Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold119
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: 3173904
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 20
Found at i:2554432 original size:42 final size:41
Alignment explanation
Indices: 2554385--2554524 Score: 124
Period size: 42 Copynumber: 3.3 Consensus size: 41
2554375 ATTTACTAAG
2554385 GACTGAGCTGACAAGTAAATAAAGAGATAAAGGTTGATCAGA
1 GACTGAGCTGACAAGTAAATAAAGAGATAAAGGTTGATC-GA
* * * *
2554427 GACTGAGCTAACAAGTTAACATAAA-TG-TAAGAGGTTTACCGA
1 GACTGAGCTGACAAG-TAA-ATAAAGAGATAA-AGGTTGATCGA
* * *
2554469 GGACTGAGCCGACAGGTAAATAATGAGATGAAA-GTTGATCGAA
1 -GACTGAGCTGACAAGTAAATAAAGAGAT-AAAGGTTGATCG-A
*
2554512 GATTGAGCTGACA
1 GACTGAGCTGACA
2554525 TGTCACCATA
Statistics
Matches: 77, Mismatches: 13, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
41 4 0.05
42 40 0.52
43 26 0.34
44 7 0.09
ACGTcount: A:0.41, C:0.12, G:0.26, T:0.21
Consensus pattern (41 bp):
GACTGAGCTGACAAGTAAATAAAGAGATAAAGGTTGATCGA
Found at i:2554497 original size:85 final size:85
Alignment explanation
Indices: 2554205--2554606 Score: 320
Period size: 85 Copynumber: 4.8 Consensus size: 85
2554195 AAGGGTAAGG
* ** *
2554205 GGGTTTACTAAGGACTGAGATGATAGGTAAACAATGAGATG-AAGGTTGA-CTGGAGACTGAGCT
1 GGGTTTACTGAGGACTGAGCCGACAGGTAAACAATGAGATGAAAGGTTGATC-GGAGACTGAGCT
* * * * *
2554268 AATAAGTCACCGTAAGGGTAA
65 AACAAGTTAACATAAAGGTAA
* * * * *
2554289 TAGG-TTA-TTAGGGACTGAGCCAACAGGTAAACAATGAGATG-AAGGTTGACCGGAGACTAAGC
1 -GGGTTTACTGA-GGACTGAGCCGACAGGTAAACAATGAGATGAAAGGTTGATCGGAGACTGAGC
* * * *
2554351 TAGC-AGGTCAC-CAAAGGATAA
64 TAACAAGTTAACATAAAGG-TAA
* * * * * *
2554372 GGGATTTACTAAGGACTGAGCTGACAAGTAAATAAAGAGAT-AAAGGTTGATCAGAGACTGAGCT
1 GGG-TTTACTGAGGACTGAGCCGACAGGTAAACAATGAGATGAAAGGTTGATCGGAGACTGAGCT
*
2554436 AACAAGTTAACATAAATGTAA
65 AACAAGTTAACATAAAGGTAA
* * * *
2554457 GAGGTTTACCGAGGACTGAGCCGACAGGTAAATAATGAGATGAAA-GTTGATCGAAGATTGAGCT
1 G-GGTTTACTGAGGACTGAGCCGACAGGTAAACAATGAGATGAAAGGTTGATCGGAGACTGAGCT
* * * * *
2554521 GACATGTCACCATAGAGGTAA
65 AACAAGTTAACATAAAGGTAA
* * * *
2554542 TGGGTTTATTGAGGACTAAGCAGATAGGTAAACAAT-AGGATGAAAGGTTGATCGGAGACTGAGC
1 -GGGTTTACTGAGGACTGAGCCGACAGGTAAACAATGA-GATGAAAGGTTGATCGGAGACTGAGC
2554606 T
64 T
2554607 GACAGGTCAC
Statistics
Matches: 251, Mismatches: 52, Indels: 27
0.76 0.16 0.08
Matches are distributed among these distances:
82 6 0.02
83 8 0.03
84 98 0.39
85 112 0.45
86 27 0.11
ACGTcount: A:0.37, C:0.12, G:0.29, T:0.22
Consensus pattern (85 bp):
GGGTTTACTGAGGACTGAGCCGACAGGTAAACAATGAGATGAAAGGTTGATCGGAGACTGAGCTA
ACAAGTTAACATAAAGGTAA
Found at i:2554752 original size:84 final size:84
Alignment explanation
Indices: 2554647--2554804 Score: 210
Period size: 84 Copynumber: 1.9 Consensus size: 84
2554637 TGCGGACTAA
* * * ** * * * *
2554647 GCCGAGAGGTAGACAAAGGATAAAAGGTGTTTCTGAGGGCTGAGCCGA-TGGGCAAACAAAGAGT
1 GCCGACAGGCAGACAAAGGATAAAAAGTGTTTCCCAAGACTAAGCCGACT-GGCAAACAAAGAAT
*
2554711 TAAGAAGTCTTTGAGTCTAG
65 AAAGAAGTCTTTGAGTCTAG
2554731 GCCGACAGGCAGACAAAGGATAAAAAGTGTTTCCCAAGACTAAGCCGACTGGCAAACAAAGAATA
1 GCCGACAGGCAGACAAAGGATAAAAAGTGTTTCCCAAGACTAAGCCGACTGGCAAACAAAGAATA
2554796 AAGAAGTCT
66 AAGAAGTCT
2554805 CTCGGGCCTA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
84 62 0.98
85 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.28, T:0.17
Consensus pattern (84 bp):
GCCGACAGGCAGACAAAGGATAAAAAGTGTTTCCCAAGACTAAGCCGACTGGCAAACAAAGAATA
AAGAAGTCTTTGAGTCTAG
Found at i:2556208 original size:9 final size:9
Alignment explanation
Indices: 2556194--2556227 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
2556184 TTTGTTGTTG
2556194 TTTTTTTGT
1 TTTTTTTGT
*
2556203 TTTTTTTAT
1 TTTTTTTGT
2556212 TTTTTTTGT
1 TTTTTTTGT
2556221 TTTTTTT
1 TTTTTTT
2556228 ACTCTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.03, C:0.00, G:0.06, T:0.91
Consensus pattern (9 bp):
TTTTTTTGT
Found at i:2556217 original size:18 final size:20
Alignment explanation
Indices: 2556194--2556238 Score: 76
Period size: 18 Copynumber: 2.4 Consensus size: 20
2556184 TTTGTTGTTG
2556194 TTTTTTTGTTTTTTTTA-T-
1 TTTTTTTGTTTTTTTTACTC
2556212 TTTTTTTGTTTTTTTTACTC
1 TTTTTTTGTTTTTTTTACTC
2556232 TTTTTTT
1 TTTTTTT
2556239 ATGCATGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 17 0.68
19 1 0.04
20 7 0.28
ACGTcount: A:0.04, C:0.04, G:0.04, T:0.87
Consensus pattern (20 bp):
TTTTTTTGTTTTTTTTACTC
Found at i:2556235 original size:29 final size:30
Alignment explanation
Indices: 2556164--2556240 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
2556154 TTTCATTCGA
*
2556164 TTTTTTA-TTTATATTTATTTTTTGTTGTTG
1 TTTTTTACTTT-TTTTTATTTTTTGTTGTTG
**
2556194 TTTTTTTGTTTTTTTTATTTTTT-TTGTT-
1 TTTTTTACTTTTTTTTATTTTTTGTTGTTG
2556222 TTTTTTACTCTTTTTTTAT
1 TTTTTTACT-TTTTTTTAT
2556241 GCATGGTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 7 0.17
29 14 0.34
30 17 0.41
31 3 0.07
ACGTcount: A:0.09, C:0.03, G:0.06, T:0.82
Consensus pattern (30 bp):
TTTTTTACTTTTTTTTATTTTTTGTTGTTG
Found at i:2556236 original size:30 final size:30
Alignment explanation
Indices: 2556177--2556240 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
2556167 TTTATTTATA
*
2556177 TTTATTTTTTGTTGTTGTTTTTTTGTTTTT
1 TTTATTTTTTGTTGTTGTTTTTTTCTTTTT
*
2556207 TTTATTTTTT-TTGTT-TTTTTTACTCTTTT
1 TTTATTTTTTGTTGTTGTTTTTTTCT-TTTT
2556236 TTTAT
1 TTTAT
2556241 GCATGGTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 7 0.23
29 14 0.45
30 10 0.32
ACGTcount: A:0.06, C:0.03, G:0.08, T:0.83
Consensus pattern (30 bp):
TTTATTTTTTGTTGTTGTTTTTTTCTTTTT
Found at i:2576912 original size:10 final size:10
Alignment explanation
Indices: 2576891--2576966 Score: 75
Period size: 10 Copynumber: 7.6 Consensus size: 10
2576881 ATTTTCTTAG
2576891 TTTTTCT-T-
1 TTTTTCTCTC
2576899 TTTTTCTCTC
1 TTTTTCTCTC
*
2576909 TTTTTCTTTC
1 TTTTTCTCTC
* *
2576919 TTTTTTCTTTTT
1 -TTTTTC-TCTC
*
2576931 TTTTTCTCAC
1 TTTTTCTCTC
2576941 TTTTTCTCTC
1 TTTTTCTCTC
*
2576951 TTTTTCCCTC
1 TTTTTCTCTC
2576961 TTTTTC
1 TTTTTC
2576967 CAACTGAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
8 7 0.12
9 1 0.02
10 34 0.60
11 12 0.21
12 3 0.05
ACGTcount: A:0.01, C:0.24, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTTCTCTC
Found at i:2576965 original size:32 final size:32
Alignment explanation
Indices: 2576895--2576965 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
2576885 TCTTAGTTTT
* * * *
2576895 TCTTTTTTTCTCTCTTTTTCTTTCTTTTTTCT
1 TCTTTTTTTCTCACTTTTTCTCTCTTTTTCCC
*
2576927 TTTTTTTTTCTCACTTTTTCTCTCTTTTTCCC
1 TCTTTTTTTCTCACTTTTTCTCTCTTTTTCCC
2576959 TCTTTTT
1 TCTTTTT
2576966 CCAACTGAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.01, C:0.24, G:0.00, T:0.75
Consensus pattern (32 bp):
TCTTTTTTTCTCACTTTTTCTCTCTTTTTCCC
Found at i:2577797 original size:143 final size:146
Alignment explanation
Indices: 2577631--2577925 Score: 409
Period size: 144 Copynumber: 2.0 Consensus size: 146
2577621 AATGAAAATG
*
2577631 AATGAATTTTTAAAAACTGATTTAATATG-AAATAAATAATAATATTTGATAAATTTTAAAAATT
1 AATGAATTTTTAAAAACTAATTTAATATGAAAATAAATAATAATATTTGATAAATTTTAAAAATT
*
2577695 AAAAACCACGAAAAATCCC-CTCAAAAAAATTTACGAACTAAAAAACTCCATATTTCGAAAATAA
66 AAAAACCAAGAAAAATCCCTC-CAAAAAAATTTACGAACTAAAAAACTCCATATTTCGAAAATAA
*
2577759 GAAAATTTCAAG-GAAA
130 GAAAATTTCAAGAAAAA
*
2577775 AATGAA-TTTTAAAAACTAATTTAATATGAAAATAAATAATAATATTTGATGAATTTTAAAAATT
1 AATGAATTTTTAAAAACTAATTTAATATGAAAATAAATAATAATATTTGATAAATTTTAAAAATT
* ** * * * * * *** *
2577839 AAAAACTAAGAAAAATCTTTCCGAAAAAATTTATGGAGTACAAAACTTTGTATTTTGAAAATAAG
66 AAAAACCAAGAAAAATCCCTCCAAAAAAATTTACGAACTAAAAAACTCCATATTTCGAAAATAAG
2577904 AAAATTTCAAGAAAAA
131 AAAATTTCAAGAAAAA
2577920 AATGAA
1 AATGAA
2577926 AACTCATGAA
Statistics
Matches: 132, Mismatches: 16, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
143 21 0.16
144 101 0.77
145 10 0.08
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.30
Consensus pattern (146 bp):
AATGAATTTTTAAAAACTAATTTAATATGAAAATAAATAATAATATTTGATAAATTTTAAAAATT
AAAAACCAAGAAAAATCCCTCCAAAAAAATTTACGAACTAAAAAACTCCATATTTCGAAAATAAG
AAAATTTCAAGAAAAA
Found at i:2579008 original size:67 final size:67
Alignment explanation
Indices: 2578929--2579065 Score: 274
Period size: 67 Copynumber: 2.0 Consensus size: 67
2578919 CCCAATTGTT
2578929 AAGACAAATCAATAACAAAATTCTTATCATTGGATAAGGTTTCATCATAATAAATTCAAAACATC
1 AAGACAAATCAATAACAAAATTCTTATCATTGGATAAGGTTTCATCATAATAAATTCAAAACATC
2578994 TC
66 TC
2578996 AAGACAAATCAATAACAAAATTCTTATCATTGGATAAGGTTTCATCATAATAAATTCAAAACATC
1 AAGACAAATCAATAACAAAATTCTTATCATTGGATAAGGTTTCATCATAATAAATTCAAAACATC
2579061 TC
66 TC
2579063 AAG
1 AAG
2579066 CTCTGGCAAC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 70 1.00
ACGTcount: A:0.47, C:0.16, G:0.08, T:0.29
Consensus pattern (67 bp):
AAGACAAATCAATAACAAAATTCTTATCATTGGATAAGGTTTCATCATAATAAATTCAAAACATC
TC
Found at i:2582249 original size:23 final size:21
Alignment explanation
Indices: 2582209--2582251 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
2582199 AAAAGTTTTG
2582209 AATAAAAAAATAAATAATAAA
1 AATAAAAAAATAAATAATAAA
*
2582230 AATAAAAATTAATAATTAATAA
1 AATAAAAA--AATAAATAATAA
2582252 TTAACAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
23 11 0.58
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (21 bp):
AATAAAAAAATAAATAATAAA
Found at i:2589907 original size:2 final size:2
Alignment explanation
Indices: 2589902--2589949 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2589892 AAAAAGACAC
2589902 AG AG AG AG AG AG 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 AG AG AG AG AG AG
2589944 AG AG AG
1 AG AG AG
2589950 TAACAAAAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2592693 original size:18 final size:19
Alignment explanation
Indices: 2592670--2592705 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
2592660 TTTCATTGTA
2592670 TTTTATTATA-TTTTAAAT
1 TTTTATTATACTTTTAAAT
2592688 TTTTATTATACTTTTAAA
1 TTTTATTATACTTTTAAA
2592706 AAACAATTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTATTATACTTTTAAAT
Found at i:2594520 original size:4 final size:4
Alignment explanation
Indices: 2594513--2594546 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
2594503 ATTAATTGAA
2594513 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT AT
