Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 124 of 187
Found at i:37569580 original size:15 final size:14
Alignment explanation
Indices: 37569551--37569593 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
37569541 GGTCTCCAGA
37569551 CTCTT-TTTTTATTT
1 CTCTTCTTTTT-TTT
37569565 CTCTTCTTTTCTTTT
1 CTCTTCTTTT-TTTT
*
37569580 CTTTTCTTTTTTTT
1 CTCTTCTTTTTTTT
37569594 GAAATCCCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 9 0.35
15 16 0.62
16 1 0.04
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (14 bp):
CTCTTCTTTTTTTT
Found at i:37585134 original size:29 final size:29
Alignment explanation
Indices: 37585102--37585210 Score: 157
Period size: 29 Copynumber: 3.8 Consensus size: 29
37585092 ATGGTCAAAG
* * *
37585102 CCATCCTTTTTTATATTCGATGGTCGTCT
1 CCATCCCTTTTCATATTCGATGGTCGTCA
37585131 CCATCCCTTTTCATATTCGATGGTCGTCA
1 CCATCCCTTTTCATATTCGATGGTCGTCA
* **
37585160 CCATCCCTTTTCATATTTGAT-GTCGAAA
1 CCATCCCTTTTCATATTCGATGGTCGTCA
37585188 CCATCCCTTTTCATATTCGATGG
1 CCATCCCTTTTCATATTCGATGG
37585211 GCATCAATAC
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
28 25 0.35
29 47 0.65
ACGTcount: A:0.18, C:0.28, G:0.13, T:0.41
Consensus pattern (29 bp):
CCATCCCTTTTCATATTCGATGGTCGTCA
Found at i:37590229 original size:23 final size:23
Alignment explanation
Indices: 37590203--37590278 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
37590193 ATAAGTGCCA
37590203 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
37590226 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
37590249 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
37590272 CACTGAT
1 CACTGAT
37590279 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:37590378 original size:8 final size:8
Alignment explanation
Indices: 37590365--37590393 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
37590355 ACCCGGGACT
37590365 CACTGTAA
1 CACTGTAA
37590373 CACTGTAA
1 CACTGTAA
37590381 CACTGTAA
1 CACTGTAA
37590389 CACTG
1 CACTG
37590394 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:37590538 original size:18 final size:17
Alignment explanation
Indices: 37590512--37590550 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
37590502 ATTTTCCTTC
37590512 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
37590529 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
37590547 CACA
1 CACA
37590551 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:37625776 original size:25 final size:25
Alignment explanation
Indices: 37625746--37625813 Score: 102
Period size: 25 Copynumber: 2.7 Consensus size: 25
37625736 CTATAAATGA
37625746 TAAGCTCATTCGAGCTGAATATCAG
1 TAAGCTCATTCGAGCTGAATATCAG
* *
37625771 TAAGCTCATGCGAGCTAAATATCAG
1 TAAGCTCATTCGAGCTGAATATCAG
37625796 TAAGCTC-TCTCGAGCTGA
1 TAAGCTCAT-TCGAGCTGA
37625814 GAATCGGTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
24 1 0.03
25 37 0.97
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (25 bp):
TAAGCTCATTCGAGCTGAATATCAG
Found at i:37635544 original size:53 final size:53
Alignment explanation
Indices: 37635464--37635569 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
37635454 ATGCAAAAGT
37635464 ATCATATGGACAAGTGAAAGTTGTCTTCTCTTGGTCGTTGGGAGCTTTAGTAG
1 ATCATATGGACAAGTGAAAGTTGTCTTCTCTTGGTCGTTGGGAGCTTTAGTAG
37635517 ATCATATGGACAAGTGAAAGTTGTCTTCTCTTGGTCGTTGGGAGCTTTAGTAG
1 ATCATATGGACAAGTGAAAGTTGTCTTCTCTTGGTCGTTGGGAGCTTTAGTAG
37635570 TCTTATTATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.23, C:0.13, G:0.28, T:0.36
Consensus pattern (53 bp):
ATCATATGGACAAGTGAAAGTTGTCTTCTCTTGGTCGTTGGGAGCTTTAGTAG
Found at i:37645572 original size:14 final size:14
Alignment explanation
Indices: 37645553--37645584 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
37645543 CCGGATATCG
37645553 AGTACATACCCCTA
1 AGTACATACCCCTA
37645567 AGTACATACCCCTA
1 AGTACATACCCCTA
37645581 AGTA
1 AGTA
37645585 AATCATATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.31, G:0.09, T:0.22
Consensus pattern (14 bp):
AGTACATACCCCTA
Found at i:37647743 original size:27 final size:28
Alignment explanation
Indices: 37647713--37647780 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 28
37647703 CAAGTTCATT
* *
37647713 ACCACAAAGGCTTCCTTTT-CGTAAATC
1 ACCACAAAGGCTTCATTTTACATAAATC
** *
37647740 ACCACAAACTCTTCATTTTACATAGATC
1 ACCACAAAGGCTTCATTTTACATAAATC
*
37647768 ACCACACAGGCTT
1 ACCACAAAGGCTT
37647781 TTTTTCTGGC
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
27 16 0.50
28 16 0.50
ACGTcount: A:0.32, C:0.31, G:0.09, T:0.28
Consensus pattern (28 bp):
ACCACAAAGGCTTCATTTTACATAAATC
Found at i:37650454 original size:25 final size:25
Alignment explanation
Indices: 37650395--37650512 Score: 98
Period size: 25 Copynumber: 4.7 Consensus size: 25
37650385 TCCTGTACAT
37650395 GTATGCTCACACGAG-TATGAAA-CG
1 GTATGCTCACACGAGCTAT-AAATCG
* *
37650419 ATATGCTCACACGAGCTATAAATTG
1 GTATGCTCACACGAGCTATAAATCG
* *
37650444 GTATGCTCACACGAGCTGTAAATCA
1 GTATGCTCACACGAGCTATAAATCG
* * *
37650469 GT-TAGCTCACATGAGCTGTGGAAATGG
1 GTAT-GCTCACACGAGCTAT--AAATCG
**
37650496 GCCTGCTCACACGAGCT
1 GTATGCTCACACGAGCT
37650513 GAGGGTCAAA
Statistics
Matches: 77, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
24 18 0.23
25 41 0.53
27 17 0.22
28 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.24
Consensus pattern (25 bp):
GTATGCTCACACGAGCTATAAATCG
Found at i:37651754 original size:25 final size:25
Alignment explanation
Indices: 37651723--37651780 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
37651713 GCTGTAAACA
*
37651723 GTAAGCTCATACGAGCTAAATATCG
1 GTAAGCTCATACAAGCTAAATATCG
* *
37651748 GTAAGCTCATGCAAGCTGAATATCG
1 GTAAGCTCATACAAGCTAAATATCG
*
37651773 ATAAGCTC
1 GTAAGCTC
37651781 TCTCGAGTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (25 bp):
GTAAGCTCATACAAGCTAAATATCG
Found at i:37654449 original size:21 final size:20
Alignment explanation
Indices: 37654412--37654450 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
37654402 TAGAGCTTAT
*
37654412 TTTAGCTCATTTGAGCTCAA
1 TTTAGCTCATTTCAGCTCAA
*
37654432 TTTAGCTTACTTTCAGCTC
1 TTTAGCTCA-TTTCAGCTC
37654451 GTCCCTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.44
Consensus pattern (20 bp):
TTTAGCTCATTTCAGCTCAA
Found at i:37661434 original size:14 final size:14
Alignment explanation
Indices: 37661413--37661448 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
37661403 TCCAACAAAG
37661413 AACA-TCCTACAAT
1 AACATTCCTACAAT
*
37661426 AACATTCCTCCAAT
1 AACATTCCTACAAT
37661440 AACATTCCT
1 AACATTCCT
37661449 GGGCACCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.39, C:0.33, G:0.00, T:0.28
Consensus pattern (14 bp):
AACATTCCTACAAT
Found at i:37665089 original size:39 final size:38
Alignment explanation
Indices: 37665040--37665139 Score: 130
Period size: 39 Copynumber: 2.6 Consensus size: 38
37665030 CGAATATAAT
* *
37665040 AATTATAATTACCATAATTATAATAATGCTT-GACCGAAA
1 AATTATAATTACAATAATTATAATAAT-ATTCGACCG-AA
* * *
37665079 AATTACAATTACAATAATTATAATAATATTCGATCGTA
1 AATTATAATTACAATAATTATAATAATATTCGACCGAA
37665117 AATTATAATTACAATAATTATAA
1 AATTATAATTACAATAATTATAA
37665140 CAAGGATTTC
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
38 25 0.46
39 29 0.54
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36
Consensus pattern (38 bp):
AATTATAATTACAATAATTATAATAATATTCGACCGAA
Found at i:37669991 original size:20 final size:20
Alignment explanation
Indices: 37669963--37670017 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
37669953 ATGGGATTGG
*
37669963 ACTTCGGTGCCTCTGTTTTC
1 ACTTTGGTGCCTCTGTTTTC
*
37669983 ACTTTGGTGTCTCTGTTTTC
1 ACTTTGGTGCCTCTGTTTTC
37670003 ACTTTGGTGCCTCTG
1 ACTTTGGTGCCTCTG
37670018 ATTGCACTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.05, C:0.25, G:0.22, T:0.47
Consensus pattern (20 bp):
ACTTTGGTGCCTCTGTTTTC
Found at i:37670025 original size:20 final size:20
Alignment explanation
Indices: 37669957--37670025 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
37669947 GCATGTATGG
* *
37669957 GATTGGACTTCGGTGCCTCT
1 GATTGCACTTTGGTGCCTCT
* * *
37669977 GTTTTCACTTTGGTGTCTCT
1 GATTGCACTTTGGTGCCTCT
* *
37669997 GTTTTCACTTTGGTGCCTCT
1 GATTGCACTTTGGTGCCTCT
37670017 GATTGCACT
1 GATTGCACT
37670026 ACCGTGCCTT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.45
Consensus pattern (20 bp):
GATTGCACTTTGGTGCCTCT
Found at i:37678903 original size:72 final size:72
Alignment explanation
Indices: 37678786--37678930 Score: 281
Period size: 72 Copynumber: 2.0 Consensus size: 72
37678776 TTTATTGCAC
*
37678786 TGTATGATTGAAATATCTAATGTGCTCCTACAGTAGCAATATTGTGAAAATGACTTTAACAGTAT
1 TGTATGATTGAAATATCTAATGTGCTCCTACAATAGCAATATTGTGAAAATGACTTTAACAGTAT
37678851 TTTCGAA
66 TTTCGAA
37678858 TGTATGATTGAAATATCTAATGTGCTCCTACAATAGCAATATTGTGAAAATGACTTTAACAGTAT
1 TGTATGATTGAAATATCTAATGTGCTCCTACAATAGCAATATTGTGAAAATGACTTTAACAGTAT
37678923 TTTCGAA
66 TTTCGAA
37678930 T
1 T
37678931 TATCTCATAT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (72 bp):
TGTATGATTGAAATATCTAATGTGCTCCTACAATAGCAATATTGTGAAAATGACTTTAACAGTAT
TTTCGAA
Found at i:37688512 original size:19 final size:19
Alignment explanation
Indices: 37688488--37688525 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
37688478 AAAGTTAATA
37688488 AAAAATTTGATTACGGTGG
1 AAAAATTTGATTACGGTGG
*
37688507 AAAAATTTTATTACGGTGG
1 AAAAATTTGATTACGGTGG
37688526 GTGATAATGG
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:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (19 bp):
