAAAATTCAAAAT-ATTTG
1 T-AAAAATTCAAAATAATTTG
39746195 TAAAAATTCTAAAAT
1 TAAAAATTC-AAAAT
39746210 TGATATTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
19 13 0.42
20 18 0.58
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (20 bp):
TAAAAATTCAAAATAATTTG
Found at i:39749869 original size:15 final size:15
Alignment explanation
Indices: 39749849--39749879 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39749839 GTTCGTTCAA
39749849 TTTTATATATAAATT
1 TTTTATATATAAATT
*
39749864 TTTTATTTATAAATT
1 TTTTATATATAAATT
39749879 T
1 T
39749880 AATTGTAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTATATATAAATT
Found at i:39750650 original size:18 final size:18
Alignment explanation
Indices: 39750627--39750666 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
39750617 TTTCTTTTTC
*
39750627 TTTCCCT-TCTTCCCCCTT
1 TTTCCCTAT-TTCCCCCCT
39750645 TTTCCCTATTTCCCCCCT
1 TTTCCCTATTTCCCCCCT
39750663 TTTC
1 TTTC
39750667 TTTTTCATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTCCCTATTTCCCCCCT
Found at i:39753269 original size:42 final size:42
Alignment explanation
Indices: 39753221--39753319 Score: 153
Period size: 42 Copynumber: 2.4 Consensus size: 42
39753211 GCTCTCGGTA
* *
39753221 TCGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAATT
1 TCGCACACTTAGTGCCCATTATCCAACATCATCATTTTAATT
* *
39753263 TCGCACACTTAGTGCCTATTATCCAACATCATTATTTTAATT
1 TCGCACACTTAGTGCCCATTATCCAACATCATCATTTTAATT
*
39753305 TCGTACACTTAGTGC
1 TCGCACACTTAGTGC
39753320 TGTTCATATA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.26, C:0.25, G:0.10, T:0.38
Consensus pattern (42 bp):
TCGCACACTTAGTGCCCATTATCCAACATCATCATTTTAATT
Found at i:39761353 original size:15 final size:15
Alignment explanation
Indices: 39761323--39761353 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39761313 AGTGCTGCTG
*
39761323 ATAAAGGAATAAAAA
1 ATAAAGGAAAAAAAA
39761338 ATAAAGGAAAAAAAA
1 ATAAAGGAAAAAAAA
39761353 A
1 A
39761354 CAGAAAATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (15 bp):
ATAAAGGAAAAAAAA
Found at i:39761769 original size:41 final size:42
Alignment explanation
Indices: 39761731--39761810 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
39761721 AATTAAATTT
39761731 AAATAACTTTTAAAATA-TATAAAAATAATAAAAATAAATCC
1 AAATAACTTTTAAAATATTATAAAAATAATAAAAATAAATCC
* * * * * *
39761772 AAATTATTTTTTAATTATTTTAAAAATAATAAAATTAAA
1 AAATAACTTTTAAAATATTATAAAAATAATAAAAATAAA
39761811 GAATTATATA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
41 13 0.41
42 19 0.59
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.38
Consensus pattern (42 bp):
AAATAACTTTTAAAATATTATAAAAATAATAAAAATAAATCC
Found at i:39766592 original size:25 final size:23
Alignment explanation
Indices: 39766548--39766595 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
39766538 ATTTAATTAA
**
39766548 TATTTTATTAAGATTTTTAATAT
1 TATTTTATTAAGATGATTAATAT
39766571 TATTTTATTATTAGATGATTAATAT
1 TATTTTATTA--AGATGATTAATAT
39766596 AAAAGGGAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 10 0.48
25 11 0.52
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (23 bp):
TATTTTATTAAGATGATTAATAT
Found at i:39769666 original size:38 final size:38
Alignment explanation
Indices: 39769611--39769688 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
39769601 TAAAAATAAA
39769611 TAAATGCCAACCAATCGAACTTGAAATTGATAAGGATT
1 TAAATGCCAACCAATCGAACTTGAAATTGATAAGGATT
*
39769649 TAAATGCCAACCGATCGAACTTGAAATTGATAAGGATT
1 TAAATGCCAACCAATCGAACTTGAAATTGATAAGGATT
39769687 TA
1 TA
39769689 TAAATAAGTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (38 bp):
TAAATGCCAACCAATCGAACTTGAAATTGATAAGGATT
Found at i:39773975 original size:14 final size:13
Alignment explanation
Indices: 39773937--39773977 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 13
39773927 TTTTATAAAC
39773937 ATTTTAATTATTT
1 ATTTTAATTATTT
*
39773950 GTTTT-A-TATTT
1 ATTTTAATTATTT
39773961 ATTTTAAATTATTT
1 ATTTT-AATTATTT
39773975 ATT
1 ATT
39773978 ATATTAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
11 9 0.39
12 1 0.04
13 5 0.22
14 8 0.35
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (13 bp):
ATTTTAATTATTT
Found at i:39777272 original size:21 final size:22