2594547 AAACACTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:2594865 original size:15 final size:15
Alignment explanation
Indices: 2594816--2594959 Score: 112
Period size: 15 Copynumber: 9.5 Consensus size: 15
2594806 GTCATGTATT
*
2594816 TAATTTATTTTCTTG
1 TAATTTATTTTTTTG
* *
2594831 CAATTT-TTAATTTATG
1 TAATTTATT--TTTTTG
2594847 TAATTTATTTTTTTG
1 TAATTTATTTTTTTG
** *
2594862 TAATTTAAATTTATG
1 TAATTTATTTTTTTG
*
2594877 TAATTTATTTTCTTG
1 TAATTTATTTTTTTG
* *
2594892 CAATTT-TTAATTTATG
1 TAATTTATT--TTTTTG
2594908 TAATTTATTTTTTTG
1 TAATTTATTTTTTTG
** *
2594923 TAATTTAAATTTATG
1 TAATTTATTTTTTTG
*
2594938 TAATTTATTTTCTTG
1 TAATTTATTTTTTTG
*
2594953 CAATTTA
1 TAATTTA
2594960 AATTTATGCA
Statistics
Matches: 98, Mismatches: 25, Indels: 12
0.73 0.19 0.09
Matches are distributed among these distances:
14 4 0.04
15 72 0.73
16 18 0.18
17 4 0.04
ACGTcount: A:0.28, C:0.04, G:0.06, T:0.62
Consensus pattern (15 bp):
TAATTTATTTTTTTG
Found at i:2594911 original size:61 final size:61
Alignment explanation
Indices: 2594816--2594991 Score: 291
Period size: 61 Copynumber: 2.9 Consensus size: 61
2594806 GTCATGTATT
2594816 TAATTTATTTTCTTGCAATTTTTAATTTATGTAATTTATTTTTTTGTAATTTAAATTTATG
1 TAATTTATTTTCTTGCAATTTTTAATTTATGTAATTTATTTTTTTGTAATTTAAATTTATG
2594877 TAATTTATTTTCTTGCAATTTTTAATTTATGTAATTTATTTTTTTGTAATTTAAATTTATG
1 TAATTTATTTTCTTGCAATTTTTAATTTATGTAATTTATTTTTTTGTAATTTAAATTTATG
* * * * *
2594938 TAATTTATTTTCTTGCAA-TTTAAATTTATGCATTTTACTTTTGTTGCAATTTAA
1 TAATTTATTTTCTTGCAATTTTTAATTTATGTAATTTA-TTTTTTTGTAATTTAA
2594992 TCTATACTTT
Statistics
Matches: 109, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
60 16 0.15
61 93 0.85
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (61 bp):
TAATTTATTTTCTTGCAATTTTTAATTTATGTAATTTATTTTTTTGTAATTTAAATTTATG
Found at i:2594990 original size:31 final size:30
Alignment explanation
Indices: 2594816--2594991 Score: 244
Period size: 30 Copynumber: 5.8 Consensus size: 30
2594806 GTCATGTATT
*
2594816 TAATTTATTTTCTTGCAATTTTTAATTTATG
1 TAATTTATTTTCTTGCAA-TTTAAATTTATG
* *
2594847 TAATTTATTTTTTTGTAATTTAAATTTATG
1 TAATTTATTTTCTTGCAATTTAAATTTATG
*
2594877 TAATTTATTTTCTTGCAATTTTTAATTTATG
1 TAATTTATTTTCTTGCAA-TTTAAATTTATG
* *
2594908 TAATTTATTTTTTTGTAATTTAAATTTATG
1 TAATTTATTTTCTTGCAATTTAAATTTATG
2594938 TAATTTATTTTCTTGCAATTTAAATTTATG
1 TAATTTATTTTCTTGCAATTTAAATTTATG
* * *
2594968 CATTTTACTTTTGTTGCAATTTAA
1 TAATTTA-TTTTCTTGCAATTTAA
2594992 TCTATACTTT
Statistics
Matches: 129, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
30 71 0.55
31 58 0.45
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (30 bp):
TAATTTATTTTCTTGCAATTTAAATTTATG
Found at i:2598786 original size:16 final size:16
Alignment explanation
Indices: 2598765--2598798 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2598755 CACGAAATCA
*
2598765 TTGATTGAATATAATT
1 TTGATTGAATACAATT
2598781 TTGATTGAATACAATT
1 TTGATTGAATACAATT
2598797 TT
1 TT
2598799 AATGTTACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.12, T:0.50
Consensus pattern (16 bp):
TTGATTGAATACAATT
Found at i:2600411 original size:21 final size:21
Alignment explanation
Indices: 2600382--2600432 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 21
2600372 ATTATGTGTT
2600382 AATC-ATTATTACT-TAATTCA
1 AATCAATTATTACTATAA-TCA
2600402 AATCAATTATTACTCAGTAATCA
1 AATCAATTATTACT-A-TAATCA
2600425 AATCAATT
1 AATCAATT
2600433 GAAATCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 4 0.15
21 9 0.33
23 11 0.41
24 3 0.11
ACGTcount: A:0.43, C:0.16, G:0.02, T:0.39
Consensus pattern (21 bp):
AATCAATTATTACTATAATCA
Found at i:2600510 original size:157 final size:159
Alignment explanation
Indices: 2600330--2600637 Score: 390
Period size: 161 Copynumber: 1.9 Consensus size: 159
2600320 TTAAATTTTT
* * *
2600330 TAGTAAAAAAGTAATTGACAATTTTATTTTTATTAAA-T-TTAAATTATGTGTTAATCATTATTA
1 TAGTAAAAAAGTAATTAACAATTTTATTTTTATTAAATTCTTAAATTACGTGTTAATCATTACTA
* * * * *
2600393 CT-TAATTCAAATCAATTATTACTCAGTAATCAAATCAATTGAAATCT-TTTTCTAATAATGTAA
66 -TAAAATTCAAATCAATTATTACTAAATAATCAAATCAATTAAAATCTGTTTT-TAATAATATAA
* *
2600456 AATAAATGGTTAATTAAAAATGCATACACAA
129 AATAAATAGTTAACTAAAAATGCATACACAA
* * * *
2600487 TAGTAAAAACGTAATTAACAATTTTATTTTTATTAAATTACCTTAAATTGCGTGTTGATTATTAC
1 TAGTAAAAAAGTAATTAACAATTTTATTTTTATTAAATT--CTTAAATTACGTGTTAATCATTAC
* * *
2600552 TATAAAATTCAAATCAATTATTATTAAATAATCAAATCTATTAAAATCTGTTTTTATTAATATAA
64 TATAAAATTCAAATCAATTATTACTAAATAATCAAATCAATTAAAATCTGTTTTTAATAATATAA
*
2600617 AATAAATAGTTGACTAAAAAT
129 AATAAATAGTTAACTAAAAAT
2600638 ATATATACAA
Statistics
Matches: 127, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
157 35 0.28
158 1 0.01
160 1 0.01
161 86 0.68
162 4 0.03
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.41
Consensus pattern (159 bp):
TAGTAAAAAAGTAATTAACAATTTTATTTTTATTAAATTCTTAAATTACGTGTTAATCATTACTA
TAAAATTCAAATCAATTATTACTAAATAATCAAATCAATTAAAATCTGTTTTTAATAATATAAAA
TAAATAGTTAACTAAAAATGCATACACAA
Found at i:2600580 original size:21 final size:22
Alignment explanation
Indices: 2600547--2600594 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
2600537 CGTGTTGATT
2600547 ATTACTATAAAAT-TCAAATCA
1 ATTACTATAAAATATCAAATCA
* * *
2600568 ATTATTATTAAATAATCAAATCT
1 ATTACTATAAAAT-ATCAAATCA
2600591 ATTA
1 ATTA
2600595 AAATCTGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 11 0.50
23 11 0.50
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (22 bp):
ATTACTATAAAATATCAAATCA
Found at i:2600777 original size:29 final size:29
Alignment explanation
Indices: 2600735--2600795 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
2600725 AATCAAATTC
*
2600735 AATAAATGACATGTGTACAA-TATTAAATA
1 AATAAATAACATGTGTA-AAGTATTAAATA
2600764 AATAAATAACATGTGTAAAGTATTAAATA
1 AATAAATAACATGTGTAAAGTATTAAATA
2600793 AAT
1 AAT
2600796 GACATGTGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 2 0.07
29 28 0.93
ACGTcount: A:0.54, C:0.05, G:0.10, T:0.31
Consensus pattern (29 bp):
AATAAATAACATGTGTAAAGTATTAAATA
Found at i:2601789 original size:13 final size:14
Alignment explanation
Indices: 2601756--2602009 Score: 164
Period size: 14 Copynumber: 19.3 Consensus size: 14
2601746 GCTAAAGCCA
*
2601756 AAAGTGCTTGTGCC
1 AAAGTACTTGTGCC
*
2601770 AAAGTACTTGTGTC
1 AAAGTACTTGTGCC
2601784 -AAGTACTTGTGCC
1 AAAGTACTTGTGCC
* *
2601797 AAAGTACATGTACC
1 AAAGTACTTGTGCC
2601811 -AAGTA----T-CC
1 AAAGTACTTGTGCC
2601819 -AAGTA-TCTGTGCC
1 AAAGTACT-TGTGCC
*
2601832 AAAGTACCTGTGCC
1 AAAGTACTTGTGCC
* *
2601846 -AAGTACCTATGCC
1 AAAGTACTTGTGCC
* * *
2601859 AAAATACTTAT-AC
1 AAAGTACTTGTGCC
*
2601872 TAAGTACTTGTGCC
1 AAAGTACTTGTGCC
* * *
2601886 AAAATACCTGTGTC
1 AAAGTACTTGTGCC
* *
2601900 -AAGTACCTGTGTC
1 AAAGTACTTGTGCC
*
2601913 AAAGTATTTGTGCC
1 AAAGTACTTGTGCC
*
2601927 AAAGTACTTGTGTC
1 AAAGTACTTGTGCC
*
2601941 -AAGTACCT-TG-C
1 AAAGTACTTGTGCC
*
2601952 TAAGTACTTGTGCC
1 AAAGTACTTGTGCC
* *
2601966 -AAGTACTTATGAC
1 AAAGTACTTGTGCC
2601979 AAAGTACTTGTGCC
1 AAAGTACTTGTGCC
* *
2601993 -AAGTACGTGTGGC
1 AAAGTACTTGTGCC
2602006 AAAG
1 AAAG
2602010 AGTATTATGG
Statistics
Matches: 192, Mismatches: 32, Indels: 32
0.75 0.12 0.12
Matches are distributed among these distances:
8 7 0.04
9 1 0.01
11 1 0.01
12 10 0.05
13 83 0.43
14 90 0.47
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.29
Consensus pattern (14 bp):
AAAGTACTTGTGCC
Found at i:2601795 original size:27 final size:28
Alignment explanation
Indices: 2601756--2602009 Score: 150
Period size: 27 Copynumber: 9.1 Consensus size: 28
2601746 GCTAAAGCCA
*
2601756 AAAGTGCTTGTGCCAAAGTACTTGTGTC
1 AAAGTACTTGTGCCAAAGTACTTGTGTC
*
2601784 -AAGTACTTGTGCCAAAGTACATGTACCAAGTATC
1 AAAGTACTTGTGCCAAAGTAC-T-T-----GTGTC
* *
2601818 CAAGTA-TCTGTGCCAAAGTACCTGTG-C
1 AAAGTACT-TGTGCCAAAGTACTTGTGTC
* * * * * *
2601845 CAAGTACCTATGCCAAAATACTTAT-AC
1 AAAGTACTTGTGCCAAAGTACTTGTGTC
* * *
2601872 TAAGTACTTGTGCCAAAATACCTGTGTC
1 AAAGTACTTGTGCCAAAGTACTTGTGTC
* * * *
2601900 -AAGTACCTGTGTCAAAGTATTTGTGCC
1 AAAGTACTTGTGCCAAAGTACTTGTGTC
* *
2601927 AAAGTACTTGTGTC-AAGTACCT-TG-C
1 AAAGTACTTGTGCCAAAGTACTTGTGTC
* * *
2601952 TAAGTACTTGTGCC-AAGTACTTATGAC
1 AAAGTACTTGTGCCAAAGTACTTGTGTC
* *
2601979 AAAGTACTTGTGCC-AAGTACGTGTGGC
1 AAAGTACTTGTGCCAAAGTACTTGTGTC
2602006 AAAG
1 AAAG
2602010 AGTATTATGG
Statistics
Matches: 180, Mismatches: 31, Indels: 31
0.74 0.13 0.13
Matches are distributed among these distances:
25 20 0.11
26 4 0.02
27 115 0.64
28 16 0.09
29 1 0.01
33 1 0.01
34 5 0.03
35 18 0.10
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.29
Consensus pattern (28 bp):
AAAGTACTTGTGCCAAAGTACTTGTGTC
Found at i:2601830 original size:35 final size:35
Alignment explanation
Indices: 2601783--2601850 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
2601773 GTACTTGTGT
2601783 CAAGTACTTGTGCCAAAGTACATGTACCAAGTATC
1 CAAGTACTTGTGCCAAAGTACATGTACCAAGTATC
* *
2601818 CAAGTA-TCTGTGCCAAAGTACCTGTGCCAAGTA
1 CAAGTACT-TGTGCCAAAGTACATGTACCAAGTA
2601851 CCTATGCCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 1 0.03
35 29 0.97
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (35 bp):
CAAGTACTTGTGCCAAAGTACATGTACCAAGTATC
Found at i:2601918 original size:41 final size:39
Alignment explanation
Indices: 2601873--2601967 Score: 136
Period size: 41 Copynumber: 2.4 Consensus size: 39
2601863 TACTTATACT
2601873 AAGTACTTGTGCCAAAATACCTGTGTCAAGTACCTGTGTCA
1 AAGTACTTGTGCCAAAATACCTGTGTCAAGTACCT-TG-CA
* * * *
2601914 AAGTATTTGTGCCAAAGTACTTGTGTCAAGTACCTTGCT
1 AAGTACTTGTGCCAAAATACCTGTGTCAAGTACCTTGCA
2601953 AAGTACTTGTGCCAA
1 AAGTACTTGTGCCAA
2601968 GTACTTATGA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
39 15 0.31
40 2 0.04
41 32 0.65
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (39 bp):
AAGTACTTGTGCCAAAATACCTGTGTCAAGTACCTTGCA
Found at i:2602350 original size:2 final size:2
Alignment explanation
Indices: 2602345--2602369 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2602335 AAAAAAATTT
2602345 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2602370 GTACGGCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2602558 original size:67 final size:67
Alignment explanation
Indices: 2602527--2602874 Score: 466
Period size: 67 Copynumber: 5.2 Consensus size: 67
2602517 GAGAGTGACA