AAAAATTTGATTACGGTGG
Found at i:37689562 original size:18 final size:16
Alignment explanation
Indices: 37689539--37689573 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
37689529 AATTTATCAT
37689539 TTTAAATTTTAATAAAAA
1 TTTAAA-TTT-ATAAAAA
37689557 TTTAAATTTATAAAAA
1 TTTAAATTTATAAAAA
37689573 T
1 T
37689574 AAAAAGTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TTTAAATTTATAAAAA
Found at i:37703091 original size:41 final size:41
Alignment explanation
Indices: 37703031--37703113 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 41
37703021 TTGCTCAGAT
* *
37703031 AATGGATAGGTGCTTGAATTAATTAACAACAAGTCAACAAA
1 AATGGATAGGTGATTGAATTAATTAACAACAAATCAACAAA
37703072 AATGGATAGGT-ATTAGAATTAATTAACAACAAATCAACAAA
1 AATGGATAGGTGATT-GAATTAATTAACAACAAATCAACAAA
37703113 A
1 A
37703114 TAAAAAGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
40 2 0.05
41 37 0.95
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.24
Consensus pattern (41 bp):
AATGGATAGGTGATTGAATTAATTAACAACAAATCAACAAA
Found at i:37708097 original size:18 final size:18
Alignment explanation
Indices: 37708045--37708090 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
37708035 TTCATTGCAA
37708045 AAATTTTCCTTGCATTAG
1 AAATTTTCCTTGCATTAG
37708063 AAATTTTCCTTGCATTAG
1 AAATTTTCCTTGCATTAG
37708081 AAATTTTCCT
1 AAATTTTCCT
37708091 ATTATTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.46
Consensus pattern (18 bp):
AAATTTTCCTTGCATTAG
Found at i:37708098 original size:3 final size:3
Alignment explanation
Indices: 37708090--37708159 Score: 140
Period size: 3 Copynumber: 23.3 Consensus size: 3
37708080 GAAATTTTCC
37708090 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
37708138 TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
37708160 TTCCTTCTCC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:37709178 original size:7 final size:7
Alignment explanation
Indices: 37709166--37709195 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
37709156 TATAATATAA
37709166 AAAATTC
1 AAAATTC
37709173 AAAATTC
1 AAAATTC
37709180 AAAATTC
1 AAAATTC
37709187 AAAATTC
1 AAAATTC
37709194 AA
1 AA
37709196 TACAACTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAATTC
Found at i:37709371 original size:17 final size:18
Alignment explanation
Indices: 37709351--37709384 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
37709341 TAATTTAATT
*
37709351 TCATTTATAA-TAATTTC
1 TCATTCATAATTAATTTC
37709368 TCATTCATAATTAATTT
1 TCATTCATAATTAATTT
37709385 AACTATTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (18 bp):
TCATTCATAATTAATTTC
Found at i:37712663 original size:20 final size:20
Alignment explanation
Indices: 37712595--37712701 Score: 92
Period size: 20 Copynumber: 5.3 Consensus size: 20
37712585 GCATCATAGA
*
37712595 TGCATAACAGGAGCACCGAAG
1 TGCA-AACAGGGGCACCGAAG
* *
37712616 TGTAGAA-AGGGGCA-CAAATG
1 TGCA-AACAGGGGCACCGAA-G
* *
37712636 TGTAAACAGGGGCACCGTAG
1 TGCAAACAGGGGCACCGAAG
* *
37712656 TGCGAACAGGGACACCGAAG
1 TGCAAACAGGGGCACCGAAG
* *
37712676 TGCAAAAAGAGGCACCGAAG
1 TGCAAACAGGGGCACCGAAG
37712696 TGCAAA
1 TGCAAA
37712702 TCTCGTACAA
Statistics
Matches: 69, Mismatches: 14, Indels: 7
0.77 0.16 0.08
Matches are distributed among these distances:
19 5 0.07
20 57 0.83
21 7 0.10
ACGTcount: A:0.38, C:0.20, G:0.32, T:0.10
Consensus pattern (20 bp):
TGCAAACAGGGGCACCGAAG
Found at i:37715116 original size:21 final size:21
Alignment explanation
Indices: 37715078--37715117 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
37715068 TTCCAAGCCA
*
37715078 TTTTAGGGTTTTAGTTAGTAG
1 TTTTAGGGTTTTACTTAGTAG
37715099 TTTTA-GGTTGTTACTTAGT
1 TTTTAGGGTT-TTACTTAGT
37715118 TTAGTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.55
Consensus pattern (21 bp):
TTTTAGGGTTTTACTTAGTAG
Found at i:37718163 original size:17 final size:16
Alignment explanation
Indices: 37718141--37718174 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
37718131 AGGGATTGTG
37718141 TTTGTTTGATGTTTATT
1 TTTGTTTG-TGTTTATT
*
37718158 TTTGTTTGTTTTTATT
1 TTTGTTTGTGTTTATT
37718174 T
1 T
37718175 CATAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.09, C:0.00, G:0.15, T:0.76
Consensus pattern (16 bp):
TTTGTTTGTGTTTATT
Found at i:37720651 original size:13 final size:13
Alignment explanation
Indices: 37720633--37720658 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
37720623 TCAAACTATC
37720633 AAATTTTCACACA
1 AAATTTTCACACA
37720646 AAATTTTCACACA
1 AAATTTTCACACA
37720659 TATAACTTAA
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:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATTTTCACACA
Found at i:37731870 original size:188 final size:189
Alignment explanation
Indices: 37731553--37731932 Score: 753
Period size: 188 Copynumber: 2.0 Consensus size: 189
37731543 GTTCTTCATG
37731553 ATGACATACTTTCACTTAGATAAAATCATCATTCATACTCGTATACAAACTATCTCAGTAACAAA
1 ATGACATACTTTCACTTAGATAAAATCATCATTCATACTCGTATACAAACTATCTCAGTAACAAA
37731618 AAAAAAGATCTCTAAACATTCATTTATTAAAACATACTTATGAAGGAAATAATTGAAGCATACTT
66 AAAAAAGATCTCTAAACATTCATTTATTAAAACATACTTATGAAGGAAATAATTGAAGCATACTT
37731683 GAAAAAAAATTTAAAAGTTTGTGCAATTTATTTGCCTTA-CCCCCTTTAAAAGGAAGCA
131 GAAAAAAAATTTAAAAGTTTGTGCAATTTATTTGCCTTACCCCCCTTTAAAAGGAAGCA
37731741 ATGACATACTTTCACTTAGATAAAATCATCATTCATACTCGTATACAAACTATCTCAGTAACAAA
1 ATGACATACTTTCACTTAGATAAAATCATCATTCATACTCGTATACAAACTATCTCAGTAACAAA
37731806 AAAAAAGATCTCTAAACATTCATTTATTAAAACATACTTATGAAGGAAATAATTGAAGCATACTT
66 AAAAAAGATCTCTAAACATTCATTTATTAAAACATACTTATGAAGGAAATAATTGAAGCATACTT
37731871 GAAAAAAAATTTAAAAGTTTGTGCAATTTATTTGCCTTACCCCCCTTTAAAAGGAAGCA
131 GAAAAAAAATTTAAAAGTTTGTGCAATTTATTTGCCTTACCCCCCTTTAAAAGGAAGCA
37731930 ATG
1 ATG
37731933 TCCTCATTGC
Statistics
Matches: 191, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
188 169 0.88
189 22 0.12
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.31
Consensus pattern (189 bp):
ATGACATACTTTCACTTAGATAAAATCATCATTCATACTCGTATACAAACTATCTCAGTAACAAA
AAAAAAGATCTCTAAACATTCATTTATTAAAACATACTTATGAAGGAAATAATTGAAGCATACTT
GAAAAAAAATTTAAAAGTTTGTGCAATTTATTTGCCTTACCCCCCTTTAAAAGGAAGCA
Found at i:37746883 original size:42 final size:42
Alignment explanation
Indices: 37746820--37746912 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
37746810 CTCAAATATG
* * *
37746820 GGCCGTGTACCCTTCGTAATAACCCCATATGCCCGTGTGCTA
1 GGCCGTGTACCCTTCGGAATAACCCCATACGCCCGTGTGCCA
*
37746862 GGCCGTGTACCCTTTGGAATAACCCCATACGCCCGTGTGCCA
1 GGCCGTGTACCCTTCGGAATAACCCCATACGCCCGTGTGCCA
*
37746904 GGTCGTGTA
1 GGCCGTGTA
37746913 ATAGCCTAAC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.18, C:0.32, G:0.25, T:0.25
Consensus pattern (42 bp):
GGCCGTGTACCCTTCGGAATAACCCCATACGCCCGTGTGCCA
Found at i:37747015 original size:43 final size:43
Alignment explanation
Indices: 37746958--37747068 Score: 177
Period size: 43 Copynumber: 2.6 Consensus size: 43
37746948 GACACACGAC
*
37746958 CACGGCTAAGACACACGACCGTGTCACCTAGCCGTGTGTCACA
1 CACGGCTGAGACACACGACCGTGTCACCTAGCCGTGTGTCACA
* * *
37747001 CACGGTTGAGACACACGACCATGTCACCTAGCCGTGTGTGACA
1 CACGGCTGAGACACACGACCGTGTCACCTAGCCGTGTGTCACA
*
37747044 CACGGCTGAGACACACGTCCGTGTC
1 CACGGCTGAGACACACGACCGTGTC
37747069 TCTGACTGTG
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 61 1.00
ACGTcount: A:0.24, C:0.33, G:0.25, T:0.17
Consensus pattern (43 bp):
CACGGCTGAGACACACGACCGTGTCACCTAGCCGTGTGTCACA
Found at i:37751528 original size:7 final size:7
Alignment explanation
Indices: 37751518--37751549 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
37751508 CATATGTCAT
37751518 ATATCAC
1 ATATCAC
37751525 ATATCAC
1 ATATCAC
37751532 ATATCAC
1 ATATCAC
37751539 ATATCAC
1 ATATCAC
37751546 ATAT
1 ATAT
37751550 TGATTGTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (7 bp):
ATATCAC
Found at i:37753590 original size:4 final size:4
Alignment explanation
Indices: 37753581--37753608 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
37753571 GGGATTCCAT
37753581 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
37753609 GGGAATACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:37757706 original size:50 final size:50
Alignment explanation
Indices: 37757557--37757846 Score: 343
Period size: 50 Copynumber: 5.8 Consensus size: 50
37757547 GATAATAACA
* ** * *
37757557 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATGTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * * * ** *
37757606 TACCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * * * *
37757656 TGCCCATGTCATGTCCTAGACATGGTCTTACAGGGGACCTCTCTTCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
37757706 TGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
37757756 TGCCAACGCCATGTCCCAAACATGGTCTTATATGGGACCTCTCATCTCAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
37757806 TGCC-ACGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
37757847 TTACCCAAAT
Statistics
Matches: 208, Mismatches: 31, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
48 1 0.00
49 73 0.35
50 134 0.64
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:37757827 original size:149 final size:149
Alignment explanation
Indices: 37757557--37757846 Score: 359
Period size: 149 Copynumber: 1.9 Consensus size: 149
37757547 GATAATAACA
** * * *
37757557 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATGTACTACCAATGCCATATCC
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTACTACCAACGCCATATCC
* * ** * * * *
37757622 CAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGTCATGTCCTAGACATGGTCTTAC
66 CAAACATGGTCTTACATGGGACCTCTCATATCAGTGCCCACGCCATGTCCCAGACATGGTCTTAC
37757687 AGGGGACCTCTCTTCTCGG
131 AGGGGACCTCTCTTCTCGG
* * * *
37757706 TGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCT-CGGTGCCAACGCCATGT
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAC--TACCAACGCCATAT
* *
37757770 CCCAAACATGGTCTTATATGGGACCTCTCATCTCAGTG-CCACGCCATGTCCCAGACATGGTCTT
64 CCCAAACATGGTCTTACATGGGACCTCTCATATCAGTGCCCACGCCATGTCCCAGACATGGTCTT
* *
37757834 ACATGGGATCTCT
129 ACAGGGGACCTCT
37757847 TTACCCAAAT
Statistics
Matches: 118, Mismatches: 21, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
148 1 0.01
149 75 0.64
150 42 0.36
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (149 bp):
TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTACTACCAACGCCATATCC
CAAACATGGTCTTACATGGGACCTCTCATATCAGTGCCCACGCCATGTCCCAGACATGGTCTTAC
AGGGGACCTCTCTTCTCGG
Found at i:37765220 original size:50 final size:50
Alignment explanation
Indices: 37765103--37765393 Score: 313
Period size: 50 Copynumber: 5.8 Consensus size: 50
37765093 GATAATAACA
* * * ** * *
37765103 TGCCAAAGCCATGTCCCAGACATTGTCTTACATAGGATGTTTCATGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* ** * ** *
37765152 TACCAATGCCACATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
37765202 TGCCCATGCCATGTCCCAGACATGGTATTAC-TGGGGACCTCTCTTCTCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAT-GGGACCTCTCATCTCGG
*
37765252 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
37765302 TGCCAGCATG--ATGTCCAAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCA--ATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
37765352 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
37765394 TTACCCAAAT
Statistics
Matches: 202, Mismatches: 32, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
48 3 0.01
49 37 0.18
50 159 0.79
51 1 0.00
52 2 0.01
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:37771680 original size:21 final size:22
Alignment explanation
Indices: 37771656--37771701 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
37771646 TAACCCAAAC
*
37771656 TAAACTAAATTAAATT-AAAAT
1 TAAAATAAATTAAATTAAAAAT
* *
37771677 TAAAATTAATTATATTAAAAAT
1 TAAAATAAATTAAATTAAAAAT
37771699 TAA
1 TAA
37771702 TATTCATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAAATAAATTAAATTAAAAAT
Found at i:37779470 original size:27 final size:25
Alignment explanation
Indices: 37779440--37779507 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 25
37779430 GTTCTGACCT
*
37779440 ACAGCTCGTGTGAGCAGGCTCATTTTC
1 ACAGCTCGTGTGAGCAGGCT-A-ATTC
* **
37779467 ACAGCTTGTGTGAGCATTCTAATTC
1 ACAGCTCGTGTGAGCAGGCTAATTC
*
37779492 ACAGCTCGTATGAGCA
1 ACAGCTCGTGTGAGCA
37779508 TACATGTACA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 17 0.49
26 1 0.03
27 17 0.49
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (25 bp):
ACAGCTCGTGTGAGCAGGCTAATTC
Found at i:37782839 original size:25 final size:25
Alignment explanation
Indices: 37782811--37782896 Score: 70
Period size: 25 Copynumber: 3.4 Consensus size: 25
37782801 TATGCTCATA
37782811 CGAGCTATGAATCGGTATGTTCACT
1 CGAGCTATGAATCGGTATGTTCACT
* *
37782836 CGAGCTGT-AGATCAGTATGCTCTCA-T
1 CGAGCTATGA-ATCGGTATG-T-TCACT
* * * *
37782862 -GAGCTATAAACCGGTATGCTCTCT
1 CGAGCTATGAATCGGTATGTTCACT
37782886 CGAGCTATGAA
1 CGAGCTATGAA
37782897 GTATCCGCAA
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
23 2 0.04
24 2 0.04
25 37 0.79
26 3 0.06
27 3 0.06
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (25 bp):
CGAGCTATGAATCGGTATGTTCACT
Found at i:37783053 original size:17 final size:18
Alignment explanation
Indices: 37783028--37783061 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
37783018 CAACCATGTA
*
37783028 AATTTATAAA-AATTCAC
1 AATTCATAAATAATTCAC
37783045 AATTCATAAATAATTCA
1 AATTCATAAATAATTCA
37783062 ATATAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (18 bp):
AATTCATAAATAATTCAC
Found at i:37792979 original size:23 final size:22
Alignment explanation
Indices: 37792936--37792979 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
37792926 TGAGAACCGG
* *
37792936 CTAAATTGTAGCCCTGATACCA
1 CTAAAATGTAGCCCTCATACCA
*
37792958 CTAAAATGTAGCACCTCTTACC
1 CTAAAATGTAGC-CCTCATACC
37792980 CATATTCATC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.32, C:0.30, G:0.11, T:0.27
Consensus pattern (22 bp):
CTAAAATGTAGCCCTCATACCA
Found at i:37794407 original size:51 final size:49
Alignment explanation
Indices: 37794289--37794469 Score: 204
Period size: 51 Copynumber: 3.6 Consensus size: 49
37794279 TCGATATACG
* * * *
37794289 TAGTAGCCTTCATATAGTACTACACATGTGATC-AAGTTTTACGGTCCAC
1 TAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTTTT-CGGTACAC
*
37794338 TAGTAGCCTCCACATAGTACTACACACGTGACCAAAGCTTTTCGGTACAC
1 TAGTAGCCTTCACATAGTACTACACACGTGACCAAAG-TTTTCGGTACAC
* * * *
37794388 ATAGTAGCCTTCACTTAGTACTACACATGTGACCATTA-TTTATCGATACAC
1 -TAGTAGCCTTCACATAGTACTACACACGTGACCA-AAGTTT-TCGGTACAC
*
37794439 GTGGTAGCCTTCACATAGTACTACACACGTG
1 -TAGTAGCCTTCACATAGTACTACACACGTG
37794470 TTCATCAATA
Statistics
Matches: 113, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
49 29 0.26
50 13 0.12
51 70 0.62
52 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (49 bp):
TAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTTTTCGGTACAC
Found at i:37801992 original size:9 final size:9
Alignment explanation
Indices: 37801978--37802003 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
37801968 AAATTAAATA
37801978 ACCAAAAGT
1 ACCAAAAGT
37801987 ACCAAAAGT
1 ACCAAAAGT
37801996 ACCAAAAG
1 ACCAAAAG
37802004 AGTCGATGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.23, G:0.12, T:0.08
Consensus pattern (9 bp):
ACCAAAAGT
Found at i:37803528 original size:37 final size:37
Alignment explanation
Indices: 37803478--37803552 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
37803468 CCACTAACTC
* *
37803478 ATAAATGGTCTAATTACCATGTAAGGATCTCCAATTT
1 ATAAATGGTCTAATTACCATATAAGGACCTCCAATTT
37803515 ATAAATGGTCTAATTACCATATAAGGACCTCCAATTT
1 ATAAATGGTCTAATTACCATATAAGGACCTCCAATTT
37803552 A
1 A
37803553 AAGTTCCATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.33
Consensus pattern (37 bp):
ATAAATGGTCTAATTACCATATAAGGACCTCCAATTT
Found at i:37804187 original size:22 final size:21
Alignment explanation
Indices: 37804155--37804196 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
37804145 TTGGTATTTA
37804155 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
37804176 GGAATTTGGTACGAATTGGTA
1 GGAA-TTGGTACGAAATGGTA
37804197 ATGGTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.31, C:0.05, G:0.33, T:0.31
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:37807938 original size:14 final size:14
Alignment explanation
Indices: 37807921--37807966 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
37807911 TTGGGAATTT
37807921 AGAATAAAAAATCG
1 AGAATAAAAAATCG
*
37807935 AGAATAAAAAATTG
1 AGAATAAAAAATCG
* * *
37807949 AGAACAATAAGTCG
1 AGAATAAAAAATCG
37807963 AGAA
1 AGAA
37807967 CAATAAGTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.61, C:0.07, G:0.17, T:0.15
Consensus pattern (14 bp):
AGAATAAAAAATCG
Found at i:37807967 original size:14 final size:14
Alignment explanation
Indices: 37807948--37807974 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
37807938 ATAAAAAATT
37807948 GAGAACAATAAGTC
1 GAGAACAATAAGTC
37807962 GAGAACAATAAGT
1 GAGAACAATAAGT
37807975 TGAAAGTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.11, G:0.22, T:0.15
Consensus pattern (14 bp):
GAGAACAATAAGTC
Found at i:37809924 original size:26 final size:26
Alignment explanation
Indices: 37809842--37809924 Score: 60
Period size: 26 Copynumber: 3.2 Consensus size: 26
37809832 AAAAAAGTTT
*
37809842 AAAAG-TTTTGGGGGAAAGCAAAAGGAA
1 AAAAGTTTTTGGGGAAAAGCAAAA-G-A
*** *** *
37809869 AAAAGTTTTTGGGGTTTAGGGGAAGT
1 AAAAGTTTTTGGGGAAAAGCAAAAGA
*
37809895 AAAAGTTTTTGGGGAAAAGTAAAAGA
1 AAAAGTTTTTGGGGAAAAGCAAAAGA
37809921 AAAA
1 AAAA
37809925 AAGTTTTGGG
Statistics
Matches: 41, Mismatches: 14, Indels: 3
0.71 0.24 0.05
Matches are distributed among these distances:
26 23 0.56
27 6 0.15
28 12 0.29
ACGTcount: A:0.45, C:0.01, G:0.31, T:0.23
Consensus pattern (26 bp):
AAAAGTTTTTGGGGAAAAGCAAAAGA
Found at i:37809929 original size:54 final size:54
Alignment explanation
Indices: 37809841--37809958 Score: 170
Period size: 54 Copynumber: 2.2 Consensus size: 54
37809831 AAAAAAAGTT
* * *
37809841 TAAAAG-TTTTGGGGGAAAGCAAAAGGAAAAAAGTTTT-TGGGGTTTAGGGGAAG
1 TAAAAGTTTTTGGGGAAAAGCAAAAGAAAAAAAGTTTTGGGGGGTTT-GGGGAAG
*
37809894 TAAAAGTTTTTGGGGAAAAGTAAAAGAAAAAAAGTTTTGGGGGGTTTGGGGAAG
1 TAAAAGTTTTTGGGGAAAAGCAAAAGAAAAAAAGTTTTGGGGGGTTTGGGGAAG
37809948 TAAAA-TTTTTG
1 TAAAAGTTTTTG
37809959 AGGGGAAGTA
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
53 12 0.20
54 40 0.68
55 7 0.12
ACGTcount: A:0.38, C:0.01, G:0.33, T:0.28
Consensus pattern (54 bp):
TAAAAGTTTTTGGGGAAAAGCAAAAGAAAAAAAGTTTTGGGGGGTTTGGGGAAG
Found at i:37809976 original size:20 final size:19
Alignment explanation
Indices: 37809941--37809991 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 19
37809931 TGGGGGGTTT
*
37809941 GGGGAAGTAAAATTTTTGA
1 GGGGAAGTAAAATTTTGGA
37809960 GGGGAAGTAACAATTTTGGA
1 GGGGAAGTAA-AATTTTGGA
*
37809980 GTGGAAGTAAAA