Alignment explanation
Indices: 39777246--39777292 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
39777236 CTCTGCTCAA
*
39777246 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
39777267 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
39777289 ACTC
1 ACTC
39777293 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:39784714 original size:49 final size:50
Alignment explanation
Indices: 39784634--39784879 Score: 298
Period size: 49 Copynumber: 4.9 Consensus size: 50
39784624 AGCTATTGTG
*
39784634 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATT
* * * *
39784684 -GGTCGCATGTGTGGTACTAAGTGCAGGCTACTATGCGTACCTGATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAA-TT
* * * ** * **
39784734 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTATCAGATGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATT
* * *
39784784 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATT
* * *
39784834 -GGTCGCATGTGTAGTACTAAGTGCAGACTACTATGCGTACCAGATA
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATA
39784880 GCTTCGGCTA
Statistics
Matches: 165, Mismatches: 29, Indels: 5
0.83 0.15 0.03
Matches are distributed among these distances:
49 82 0.50
50 47 0.28
51 36 0.22
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATT
Found at i:39803233 original size:49 final size:49
Alignment explanation
Indices: 39803094--39803321 Score: 178
Period size: 49 Copynumber: 4.7 Consensus size: 49
39803084 TTGAGACAAG
* * * *
39803094 AGCTAGTGTAAGACATGTTTGGGACAT-GCATCGGCCTCGAGATAT-ACA
1 AGCTAGTGTAAGACCTGTCTGGGACATGGCATCAGCCTCGATATATGA-A
** * * *
39803142 AGCTAGTGTAAGACCTGTCTGAAACATGGCATCAACAC-CGATAGATGAG
1 AGCTAGTGTAAGACCTGTCTGGGACATGGCATCAGC-CTCGATATATGAA
*
39803191 AGCTAGTGTAAGACCTGTCTGGGACATGGCATTAGCCTCGATATATGAA
1 AGCTAGTGTAAGACCTGTCTGGGACATGGCATCAGCCTCGATATATGAA
* ** * * * * * ** **
39803240 AGTTAGCATAAGATCTGTCTAGGACACGACATC-GACTTTA-ATATGCT
1 AGCTAGTGTAAGACCTGTCTGGGACATGGCATCAGCCTCGATATATGAA
* *
39803287 AGCCAGTGTAAGACCATGTTTGGGACATGGCATCA
1 AGCTAGTGTAAGACC-TGTCTGGGACATGGCATCA
39803322 ACATCTTATC
Statistics
Matches: 137, Mismatches: 37, Indels: 11
0.74 0.20 0.06
Matches are distributed among these distances:
47 15 0.11
48 42 0.31
49 78 0.57
50 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (49 bp):
AGCTAGTGTAAGACCTGTCTGGGACATGGCATCAGCCTCGATATATGAA
Found at i:39807887 original size:28 final size:28
Alignment explanation
Indices: 39807855--39807953 Score: 153
Period size: 28 Copynumber: 3.5 Consensus size: 28
39807845 TCGACAGCAG
*
39807855 CTAAGACACATTAAAAACACGTATTAAA
1 CTAAGACACATTAAAAACATGTATTAAA
*
39807883 CTAAGACACATTAATAACATGTATTAAA
1 CTAAGACACATTAAAAACATGTATTAAA
* * *
39807911 CTAAGACACATTAATAATATGTAATAAA
1 CTAAGACACATTAAAAACATGTATTAAA
39807939 CTAAGACACATTAAA
1 CTAAGACACATTAAA
39807954 CACTTTAATT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 66 1.00
ACGTcount: A:0.53, C:0.15, G:0.07, T:0.25
Consensus pattern (28 bp):
CTAAGACACATTAAAAACATGTATTAAA
Found at i:39810082 original size:27 final size:27
Alignment explanation
Indices: 39810041--39810094 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
39810031 TGTCATGTGA
* *
39810041 AATTGAATGGCAAATTATTGTTACATG
1 AATTGAATGGCAAATTACTATTACATG
**
39810068 AATTGAATGTTAAATTACTATTACATG
1 AATTGAATGGCAAATTACTATTACATG
39810095 GGTTGTATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (27 bp):
AATTGAATGGCAAATTACTATTACATG
Found at i:39810454 original size:49 final size:48
Alignment explanation
Indices: 39810339--39810461 Score: 140
Period size: 48 Copynumber: 2.5 Consensus size: 48
39810329 TGAGGTCACG
* * * * **
39810339 TGTGTAGTATTAAGTGCAGGTTACTACGTGTATCAGATGGTTAGGTCA
1 TGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATAATTAGGTCA
* * *
39810387 CGTATAGTACTAAGTGCAGGCTACTACATGTACCGGATAATT-GGTCATA
1 TGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATAATTAGGTC--A
39810436 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
39810462 TGCGTACCAG
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
47 4 0.06
48 33 0.53
49 25 0.40
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.32
Consensus pattern (48 bp):
TGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATAATTAGGTCA
Found at i:39815650 original size:47 final size:46
Alignment explanation
Indices: 39815556--39815670 Score: 140
Period size: 47 Copynumber: 2.5 Consensus size: 46
39815546 TTAGTTTAAG
* * * **
39815556 TATTTAATTGTCTTAAGTTTATTTAATGTGTTCTAATTAGTTTAGC
1 TATTTAATTGTCCTAAGTTTATTTAATATGTTCTAATTAATACAGC
* *
39815602 TATTTAATATGTCCTAAGTTTATTTAATATGTTTTAGTTAATACAGC
1 TATTTAAT-TGTCCTAAGTTTATTTAATATGTTCTAATTAATACAGC
*
39815649 TACTTAATGTGTCCTAAGTTTA
1 TATTTAAT-TGTCCTAAGTTTA
39815671 GTCAACTTAA
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
46 8 0.14
47 51 0.86
ACGTcount: A:0.29, C:0.09, G:0.12, T:0.50
Consensus pattern (46 bp):
TATTTAATTGTCCTAAGTTTATTTAATATGTTCTAATTAATACAGC
Found at i:39818298 original size:40 final size:40
Alignment explanation
Indices: 39818247--39818631 Score: 619
Period size: 40 Copynumber: 9.6 Consensus size: 40
39818237 CATTTGAATG
*
39818247 ATATCCGGGCTAAGACCCGAAGGCATTAGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
39818287 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
39818327 ATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
39818367 ATATCCGGGCTAAGACCTGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
39818407 ATATCCGGGCTAAGACCAGAAGGCATTAGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
39818447 ATATCCGGGCTAAGACCTGAAGGCATTTGTGCGAACTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
39818487 ATATCCGGGCTAAGACCCGACGGCGTTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
39818527 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-AAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAA-TTGAT
* * *
39818567 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
39818607 ATACCCGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCA
39818632 ATTGAGCTTG
Statistics
Matches: 321, Mismatches: 22, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
39 2 0.01
40 318 0.99
41 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
Found at i:39821075 original size:56 final size:56
Alignment explanation
Indices: 39821015--39821136 Score: 199
Period size: 56 Copynumber: 2.2 Consensus size: 56
39821005 TCCCAAACAG
* *
39821015 GGTCTTACTCGCACATATATATCAGAATCACATATCGATGGCAACATTTTAAACGT
1 GGTCTTACTCGCACACATATATCAGAATCACATATCGATGGCAACATATTAAACGT
* * *
39821071 GGTCTTACTCGTACACATATATCAGAATCACATATCGATGTCAACGTATTAAACGT
1 GGTCTTACTCGCACACATATATCAGAATCACATATCGATGGCAACATATTAAACGT
39821127 GGTCTTACTC
1 GGTCTTACTC
39821137 ATGATCACAA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 61 1.00
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (56 bp):
GGTCTTACTCGCACACATATATCAGAATCACATATCGATGGCAACATATTAAACGT
Found at i:39828590 original size:4 final size:4
Alignment explanation
Indices: 39828583--39828621 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
39828573 AATATCAAAA
*
39828583 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AGAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
39828622 AACATTAGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:39828938 original size:11 final size:11
Alignment explanation
Indices: 39828909--39828938 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
39828899 TTGATTAATG
*
39828909 AAATATAATAA
1 AAATATATTAA
39828920 AAATATATTAA
1 AAATATATTAA
39828931 AAATATAT
1 AAATATAT
39828939 ATTGAGTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATATATTAA
Found at i:39831681 original size:22 final size:22
Alignment explanation
Indices: 39831656--39831697 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
39831646 CTGAATTTAA
39831656 AATTTATCACACAT-ATTAATCC
1 AATTTATCA-ACATCATTAATCC
*
39831678 AATTTATTAACATCATTAAT
1 AATTTATCAACATCATTAAT
39831698 TTTTTAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (22 bp):
AATTTATCAACATCATTAATCC
Found at i:39838691 original size:37 final size:37
Alignment explanation
Indices: 39838641--39838719 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
39838631 TTATTACGAA
* *
39838641 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
39838678 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
39838715 GTCTT
1 GTCTT
39838720 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Done.