* *
2602527 CATAAGACCACAATGATCGACTTCTCTATTAAGAGTAATTGCATTGGGAAAAGTAACGGAAGTGG
1 CATAAGACCACAATGATCGACTTCTCTATTAAGAGTACTTGCATTGGGAAAAGTGACGGAAGTGG
*
2602592 TG
66 CG
* * * *
2602594 CATAAGACCACAACGATTGACTTCTCTATTAAGAGTACTTGCATTGGGAAAAATGATGGAAGTGG
1 CATAAGACCACAATGATCGACTTCTCTATTAAGAGTACTTGCATTGGGAAAAGTGACGGAAGTGG
**
2602659 TA
66 CG
** * *
2602661 CATATA-ACCACAATGATTAACTTCTCTATTAAGAGTCCTTGCATTGGCAAAAGTGACGGAAGTG
1 CATA-AGACCACAATGATCGACTTCTCTATTAAGAGTACTTGCATTGGGAAAAGTGACGGAAGTG
2602725 GCG
65 GCG
* * *
2602728 CATGAGACCACAACGATCGACTTCTCTATTAAGAGTACTTGCATTGGGAAAAGTGACAGAAGTGG
1 CATAAGACCACAATGATCGACTTCTCTATTAAGAGTACTTGCATTGGGAAAAGTGACGGAAGTGG
2602793 CG
66 CG
* **
2602795 CATATGACCACAATGATCGACTTCTCTATTAAGAGTACTTATATTAGGG-AAAGTGACGGAAGTG
1 CATAAGACCACAATGATCGACTTCTCTATTAAGAGTACTTGCATT-GGGAAAAGTGACGGAAGTG
*
2602859 ACG
65 GCG
* *
2602862 CATAGGATCACAA
1 CATAAGACCACAA
2602875 CGGTCAACTT
Statistics
Matches: 247, Mismatches: 31, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
66 1 0.00
67 242 0.98
68 4 0.02
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (67 bp):
CATAAGACCACAATGATCGACTTCTCTATTAAGAGTACTTGCATTGGGAAAAGTGACGGAAGTGG
CG
Found at i:2604066 original size:20 final size:20
Alignment explanation
Indices: 2604041--2604106 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
2604031 TTACAGGCCA
2604041 ATGTATCGATACATTTGGTC
1 ATGTATCGATACATTTGGTC
*
2604061 ATGTATCAATACA-------
1 ATGTATCGATACATTTGGTC
2604074 ATGTATCGATACATTTGGTC
1 ATGTATCGATACATTTGGTC
2604094 ATGTATCGATACA
1 ATGTATCGATACA
2604107 ATGTATCGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
13 12 0.32
20 25 0.68
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTTGGTC
Found at i:2604081 original size:33 final size:33
Alignment explanation
Indices: 2604039--2604139 Score: 161
Period size: 33 Copynumber: 3.1 Consensus size: 33
2604029 CGTTACAGGC
*
2604039 CAATGTATCGATACATTTGGTCATGTATCAATA
1 CAATGTATCGATACATTTGGTCATGTATCGATA
2604072 CAATGTATCGATACATTTGGTCATGTATCGATA
1 CAATGTATCGATACATTTGGTCATGTATCGATA
*
2604105 CAATGTATCGATAAATCTT-GT-ATGTATCGATA
1 CAATGTATCGATACAT-TTGGTCATGTATCGATA
2604137 CAA
1 CAA
2604140 ACAGTTAAGG
Statistics
Matches: 65, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
32 14 0.22
33 49 0.75
34 2 0.03
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Consensus pattern (33 bp):
CAATGTATCGATACATTTGGTCATGTATCGATA
Found at i:2604112 original size:13 final size:12
Alignment explanation
Indices: 2604041--2604117 Score: 53
Period size: 13 Copynumber: 6.9 Consensus size: 12
2604031 TTACAGGCCA
2604041 ATGTATCGATAC
1 ATGTATCGATAC
*
2604053 AT-T-T-GGT-C
1 ATGTATCGATAC
*
2604061 ATGTATCAATAC
1 ATGTATCGATAC
2604073 AATGTATCGATAC
1 -ATGTATCGATAC
*
2604086 AT-T-T-GGT-C
1 ATGTATCGATAC
2604094 ATGTATCGATAC
1 ATGTATCGATAC
2604106 AATGTATCGATA
1 -ATGTATCGATA
2604118 AATCTTGTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 19
0.66 0.08 0.26
Matches are distributed among these distances:
8 6 0.12
9 6 0.12
10 4 0.08
11 5 0.10
12 6 0.12
13 22 0.45
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.36
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:2604237 original size:13 final size:13
Alignment explanation
Indices: 2604219--2604243 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2604209 TACAGTGGTC
2604219 ATGTATCGATACA
1 ATGTATCGATACA
2604232 ATGTATCGATAC
1 ATGTATCGATAC
2604244 TGTGCATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2612888 original size:13 final size:13
Alignment explanation
Indices: 2612870--2612894 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2612860 TATAGTGGTC
2612870 ATGTATCGATACA
1 ATGTATCGATACA
2612883 ATGTATCGATAC
1 ATGTATCGATAC
2612895 TGTGCATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2614317 original size:20 final size:20
Alignment explanation
Indices: 2614271--2614320 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
2614261 TTTTACCCAG
* *
2614271 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATGTATCA
* *
2614291 ATATATCGATACATGTATGA
1 ATGTATCGATACATGTATCA
2614311 ATGTATCGAT
1 ATGTATCGAT
2614321 GCATTCTGTC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATGTATCA
Found at i:2614367 original size:20 final size:20
Alignment explanation
Indices: 2614342--2614416 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 20
2614332 TTTTACCCAG
2614342 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
2614362 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
2614382 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
*
2614402 ATATATCGATACATT
1 ATGTATCGATACATT
2614417 ATGTCTTTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:2614376 original size:71 final size:71
Alignment explanation
Indices: 2614260--2614398 Score: 260
Period size: 71 Copynumber: 2.0 Consensus size: 71
2614250 AAAAGTCATA
*
2614260 TTTTTACCCAGATGTATCGATACATTTTTCAATATATCGATACATGTATGAATGTATCGATGCAT
1 TTTTTACCCAGATGTATCGATACATTTTTCAATATATCGATACATGTATGAATGTATCGATACAT
2614325 TCTGTC
66 TCTGTC
*
2614331 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
1 TTTTTACCCAGATGTATCGATACATTTTTCAATATATCGATACATGTATGAATGTATCGATACAT
2614396 TCT
66 TCT
2614399 TCAATATATC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 66 1.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.41
Consensus pattern (71 bp):
TTTTTACCCAGATGTATCGATACATTTTTCAATATATCGATACATGTATGAATGTATCGATACAT
TCTGTC
Found at i:2614402 original size:40 final size:39
Alignment explanation
Indices: 2614342--2614419 Score: 129
Period size: 40 Copynumber: 2.0 Consensus size: 39
2614332 TTTTACCCAG
* *
2614342 ATGTATCGATACATTTTTCAATGTATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATATATCGATACAT-TATGA
2614382 ATGTATCGATACATTCTTCAATATATCGATACATTATG
1 ATGTATCGATACATTCTTCAATATATCGATACATTATG
2614420 TCTTTTTACC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 4 0.11
40 32 0.89
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATATATCGATACATTATGA
Found at i:2614426 original size:91 final size:91
Alignment explanation
Indices: 2614271--2614446 Score: 246
Period size: 91 Copynumber: 1.9 Consensus size: 91
2614261 TTTTACCCAG
* * * * * *
2614271 ATGTATCGATACATTTTTCAATATATCGATACATGTATGAATGTATCGATGCATTCTGTCTTTTT
1 ATGTATCGATACATGTATCAATATATCGATACATGTATCAATATATCGATACATTATGTCTTTTT
2614336 ACCCAGATGTATCGATACATTTTTCA
66 ACCCAGATGTATCGATACATTTTTCA
* * *
2614362 ATGTATCGATACATGTATGAATGTATCGATACAT-TCTTCAATATATCGATACATTATGTCTTTT
1 ATGTATCGATACATGTATCAATATATCGATACATGT-ATCAATATATCGATACATTATGTCTTTT
*
2614426 TACCTAGATGTATCGATACAT
65 TACCCAGATGTATCGATACAT
2614447 CTAGTTAAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
90 1 0.01
91 73 0.99
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (91 bp):
ATGTATCGATACATGTATCAATATATCGATACATGTATCAATATATCGATACATTATGTCTTTTT
ACCCAGATGTATCGATACATTTTTCA
Found at i:2615622 original size:13 final size:13
Alignment explanation
Indices: 2615604--2615629 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2615594 CAATTTTTTG
2615604 TGTATCGATACAT
1 TGTATCGATACAT
2615617 TGTATCGATACAT
1 TGTATCGATACAT
2615630 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2618172 original size:13 final size:13
Alignment explanation
Indices: 2618154--2618192 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2618144 ATAATCACCC
*
2618154 TGTATCGATACAG
1 TGTATCGATACAA
2618167 TGTATCGATACAA
1 TGTATCGATACAA
2618180 TGTATCGATACAA
1 TGTATCGATACAA
2618193 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2618203 original size:20 final size:20
Alignment explanation
Indices: 2618178--2618256 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
2618168 GTATCGATAC
2618178 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
2618198 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
2618223 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
2618243 CATGTATCGATACA
1 AATGTATCGATACA
2618257 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:2620291 original size:15 final size:15
Alignment explanation
Indices: 2620271--2620301 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2620261 ATTTCGTTTG
*
2620271 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
2620286 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
2620301 G
1 G
2620302 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:2622134 original size:21 final size:21
Alignment explanation
Indices: 2622105--2622149 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2622095 AAGTTTTCAT
*
2622105 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
2622125 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
2622147 TTT
1 TTT
2622150 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:2624385 original size:13 final size:13
Alignment explanation
Indices: 2624367--2624392 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2624357 CAATTTTTTG
2624367 TGTATCGATACAT
1 TGTATCGATACAT
2624380 TGTATCGATACAT
1 TGTATCGATACAT
2624393 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2626074 original size:13 final size:13
Alignment explanation
Indices: 2626056--2626080 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2626046 TTCAACGATT
2626056 TGTATCGATACAA
1 TGTATCGATACAA
2626069 TGTATCGATACA
1 TGTATCGATACA
2626081 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2626093 original size:19 final size:19
Alignment explanation
Indices: 2626069--2626118 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
2626059 ATCGATACAA
2626069 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
*
2626088 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAGTGT
2626107 TGTATCGATACA
1 TGTATCGATACA
2626119 ATGTAAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:2626239 original size:52 final size:52
Alignment explanation
Indices: 2626195--2626323 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
2626185 CACTGATCTT
*
2626195 TGTATCGATACATGCAGGCAAATTTGCCCATATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* * *
2626247 TGCATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
2626299 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
2626324 TCATATTTCG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2639541 original size:8 final size:8