1 GGGGAAGTAAAA
37809992 GAAAAAAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.39, C:0.02, G:0.33, T:0.25
Consensus pattern (19 bp):
GGGGAAGTAAAATTTTGGA
Found at i:37810624 original size:23 final size:22
Alignment explanation
Indices: 37810594--37810636 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
37810584 AAAAAAATCG
*
37810594 AATTGATTTGATTAACTCGATT
1 AATTGATTTGAATAACTCGATT
*
37810616 AATTCGATTTGAATAATTCGA
1 AATT-GATTTGAATAACTCGA
37810637 AATTTGAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (22 bp):
AATTGATTTGAATAACTCGATT
Found at i:37812358 original size:29 final size:29
Alignment explanation
Indices: 37812315--37812371 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
37812305 TTACGTCAAC
* *
37812315 TATGGTTAAATTTTAATTTTATAAAATTG
1 TATGGTAAAAATTTAATTTTATAAAATTG
37812344 TATGGTAAAAATTTAATTTTATAAAATT
1 TATGGTAAAAATTTAATTTTATAAAATT
37812372 AATCAAGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (29 bp):
TATGGTAAAAATTTAATTTTATAAAATTG
Found at i:37812371 original size:15 final size:15
Alignment explanation
Indices: 37812321--37812371 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
37812311 CAACTATGGT
*
37812321 TAAATTTTAATTTTA
1 TAAAATTTAATTTTA
**
37812336 TAAAATTGT-ATGGTA
1 TAAAATT-TAATTTTA
37812351 -AAAATTTAATTTTA
1 TAAAATTTAATTTTA
37812365 TAAAATT
1 TAAAATT
37812372 AATCAAGTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
13 1 0.04
14 10 0.36
15 16 0.57
16 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (15 bp):
TAAAATTTAATTTTA
Found at i:37818304 original size:2 final size:2
Alignment explanation
Indices: 37818297--37818323 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
37818287 CTTGCTCTTT
37818297 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 T
37818324 TTTGGTAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:37819093 original size:51 final size:52
Alignment explanation
Indices: 37819033--37819148 Score: 180
Period size: 52 Copynumber: 2.2 Consensus size: 52
37819023 TCCTCTCTAA
37819033 TCCTCTCAATTTCCTTCCAAAA-TTCTCTCAAACCCATATTTAATGTCAATT
1 TCCTCTCAATTTCCTTCCAAAATTTCTCTCAAACCCATATTTAATGTCAATT
* * *
37819084 TCCTCTCAATTTCCTTCCAAAATTTCTCTCAAATCCATATTTAATTTTAATT
1 TCCTCTCAATTTCCTTCCAAAATTTCTCTCAAACCCATATTTAATGTCAATT
* *
37819136 TCCCCTAAATTTC
1 TCCTCTCAATTTC
37819149 ATTTTTTTAA
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
51 22 0.37
52 37 0.63
ACGTcount: A:0.28, C:0.28, G:0.01, T:0.42
Consensus pattern (52 bp):
TCCTCTCAATTTCCTTCCAAAATTTCTCTCAAACCCATATTTAATGTCAATT
Found at i:37819177 original size:10 final size:10
Alignment explanation
Indices: 37819149--37819214 Score: 60
Period size: 10 Copynumber: 6.5 Consensus size: 10
37819139 CCTAAATTTC
37819149 ATTTTTTTAAA
1 ATTTTTTT-AA
**
37819160 ATAATTTTAA
1 ATTTTTTTAA
*
37819170 ATTTTTTTAT
1 ATTTTTTTAA
*
37819180 ATTTTTTAAA
1 ATTTTTTTAA
**
37819190 ATAATTTTAA
1 ATTTTTTTAA
*
37819200 ATTTTTTTAT
1 ATTTTTTTAA
37819210 ATTTT
1 ATTTT
37819215 CATCAATGGC
Statistics
Matches: 42, Mismatches: 13, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
10 36 0.86
11 6 0.14
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
ATTTTTTTAA
Found at i:37819185 original size:30 final size:30
Alignment explanation
Indices: 37819151--37819214 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
37819141 TAAATTTCAT
37819151 TTTTTTAAAATAATTTTAAATTTTTTTATA
1 TTTTTTAAAATAATTTTAAATTTTTTTATA
37819181 TTTTTTAAAATAATTTTAAATTTTTTTATA
1 TTTTTTAAAATAATTTTAAATTTTTTTATA
37819211 TTTT
1 TTTT
37819215 CATCAATGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (30 bp):
TTTTTTAAAATAATTTTAAATTTTTTTATA
Found at i:37819314 original size:18 final size:18
Alignment explanation
Indices: 37819291--37819353 Score: 51
Period size: 18 Copynumber: 3.5 Consensus size: 18
37819281 TAAGTATTAA
37819291 ATTTAATTTTTAAATATT
1 ATTTAATTTTTAAATATT
**
37819309 ATTTAAGATTTTTTTAT-TT
1 ATTT-A-ATTTTTAAATATT
*
37819328 ATTT-ATTTTTAGATAATT
1 ATTTAATTTTTAAAT-ATT
37819346 A-TTAATTT
1 ATTTAATTT
37819354 ATTATTTGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
16 8 0.22
17 2 0.06
18 11 0.31
19 7 0.19
20 8 0.22
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
ATTTAATTTTTAAATATT
Found at i:37820308 original size:7 final size:7
Alignment explanation
Indices: 37820296--37820320 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
37820286 AGTCGATTGA
37820296 TATTTAG
1 TATTTAG
37820303 TATTTAG
1 TATTTAG
37820310 TATTTAG
1 TATTTAG
37820317 TATT
1 TATT
37820321 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:37820998 original size:18 final size:18
Alignment explanation
Indices: 37820972--37821006 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
37820962 AGGTGTGTTT
* *
37820972 CCTAGCCCTTATATGTAC
1 CCTAACCCTTACATGTAC
37820990 CCTAACCCTTACATGTA
1 CCTAACCCTTACATGTA
37821007 TCCTTTTCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (18 bp):
CCTAACCCTTACATGTAC
Found at i:37821474 original size:26 final size:25
Alignment explanation
Indices: 37821410--37821478 Score: 102
Period size: 25 Copynumber: 2.7 Consensus size: 25
37821400 TTTAAATTTA
*
37821410 TTATCTAATGTAATAAAATAGAAGT
1 TTATTTAATGTAATAAAATAGAAGT
*
37821435 TTATTTAATATAATAAAATAGAAGT
1 TTATTTAATGTAATAAAATAGAAGT
*
37821460 TCTATTTGATGTAATAAAA
1 T-TATTTAATGTAATAAAA
37821479 ATCCTAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
25 24 0.62
26 15 0.38
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.39
Consensus pattern (25 bp):
TTATTTAATGTAATAAAATAGAAGT
Found at i:37821497 original size:18 final size:18
Alignment explanation
Indices: 37821474--37821522 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
37821464 TTTGATGTAA
* *
37821474 TAAAAATCCTAATTTAAT
1 TAAAAACCCTAACTTAAT
37821492 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
*
37821510 TCAAAACCCTAAC
1 TAAAAACCCTAAC
37821523 CCTAACCTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAAAACCCTAACTTAAT
Found at i:37821544 original size:29 final size:29
Alignment explanation
Indices: 37821499--37821580 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
37821489 AATTAAAAAC
* *
37821499 CCTAACTTAATTCAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
37821528 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
37821557 CCTAATTTAATTAAAAACCCTAAC
1 CCTAATTTAATTAAAAACCCTAAC
37821581 TTAATTAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.27
Consensus pattern (29 bp):
CCTAATTTAATTAAAAACCCTAACCCTAA
Found at i:37821579 original size:47 final size:47
Alignment explanation
Indices: 37821528--37821731 Score: 266
Period size: 47 Copynumber: 4.1 Consensus size: 47
37821518 CTAACCCTAA
* *
37821528 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAAC
1 CCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAAC
37821575 CCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCC
1 CCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAA--C
* *
37821624 TAACTCTAACCTAATTTAATTAAAAATCCTAACCCTAACCTAATTTAATT-AAAAC
1 ---C-CTAA-C----TTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAAC
37821679 CCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAAC
37821726 CCTAAC
1 CCTAAC
37821732 ACTAACCTAA
Statistics
Matches: 139, Mismatches: 6, Indels: 24
0.82 0.04 0.14
Matches are distributed among these distances:
46 33 0.24
47 55 0.40
49 1 0.01
50 1 0.01
51 4 0.03
52 2 0.01
53 4 0.03
54 1 0.01
55 1 0.01
57 4 0.03
58 33 0.24
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (47 bp):
CCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAAC
Found at i:37821584 original size:18 final size:18
Alignment explanation
Indices: 37821557--37821598 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
37821547 CTAACCCTAA
*
37821557 CCTAATTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
37821575 CCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
37821593 CCTAAC
1 CCTAAC
37821599 CCTAACCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.29
Consensus pattern (18 bp):
CCTAACTTAATTAAAAAC
Found at i:37821602 original size:76 final size:76
Alignment explanation
Indices: 37821481--37821731 Score: 334
Period size: 76 Copynumber: 3.3 Consensus size: 76
37821471 TAATAAAAAT
* *
37821481 CCTAATTTAATTAAAAACCCTAACTTAATTCAAAACCCTAACCCTAACCTAATTTAATTAAAAAC
1 CCTAATTTAATTAAAAACCCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAAC
37821546 CCTAACCCTAA
66 CCTAACCCTAA
37821557 CCTAATTTAATTAAAAACCCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAAC
1 CCTAATTTAATTAAAAACCCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAAC
*
37821622 CCTAACTCTAA
66 CCTAACCCTAA
* * * * *
37821633 CCTAATTTAATTAAAAATCCTAACCCTAACCTAATTTAA--TTAA----AACCCTAACTTAATTA
1 CCTAATTTAATTAAAAACCCTAA-CTTAA-TTAA--AAACCCTAACCCTAA-CCTAACTTAATTA
37821692 AAAACCCTAACCCTAA
61 AAAACCCTAACCCTAA
*
37821708 CCTAACTTAATTAAAAACCCTAAC
1 CCTAATTTAATTAAAAACCCTAAC
37821732 ACTAACCTAA
Statistics
Matches: 159, Mismatches: 11, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
74 3 0.02
75 49 0.31
76 95 0.60
77 4 0.03
78 6 0.04
80 2 0.01
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.28
Consensus pattern (76 bp):
CCTAATTTAATTAAAAACCCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAAC
CCTAACCCTAA
Found at i:37821607 original size:29 final size:29
Alignment explanation
Indices: 37821575--37821684 Score: 177
Period size: 29 Copynumber: 3.8 Consensus size: 29
37821565 AATTAAAAAC
37821575 CCTAACTTAATTAAAAACCCTAACCCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
*
37821604 CCTAACTTAATTAAAAACCCTAACTCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
* *
37821633 CCTAATTTAATTAAAAATCCTAACCCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
*
37821662 CCTAATTTAATT-AAAACCCTAAC
1 CCTAACTTAATTAAAAACCCTAAC
37821685 TTAATTAAAA
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
28 10 0.13
29 66 0.87
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.28
Consensus pattern (29 bp):
CCTAACTTAATTAAAAACCCTAACCCTAA
Found at i:37821659 original size:105 final size:104
Alignment explanation
Indices: 37821499--37821744 Score: 447
Period size: 104 Copynumber: 2.4 Consensus size: 104
37821489 AATTAAAAAC
* *
37821499 CCTAACTTAATTCAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATT
1 CCTAACTTAATTAAAAACCCTAACACTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATT
37821564 TAATTAAAAACCCTAACTTAATTAAAAACCCTAACCCTAA
66 TAATT-AAAACCCTAACTTAATTAAAAACCCTAACCCTAA
* *
37821604 CCTAACTTAATTAAAAACCCTAACTCTAACCTAATTTAATTAAAAATCCTAACCCTAACCTAATT
1 CCTAACTTAATTAAAAACCCTAACACTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATT
37821669 TAATTAAAACCCTAACTTAATTAAAAACCCTAACCCTAA
66 TAATTAAAACCCTAACTTAATTAAAAACCCTAACCCTAA
37821708 CCTAACTTAATTAAAAACCCTAACACTAACCTAATTT
1 CCTAACTTAATTAAAAACCCTAACACTAACCTAATTT
37821745 TACATAATTT
Statistics
Matches: 137, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
104 70 0.51
105 67 0.49
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.28
Consensus pattern (104 bp):
CCTAACTTAATTAAAAACCCTAACACTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATT
TAATTAAAACCCTAACTTAATTAAAAACCCTAACCCTAA
Found at i:37821688 original size:17 final size:18
Alignment explanation
Indices: 37821662--37821702 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
37821652 CTAACCCTAA
*
37821662 CCTAATTTAATT-AAAAC
1 CCTAACTTAATTAAAAAC
37821679 CCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
37821697 CCTAAC
1 CCTAAC
37821703 CCTAACCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.29
Consensus pattern (18 bp):
CCTAACTTAATTAAAAAC
Found at i:37821689 original size:46 final size:47
Alignment explanation
Indices: 37821633--37821731 Score: 164
Period size: 46 Copynumber: 2.1 Consensus size: 47
37821623 CTAACTCTAA
* * *
37821633 CCTAATTTAATTAAAAATCCTAACCCTAACCTAATTTAATT-AAAAC
1 CCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAAC
37821679 CCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAAC
37821726 CCTAAC
1 CCTAAC
37821732 ACTAACCTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
46 38 0.78
47 11 0.22
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.28
Consensus pattern (47 bp):
CCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAAC
Found at i:37821721 original size:29 final size:29
Alignment explanation
Indices: 37821679--37821741 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
37821669 TAATTAAAAC
*
37821679 CCTAACTTAATTAAAAACCCTAACCCTAA
1 CCTAACTTAATTAAAAACCCTAACACTAA
37821708 CCTAACTTAATTAAAAACCCTAACACTAA
1 CCTAACTTAATTAAAAACCCTAACACTAA
37821737 CCTAA
1 CCTAA
37821742 TTTTACATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (29 bp):
CCTAACTTAATTAAAAACCCTAACACTAA
Found at i:37821804 original size:55 final size:55
Alignment explanation
Indices: 37821743--37821985 Score: 240
Period size: 55 Copynumber: 4.2 Consensus size: 55
37821733 CTAACCTAAT
*
37821743 TTTACATAATTTGGTAATTTTACTAACCATTAACACAATTGTTGGACTTAATAAG
1 TTTACATAATTTGATAATTTTACTAACCATTAACACAATTGTTGGACTTAATAAG
* *
37821798 TTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAATAAT
1 TTTACATAATTTGATAATTTTACTAACCATTAACACAATTGTTGGACTTAATAAG
** * * *
37821853 TTTACATAATTTGATAATTTTACCTAATTTAATTAA-A-ATTTTTTTGGCTTAATAATTTTACAT
1 TTTACATAATTTGATAATTTTA-CTAA--CCATTAACACA-ATTGTTGG-------A-CTTA-AT
*
37821916 AAT
53 AAG
* *
37821919 TTTACATAATTTGATAATTTTACTAACCATTAACAAAATT-TTGAGACTTAATAAT
1 TTTACATAATTTGATAATTTTACTAACCATTAACACAATTGTTG-GACTTAATAAG
37821974 TTTACATAATTT
1 TTTACATAATTT
37821986 TACATAATGT
Statistics
Matches: 161, Mismatches: 11, Indels: 32
0.79 0.05 0.16
Matches are distributed among these distances:
55 91 0.57
56 8 0.05
57 9 0.06
58 5 0.03
63 8 0.05
64 5 0.03
65 8 0.05
66 27 0.17
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (55 bp):
TTTACATAATTTGATAATTTTACTAACCATTAACACAATTGTTGGACTTAATAAG
Found at i:37821871 original size:18 final size:18
Alignment explanation
Indices: 37821848--37821882 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
37821838 TTTGGACTTA
37821848 ATAATTTTACATAATTTG
1 ATAATTTTACATAATTTG
*
37821866 ATAATTTTACCTAATTT
1 ATAATTTTACATAATTT
37821883 AATTAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (18 bp):
ATAATTTTACATAATTTG
Found at i:37821919 original size:10 final size:10
Alignment explanation
Indices: 37821904--37821930 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
37821894 TTTTGGCTTA
37821904 ATAATTTTAC
1 ATAATTTTAC
37821914 ATAATTTTAC
1 ATAATTTTAC
37821924 ATAATTT
1 ATAATTT
37821931 GATAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:37821922 original size:66 final size:64
Alignment explanation
Indices: 37821848--37821993 Score: 204
Period size: 65 Copynumber: 2.2 Consensus size: 64
37821838 TTTGGACTTA
* * ** *
37821848 ATAATTTTACATAATTTGATAATTTTACCTAA-TTTAATTAAAATTTTTTTGGCTTAATAATTTT
1 ATAATTTTACATAATTTGATAATTTTA-CTAACATTAA-CAAAA-TTTTGAGACTTAATAATTTT
37821912 AC
63 AC
37821914 ATAATTTTACATAATTTGATAATTTTACTAACCATTAACAAAATTTTGAGACTTAATAATTTTAC
1 ATAATTTTACATAATTTGATAATTTTACTAA-CATTAACAAAATTTTGAGACTTAATAATTTTAC
37821979 ATAATTTTACATAAT
1 ATAATTTTACATAAT
37821994 GTTAGATTTG
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
65 38 0.52
66 31 0.42
67 4 0.05
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (64 bp):
ATAATTTTACATAATTTGATAATTTTACTAACATTAACAAAATTTTGAGACTTAATAATTTTAC
Found at i:37821984 original size:10 final size:10
Alignment explanation
Indices: 37821969--37821993 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
37821959 TTGAGACTTA
37821969 ATAATTTTAC
1 ATAATTTTAC
37821979 ATAATTTTAC
1 ATAATTTTAC
37821989 ATAAT
1 ATAAT
37821994 GTTAGATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:37825400 original size:124 final size:125
Alignment explanation
Indices: 37825180--37825525 Score: 588
Period size: 125 Copynumber: 2.8 Consensus size: 125
37825170 CCCAAACTTG
*
37825180 CTACTGTAGCAAAATCGCGTCCACGAGGGCGTGATTTCACAATTTCTTCTCAAATAACATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAACATCCTGG
37825245 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTC-AAAAAAAATTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGAC
*
37825304 CTACTGTAGCAAAATCGCGTCCACGAGGGTGCGATTTCACAATTTCTTCTCAAATAACATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAACATCCTGG
* *
37825369 TAGAGGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTTTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGAC
* * * *
37825429 CTACTATAGCAAAATCGCGTCCAGGAGGGCGCGATTTCATAATTTCTTCTCAAATATCATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAACATCCTGG
*
37825494 TAGAAGCGATTATATACTATTTGAC-CAGAAAC
66 TAGAAGCGATTTTATACTATTTG-CTCAGAAAC
37825526 ACCAACTCGA
Statistics
Matches: 209, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
124 97 0.46
125 111 0.53
126 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (125 bp):
CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAACATCCTGG
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGAC
Found at i:37825807 original size:28 final size:28
Alignment explanation
Indices: 37825746--37825808 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
37825736 CGCAATTTCC
37825746 TGAAAAATGGCCCATTCCGGTAAATAAT
1 TGAAAAATGGCCCATTCCGGTAAATAAT
** * *
37825774 CAAAAAATCGGCCCATTTCGGTAAAT-TT
1 TGAAAAAT-GGCCCATTCCGGTAAATAAT
37825802 TGAAAAA
1 TGAAAAA
37825809 AAACGGCTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
28 12 0.43
29 16 0.57
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.25
Consensus pattern (28 bp):
TGAAAAATGGCCCATTCCGGTAAATAAT
Found at i:37828333 original size:5 final size:5
Alignment explanation
Indices: 37828323--37828395 Score: 83
Period size: 5 Copynumber: 14.6 Consensus size: 5
37828313 ATATATATAT
* * * * *
37828323 ATTCC ATTCC ATACC ATTCC ATTCC ATACT ATTCC ATTTC ATACC ATTCC
1 ATTCC ATTCC ATTCC ATTCC ATTCC ATTCC ATTCC ATTCC ATTCC ATTCC
* *
37828373 ATTTC ATACC ATTCC ATTCC ATT
1 ATTCC ATTCC ATTCC ATTCC ATT
37828396 TCATCAAGCT
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
5 54 1.00
ACGTcount: A:0.26, C:0.34, G:0.00, T:0.40
Consensus pattern (5 bp):
ATTCC
Found at i:37828343 original size:15 final size:15
Alignment explanation
Indices: 37828323--37828394 Score: 117
Period size: 15 Copynumber: 4.8 Consensus size: 15
37828313 ATATATATAT
37828323 ATTCCATTCCATACC
1 ATTCCATTCCATACC
*
37828338 ATTCCATTCCATACT
1 ATTCCATTCCATACC
*
37828353 ATTCCATTTCATACC
1 ATTCCATTCCATACC
*
37828368 ATTCCATTTCATACC
1 ATTCCATTCCATACC
37828383 ATTCCATTCCAT
1 ATTCCATTCCAT
37828395 TTCATCAAGC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 53 1.00
ACGTcount: A:0.26, C:0.35, G:0.00, T:0.39
Consensus pattern (15 bp):
ATTCCATTCCATACC
Found at i:37829361 original size:50 final size:50
Alignment explanation
Indices: 37829299--37829587 Score: 271
Period size: 51 Copynumber: 5.7 Consensus size: 50