Alignment explanation
Indices: 2639530--2639582 Score: 63
Period size: 8 Copynumber: 6.5 Consensus size: 8
2639520 GCAAAAAAAA
2639530 AAAACAAC
1 AAAACAAC
*
2639538 AAAACAAA
1 AAAACAAC
2639546 AAAACAAAAC
1 AAAAC--AAC
2639556 AAAACAA-
1 AAAACAAC
*
2639563 AAAACAAA
1 AAAACAAC
2639571 AAAACAAC
1 AAAACAAC
2639579 AAAA
1 AAAA
2639583 AGGGTCCGGA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
7 7 0.18
8 25 0.64
10 7 0.18
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAACAAC
Found at i:2639546 original size:18 final size:17
Alignment explanation
Indices: 2639521--2639583 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 17
2639511 GCGTCCTCCG
*
2639521 CAAAA-AAAAAAAACAA
1 CAAAACAAAAAAAAAAA
2639537 CAAAACAAAAAAACAAAA
1 CAAAACAAAAAAA-AAAA
2639555 CAAAACAAAAAACAAAAA
1 CAAAACAAAAAA-AAAAA
2639573 -AACAACAAAAA
1 CAA-AACAAAAA
2639584 GGGTCCGGAT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
16 5 0.12
17 9 0.21
18 27 0.64
19 1 0.02
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (17 bp):
CAAAACAAAAAAAAAAA
Found at i:2639566 original size:25 final size:25
Alignment explanation
Indices: 2639522--2639583 Score: 92
Period size: 25 Copynumber: 2.5 Consensus size: 25
2639512 CGTCCTCCGC
2639522 AAAA-AAAAAAAACAACAAAACAAA
1 AAAACAAAAAAAACAACAAAACAAA
2639546 AAAACAAAACAAAACAA-AAAACAAA
1 AAAACAAAA-AAAACAACAAAACAAA
*
2639571 AAAACAACAAAAA
1 AAAACAAAAAAAA
2639584 GGGTCCGGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
24 8 0.23
25 20 0.57
26 7 0.20
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (25 bp):
AAAACAAAAAAAACAACAAAACAAA
Found at i:2641144 original size:34 final size:34
Alignment explanation
Indices: 2641073--2641422 Score: 217
Period size: 34 Copynumber: 10.7 Consensus size: 34
2641063 CTTCTAAAGT
** *
2641073 CCACAACTTAGTGGCACCTTTTTTTTCTTTTTAAAGC
1 CCACAACTCCGTGGCACC--TTTTTTCCTTTT-AAGC
*
2641110 CCACAACTCCGTGGCACCTTTTTTCCTTCTAAGC
1 CCACAACTCCGTGGCACCTTTTTTCCTTTTAAGC
* *
2641144 CCACAACTCCGTGGCA-TTCTTTTTCCTTTTAAGT
1 CCACAACTCCGTGGCACCT-TTTTTCCTTTTAAGC
*
2641178 CCACAACTCTGTGGCA-C------CCTTTTAAGC
1 CCACAACTCCGTGGCACCTTTTTTCCTTTTAAGC
* **
2641205 CCACAAGTTGGTGGCACC------CCTTTTAAAGC
1 CCACAACTCCGTGGCACCTTTTTTCCTTTT-AAGC
* * *
2641234 CCACAAGC-CAGTGGCAACC----TT-C--TAAAGT
1 CCACAA-CTCCGTGGC-ACCTTTTTTCCTTTTAAGC
* * *
2641262 CCACAACTCAGTGGCACTTTTTTTTTCTTTTTAAAGC
1 CCACAACTCCGTGGCAC--CTTTTTTCCTTTT-AAGC
* * * *
2641299 CCACAACTCTGTGGCA-CTCTTTTCCTTCTAAGT
1 CCACAACTCCGTGGCACCTTTTTTCCTTTTAAGC
*
2641332 CCACAACTCCGTGGCACCTTCTTTCCTTTTAAGC
1 CCACAACTCCGTGGCACCTTTTTTCCTTTTAAGC
* *
2641366 CCACAACTCCGTGGCA-TTCTTTTTCCTTTTAAGT
1 CCACAACTCCGTGGCACCT-TTTTTCCTTTTAAGC
*
2641400 CCACAACTCTGTGGCACCTTTTT
1 CCACAACTCCGTGGCACCTTTTT
2641423 AAGCCCACAA
Statistics
Matches: 254, Mismatches: 38, Indels: 45
0.75 0.11 0.13
Matches are distributed among these distances:
27 25 0.10
28 23 0.09
29 16 0.06
30 3 0.01
31 1 0.00
33 22 0.09
34 118 0.46
35 11 0.04
36 1 0.00
37 34 0.13
ACGTcount: A:0.21, C:0.32, G:0.13, T:0.35
Consensus pattern (34 bp):
CCACAACTCCGTGGCACCTTTTTTCCTTTTAAGC
Found at i:2641208 original size:27 final size:27
Alignment explanation
Indices: 2641168--2641278 Score: 107
Period size: 28 Copynumber: 4.0 Consensus size: 27
2641158 CATTCTTTTT
* *
2641168 CCTTTTAAGTCCACAACTCTGTGGCAC
1 CCTTTTAAGCCCACAACTCAGTGGCAC
* **
2641195 CCTTTTAAGCCCACAAGTTGGTGGCACC
1 CCTTTTAAGCCCACAACTCAGTGGCA-C
*
2641223 CCTTTTAAAGCCCACAAGC-CAGTGGCAA
1 CCTTTT-AAGCCCACAA-CTCAGTGGCAC
* *
2641251 CCTTCTAAAGTCCACAACTCAGTGGCAC
1 CCTT-TTAAGCCCACAACTCAGTGGCAC
2641279 TTTTTTTTTC
Statistics
Matches: 68, Mismatches: 11, Indels: 9
0.77 0.12 0.10
Matches are distributed among these distances:
27 23 0.34
28 28 0.41
29 17 0.25
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.23
Consensus pattern (27 bp):
CCTTTTAAGCCCACAACTCAGTGGCAC
Found at i:2641403 original size:68 final size:68
Alignment explanation
Indices: 2641062--2641419 Score: 256
Period size: 68 Copynumber: 5.4 Consensus size: 68
2641052 CCAGTAGCAA
* * *
2641062 CCTTCTAAAGTCCACAACTTAGTGGCACCTTTTTTTTCTTTTTAAAGCCCACAACTCCGTGGCAC
1 CCTTCT-AAGTCCACAACTCAGTGGCACC--TTCTTTCCTTTTAAAGCCCACAACTCCGTGGCA-
*
2641127 CTTTTTT
62 CTCTTTT
* * * * *
2641134 CCTTCTAAGCCCACAACTCCGTGGCATTCTT-TTTCCTTTT-AAGTCCACAACTCTGTGGCA--C
1 CCTTCTAAGTCCACAACTCAGTGGCA-CCTTCTTTCCTTTTAAAGCCCACAACTCCGTGGCACTC
2641195 ----
65 TTTT
* * * ** *
2641195 CCTTTTAAGCCCACAAGTTGGTGGCA-C--C---CCTTTTAAAGCCCACAAGC-CAGTGGCAAC-
1 CCTTCTAAGTCCACAACTCAGTGGCACCTTCTTTCCTTTTAAAGCCCACAA-CTCCGTGGC-ACT
2641252 C--TT
64 CTTTT
* * * * *
2641255 -C-T-AAAGTCCACAACTCAGTGGCACTTTTTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACT
1 CCTTCTAAGTCCACAACTCAGTGGCAC--CTTCTTTCCTTTTAAAGCCCACAACTCCGTGGCACT
2641317 CTTTT
64 CTTTT
* *
2641322 CCTTCTAAGTCCACAACTCCGTGGCACCTTCTTTCCTTTT-AAGCCCACAACTCCGTGGCATTCT
1 CCTTCTAAGTCCACAACTCAGTGGCACCTTCTTTCCTTTTAAAGCCCACAACTCCGTGGCACTC-
2641386 TTTT
65 TTTT
* *
2641390 CCTTTTAAGTCCACAACTCTGTGGCACCTT
1 CCTTCTAAGTCCACAACTCAGTGGCACCTT
2641420 TTTAAGCCCA
Statistics
Matches: 230, Mismatches: 32, Indels: 52
0.73 0.10 0.17
Matches are distributed among these distances:
55 6 0.03
56 15 0.07
57 18 0.08
58 2 0.01
59 2 0.01
61 22 0.10
64 3 0.01
65 23 0.10
67 23 0.10
68 61 0.27
69 9 0.04
70 22 0.10
71 17 0.07
72 7 0.03
ACGTcount: A:0.21, C:0.32, G:0.13, T:0.34
Consensus pattern (68 bp):
CCTTCTAAGTCCACAACTCAGTGGCACCTTCTTTCCTTTTAAAGCCCACAACTCCGTGGCACTCT
TTT
Found at i:2641440 original size:27 final size:28
Alignment explanation
Indices: 2641392--2641464 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 28
2641382 TTCTTTTTCC
* *
2641392 TTTTAAGTCCACAACTCTGTGGCA-CCT
1 TTTTAAGCCCACAAGTCTGTGGCACCCT
2641419 TTTTAAGCCCACAAGT-TGGTGGCACCCCT
1 TTTTAAGCCCACAAGTCT-GTGGCA-CCCT
* *
2641448 TTTAAAACCCACAAGTC
1 TTTTAAGCCCACAAGTC
2641465 AATGGCAACC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
26 1 0.03
27 20 0.53
29 17 0.45
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.29
Consensus pattern (28 bp):
TTTTAAGCCCACAAGTCTGTGGCACCCT
Found at i:2641489 original size:28 final size:30
Alignment explanation
Indices: 2641444--2641522 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 30
2641434 TTGGTGGCAC
*
2641444 CCCTTTTAAAA-CC-CACAAGTCAATGGCAA
1 CCCTTTCAAAAGCCACACAAGTCAAT-GCAA
**
2641473 -CC-TTCAAAAG-CACACAAGTTGATGCAA
1 CCCTTTCAAAAGCCACACAAGTCAATGCAA
2641500 CCCTTTCAAAAGCCCACACAAGT
1 CCCTTTCAAAAG-CCACACAAGT
2641523 TGATGGCGTC
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
27 11 0.27
28 13 0.32
29 8 0.20
31 9 0.22
ACGTcount: A:0.38, C:0.32, G:0.11, T:0.19
Consensus pattern (30 bp):
CCCTTTCAAAAGCCACACAAGTCAATGCAA
Found at i:2641517 original size:29 final size:30
Alignment explanation
Indices: 2641423--2641529 Score: 114
Period size: 29 Copynumber: 3.6 Consensus size: 30
2641413 GCACCTTTTT
* * *
2641423 AAGCCCACAAGTTGGTGGCACCCCTTTTAA
1 AAGCCCACAAGTTGATGGCAACCCTTTCAA
**
2641453 AA-CCCACAAGTCAATGGCAA-CC-TTCAA
1 AAGCCCACAAGTTGATGGCAACCCTTTCAA
*
2641480 AAGCACACAAGTTGAT-GCAACCCTTTCAA
1 AAGCCCACAAGTTGATGGCAACCCTTTCAA
2641509 AAGCCCACACAAGTTGATGGC
1 AAG-CC-CACAAGTTGATGGC
2641530 GTCTTTTTCT
Statistics
Matches: 62, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
27 10 0.16
28 14 0.23
29 22 0.35
30 3 0.05
31 11 0.18
32 2 0.03
ACGTcount: A:0.35, C:0.30, G:0.17, T:0.19
Consensus pattern (30 bp):
AAGCCCACAAGTTGATGGCAACCCTTTCAA
Found at i:2641712 original size:49 final size:49
Alignment explanation
Indices: 2641539--2641820 Score: 247
Period size: 49 Copynumber: 5.8 Consensus size: 49
2641529 CGTCTTTTTC
* * * * *
2641539 TAAGTCCAATATCGCTGGCCTTGAACCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCCTCATCTT
** * * *
2641588 TAAAACTCAATATCGCTGGCCTTGAATCAGCATATT-G-A----CACCTT
1 TAAGTC-CAATGTCGCTGGCCTTGAATCAGCACATTGGCACCCTCATCTT
* *
2641632 GAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCCTCATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCCTCATCTT
* * * * *
2641681 TAAGTCCAATGTAGCTGGCCTTGAATTAGCACATTGGCATCTTCACCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCCTCATCTT
* * **
2641730 TAAGTCCAATAG-CGCTGGCCTTGAATCAGCATATTAGCA-CCTTTTCCGTCT
1 TAAGTCCAAT-GTCGCTGGCCTTGAATCAGCACATTGGCACCCTCAT-C-T-T
* * *
2641781 TGAGTCCAATGTAGCTGGCCTTGAATCAGCACATTAGCAC
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
2641821 AAGTCCAATA
Statistics
Matches: 192, Mismatches: 28, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
43 27 0.14
44 9 0.05
45 1 0.01
48 3 0.02
49 86 0.45
50 31 0.16
51 35 0.18
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (49 bp):
TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCCTCATCTT
Found at i:2642061 original size:154 final size:154
Alignment explanation
Indices: 2641880--2642392 Score: 873
Period size: 154 Copynumber: 3.3 Consensus size: 154
2641870 TTTCTCACCT
* * *
2641880 TCATCTTTAAGTCTAATATCGTTGGCCTTGAATTAGCGTATTGGCATCTTTAACATCCCTAAGCC
1 TCATCTTTAAGCCCAATATCGTTGGCCTTGAATCAGCGTATTGGCATCTTTAACATCCCTAAGCC
* * *
2641945 CAATGTCGTTGGCCTTGTCTCAGCACATTGACATTCTTTTCCAAGTCTAATGCCACTGACTGTGA
66 CAATGTCGTTGGCCTTGTCTCAGCACATTGACATTCTTCTCCAAGTCTAATGCCGCTGACCGTGA
2642010 ATCAGCACATTAACATCCTTTTTC
131 ATCAGCACATTAACATCCTTTTTC
2642034 TCATCTTTAAGCCCAATATCGTTGGCCTTGAATCAGCGTATTGGCATCTTTAACATCCCTAAGCC
1 TCATCTTTAAGCCCAATATCGTTGGCCTTGAATCAGCGTATTGGCATCTTTAACATCCCTAAGCC
*
2642099 TAATGTCGTTGGCCTTGTCTCAGCACATTGACATTCTTCTCCAAGTCTAATGCCGCTGACCGTGA
66 CAATGTCGTTGGCCTTGTCTCAGCACATTGACATTCTTCTCCAAGTCTAATGCCGCTGACCGTGA
*
2642164 ATCAGCACATTAACAGCCTTTTTC
131 ATCAGCACATTAACATCCTTTTTC
2642188 TCATCTTTAAGCCCAATATCGTTGGCCTTGAATCAGCGTATTGGCATCTTTAACATCCCTAAGCC
1 TCATCTTTAAGCCCAATATCGTTGGCCTTGAATCAGCGTATTGGCATCTTTAACATCCCTAAGCC
* *
2642253 CAATGTTGTTGGCCTTGTCTCGGCACATTGACATTCTTCTCCAAGTCTAATGCCGCTGACCGTGA
66 CAATGTCGTTGGCCTTGTCTCAGCACATTGACATTCTTCTCCAAGTCTAATGCCGCTGACCGTGA
* *
2642318 ATCAGCACATTGACATCTTTTTTC
131 ATCAGCACATTAACATCCTTTTTC
* * * * *
2642342 TCATTTTTAAGCCTAATATCGTTGGCCGTGAATCAGCATATTGGTATCTTT
1 TCATCTTTAAGCCCAATATCGTTGGCCTTGAATCAGCGTATTGGCATCTTT
2642393 CTCACTTTTC
Statistics
Matches: 340, Mismatches: 19, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