37829289 TCATTCGATA
37829299 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAT-TTTTACGGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGA-CAATCTTTTACGGTT
* *
37829349 CACGTAATAGCCTTCACATAGTACTACACACGTGATCAA-GTTTTACGGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGA-CAATCTTTTACGGTT
* * *
37829399 CACATAGTAGCCTTCACATAGTACTACATACGTGACTAATGCTTTT-CGGTA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGAC-AAT-CTTTTACGGTT
* * * * * * * **
37829450 CACATAGTAGTCTTCACTTAGTACAACACATGTGACCATCATTTATCAATT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACAATCTTTTA-CGGTT
* * * * *
37829501 CATGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCT-CGGTA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGA-C-AATCTTTTACGGTT
** * * *
37829552 CATATTGTAGCCTTCACTTAGTACTACACATGTGAC
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGAC
37829588 CATTATTTAT
Statistics
Matches: 196, Mismatches: 35, Indels: 16
0.79 0.14 0.06
Matches are distributed among these distances:
49 5 0.03
50 85 0.43
51 97 0.49
52 5 0.03
53 4 0.02
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (50 bp):
CACGTAGTAGCCTTCACATAGTACTACACACGTGACAATCTTTTACGGTT
Found at i:37829535 original size:102 final size:102
Alignment explanation
Indices: 37829299--37829598 Score: 347
Period size: 102 Copynumber: 3.0 Consensus size: 102
37829289 TCATTCGATA
* * *
37829299 CACGTAGTAGCCTTCACATAGTACTACACACGTGA-TCAAT--TTTTACGGTTCACGTAATAGCC
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACT-AATGCTTTT-CGGTACACATAGTAGCC
* * * *** **
37829361 TTCACATAGTACTACACACGTGATCAAGTTTTA-CGGTT
64 TTCACTTAGTACTACACATGTGACCATCATTTATCAATT
* * *
37829399 CACATAGTAGCCTTCACATAGTACTACATACGTGACTAATGCTTTTCGGTACACATAGTAGTCTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACTAATGCTTTTCGGTACACATAGTAGCCTT
*
37829464 CACTTAGTACAACACATGTGACCATCATTTATCAATT
66 CACTTAGTACTACACATGTGACCATCATTTATCAATT
* * * * * * *
37829501 CATGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACATATTGTAGCCTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACTAATGCTTTTCGGTACACATAGTAGCCTT
*
37829566 CACTTAGTACTACACATGTGACCATTATTTATC
66 CACTTAGTACTACACATGTGACCATCATTTATC
37829599 GATTACCATT
Statistics
Matches: 169, Mismatches: 27, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
100 36 0.21
101 40 0.24
102 93 0.55
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (102 bp):
CACGTAGTAGCCTTCACATAGTACTACACACGTGACTAATGCTTTTCGGTACACATAGTAGCCTT
CACTTAGTACTACACATGTGACCATCATTTATCAATT
Found at i:37829981 original size:37 final size:37
Alignment explanation
Indices: 37829931--37830007 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
37829921 ATTCTCATGA
37829931 AACACGTTTACTAACTTTCCAAATCACTAATCAATTT
1 AACACGTTTACTAACTTTCCAAATCACTAATCAATTT
*
37829968 AACACTTTTACTAACTTTCCAAATCACTAATCAATTT
1 AACACGTTTACTAACTTTCCAAATCACTAATCAATTT
37830005 AAC
1 AAC
37830008 TCTATAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.39, C:0.25, G:0.01, T:0.35
Consensus pattern (37 bp):
AACACGTTTACTAACTTTCCAAATCACTAATCAATTT
Found at i:37831123 original size:18 final size:19
Alignment explanation
Indices: 37831095--37831130 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
37831085 CTAATATTTC
*
37831095 TTCCAAAACTATTTTTACT
1 TTCCAAAACTATTATTACT
37831114 TTCC-AAACTATTATTAC
1 TTCCAAAACTATTATTAC
37831131 CTCTGTATGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.44
Consensus pattern (19 bp):
TTCCAAAACTATTATTACT
Found at i:37832666 original size:5 final size:5
Alignment explanation
Indices: 37832656--37832718 Score: 81
Period size: 5 Copynumber: 12.6 Consensus size: 5
37832646 TCATATATAT
* * * * *
37832656 ATTCC ATTCC ATACC ATTCC ATTCC ATACT ATTCC ATTTC ATACC ATTCC
1 ATTCC ATTCC ATTCC ATTCC ATTCC ATTCC ATTCC ATTCC ATTCC ATTCC
37832706 ATTCC ATTCC ATT
1 ATTCC ATTCC ATT
37832719 TCATCAAGCA
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
5 48 1.00
ACGTcount: A:0.25, C:0.35, G:0.00, T:0.40
Consensus pattern (5 bp):
ATTCC
Found at i:37832676 original size:15 final size:15
Alignment explanation
Indices: 37832656--37832718 Score: 99
Period size: 15 Copynumber: 4.2 Consensus size: 15
37832646 TCATATATAT
37832656 ATTCCATTCCATACC
1 ATTCCATTCCATACC
*
37832671 ATTCCATTCCATACT
1 ATTCCATTCCATACC
*
37832686 ATTCCATTTCATACC
1 ATTCCATTCCATACC
*
37832701 ATTCCATTCCATTCC
1 ATTCCATTCCATACC
37832716 ATT
1 ATT
37832719 TCATCAAGCA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 43 1.00
ACGTcount: A:0.25, C:0.35, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTCCATTCCATACC
Found at i:37833849 original size:102 final size:102
Alignment explanation
Indices: 37833618--37834068 Score: 570
Period size: 102 Copynumber: 4.4 Consensus size: 102
37833608 CTATTATCAT
* * * * * * * * * *
37833618 TCGATACATGTAGTAGCCTTCACATAGTGCTACACACGTGATC-AA-TTTTTACGGTTCACGTAA
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCT-CGGTACACATAG
* * *
37833681 TAGCCTTCACATAGTACTACACACGTGATCA--AGTTT-
65 TAGCCTTCACTTAGTACTACACATGTGACCATTA-TTTA
* * * * * * * *
37833717 TGCGGTTCACATAGTAGCCTTCACATAGTACTACATACGTGACTAATGCTTTTCTGTACACATAG
1 T-CGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATAG
*
37833782 TAGCCTTCACTTAGTACTACACATGTGACCATCATTTA
65 TAGCCTTCACTTAGTACTACACATGTGACCATTATTTA
* * * *
37833820 TCAATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACATATTGG
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATAGT
37833885 AGCCTTCACTTAGTACTACACATGTGACCATTATTTA
66 AGCCTTCACTTAGTACTACACATGTGACCATTATTTA
* *
37833922 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACATATTGT
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATAGT
37833987 AGCCTTCACTTAGTACTACACATGTGACCATTATTTA
66 AGCCTTCACTTAGTACTACACATGTGACCATTATTTA
* *
37834024 TCGATTCACGTAGTTGCCTTCACACAATACTACACACGTGACCAA
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAA
37834069 CACTTTCACT
Statistics
Matches: 312, Mismatches: 34, Indels: 9
0.88 0.10 0.03
Matches are distributed among these distances:
99 1 0.00
100 34 0.11
101 37 0.12
102 238 0.76
103 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (102 bp):
TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATAGT
AGCCTTCACTTAGTACTACACATGTGACCATTATTTA
Found at i:37834066 original size:51 final size:51
Alignment explanation
Indices: 37833618--37834067 Score: 369
Period size: 51 Copynumber: 8.9 Consensus size: 51
37833608 CTATTATCAT
* * * *
37833618 TCGATACATGTAGTAGCCTTCACATAGTGCTACACACGTGATCAATT-TTTA
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGA-CCATTATTTA
* * *
37833669 -CGGTTCACGTAATAGCCTTCACATAGTACTACACACGTGATCA--AGTTT-
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCATTA-TTTA
* * * * **
37833717 TGCGGTTCACATAGTAGCCTTCACATAGTACTACATACGTGACTAATGCTTT-
1 T-CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGAC-CATTATTTA
* * * * *
37833769 TCTG-TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTA
1 TC-GATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCATTATTTA
* * * * *
37833820 TCAATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCA-AAGCTTC
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCATTA-TTTA
* * ** * * * *
37833871 TCGGTACATATTGGAGCCTTCACTTAGTACTACACATGTGACCATTATTTA
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCATTATTTA
* * * *
37833922 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCA-AAGCTTC
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCATTA-TTTA
* * ** * * *
37833973 TCGGTACATATTGTAGCCTTCACTTAGTACTACACATGTGACCATTATTTA
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCATTATTTA
* * *
37834024 TCGATTCACGTAGTTGCCTTCACACAATACTACACACGTGACCA
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCA
37834068 ACACTTTCAC
Statistics
Matches: 310, Mismatches: 75, Indels: 28
0.75 0.18 0.07
Matches are distributed among these distances:
49 4 0.01
50 79 0.25
51 220 0.71
52 7 0.02
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (51 bp):
TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCATTATTTA
Found at i:37841382 original size:19 final size:20
Alignment explanation
Indices: 37841358--37841398 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
37841348 CATGCAGATT
37841358 AAATAAACAAAA-AAATAAA
1 AAATAAACAAAACAAATAAA
*
37841377 AAATAAATAAAACCAAATAAA
1 AAATAAACAAAA-CAAATAAA
37841398 A
1 A
37841399 TAAAATTCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
21 8 0.42
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.12
Consensus pattern (20 bp):
AAATAAACAAAACAAATAAA
Found at i:37844373 original size:29 final size:29
Alignment explanation
Indices: 37844340--37844398 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 29
37844330 TAAAAGCTAC
37844340 ATGAATG-CATG-AAATAGATAAAAATCAAA
1 ATGAATGACATGAAAATAG--AAAAATCAAA
37844369 ATGAATGATCATGAAAATAGAAAAATCAAA
1 ATGAATGA-CATGAAAATAGAAAAATCAAA
37844399 GCTTGGAGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 7 0.26
30 10 0.37
31 4 0.15
32 6 0.22
ACGTcount: A:0.59, C:0.07, G:0.14, T:0.20
Consensus pattern (29 bp):
ATGAATGACATGAAAATAGAAAAATCAAA
Found at i:37863991 original size:43 final size:42
Alignment explanation
Indices: 37863887--37864058 Score: 204
Period size: 43 Copynumber: 4.0 Consensus size: 42
37863877 AAATGCCACA
* *
37863887 AAAGATCATGTTCTTTAGCGGCGTTTGTAGTAAAATGCCGTT
1 AAAGATCATGTTCTTTAGCGGCGTTTGTAGTAAAACGCCGCT
* * *
37863929 AAAAATCATGTT-TTATAGCGGTGTTTGTAGTAAAACCACCGCT
1 AAAGATCATGTTCTT-TAGCGGCGTTTGTAGTAAAA-CGCCGCT
* * *
37863972 AAAGATCATGTTCTTTAGCGGCATTTGTTGTAAAAGCGTCGCT
1 AAAGATCATGTTCTTTAGCGGCGTTTGTAGTAAAA-CGCCGCT
* *
37864015 AAAGACCATGTTCTATAGCGGCGTTTGTGAG-AAAACGCCGCT
1 AAAGATCATGTTCTTTAGCGGCGTTTGT-AGTAAAACGCCGCT
37864057 AA
1 AA
37864059 CATTAATAGA
Statistics
Matches: 109, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
41 2 0.02
42 38 0.35
43 66 0.61
44 3 0.03
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (42 bp):
AAAGATCATGTTCTTTAGCGGCGTTTGTAGTAAAACGCCGCT
Found at i:37864056 original size:85 final size:85
Alignment explanation
Indices: 37863887--37864058 Score: 224
Period size: 85 Copynumber: 2.0 Consensus size: 85
37863877 AAATGCCACA
* * * * *
37863887 AAAGATCATGTTCTTTAGCGGCGTTTGTAGTAAAATGCCGTTAAAAATCATGTTTTATAGCGGTG
1 AAAGATCATGTTCTTTAGCGGCATTTGTAGTAAAATGCCGCTAAAAACCATGTTCTATAGCGGCG
37863952 TTTGTAGTAAAACCACCGCT
66 TTTGTAGTAAAACCACCGCT
* *
37863972 AAAGATCATGTTCTTTAGCGGCATTTGTTGTAAAA-GCGTCGCTAAAGACCATGTTCTATAGCGG
1 AAAGATCATGTTCTTTAGCGGCATTTGTAGTAAAATGC--CGCTAAAAACCATGTTCTATAGCGG
*
37864036 CGTTTGTGAG-AAAA-CGCCGCT
64 CGTTTGT-AGTAAAACCACCGCT
37864057 AA
1 AA
37864059 CATTAATAGA
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
84 2 0.03
85 41 0.54
86 31 0.41
87 2 0.03
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (85 bp):
AAAGATCATGTTCTTTAGCGGCATTTGTAGTAAAATGCCGCTAAAAACCATGTTCTATAGCGGCG
TTTGTAGTAAAACCACCGCT
Found at i:37865421 original size:15 final size:16
Alignment explanation
Indices: 37865401--37865430 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
37865391 GGTCTCTCCA
37865401 TTTCTTTAC-TAATTC
1 TTTCTTTACATAATTC
37865416 TTTCTTTACATAATT
1 TTTCTTTACATAATT
37865431 ATCCTAGACC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTCTTTACATAATTC
Found at i:37866637 original size:32 final size:32
Alignment explanation
Indices: 37866601--37866661 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
37866591 GAATTCTTTA
37866601 CTTCTGTTCTTTCATGGAGGACCAGTGTTTTG
1 CTTCTGTTCTTTCATGGAGGACCAGTGTTTTG
37866633 CTTCTGTTCTTTCATGGAGGACCAGTGTT
1 CTTCTGTTCTTTCATGGAGGACCAGTGTT
37866662 CTTTCATGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.13, C:0.20, G:0.25, T:0.43
Consensus pattern (32 bp):
CTTCTGTTCTTTCATGGAGGACCAGTGTTTTG
Found at i:37866663 original size:21 final size:21
Alignment explanation
Indices: 37866637--37866677 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
37866627 GTTTTGCTTC
37866637 TGTTCTTTCATGGAGGACCAG
1 TGTTCTTTCATGGAGGACCAG
37866658 TGTTCTTTCATGGAGGACCA
1 TGTTCTTTCATGGAGGACCA
37866678 AACTTTTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.34
Consensus pattern (21 bp):
TGTTCTTTCATGGAGGACCAG
Found at i:37868241 original size:20 final size:20
Alignment explanation
Indices: 37868216--37868255 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
37868206 AATATTTTCC
*
37868216 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
37868236 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
37868256 TCATTTTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:37869627 original size:27 final size:27
Alignment explanation
Indices: 37869589--37869823 Score: 317
Period size: 27 Copynumber: 8.6 Consensus size: 27
37869579 ATTTTTGGGC
*
37869589 AAATGACCGAATTACCCCCAAAGGGTA
1 AAATGACCGAATTACCCCCGAAGGGTA
*
37869616 AAATGACCGAATTACCCCCGAGGGGTA
1 AAATGACCGAATTACCCCCGAAGGGTA
*
37869643 AAATGACCGAATTACCCTCGAAGGGTA
1 AAATGACCGAATTACCCCCGAAGGGTA
*
37869670 AAATGACCGAATTACCCCCCGAAGGTTA
1 AAATGACCGAATTA-CCCCCGAAGGGTA
* *
37869698 AAATGATCGAATTACCCCCAAAGGGTA
1 AAATGACCGAATTACCCCCGAAGGGTA
* *
37869725 AAATGACCGAATTATCCTCGAAGGGTA
1 AAATGACCGAATTACCCCCGAAGGGTA
* * *
37869752 AAATGACTGAATTACCCCCAAAGGTTA
1 AAATGACCGAATTACCCCCGAAGGGTA
**
37869779 AAATGACTAAATTACCCCCCGAAGGGTA
1 AAATGACCGAATTA-CCCCCGAAGGGTA
* *
37869807 AAATGACCAAAATACCC
1 AAATGACCGAATTACCC
37869824 TTGTAAGGTA
Statistics
Matches: 183, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
27 136 0.74
28 47 0.26
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.18
Consensus pattern (27 bp):
AAATGACCGAATTACCCCCGAAGGGTA
Found at i:37869725 original size:82 final size:80
Alignment explanation
Indices: 37869589--37869842 Score: 348
Period size: 82 Copynumber: 3.1 Consensus size: 80
37869579 ATTTTTGGGC
* *
37869589 AAATGACCGAATTACCCCCAAAGGGTAAAATGACCGAATTACCCCCGAGGGGTAAAATGACCGAA
1 AAATGACCGAATTACCCCCAAAGGTTAAAATGA-CGAATTACCCCCGAAGGGTAAAATGACCGAA
37869654 TTACCCTCGAAGGGTA
65 TTACCCTCGAAGGGTA
* *
37869670 AAATGACCGAATTACCCCCCGAAGGTTAAAATGATCGAATTACCCCCAAAGGGTAAAATGACCGA
1 AAATGACCGAATTA-CCCCCAAAGGTTAAAATGA-CGAATTACCCCCGAAGGGTAAAATGACCGA
*
37869735 ATTATCCTCGAAGGGTA
64 ATTACCCTCGAAGGGTA
* * *
37869752 AAATGACTGAATTACCCCCAAAGGTTAAAATGACTAAATTACCCCCCGAAGGGTAAAATGACCAA
1 AAATGACCGAATTACCCCCAAAGGTTAAAATGAC-GAATTA-CCCCCGAAGGGTAAAATGACCGA
* *
37869817 AATACCCTTGTAA-GGTA
64 ATTACCCTCG-AAGGGTA
*
37869834 GAATGACCG
1 AAATGACCG
37869843 TAATGCCCCT
Statistics
Matches: 153, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
80 1 0.01
81 37 0.24
82 113 0.74
83 2 0.01
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.19
Consensus pattern (80 bp):
AAATGACCGAATTACCCCCAAAGGTTAAAATGACGAATTACCCCCGAAGGGTAAAATGACCGAAT
TACCCTCGAAGGGTA
Found at i:37869781 original size:109 final size:109
Alignment explanation
Indices: 37869589--37869823 Score: 353
Period size: 109 Copynumber: 2.2 Consensus size: 109
37869579 ATTTTTGGGC
*
37869589 AAATGACCGAATTACCCCCAAAGGGTAAAATGACCGAATTACCCCCGAGGGGTAAAATGACCGAA
1 AAATGACCGAATTACCCCCAAAGGGTAAAATGACCGAATTACCCCCGAAGGGTAAAATGACCGAA
* * * *
37869654 TTACCCTCGAAGGGTAAAATGACCGAATTACCCCCCGAAGGTTA
66 TTACCCCCAAAGGGTAAAATGACCAAATTACCCCCCGAAGGGTA
* * * *
37869698 AAATGATCGAATTACCCCCAAAGGGTAAAATGACCGAATTATCCTCGAAGGGTAAAATGACTGAA
1 AAATGACCGAATTACCCCCAAAGGGTAAAATGACCGAATTACCCCCGAAGGGTAAAATGACCGAA
* *
37869763 TTACCCCCAAAGGTTAAAATGACTAAATTACCCCCCGAAGGGTA
66 TTACCCCCAAAGGGTAAAATGACCAAATTACCCCCCGAAGGGTA
* *
37869807 AAATGACCAAAATACCC
1 AAATGACCGAATTACCC
37869824 TTGTAAGGTA
Statistics
Matches: 112, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
109 112 1.00
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.18
Consensus pattern (109 bp):
AAATGACCGAATTACCCCCAAAGGGTAAAATGACCGAATTACCCCCGAAGGGTAAAATGACCGAA
TTACCCCCAAAGGGTAAAATGACCAAATTACCCCCCGAAGGGTA
Found at i:37869896 original size:25 final size:24
Alignment explanation
Indices: 37869849--37869897 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
37869839 ACCGTAATGC
* *
37869849 CCCTTGAGGGTAAATGACTATTTG
1 CCCTCGAGGGTAAATGACGATTTG
*
37869873 CCCTCGAGGTTAAATGATCGATTTG
1 CCCTCGAGGGTAAATGA-CGATTTG
37869898 TCTGTGATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (24 bp):
CCCTCGAGGGTAAATGACGATTTG
Found at i:37869911 original size:24 final size:24
Alignment explanation
Indices: 37869884--37869952 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
37869874 CCTCGAGGTT
37869884 AAATGATCGATTTGTCTGTGATGA
1 AAATGATCGATTTGTCTGTGATGA
* * **
37869908 AAATGATTGATTTGTTTGTGATTT
1 AAATGATCGATTTGTCTGTGATGA
*
37869932 AAATGA-CTATTTTGTCTGTGA
1 AAATGATCGA-TTTGTCTGTGA
37869953 ATTGTATGAC
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
23 1 0.03
24 36 0.97
ACGTcount: A:0.28, C:0.06, G:0.22, T:0.45
Consensus pattern (24 bp):
AAATGATCGATTTGTCTGTGATGA
Found at i:37870109 original size:32 final size:32
Alignment explanation
Indices: 37870073--37870220 Score: 154
Period size: 32 Copynumber: 4.7 Consensus size: 32
37870063 GATGCTGCTA
* *
37870073 ATGGCTTTGTGCCGATCATATTACCGTTGCTG
1 ATGGCTTTGTGCCGATCATATTACCGCTACTG
* * * * * *
37870105 ATGGCTGTGTGTCGATAATATCACTGCTATTG
1 ATGGCTTTGTGCCGATCATATTACCGCTACTG
* **
37870137 ATGGCTTTGTACCGATCATATTACCATTAC-G
1 ATGGCTTTGTGCCGATCATATTACCGCTACTG
* * *
37870168 ATGGCTGTGTGCCGATCATATTGCTGCTACTG
1 ATGGCTTTGTGCCGATCATATTACCGCTACTG
*
37870200 ATGGCTTTGTGCCAATCATAT
1 ATGGCTTTGTGCCGATCATAT
37870221 AACTGTATTT
Statistics
Matches: 90, Mismatches: 25, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
31 25 0.28
32 65 0.72
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.36
Consensus pattern (32 bp):
ATGGCTTTGTGCCGATCATATTACCGCTACTG
Found at i:37870203 original size:63 final size:64
Alignment explanation
Indices: 37870073--37870220 Score: 208
Period size: 63 Copynumber: 2.3 Consensus size: 64
37870063 GATGCTGCTA
* * * *
37870073 ATGGCTTTGTGCCGATCATATTACCGTTGCTGATGGCTGTGTGTCGATAATATCACTGCTATTG
1 ATGGCTTTGTGCCGATCATATTACCATTACTGATGGCTGTGTGCCGATAATATCACTGCTACTG
* * **
37870137 ATGGCTTTGTACCGATCATATTACCATTAC-GATGGCTGTGTGCCGATCATATTGCTGCTACTG
1 ATGGCTTTGTGCCGATCATATTACCATTACTGATGGCTGTGTGCCGATAATATCACTGCTACTG
*
37870200 ATGGCTTTGTGCCAATCATAT
1 ATGGCTTTGTGCCGATCATAT
37870221 AACTGTATTT
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
63 47 0.64
64 27 0.36
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.36
Consensus pattern (64 bp):
ATGGCTTTGTGCCGATCATATTACCATTACTGATGGCTGTGTGCCGATAATATCACTGCTACTG
Found at i:37870275 original size:22 final size:22
Alignment explanation
Indices: 37870226--37870275 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
37870216 CATATAACTG
* * *
37870226 TATTTATGGCTTGTAGCCATTC
1 TATTTATAGCTTATAGCCATCC
* *
37870248 TGTTTATAGCTTATAGCTATCC
1 TATTTATAGCTTATAGCCATCC
37870270 TATTTA
1 TATTTA
37870276 CGACTCTTAG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.22, C:0.16, G:0.14, T:0.48