154 340 1.00
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35
Consensus pattern (154 bp):
TCATCTTTAAGCCCAATATCGTTGGCCTTGAATCAGCGTATTGGCATCTTTAACATCCCTAAGCC
CAATGTCGTTGGCCTTGTCTCAGCACATTGACATTCTTCTCCAAGTCTAATGCCGCTGACCGTGA
ATCAGCACATTAACATCCTTTTTC
Found at i:2642108 original size:52 final size:52
Alignment explanation
Indices: 2641898--2642269 Score: 194
Period size: 52 Copynumber: 7.2 Consensus size: 52
2641888 AAGTCTAATA
* **
2641898 TCGTTGGCCTTGAATTAGCGTATTGGCATCTTTAACATCCCTAAGCCCAATG
1 TCGTTGGCCTTGAATCAGCACATTGGCATCTTTAACATCCCTAAGCCCAATG
** * * *
2641950 TCGTTGGCCTTGTCTCAGCACATTGACATTCTTT----T-CC-AAGTCTAATG
1 TCGTTGGCCTTGAATCAGCACATTGGCA-TCTTTAACATCCCTAAGCCCAATG
* ** * ** ** ** *
2641997 CCACT-GACTGTGAATCAGCACATTAACATCCTTTTTCTCATCTTTAAGCCCAATA
1 TCGTTGGCCT-TGAATCAGCACATTGGCAT-C--TTTAACATCCCTAAGCCCAATG
** *
2642052 TCGTTGGCCTTGAATCAGCGTATTGGCATCTTTAACATCCCTAAGCCTAATG
1 TCGTTGGCCTTGAATCAGCACATTGGCATCTTTAACATCCCTAAGCCCAATG
** * * *
2642104 TCGTTGGCCTTGTCTCAGCACATTGACAT-TCTT--C-T-CC-AAGTCTAATG
1 TCGTTGGCCTTGAATCAGCACATTGGCATCT-TTAACATCCCTAAGCCCAATG
* * * * * * * ** ** *
2642151 CCGCTGACCGTGAATCAGCACATTAACAGCCTTTTTCTCATCTTTAAGCCCAATA
1 TCGTTGGCCTTGAATCAGCACATT---GGCATCTTTAACATCCCTAAGCCCAATG
**
2642206 TCGTTGGCCTTGAATCAGCGTATTGGCATCTTTAACATCCCTAAGCCCAATG
1 TCGTTGGCCTTGAATCAGCACATTGGCATCTTTAACATCCCTAAGCCCAATG
*
2642258 TTGTTGGCCTTG
1 TCGTTGGCCTTG
2642270 TCTCGGCACA
Statistics
Matches: 229, Mismatches: 69, Indels: 44
0.67 0.20 0.13
Matches are distributed among these distances:
46 4 0.02
47 53 0.23
48 4 0.02
49 5 0.02
50 5 0.02
51 2 0.01
52 96 0.42
53 7 0.03
54 1 0.00
55 49 0.21
56 3 0.01
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.34
Consensus pattern (52 bp):
TCGTTGGCCTTGAATCAGCACATTGGCATCTTTAACATCCCTAAGCCCAATG
Found at i:2643011 original size:20 final size:20
Alignment explanation
Indices: 2642965--2643014 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
2642955 TTTTACCTAG
* *
2642965 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATATATCA
* *
2642985 ATATATCGATACATATATGA
1 ATGTATCGATACATATATCA
2643005 ATGTATCGAT
1 ATGTATCGAT
2643015 GCATTCTGTC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATATATCA
Found at i:2643061 original size:20 final size:20
Alignment explanation
Indices: 2643036--2643110 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
2643026 TTTTACCCAG
2643036 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
2643056 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
2643076 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
* *
2643096 ATATATCAATACATT
1 ATGTATCGATACATT
2643111 CTGTCTTTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:2643075 original size:71 final size:71
Alignment explanation
Indices: 2642954--2643092 Score: 242
Period size: 71 Copynumber: 2.0 Consensus size: 71
2642944 AAAAGTCATA
* *
2642954 TTTTTACCTAGATGTATCGATACATTTTTCAATATATCGATACATATATGAATGTATCGATGCAT
1 TTTTTACCCAGATGTATCGATACATTTTTCAATATATCGATACATATATGAATGTATCGATACAT
2643019 TCTGTC
66 TCTGTC
* *
2643025 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
1 TTTTTACCCAGATGTATCGATACATTTTTCAATATATCGATACATATATGAATGTATCGATACAT
2643090 TCT
66 TCT
2643093 TCAATATATC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 64 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (71 bp):
TTTTTACCCAGATGTATCGATACATTTTTCAATATATCGATACATATATGAATGTATCGATACAT
TCTGTC
Found at i:2643120 original size:91 final size:91
Alignment explanation
Indices: 2642965--2643160 Score: 252
Period size: 91 Copynumber: 2.2 Consensus size: 91
2642955 TTTTACCTAG
* * * * * *
2642965 ATGTATCGATACATTTTTCAATATATCGATACATATATGAATGTATCGATGCATTCTGTCTTTTT
1 ATGTATCGATACATGTATCAATATATCGATACATATATCAATATATCAATACATTCTGTCTTTTT
**
2643030 ACCCAGATGTATCGATACATT-TTTCA
66 ACCCAGATGTATCGATACATTGACT-A
* * *
2643056 ATGTATCGATACATGTATGAATGTATCGATACAT-TCTTCAATATATCAATACATTCTGTCTTTT
1 ATGTATCGATACATGTATCAATATATCGATACATAT-ATCAATATATCAATACATTCTGTCTTTT
*
2643120 TACCTAGATGTATCGATACATTGACTA
65 TACCCAGATGTATCGATACATTGACTA
2643147 ATGTATCGATACAT
1 ATGTATCGATACAT
2643161 CTAGTTAAAA
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
90 1 0.01
91 89 0.98
92 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.40
Consensus pattern (91 bp):
ATGTATCGATACATGTATCAATATATCGATACATATATCAATATATCAATACATTCTGTCTTTTT
ACCCAGATGTATCGATACATTGACTA
Found at i:2645008 original size:19 final size:19
Alignment explanation
Indices: 2644950--2645033 Score: 99
Period size: 19 Copynumber: 4.7 Consensus size: 19
2644940 TTTCAATGAT
2644950 TTGTATCGATACATAAAGTG
1 TTGTATCGATACAT-AAGTG
*
2644970 TTCTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
2644984 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
*
2645002 TTGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
2645021 TTGTATCGATACA
1 TTGTATCGATACA
2645034 ATGTAAGCTA
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
13 10 0.18
15 2 0.04
17 2 0.04
19 30 0.55
20 11 0.20
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:2645009 original size:32 final size:33
Alignment explanation
Indices: 2644951--2645014 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
2644941 TTCAATGATT
2644951 TGTATCGATACATAAAGTGTTCTATCGATACAA
1 TGTATCGATACATAAAGTGTTCTATCGATACAA
*
2644984 TGTATCGATACAT-AAGTGTTGTATCGATACA
1 TGTATCGATACATAAAGTGTTCTATCGATACA
2645015 TAAGTTTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTCTATCGATACAA
Found at i:2645169 original size:52 final size:52
Alignment explanation
Indices: 2645113--2645238 Score: 216
Period size: 52 Copynumber: 2.4 Consensus size: 52
2645103 TGATCTTTGT
*
2645113 ATCGATACATGCAGGCAAATTTGCCCAGATTTATCGATACACTATAAAATGC
1 ATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAATGC
* * *
2645165 ATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATGT
1 ATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAATGC
2645217 ATCGATACATGCAGGCAAATTT
1 ATCGATACATGCAGGCAAATTT
2645239 TCATATTTCG
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.27
Consensus pattern (52 bp):
ATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAATGC
Found at i:2648310 original size:40 final size:40
Alignment explanation
Indices: 2648255--2648343 Score: 142
Period size: 40 Copynumber: 2.2 Consensus size: 40
2648245 CATAGAAATC
* *
2648255 CCCAATCGCGAGGGATATTAAGTTAAGCGCGCCTCTTTTG
1 CCCAATCGCGAGGGATATTAAGTCAAGCGCGCCTCATTTG
*
2648295 CCCAATCGCGAGGGATATTAAGTCGAGCGCGCCTCATTTG
1 CCCAATCGCGAGGGATATTAAGTCAAGCGCGCCTCATTTG
*
2648335 CCCTATCGC
1 CCCAATCGC
2648344 CGTTATCAGC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.21, C:0.29, G:0.25, T:0.25
Consensus pattern (40 bp):
CCCAATCGCGAGGGATATTAAGTCAAGCGCGCCTCATTTG
Found at i:2648408 original size:10 final size:11
Alignment explanation
Indices: 2648393--2648421 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
2648383 CCACTAGATG
2648393 ATTTTTCAAA-
1 ATTTTTCAAAC
2648403 ATTTTTCAAAC
1 ATTTTTCAAAC
2648414 ATTTTTCA
1 ATTTTTCA
2648422 TAAAAACTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (11 bp):
ATTTTTCAAAC
Found at i:2660705 original size:1 final size:1
Alignment explanation
Indices: 2660699--2660765 Score: 53
Period size: 1 Copynumber: 67.0 Consensus size: 1
2660689 CAAAACAAAC
* * * * ** * * *
2660699 AAAAAAACAAAAAAAAATAAAATAAAGAAAAAACCAAAAAAAAAAAAAAACAAAAACAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2660764 AA
1 AA
2660766 TGGTCCAGAT
Statistics
Matches: 50, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.87, C:0.09, G:0.01, T:0.03
Consensus pattern (1 bp):
A
Found at i:2660712 original size:10 final size:10
Alignment explanation
Indices: 2660699--2660765 Score: 64
Period size: 10 Copynumber: 6.4 Consensus size: 10
2660689 CAAAACAAAC
2660699 AAAAAAACAA
1 AAAAAAACAA
*
2660709 AAAAAAATAA
1 AAAAAAACAA
2660719 AATAAAGAA-AA
1 AA-AAA-AACAA
*
2660730 AACCAAAAAAAA
1 AA--AAAAACAA
2660742 AAAAAAACAA
1 AAAAAAACAA
*
2660752 AAACAAACAA
1 AAAAAAACAA
2660762 AAAA
1 AAAA
2660766 TGGTCCAGAT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
10 30 0.62
11 9 0.19
12 9 0.19
ACGTcount: A:0.87, C:0.09, G:0.01, T:0.03
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:2660720 original size:27 final size:25
Alignment explanation
Indices: 2660690--2660765 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 25
2660680 CCTTCGTACC
*
2660690 AAAACAAACAAAAAAACAAAAAAAA
1 AAAAAAAACAAAAAAACAAAAAAAA
* *
2660715 ATAAAATAAA-GAAAAAACCAAAAAAA
1 A-AAAA-AAACAAAAAAACAAAAAAAA
2660741 AAAAAAAACAAAAACAAACAAAAAA
1 AAAAAAAAC-AAAA-AAACAAAAAA
2660766 TGGTCCAGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
24 3 0.07
25 5 0.12
26 21 0.51
27 12 0.29
ACGTcount: A:0.86, C:0.11, G:0.01, T:0.03
Consensus pattern (25 bp):
AAAAAAAACAAAAAAACAAAAAAAA
Found at i:2662047 original size:28 final size:28
Alignment explanation
Indices: 2662007--2662471 Score: 422
Period size: 28 Copynumber: 16.2 Consensus size: 28
2661997 TAGAACGTTT
* * *
2662007 ATCTCTTCAAAGCTCACAGGTCCA-TGGC
1 ATCTTTTCAAAGCCCACAAGT-CAGTGGC
*
2662035 ATCTTTTCAAAGCCCACAAGTCAATGGC
1 ATCTTTTCAAAGCCCACAAGTCAGTGGC
* *
2662063 ATCTTTTCAAAGCCCACAGGTCAATGGC
1 ATCTTTTCAAAGCCCACAAGTCAGTGGC
2662091 ATCCTTTT-AAAGCCCACAAGTCAGTGGC
1 AT-CTTTTCAAAGCCCACAAGTCAGTGGC
* * *
2662119 ATCCTTCCAAAGCCCACAAGTTAGTGGC
1 ATCTTTTCAAAGCCCACAAGTCAGTGGC
*
2662147 ATCCTTTCAAAGCCCACAAGTCAGTGGC
1 ATCTTTTCAAAGCCCACAAGTCAGTGGC
*
2662175 ATCCTTTT-AAAGCCCACAAGTTAGTGGC
1 AT-CTTTTCAAAGCCCACAAGTCAGTGGC
* **
2662203 ATCTCTTCAAAAGATCACAAGTCAGTGGC
1 ATCTTTTC-AAAGCCCACAAGTCAGTGGC
*
2662232 ATCCTTTCAAAGCCCACAAGTCAGTGGC
1 ATCTTTTCAAAGCCCACAAGTCAGTGGC
* * * *
2662260 ACCTTTTCAAAGCTCAAAAGTTAGTGGC
1 ATCTTTTCAAAGCCCACAAGTCAGTGGC
** * *
2662288 ATACCCCTTCAAAGCCCACAAGACAGTAGC
1 AT--CTTTTCAAAGCCCACAAGTCAGTGGC
* *
2662318 ACCCTTTCAAAGCCCACAAGTCAGTGGC
1 ATCTTTTCAAAGCCCACAAGTCAGTGGC
** * *
2662346 ATACCCATTCAAAGCCTACAAGTCAGTGGT
1 AT--CTTTTCAAAGCCCACAAGTCAGTGGC
2662376 ATACCCTTTT-AAAGCCCACAAGT--GTGGC
1 AT---CTTTTCAAAGCCCACAAGTCAGTGGC
* * *
2662404 ACCCTTTCAAAGCCTACACAAGTCCGTGGC
1 ATCTTTTCAAAGCC--CACAAGTCAGTGGC
* *
2662434 AACTCTTTTCAAAGCTCACACAAGTTAGTAGC
1 -A-TCTTTTCAAAGC-C-CACAAGTCAGTGGC
2662466 A-CTTTT
1 ATCTTTT
2662472 TTTATTAAAA
Statistics
Matches: 364, Mismatches: 54, Indels: 37
0.80 0.12 0.08
Matches are distributed among these distances:
25 4 0.01
26 6 0.02
27 9 0.02
28 217 0.60
29 37 0.10
30 62 0.17
31 6 0.02
32 22 0.06
33 1 0.00
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (28 bp):
ATCTTTTCAAAGCCCACAAGTCAGTGGC
Found at i:2663408 original size:20 final size:20
Alignment explanation
Indices: 2663383--2663436 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
2663373 CTTTACCCAG
2663383 ATGTATCGATACATGTATGA
1 ATGTATCGATACATGTATGA
*
2663403 ATGTATCGATATATGTATGA
1 ATGTATCGATACATGTATGA
*
2663423 ATGTTTCGATACAT
1 ATGTATCGATACAT
2663437 TCTTTAATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATGTATGA
Found at i:2667740 original size:20 final size:19
Alignment explanation
Indices: 2667693--2667767 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 19
2667683 AAAAAGACAG
2667693 AATGTATCGATACATTGAA
1 AATGTATCGATACATTGAA
* *
2667712 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTGA-A
* *
2667733 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTG-AA
*
2667753 AATGTAACGATACAT
1 AATGTATCGATACAT
2667768 CTGGGTAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 42 0.95
21 2 0.05
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:2668492 original size:29 final size:29
Alignment explanation
Indices: 2668346--2668767 Score: 543
Period size: 29 Copynumber: 14.5 Consensus size: 29
2668336 CACTAACTTG
**
2668346 TGTGGGCTTTGAAAAGAGTTGCCACCAACT
1 TGTGGGCTTTGAAAAGAG-TGCCACTGACT
2668376 CGTGTGGGCTTTGAAAAGAGTGCCACTGACT
1 --TGTGGGCTTTGAAAAGAGTGCCACTGACT
* * *
2668407 TATGGGCTTTG-AAAGGGTACCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
** *
2668435 TGTCTGCTTTG-AAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
2668463 TGTGGGCTTTGAAAAGAGTGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
2668492 TGTGGGCTTTG-AAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
2668520 TACGTGGGCTTTGAAAGGA-TGCCACTGACT
1 T--GTGGGCTTTGAAAAGAGTGCCACTGACT
*
2668550 TACGTGGGCTTTGAAAGGA-TGCCTACTGACT
1 T--GTGGGCTTTGAAAAGAGTGCC-ACTGACT
2668581 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
2668610 TGTGGGCTTTGAAAA-TGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* * *
2668638 TGTGGGCTTTAAAAAGAGTGACACTGATT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
2668667 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
2668696 TGTGGGCTTTG-AAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
2668724 CAGTGGACTTTGAAAAGAGTGCCACTGACT
1 -TGTGGGCTTTGAAAAGAGTGCCACTGACT
2668754 TGTGGGCTTTGAAA
1 TGTGGGCTTTGAAA
2668768 GGGATGAACA
Statistics
Matches: 349, Mismatches: 32, Indels: 21
0.87 0.08 0.05
Matches are distributed among these distances:
28 106 0.30
29 141 0.40
30 64 0.18
31 20 0.06
32 18 0.05
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (29 bp):
TGTGGGCTTTGAAAAGAGTGCCACTGACT
Found at i:2668493 original size:57 final size:57
Alignment explanation
Indices: 2668346--2668767 Score: 530
Period size: 57 Copynumber: 7.2 Consensus size: 57
2668336 CACTAACTTG
**
2668346 TGTGGGCTTTGAAAAGAGTTGCCACCAACTCGTGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAG-TGCCACTGACT--TGTGGGCTTTG-AAAGAGTGCCACTGACT
* * * ** *
2668407 TATGGGCTTTG-AAAGGGTACCACTGACTTGTCTGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
* *
2668463 TGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
*
2668520 TACGTGGGCTTTGAAAGGA-TGCCACTGACTTACGTGGGCTTTGAAAG-GATGCCTACTGACT
1 T--GTGGGCTTTGAAAAGAGTGCCACTGACTT--GTGGGCTTTGAAAGAG-TGCC-ACTGACT
2668581 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA-ATGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGA-GTGCCACTGACT
* * *
2668638 TGTGGGCTTTAAAAAGAGTGACACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACT
* * *
2668696 TGTGGGCTTTG-AAAGGGTGCCACTGACTCAGTGGACTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT-TGTGGGCTTTG-AAAGAGTGCCACTGACT
2668754 TGTGGGCTTTGAAA
1 TGTGGGCTTTGAAA
2668768 GGGATGAACA
Statistics
Matches: 321, Mismatches: 26, Indels: 30
0.85 0.07 0.08
Matches are distributed among these distances:
56 26 0.08
57 108 0.34
58 91 0.28
59 43 0.13
60 35 0.11
61 18 0.06
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (57 bp):
TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
Found at i:2670017 original size:1 final size:1
Alignment explanation
Indices: 2670013--2670044 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
2670003 TTTTTCTTGG
*
2670013 TTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2670045 GGGTGTAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:2670025 original size:9 final size:9
Alignment explanation
Indices: 2670002--2670045 Score: 56
Period size: 8 Copynumber: 5.0 Consensus size: 9
2669992 TTTTTTGCTA
2670002 TTTTTTCTTG
1 TTTTTT-TTG
*
2670012 GTTTTTTTG
1 TTTTTTTTG
2670021 TTTTTTTT-
1 TTTTTTTTG
2670029 TTTTTTTT-
1 TTTTTTTTG
2670037 TTTTTTTTG
1 TTTTTTTTG
2670046 GGTGTAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
8 16 0.52
9 10 0.32
10 5 0.16
ACGTcount: A:0.00, C:0.02, G:0.09, T:0.89
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:2679762 original size:20 final size:20
Alignment explanation
Indices: 2679737--2679778 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2679727 AAATAATGGG
*
2679737 AATGAATAGCAAGAAAAAAA
1 AATGAACAGCAAGAAAAAAA
* *
2679757 AATGAACATCAATAAAAAAA
1 AATGAACAGCAAGAAAAAAA
2679777 AA
1 AA
2679779 AAAGTGGCCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.71, C:0.07, G:0.10, T:0.12
Consensus pattern (20 bp):
AATGAACAGCAAGAAAAAAA
Found at i:2683046 original size:23 final size:21
Alignment explanation
Indices: 2683020--2683068 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
2683010 GCATCTTGAC
2683020 ATGACAAATGTGATAATCATACA
1 ATGACAAATG-GATAA-CATACA
* *
2683043 ATGAACTAATGGATAACATTCA
1 ATG-ACAAATGGATAACATACA
2683065 ATGA
1 ATGA
2683069 GATGCTGGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 1 0.04
22 8 0.35
23 8 0.35
24 6 0.26
ACGTcount: A:0.47, C:0.12, G:0.14, T:0.27
Consensus pattern (21 bp):
ATGACAAATGGATAACATACA
Found at i:2684054 original size:20 final size:20
Alignment explanation
Indices: 2684025--2684102 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
2684015 GTAAAAAGAT
2684025 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
* *
2684045 AGAATATATCGATACATTCA
1 AGAATGTATCGATACATTGA
* * *
2684065 TA-CATGTATCAATATATTGA
1 -AGAATGTATCGATACATTGA
*
2684085 AAAATGTATCGATACATT
1 AGAATGTATCGATACATT
2684103 TGGGTAAAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
19 1 0.02
20 44 0.96
21 1 0.02
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:2687940 original size:14 final size:13
Alignment explanation
Indices: 2687921--2687967 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
2687911 GAAATATTAT
2687921 TGCCAAAGTACATG
1 TGCCAAAGTAC-TG
*
2687935 TGCCAAAGTACTT
1 TGCCAAAGTACTG
2687948 TGCC-AAGTACCTG
1 TGCCAAAGTA-CTG
*
2687961 TGTCAAA
1 TGCCAAA
2687968 ACTAAAAGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 5 0.18
13 10 0.36
14 13 0.46
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (13 bp):
TGCCAAAGTACTG
Found at i:2688040 original size:40 final size:40
Alignment explanation
Indices: 2687996--2688166 Score: 132
Period size: 40 Copynumber: 4.3 Consensus size: 40
2687986 AAAGTGTCTG
* * * * *
2687996 TGCCAGGTACCTGTGACAAAGTACCTGTGTCAGGTACCTA
1 TGCCAAGTACCTGTGCCAAAATACCTGTGCCAAGTACCTA
* * *
2688036 TGCCAAGTATCTATGCCAAAATACCTGTGCCAAGTACCTG
1 TGCCAAGTACCTGTGCCAAAATACCTGTGCCAAGTACCTA
** * * *
2688076 TGCCAAAGTACCTGTGCC-AAATATTTATGCCAAAGTACTTG
1 TGCC-AAGTACCTGTGCCAAAATACCTGTGCC-AAGTACCTA
* * * *
2688117 TGCTAAGTACCT-TGCC-AAGTACCTGTGCCAAAGTATCTG
1 TGCCAAGTACCTGTGCCAAAATACCTGTGCC-AAGTACCTA
*
2688156 TGCTAAGTACC
1 TGCCAAGTACC
2688167 CTAGGTACTT
Statistics
Matches: 108, Mismatches: 21, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
39 32 0.30
40 54 0.50
41 22 0.20
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (40 bp):
TGCCAAGTACCTGTGCCAAAATACCTGTGCCAAGTACCTA
Found at i:2688049 original size:13 final size:13
Alignment explanation
Indices: 2687993--2688166 Score: 152
Period size: 13 Copynumber: 13.1 Consensus size: 13
2687983 ACCAAAGTGT
*
2687993 CTGTGCCAGGTAC
1 CTGTGCCAAGTAC
*
2688006 CTGTGACAAAGTAC
1 CTGTG-CCAAGTAC
* *
2688020 CTGTGTCAGGTAC
1 CTGTGCCAAGTAC
* *
2688033 CTATGCCAAGTAT
1 CTGTGCCAAGTAC
* *
2688046 CTATGCCAAAATAC
1 CTGTGCC-AAGTAC
2688060 CTGTGCCAAGTAC
1 CTGTGCCAAGTAC
2688073 CTGTGCCAAAGTAC
1 CTGTGCC-AAGTAC
* *
2688087 CTGTGCCAAATAT
1 CTGTGCCAAGTAC
* *
2688100 TTATGCCAAAGTAC
1 CTGTGCC-AAGTAC
* *
2688114 TTGTGCTAAGTAC
1 CTGTGCCAAGTAC
2688127 CT-TGCCAAGTAC
1 CTGTGCCAAGTAC
*
2688139 CTGTGCCAAAGTAT
1 CTGTGCC-AAGTAC
*
2688153 CTGTGCTAAGTAC
1 CTGTGCCAAGTAC
2688166 C
1 C
2688167 CTAGGTACTT
Statistics
Matches: 129, Mismatches: 26, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
12 11 0.09
13 64 0.50
14 54 0.42
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (13 bp):
CTGTGCCAAGTAC
Found at i:2688060 original size:27 final size:27
Alignment explanation
Indices: 2688029--2688154 Score: 148
Period size: 27 Copynumber: 4.7 Consensus size: 27
2688019 CCTGTGTCAG
*
2688029 GTACCTATGCCAAGTATCTATGCCAAA
1 GTACCTGTGCCAAGTATCTATGCCAAA
* * *
2688056 ATACCTGTGCCAAGTACCTGTGCCAAA
1 GTACCTGTGCCAAGTATCTATGCCAAA
* *
2688083 GTACCTGTGCCAAATATTTATGCCAAA
1 GTACCTGTGCCAAGTATCTATGCCAAA
* * *
2688110 GTACTTGTGCTAAGTACCT-TGCC-AA
1 GTACCTGTGCCAAGTATCTATGCCAAA
2688135 GTACCTGTGCCAAAGTATCT
1 GTACCTGTGCC-AAGTATCT
2688155 GTGCTAAGTA
Statistics
Matches: 81, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
25 11 0.14
26 11 0.14
27 59 0.73
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.28
Consensus pattern (27 bp):
GTACCTGTGCCAAGTATCTATGCCAAA
Found at i:2688164 original size:27 final size:27
Alignment explanation
Indices: 2687984--2688166 Score: 135
Period size: 27 Copynumber: 6.9 Consensus size: 27
2687974 AGTGTCTATA
* * *
2687984 CCAAAGTGTCTGTGCCAGGTACCTGTG
1 CCAAAGTATCTGTGCAAAGTACCTGTG
* * * *
2688011 ACAAAGTACCTGTGTC-AGGTACCTATG
1 CCAAAGTATCTGTG-CAAAGTACCTGTG
* *
2688038 CC-AAGTATCTATGCCAAAATACCTGTG