Consensus pattern (22 bp):
TATTTATAGCTTATAGCCATCC
Found at i:37879369 original size:25 final size:25
Alignment explanation
Indices: 37879314--37879374 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
37879304 TTTTAAGTGT
* * *
37879314 TTTCAGTATAGTCTATCTATAGTAG
1 TTTCAGTATATTCTACCTATAGCAG
* *
37879339 TCTCAGTATATTCTACCTGTAGCAG
1 TTTCAGTATATTCTACCTATAGCAG
*
37879364 TTTCAGGATAT
1 TTTCAGTATAT
37879375 ACTATCCAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.41
Consensus pattern (25 bp):
TTTCAGTATATTCTACCTATAGCAG
Found at i:37886275 original size:53 final size:53
Alignment explanation
Indices: 37886208--37886321 Score: 221
Period size: 53 Copynumber: 2.2 Consensus size: 53
37886198 CTCTCAAACA
37886208 TTTT-AAGTGAAAAAGACGAATGCAAAAGGATAGTTTTGAAAATTTCGATCTC
1 TTTTAAAGTGAAAAAGACGAATGCAAAAGGATAGTTTTGAAAATTTCGATCTC
37886260 TTTTAAAGTGAAAAAGACGAATGCAAAAGGATAGTTTTGAAAATTTCGATCTC
1 TTTTAAAGTGAAAAAGACGAATGCAAAAGGATAGTTTTGAAAATTTCGATCTC
37886313 TTTTAAAGT
1 TTTTAAAGT
37886322 TTTTCATTCA
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 4 0.07
53 57 0.93
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.32
Consensus pattern (53 bp):
TTTTAAAGTGAAAAAGACGAATGCAAAAGGATAGTTTTGAAAATTTCGATCTC
Found at i:37886882 original size:22 final size:23
Alignment explanation
Indices: 37886845--37886912 Score: 79
Period size: 22 Copynumber: 3.0 Consensus size: 23
37886835 TTACGGTTAC
37886845 TTAAGTGTTCTAAATAGATTTAA
1 TTAAGTGTTCTAAATAGATTTAA
* *
37886868 TTCA-TGTT-TATAATATGA-TTAC
1 TTAAGTGTTCTA-AATA-GATTTAA
37886890 TTAAGTGTTCTAAATAGATTTAA
1 TTAAGTGTTCTAAATAGATTTAA
37886913 GTCAAATTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
21 2 0.06
22 16 0.44
23 16 0.44
24 2 0.06
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.46
Consensus pattern (23 bp):
TTAAGTGTTCTAAATAGATTTAA
Found at i:37886898 original size:23 final size:23
Alignment explanation
Indices: 37886841--37886911 Score: 85
Period size: 23 Copynumber: 3.1 Consensus size: 23
37886831 TAAATTACGG
37886841 TTACTTAAGTGTTCTAAATAGAT
1 TTACTTAAGTGTTCTAAATAGAT
* *
37886864 TTAATTCA-TGTT-TATAATATGA-
1 TTACTTAAGTGTTCTA-AATA-GAT
37886886 TTACTTAAGTGTTCTAAATAGAT
1 TTACTTAAGTGTTCTAAATAGAT
37886909 TTA
1 TTA
37886912 AGTCAAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
21 2 0.05
22 16 0.41
23 19 0.49
24 2 0.05
ACGTcount: A:0.35, C:0.07, G:0.11, T:0.46
Consensus pattern (23 bp):
TTACTTAAGTGTTCTAAATAGAT
Found at i:37890965 original size:21 final size:21
Alignment explanation
Indices: 37890941--37890980 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
37890931 ATAAACTTTT
*
37890941 CAATTGATTGAATAAAACAAA
1 CAATAGATTGAATAAAACAAA
* *
37890962 CAATAGGTTGTATAAAACA
1 CAATAGATTGAATAAAACA
37890981 GTATACATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.10, G:0.12, T:0.25
Consensus pattern (21 bp):
CAATAGATTGAATAAAACAAA
Found at i:37891529 original size:13 final size:13
Alignment explanation
Indices: 37891508--37891542 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
37891498 ACATTATTCG
*
37891508 AAATTTAGAAAAA
1 AAATATAGAAAAA
37891521 AAATATAG-AAAA
1 AAATATAGAAAAA
37891533 AAATATAGAA
1 AAATATAGAA
37891543 TGAAATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (13 bp):
AAATATAGAAAAA
Found at i:37892018 original size:41 final size:40
Alignment explanation
Indices: 37891925--37892025 Score: 157
Period size: 40 Copynumber: 2.5 Consensus size: 40
37891915 GAAAAATGGT
* *
37891925 GCTATTGCTTTACCATTAGCGGCGTTTATGAAAAAACACC
1 GCTATTGCTTTACCTTTTGCGGCGTTTATGAAAAAACACC
*
37891965 GCTATTGTTTTACCTTTTGCGGCGTTTATGAGAAAAACACC
1 GCTATTGCTTTACCTTTTGCGGCGTTTATGA-AAAAACACC
*
37892006 GCTACTGCTTTACCTTTTGC
1 GCTATTGCTTTACCTTTTGC
37892026 AGCTTTTTTC
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
40 28 0.51
41 27 0.49
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.36
Consensus pattern (40 bp):
GCTATTGCTTTACCTTTTGCGGCGTTTATGAAAAAACACC
Found at i:37893540 original size:18 final size:20
Alignment explanation
Indices: 37893510--37893547 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
37893500 TAAAATCAAT
37893510 TTTTCTAAAAATATT-TTTA
1 TTTTCTAAAAATATTATTTA
37893529 TTTTCT-AAAATATTATTTA
1 TTTTCTAAAAATATTATTTA
37893548 CCAATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTCTAAAAATATTATTTA
Found at i:37898066 original size:16 final size:15
Alignment explanation
Indices: 37898045--37898088 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
37898035 TTTTAAAGGT
*
37898045 TAATTAAGTAATTTGA
1 TAATTAAGTAA-ATGA
*
37898061 TAATTAAGTTAAATGT
1 TAATTAAG-TAAATGA
37898077 TAATTAAGTAAA
1 TAATTAAGTAAA
37898089 AGATGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 4 0.16
16 18 0.72
17 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (15 bp):
TAATTAAGTAAATGA
Found at i:37898079 original size:32 final size:31
Alignment explanation
Indices: 37898016--37898087 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 31
37898006 TGGATAGGTT
*
37898016 TTAATGTAATTATGATAATTTTTAAAGGTTAA
1 TTAA-GTAATTATGATAATTGTTAAAGGTTAA
*
37898048 TTAAGTAATT-TGATAATTAAGTTAAATGTTAA
1 TTAAGTAATTATGATAATT--GTTAAAGGTTAA
37898080 TTAAGTAA
1 TTAAGTAA
37898088 AAGATGAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
30 8 0.22
31 6 0.17
32 22 0.61
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.44
Consensus pattern (31 bp):
TTAAGTAATTATGATAATTGTTAAAGGTTAA
Found at i:37898897 original size:40 final size:39
Alignment explanation
Indices: 37898842--37898973 Score: 167
Period size: 40 Copynumber: 3.3 Consensus size: 39
37898832 TACCCGTGTG
*
37898842 TGTACTTCGGTACCCCTAATTTCACATACGTGCCCCTAGT
1 TGTACTTCGGTACCCCTAATTGCACATACGTGCCCCT-GT
* *
37898882 TGTACTTCAGTACCCCTGAA-TGCACATACGTGCCCATGTT
1 TGTACTTCGGTACCCCT-AATTGCACATACGTGCCCCTG-T
* *
37898922 TGTACTTTGGTACCCCTAATTGCAGATACGTGCCCCTGGT
1 TGTACTTCGGTACCCCTAATTGCACATACGTGCCCCT-GT
*
37898962 TGTACTTTGGTA
1 TGTACTTCGGTA
37898974 ATCCTGAATT
Statistics
Matches: 81, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
39 3 0.04
40 75 0.93
41 3 0.04
ACGTcount: A:0.20, C:0.28, G:0.19, T:0.33
Consensus pattern (39 bp):
TGTACTTCGGTACCCCTAATTGCACATACGTGCCCCTGT
Found at i:37901130 original size:50 final size:50
Alignment explanation
Indices: 37901027--37901316 Score: 287
Period size: 50 Copynumber: 5.7 Consensus size: 50
37901017 TAAAGAGATT
**
37901027 CCATGTAAGACCATGTCTGACACATGGCATTGGCATCCTTGAGACCATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA--C-TGAG---ATGAGAGGTC
* *
37901083 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGACGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTC
* * *
37901133 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGGGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTC
* * * * **
37901183 TCC-CGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTC
1 -CCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTC
* * * * * * * **
37901233 CCATGTAAGACCATATATGGGATATGGCATTGGAAGT-ACATGAAACATC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTC
* *
37901282 CCATGTAATACCATGTCTGGGACATGGCTTTGGCA
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA
37901317 TGTTATTATC
Statistics
Matches: 200, Mismatches: 32, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
49 39 0.19
50 122 0.61
51 2 0.01
53 4 0.02
54 1 0.00
56 32 0.16
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (50 bp):
CCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTC
Found at i:37902731 original size:12 final size:12
Alignment explanation
Indices: 37902714--37902739 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
37902704 TGAGTTACAT
37902714 GGCCTAGCACAC
1 GGCCTAGCACAC
37902726 GGCCTAGCACAC
1 GGCCTAGCACAC
37902738 GG
1 GG
37902740 GTGTGTGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.38, G:0.31, T:0.08
Consensus pattern (12 bp):
GGCCTAGCACAC
Found at i:37904432 original size:20 final size:20
Alignment explanation
Indices: 37904409--37904447 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
37904399 GTATACATGT
*
37904409 TGGTGTCCCTGTTTGCACTA
1 TGGTGCCCCTGTTTGCACTA
37904429 TGGTGCCCCTGTTTGCACT
1 TGGTGCCCCTGTTTGCACT
37904448 TCAGTGCTCT
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:0.08, C:0.28, G:0.26, T:0.38
Consensus pattern (20 bp):
TGGTGCCCCTGTTTGCACTA
Found at i:37906764 original size:24 final size:24
Alignment explanation
Indices: 37906737--37906826 Score: 101
Period size: 24 Copynumber: 3.8 Consensus size: 24
37906727 TGTCTATGAC
* *
37906737 GCCTTTATGGTGTATTCTATTAAT
1 GCCTTTATGGCGTATTCTATAAAT
37906761 GCCTTTATGGCGTATTCTATAAAT
1 GCCTTTATGGCGTATTCTATAAAT
* *
37906785 ACC-CTATTGGCGTATTCTATAAAT
1 GCCTTTA-TGGCGTATTCTATAAAT
* * *
37906809 TCCTTTGTGGTGTATTCT
1 GCCTTTATGGCGTATTCT
37906827 GTGTTGCCTT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
23 2 0.04
24 53 0.95
25 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.46
Consensus pattern (24 bp):
GCCTTTATGGCGTATTCTATAAAT
Found at i:37909031 original size:19 final size:20
Alignment explanation
Indices: 37909007--37909049 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
37908997 GCATTAGAAC
37909007 TTTTATTTT-TATTTACTTA-
1 TTTTATTTTAT-TTTACTTAG
37909026 TTTTATTTTATTTTACTTAG
1 TTTTATTTTATTTTACTTAG
37909046 TTTT
1 TTTT
37909050 TTAATCACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (20 bp):
TTTTATTTTATTTTACTTAG
Done.