1 CCAAAGTATCTGTG-CAAAGTACCTGTG
*
2688065 CC-AAGTACCTGTGCCAAAGTACCTGTG
1 CCAAAGTATCTGTG-CAAAGTACCTGTG
* * *
2688092 CCAAA-TATTTATGCCAAAGTACTTGTG
1 CCAAAGTATCTGTG-CAAAGTACCTGTG
* * *
2688119 -CTAAGTACCT-TGCCAAGTACCTGTG
1 CCAAAGTATCTGTGCAAAGTACCTGTG
*
2688144 CCAAAGTATCTGTGCTAAGTACC
1 CCAAAGTATCTGTGCAAAGTACC
2688167 CTAGGTACTT
Statistics
Matches: 124, Mismatches: 26, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
25 11 0.09
26 23 0.19
27 87 0.70
28 3 0.02
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (27 bp):
CCAAAGTATCTGTGCAAAGTACCTGTG
Found at i:2688252 original size:13 final size:14
Alignment explanation
Indices: 2688222--2688256 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
2688212 ACTTATGTCA
*
2688222 AAATACTTGTGCCC
1 AAATACCTGTGCCC
2688236 AAATACCTGTG-CC
1 AAATACCTGTGCCC
2688249 AAATACCT
1 AAATACCT
2688257 ATGACAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.34, C:0.29, G:0.11, T:0.26
Consensus pattern (14 bp):
AAATACCTGTGCCC
Found at i:2689088 original size:18 final size:18
Alignment explanation
Indices: 2689045--2689088 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2689035 AGTTCTTTTA
**
2689045 AAAATTAATTTCAAAATC
1 AAAATTAATTAAAAAATC
* *
2689063 AAATTTAATTAAAAAATT
1 AAAATTAATTAAAAAATC
2689081 AAAATTAA
1 AAAATTAA
2689089 ATAAGATAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAATTAATTAAAAAATC
Found at i:2689751 original size:21 final size:22
Alignment explanation
Indices: 2689725--2689766 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
2689715 TGTTACAAGC
*
2689725 CATATATCAATA-TATCTATAT
1 CATATATCAATACAATCTATAT
2689746 CATATATCAATACAATCTATA
1 CATATATCAATACAATCTATA
2689767 GGGTATCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (22 bp):
CATATATCAATACAATCTATAT
Found at i:2694902 original size:196 final size:195
Alignment explanation
Indices: 2694488--2695068 Score: 939
Period size: 195 Copynumber: 3.0 Consensus size: 195
2694478 TCCCTACTAT
* * *
2694488 ATAAGCATGGCCATCAAATTAATTTAACTTAAAACCAAATGTAATATTCCAAATATGATAAGACC
1 ATAAGCATGGCCATCAAATAAATTTAACTTGAAACCAAATGTAACATTCCAAATATGATAAGACC
* * *
2694553 TAATAATATCCACCATCAGATATCAGTTTTATGATGAAAAGCAACTCTAGACCTCAGATTTGTTA
66 TAATAATATCCACCATCAGAAATCAG-TTTATGATGACAAGCAACTCTAGGCCTCAGATTTGTTA
* * *
2694618 -TTTTATTGTCATCAGAATGAAGATCAGACAATGTAGGCAATTCATAATCATCATAAGCCTGCCA
130 TTTTTATTGTCATCAGAATGAAGATCAGACAATGTAGGCAATTCTTAATCATCATAGGCCTACCA
2694682 C
195 C
* *
2694683 ATAAGCATGGCCATCAAATAAATTTAACTTGAAACTAAATGTAACATTCCAAATATGATAAGGCC
1 ATAAGCATGGCCATCAAATAAATTTAACTTGAAACCAAATGTAACATTCCAAATATGATAAGACC
* ** * *
2694748 TAACAATATCTGCCATAAGACATCAGTTTCATGATGACAAGCAACTCTAGGCCTCAGATTTGTTA
66 TAATAATATCCACCATCAGAAATCAGTTT-ATGATGACAAGCAACTCTAGGCCTCAGATTTGTTA
*
2694813 TTTTTATTGTCATCAGAATGAAGATCAGACAATGTGGGCAATTCTTAATCATCATAGGCCTACCA
130 TTTTTATTGTCATCAGAATGAAGATCAGACAATGTAGGCAATTCTTAATCATCATAGGCCTACCA
2694878 C
195 C
*
2694879 ATAAGCATGGCCATCAGATAAATTTAACTTGAAACCAAATGTAACATTCCAAATATGATAAGACC
1 ATAAGCATGGCCATCAAATAAATTTAACTTGAAACCAAATGTAACATTCCAAATATGATAAGACC
2694944 TAATAATATCCACCATCAGAAATCAGTTTATGATGACAAGCAACTCTAGGCCTCAGATTTGTTAT
66 TAATAATATCCACCATCAGAAATCAGTTTATGATGACAAGCAACTCTAGGCCTCAGATTTGTTAT
* * * *
2695009 ATTTATTGTCATCAGAGTGAAGATCAGACAATGTAGGCAATTCTTAATAAACATAGGCCT
131 TTTTATTGTCATCAGAATGAAGATCAGACAATGTAGGCAATTCTTAATCATCATAGGCCT
2695069 TCTAAAAGCA
Statistics
Matches: 355, Mismatches: 29, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
194 3 0.01
195 205 0.58
196 147 0.41
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (195 bp):
ATAAGCATGGCCATCAAATAAATTTAACTTGAAACCAAATGTAACATTCCAAATATGATAAGACC
TAATAATATCCACCATCAGAAATCAGTTTATGATGACAAGCAACTCTAGGCCTCAGATTTGTTAT
TTTTATTGTCATCAGAATGAAGATCAGACAATGTAGGCAATTCTTAATCATCATAGGCCTACCAC
Found at i:2696906 original size:2 final size:2
Alignment explanation
Indices: 2696899--2696939 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2696889 TCTATCTGTC
2696899 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2696940 TAATTTAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2698701 original size:22 final size:22
Alignment explanation
Indices: 2698676--2698722 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2698666 TAAAATTTAT
*
2698676 TTTTTAAATATATAATATATTA
1 TTTTTAAATATATAATATATAA
** *
2698698 TTTTTATTTATATATTATATAA
1 TTTTTAAATATATAATATATAA
2698720 TTT
1 TTT
2698723 ATATTATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTTTAAATATATAATATATAA
Found at i:2698727 original size:22 final size:21
Alignment explanation
Indices: 2698684--2698764 Score: 72
Period size: 22 Copynumber: 3.7 Consensus size: 21
2698674 ATTTTTTAAA
* *
2698684 TATATAATATATTATTTTTATT
1 TATATAATATATAATTTATA-T
*
2698706 TATATATTATATAATTTATAT
1 TATATAATATATAATTTATAT
* * *
2698727 TATATAAAAATAAAATATATAT
1 TATAT-AATATATAATTTATAT
2698749 ATATATAATATTATAA
1 -TATATAATA-TATAA
2698765 AATAAAAATT
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
21 6 0.13
22 32 0.68
23 9 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TATATAATATATAATTTATAT
Found at i:2698748 original size:31 final size:30
Alignment explanation
Indices: 2698713--2698783 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
2698703 ATTTATATAT
* *
2698713 TATATAATTTATATTA-TATAAAA-ATAAAA
1 TATATAATATATAATATTATAAAATA-AAAA
2698742 TATATATATATATAATATTATAAAATAAAAA
1 TATATA-ATATATAATATTATAAAATAAAAA
2698773 T-TATAATATAT
1 TATATAATATAT
2698784 GTGTTAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
29 12 0.32
30 12 0.32
31 12 0.32
32 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (30 bp):
TATATAATATATAATATTATAAAATAAAAA
Found at i:2698760 original size:33 final size:29
Alignment explanation
Indices: 2698715--2698783 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
2698705 TTATATATTA
* * *
2698715 TATAATTTATATTA-TATAAAAATAAAAT
1 TATAATATATAATATTATAAAAAAAAAAT
*
2698743 ATATATATATATAATATTATAAAATAAAAAT
1 -TATA-ATATATAATATTATAAAAAAAAAAT
2698774 TATAATATAT
1 TATAATATAT
2698784 GTGTTAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 12 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
TATAATATATAATATTATAAAAAAAAAAT
Found at i:2700695 original size:16 final size:16
Alignment explanation
Indices: 2700673--2700710 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
2700663 TATTCATTTA
*
2700673 TAAAAAAGGAAAAAA-
1 TAAAAAAAGAAAAAAG
2700688 TAAAAAAAGAAAAAAG
1 TAAAAAAAGAAAAAAG
2700704 TAAAAAA
1 TAAAAAA
2700711 CTTTAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.08
Consensus pattern (16 bp):
TAAAAAAAGAAAAAAG
Found at i:2700911 original size:19 final size:20
Alignment explanation
Indices: 2700874--2700913 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2700864 AATTAAATGA
* *
2700874 ATTTTATATTTTTATAAATT
1 ATTTAATATTTATATAAATT
2700894 ATTTAATATTTATA-AAATT
1 ATTTAATATTTATATAAATT
2700913 A
1 A
2700914 ATCTAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTAATATTTATATAAATT
Found at i:2701173 original size:23 final size:23
Alignment explanation
Indices: 2701144--2701196 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
2701134 ATATAAAATT
* * *
2701144 TTAAAAGGAAAATAAAAGAATAAG
1 TTAAAAGAAAAAGAAAAAAAT-AG
2701168 -TAAAAGAAAAAGAAAAAAATAG
1 TTAAAAGAAAAAGAAAAAAATAG
2701190 TTAAAAG
1 TTAAAAG
2701197 CTTATATTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 2 0.08
23 23 0.92
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (23 bp):
TTAAAAGAAAAAGAAAAAAATAG
Found at i:2701684 original size:23 final size:23
Alignment explanation
Indices: 2701645--2701688 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2701635 ATAAAAATAT
*
2701645 AATATATTTATACAATAATTTAA
1 AATATATATATACAATAATTTAA
2701668 AATATATAATATA-AATAATTT
1 AATATAT-ATATACAATAATTT
2701689 TTTATAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
AATATATATATACAATAATTTAA
Found at i:2702281 original size:15 final size:15
Alignment explanation
Indices: 2702256--2702303 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
2702246 TTGAAAATAT
2702256 TTTTATTTAAATTAA
1 TTTTATTTAAATTAA
2702271 TTATT-TTTAAATTAA
1 TT-TTATTTAAATTAA
2702286 TTTTATTTAAATT-A
1 TTTTATTTAAATTAA
2702300 TTTT
1 TTTT
2702304 TTAATTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
14 7 0.23
15 22 0.71
16 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTATTTAAATTAA
Found at i:2702313 original size:7 final size:7
Alignment explanation
Indices: 2702301--2702328 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
2702291 TTTAAATTAT
2702301 TTTTTAA
1 TTTTTAA
2702308 TTTTTAA
1 TTTTTAA
2702315 TTTTTAA
1 TTTTTAA
2702322 TTTTTAA
1 TTTTTAA
2702329 ATTTCAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTTAA
Found at i:2704298 original size:2 final size:2
Alignment explanation
Indices: 2704293--2704325 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2704283 TATATATATA
2704293 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
2704326 TTCTCATAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2706477 original size:89 final size:88
Alignment explanation
Indices: 2706356--2706532 Score: 327
Period size: 89 Copynumber: 2.0 Consensus size: 88
2706346 GGAAATAGAA
*
2706356 ATTTAGCAGAATCCTTTCACAATCACATTATATTTCATCCTCCTCAAAGGGATCTCGTTCAGGAT
1 ATTTAGCAGAACCCTTTCACAATCACATTATATTTCATCCTCCTCAAAGGGATCTCGTTCAGGAT
2706421 AGTCACCAACCTGGAAATGACAG
66 AGTCACCAACCTGGAAATGACAG
*
2706444 ATTTAGCAGTACCCTTTTCACAATCACATTATATTTCATCCTCCTCAAAGGGATCTCGTTCAGGA
1 ATTTAGCAGAACCC-TTTCACAATCACATTATATTTCATCCTCCTCAAAGGGATCTCGTTCAGGA
2706509 TAGTCACCAACCTGGAAATGACAG
65 TAGTCACCAACCTGGAAATGACAG
2706533 TAAAGTGCCA
Statistics
Matches: 86, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
88 12 0.14
89 74 0.86
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (88 bp):
ATTTAGCAGAACCCTTTCACAATCACATTATATTTCATCCTCCTCAAAGGGATCTCGTTCAGGAT
AGTCACCAACCTGGAAATGACAG
Found at i:2709771 original size:178 final size:178
Alignment explanation
Indices: 2709469--2709814 Score: 541
Period size: 178 Copynumber: 1.9 Consensus size: 178
2709459 TTACTCCATG
* *
2709469 AAAATAGGGTGCAAAACAAATTCCAGAAGTAATATATACATAATACATTTAATATGGTTGAATTT
1 AAAATAGGGCGCAAAACAAATTCCAGAAGTAATATATACATAATACATTTAACATGGTTGAATTT
* * *
2709534 AAAACTGTGTTTGCTCGTAGGTAAGCATTATCAAGCATATAGTGGTAAATTTGTTGAGATTTTGG
66 AAAACTGTGTTTGCTCGTAGGTAAGCACTATCAAGCATACAGTGGTAAATTTATTGAGATTTTGG
**
2709599 CCTTACAAAATCACTTT-ATGTTTTGATAAGTACAACTACTGTCTGTCA
131 CCTTACAAAATCA-TTTCATGTTTCAATAAGTACAACTACTGTCTGTCA
*
2709647 AAAATAGGGCGCAAAACAAATTCCAGAAGTAATGTATACATAATACATTTAACATGGTTGAATTT
1 AAAATAGGGCGCAAAACAAATTCCAGAAGTAATATATACATAATACATTTAACATGGTTGAATTT
* * * * *
2709712 AAAACTGTTTTTGCTTGTAGGTAAGCACTATGAAGCATGCAGTGGTGAATTTATTGAGATTTTGG
66 AAAACTGTGTTTGCTCGTAGGTAAGCACTATCAAGCATACAGTGGTAAATTTATTGAGATTTTGG
* *
2709777 CCTTCCAAAATCATTTCATGTTTCAATGAGTACAACTA
131 CCTTACAAAATCATTTCATGTTTCAATAAGTACAACTA
2709815 AACTTGATTA
Statistics
Matches: 152, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
177 3 0.02
178 149 0.98
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (178 bp):
AAAATAGGGCGCAAAACAAATTCCAGAAGTAATATATACATAATACATTTAACATGGTTGAATTT
AAAACTGTGTTTGCTCGTAGGTAAGCACTATCAAGCATACAGTGGTAAATTTATTGAGATTTTGG
CCTTACAAAATCATTTCATGTTTCAATAAGTACAACTACTGTCTGTCA
Found at i:2713947 original size:2 final size:2
Alignment explanation
Indices: 2713942--2713966 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2713932 ATATGCCTAG
2713942 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
2713967 GTGTGTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2717512 original size:17 final size:17
Alignment explanation
Indices: 2717490--2717522 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2717480 ATAAGGTGTT
*
2717490 GACATGCTCCTGCTCTG
1 GACATGCTCCTACTCTG
2717507 GACATGCTCCTACTCT
1 GACATGCTCCTACTCT
2717523 ATCTCTACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.36, G:0.18, T:0.30
Consensus pattern (17 bp):
GACATGCTCCTACTCTG
Found at i:2718956 original size:88 final size:86
Alignment explanation
Indices: 2718784--2718958 Score: 228
Period size: 88 Copynumber: 2.0 Consensus size: 86
2718774 TAATGCATTT
* *
2718784 AATAATTTTCAGTACATTGAGATAATTGTTTTTCTTTAAAAAAAAAATGAAGAAGAAAAAAGCCC
1 AATAATTTTCAGTAAATTGAGATAATTATTTTTCTTTAAAAAAAAAA-GAAGAAGAAAAAAGCCC
**
2718849 TTTGTATGCATGAACACTTTTA
65 TTTGTATGCACAAACACTTTTA
*
2718871 AATAACTTTT-AGTAAATTGAGATAATTATTTTTCTTTTTTTAAAAAAAAA-AAGAAGAAAAAAG
1 AATAA-TTTTCAGTAAATTGAGATAATTATTTTTC---TTTAAAAAAAAAAGAAGAAGAAAAAAG
* *
2718934 CTCTTTGTATTCACAAACACTTTTA
62 CCCTTTGTATGCACAAACACTTTTA
2718959 GTTGCCGATC
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
87 27 0.35
88 38 0.49
90 12 0.16
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (86 bp):
AATAATTTTCAGTAAATTGAGATAATTATTTTTCTTTAAAAAAAAAAGAAGAAGAAAAAAGCCCT
TTGTATGCACAAACACTTTTA
Found at i:2721400 original size:9 final size:9
Alignment explanation
Indices: 2721386--2721415 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
2721376 AAATAAAAAA
2721386 TTTAATTAT
1 TTTAATTAT
2721395 TTTAATTAT
1 TTTAATTAT
2721404 TTTAATTAT
1 TTTAATTAT
2721413 TTT
1 TTT
2721416 TTTATTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTAATTAT
Found at i:2723777 original size:52 final size:52
Alignment explanation
Indices: 2723695--2723795 Score: 148
Period size: 52 Copynumber: 1.9 Consensus size: 52
2723685 TCCCATAGCA
* * *
2723695 AGAACCAAGCCCAACATAGCTGGCAGGTTTAGCTTTAGTGAAGTTAGCCCAT
1 AGAACCAAGCCCAACATAGCTGGCAAGTTTAGCTCTAGTGAAATTAGCCCAT
* * *
2723747 AGAACCAAGCTCAACATAGTTGGTAAGTTTAGCTCTAGTGAAATTAGCC
1 AGAACCAAGCCCAACATAGCTGGCAAGTTTAGCTCTAGTGAAATTAGCC
2723796 AATTAAACCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.25
Consensus pattern (52 bp):
AGAACCAAGCCCAACATAGCTGGCAAGTTTAGCTCTAGTGAAATTAGCCCAT
Found at i:2724017 original size:106 final size:107
Alignment explanation
Indices: 2723858--2724198 Score: 332
Period size: 106 Copynumber: 3.2 Consensus size: 107
2723848 AATGTAACTA
* * ** *
2723858 GTAGGTAGGCTCTAGTGAAGTTGGTTCATAGTAAGAATCAAGCCTAACATAGCTGGTAGGTAGGC
1 GTAGGTAGGCTCTAATGAAGTTGGCTCATAACAAGAATCAAGCCTAACGTAGCTGGTAGGTAGGC
* * * *
2723923 TCTAGTGAAGTTGGCCTATAGTA-TCAAGCCTAACGTAGGTA
66 TCTAATGAAGTTGGCCTATAGTAGTCAAGCCAAACGTAGCTG
* * ** * * *
2723964 ATAGGTAGGCTCTAATGAAGTTGGCACATAACAAGAAAAAACCCTAATGTAGCTGGCAGGTTTA-
1 GTAGGTAGGCTCTAATGAAGTTGGCTCATAACAAGAATCAAGCCTAACGTAGCTGGTAGG--TAG
* * * *
2724028 GCTCTAATGAAGTTGGCCAATAG-ATTTAAGCCCAACGTAGCTG
64 GCTCTAATGAAGTTGGCCTATAGTAGTCAAGCCAAACGTAGCTG
* * ** * * *** *
2724071 GTAAGTAGGCTCCAAAAAAGTTAGCTCGT-AGTTG-ATCAAGCCTAACGTAGTTGGTAGGTAGGC
1 GTAGGTAGGCTCTAATGAAGTTGGCTCATAACAAGAATCAAGCCTAACGTAGCTGGTAGGTAGGC
*
2724134 TCTAATGAAGTTGGCCTATAATCAGTCAAGCCAAACGTAGCTG
66 TCTAATGAAGTTGGCCTATAGT-AGTCAAGCCAAACGTAGCTG
*
2724177 GTAGGTAGGCTCTAGTGAAGTT
1 GTAGGTAGGCTCTAATGAAGTT
2724199 AGCCCATTGA
Statistics
Matches: 184, Mismatches: 45, Indels: 12
0.76 0.19 0.05
Matches are distributed among these distances:
103 2 0.01
104 21 0.11
105 18 0.10
106 85 0.46
107 56 0.30
108 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.26
Consensus pattern (107 bp):
GTAGGTAGGCTCTAATGAAGTTGGCTCATAACAAGAATCAAGCCTAACGTAGCTGGTAGGTAGGC
TCTAATGAAGTTGGCCTATAGTAGTCAAGCCAAACGTAGCTG
Found at i:2724145 original size:53 final size:53
Alignment explanation
Indices: 2723858--2724198 Score: 284
Period size: 53 Copynumber: 6.4 Consensus size: 53
2723848 AATGTAACTA
* * *
2723858 GTAGGTAGGCTCTAGTGAAGTTGGTTCATAGTAAGAATCAAGCCTAACATAGCTG
1 GTAGGTAGGCTCTAATGAAGTTGG-CCATAGT-AGAATCAAGCCTAACGTAGCTG
* * * *
2723913 GTAGGTAGGCTCTAGTGAAGTTGGCC-TA-TAGTATCAAGCCTAACGTAGGTA
1 GTAGGTAGGCTCTAATGAAGTTGGCCATAGTAGAATCAAGCCTAACGTAGCTG
* ** ** * *
2723964 ATAGGTAGGCTCTAATGAAGTTGGCACATAACAAGAAAAAACCCTAATGTAGCTG
1 GTAGGTAGGCTCTAATGAAGTTGGC-CAT-AGTAGAATCAAGCCTAACGTAGCTG
* * * *
2724019 GCAGGTTTA-GCTCTAATGAAGTTGGCCA-A-TAGATTTAAGCCCAACGTAGCTG
1 GTAGG--TAGGCTCTAATGAAGTTGGCCATAGTAGAATCAAGCCTAACGTAGCTG
* * ** * * * *
2724071 GTAAGTAGGCTCCAAAAAAGTTAGCTCGTAGTTG-ATCAAGCCTAACGTAGTTG
1 GTAGGTAGGCTCTAATGAAGTTGGC-CATAGTAGAATCAAGCCTAACGTAGCTG
* *
2724124 GTAGGTAGGCTCTAATGAAGTTGGCCTATAATCAG--TCAAGCCAAACGTAGCTG
1 GTAGGTAGGCTCTAATGAAGTTGGCC-ATAGT-AGAATCAAGCCTAACGTAGCTG
*
2724177 GTAGGTAGGCTCTAGTGAAGTT
1 GTAGGTAGGCTCTAATGAAGTT
2724199 AGCCCATTGA
Statistics
Matches: 227, Mismatches: 47, Indels: 26
0.76 0.16 0.09
Matches are distributed among these distances:
50 2 0.01
51 54 0.24
52 23 0.10
53 80 0.35
54 5 0.02
55 44 0.19
56 17 0.07
57 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.26
Consensus pattern (53 bp):
GTAGGTAGGCTCTAATGAAGTTGGCCATAGTAGAATCAAGCCTAACGTAGCTG
Found at i:2724381 original size:65 final size:65
Alignment explanation
Indices: 2724312--2724444 Score: 153
Period size: 65 Copynumber: 2.0 Consensus size: 65
2724302 CTTTTAACTT
* *
2724312 GAACTTG-TTTTCTTAAAAATAGATCGAACATTAAAGCAAAATAGAGACCATG-TTCTTTTTTAG
1 GAACTTGTTTTTC-TAAAAATAGATCGAACATCAAAGCAAAATAAAGACCATGTTTC-TTTTTAG
2724375 TC
64 TC
* * * * * * *
2724377 GAACTTGTTTTTCTAGAAATAGATTGAGCCTCAGAGCAAAATAAAGGCCTTGTTTCTTTTTAGTC
1 GAACTTGTTTTTCTAAAAATAGATCGAACATCAAAGCAAAATAAAGACCATGTTTCTTTTTAGTC
2724442 GAA
1 GAA
2724445 TCTCTTTTCC
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
65 49 0.86
66 8 0.14
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (65 bp):
GAACTTGTTTTTCTAAAAATAGATCGAACATCAAAGCAAAATAAAGACCATGTTTCTTTTTAGTC
Found at i:2724676 original size:21 final size:21
Alignment explanation
Indices: 2724650--2724697 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
2724640 TTAGAGATAG
*
2724650 GTCTAGTAGCCTAGGAATACA
1 GTCTAGTAGCATAGGAATACA
**
2724671 GTCTAGTAGCATAGGAATGGA
1 GTCTAGTAGCATAGGAATACA
2724692 GTCTAG
1 GTCTAG
2724698 GTCCTTTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.25
Consensus pattern (21 bp):
GTCTAGTAGCATAGGAATACA
Found at i:2725231 original size:27 final size:27
Alignment explanation
Indices: 2725201--2725256 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
2725191 CACCAATTTT
2725201 ATGCATTCACCAATCATTGCATGACAA
1 ATGCATTCACCAATCATTGCATGACAA
*
2725228 ATGCATTCGCCAATCATTGCATGACAA
1 ATGCATTCACCAATCATTGCATGACAA
2725255 AT
1 AT
2725257 TAAGCCTGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.27
Consensus pattern (27 bp):
ATGCATTCACCAATCATTGCATGACAA
Found at i:2728460 original size:52 final size:52
Alignment explanation
Indices: 2728312--2728440 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
2728302 CGAAATATGA
*
2728312 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCAATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
2728364 AAATTTGCCTACATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
2728416 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
2728441 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:2728467 original size:13 final size:13
Alignment explanation
Indices: 2728449--2728473 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2728439 CAAAGATCAG
2728449 TGTATCGATACAA
1 TGTATCGATACAA
2728462 TGTATCGATACA
1 TGTATCGATACA
2728474 GTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2728553 original size:13 final size:13
Alignment explanation
Indices: 2728535--2728559 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2728525 ACAAAACTTA
2728535 TGTATCGATACAT
1 TGTATCGATACAT
2728548 TGTATCGATACA
1 TGTATCGATACA
2728560 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2728555 original size:32 final size:33
Alignment explanation
Indices: 2728514--2728579 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
2728504 AGTAGCTTAA
2728514 ATTGTATCGATACAAAAC-TTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
*
2728546 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
2728579 A
1 A
2728580 AATTGTTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 17 0.53
33 15 0.47
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (33 bp):
ATTGTATCGATACAAAACTTTATGTATCGATAC
Found at i:2730551 original size:19 final size:19
Alignment explanation
Indices: 2730527--2730594 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
2730517 AATTCAACGA
2730527 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
2730546 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
2730561 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
2730578 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
2730595 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Done.