Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 195 of 221
Found at i:57113493 original size:40 final size:40
Alignment explanation
Indices: 57113424--57113535 Score: 147
Period size: 40 Copynumber: 2.8 Consensus size: 40
57113414 TTCCCAAAAA
* *
57113424 CGCCGCTAATACT-TATTTTTAGCGGCGTTTTTCAG-AATG
1 CGCCGCTAATACTCGATTTTTAGCGGCGTTTTTC-GTAAAG
* *
57113463 CGCCGCTAATACTCGATCTTTAGCGGCGTTTTACGTAAAG
1 CGCCGCTAATACTCGATTTTTAGCGGCGTTTTTCGTAAAG
* *
57113503 CGCCGCTAATGCTCGATTTTTAGTGGCGTTTTT
1 CGCCGCTAATACTCGATTTTTAGCGGCGTTTTT
57113536 TATCCAAACG
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
39 14 0.22
40 49 0.78
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (40 bp):
CGCCGCTAATACTCGATTTTTAGCGGCGTTTTTCGTAAAG
Found at i:57122633 original size:3 final size:3
Alignment explanation
Indices: 57122627--57122661 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
57122617 TCCTCCTCCT
*
57122627 CCA CCA CCA CCA CCA CCA CCA CCC CCA CCA CCA CC
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CC
57122662 TCCTCCTCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.71, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:57126568 original size:13 final size:13
Alignment explanation
Indices: 57126552--57126577 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
57126542 AATAGATATG
57126552 GATAACAAATACA
1 GATAACAAATACA
57126565 GATAACAAATACA
1 GATAACAAATACA
57126578 AATTTACAGA
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:0.62, C:0.15, G:0.08, T:0.15
Consensus pattern (13 bp):
GATAACAAATACA
Found at i:57130767 original size:9 final size:9
Alignment explanation
Indices: 57130750--57130786 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
57130740 TGAGTTTTCG
57130750 AATTCGAAT
1 AATTCGAAT
*
57130759 AACTCGAAT
1 AATTCGAAT
57130768 AATTCGAAT
1 AATTCGAAT
57130777 AATTCGAAT
1 AATTCGAAT
57130786 A
1 A
57130787 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:57143851 original size:2 final size:2
Alignment explanation
Indices: 57143836--57143869 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
57143826 GTTTGTACAT
*
57143836 TA TA TA CA TA -A 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 T
57143870 TTGAAGGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:57149070 original size:21 final size:21
Alignment explanation
Indices: 57149044--57149083 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
57149034 GACGAGCAAT
* *
57149044 ACTCCACAGCAGGTGGAGTGA
1 ACTCCAAAACAGGTGGAGTGA
57149065 ACTCCAAAACAGGTGGAGT
1 ACTCCAAAACAGGTGGAGT
57149084 TTGAGCAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.30, T:0.15
Consensus pattern (21 bp):
ACTCCAAAACAGGTGGAGTGA
Found at i:57151021 original size:16 final size:16
Alignment explanation
Indices: 57150988--57151021 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
57150978 GGAGATTGTT
* *
57150988 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
57151004 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
57151020 AA
1 AA
57151022 TACAGAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:57156761 original size:18 final size:19
Alignment explanation
Indices: 57156723--57156759 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
57156713 TAATAAACAT
*
57156723 TAAAAAATTATTTTAAAAA
1 TAAAAAAATATTTTAAAAA
57156742 TAAAAAAATATTTTAAAA
1 TAAAAAAATATTTTAAAA
57156760 TACTTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAAAATATTTTAAAAA
Found at i:57158242 original size:21 final size:22
Alignment explanation
Indices: 57158218--57158272 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
57158208 TAGGGATCCT
*
57158218 ACACGGGCGTGTGTT-TTG-GAC
1 ACACGGGCGTGTGTTGATGAG-C
*
57158239 ACACGGTCGTGT-TTGATGAGC
1 ACACGGGCGTGTGTTGATGAGC
57158260 ACACGGGCGTGTG
1 ACACGGGCGTGTG
57158273 AGACCCTCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 2 0.07
21 25 0.89
22 1 0.04
ACGTcount: A:0.16, C:0.20, G:0.38, T:0.25
Consensus pattern (22 bp):
ACACGGGCGTGTGTTGATGAGC
Found at i:57160199 original size:19 final size:19
Alignment explanation
Indices: 57160139--57160201 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 19
57160129 ATAATATTAC
57160139 TATTATTAAATTCAT-A-T
1 TATTATTAAATTCATCATT
* *
57160156 TATTAAATTTAACTTGA-CATAT
1 TATT--A-TTAAATTCATCAT-T
57160178 TATTATTAAATTCATCATT
1 TATTATTAAATTCATCATT
57160197 TATTA
1 TATTA
57160202 ATATATTTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
17 4 0.11
19 14 0.40
20 12 0.34
22 5 0.14
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.51
Consensus pattern (19 bp):
TATTATTAAATTCATCATT
Found at i:57163389 original size:15 final size:15
Alignment explanation
Indices: 57163371--57163403 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
57163361 TTATTTTTGC
57163371 TTTTATTTT-CTCCCT
1 TTTTATTTTACT-CCT
57163386 TTTTATTTTACTCCT
1 TTTTATTTTACTCCT
57163401 TTT
1 TTT
57163404 CAATTTGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 15 0.88
16 2 0.12
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTATTTTACTCCT
Found at i:57163904 original size:16 final size:16
Alignment explanation
Indices: 57163880--57163920 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
57163870 TATTTTATCT
*
57163880 TTTATTTTGTTTATTTA
1 TTTA-TTTGTTCATTTA
57163897 TTTATTTGTTCATTTA
1 TTTATTTGTTCATTTA
57163913 TTTATTTG
1 TTTATTTG
57163921 CCTATCATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.17, C:0.02, G:0.07, T:0.73
Consensus pattern (16 bp):
TTTATTTGTTCATTTA
Found at i:57165473 original size:44 final size:45
Alignment explanation
Indices: 57165378--57165730 Score: 188
Period size: 44 Copynumber: 7.7 Consensus size: 45
57165368 TCTTATCTCT
* *
57165378 CTGAAGTTGCAGTGGAATAGATTAAAGCTACGAATAT-C-AT-CTCC
1 CTGAAGTTGCAGTGGAGTAGATTGAAGCTAC-AA-ATCCTATACTCC
* *
57165422 CTAAAGTTGCAATGGAGTAGATTGAAGCTACAAATCCTATAC-CC
1 CTGAAGTTGCAGTGGAGTAGATTGAAGCTACAAATCCTATACTCC
* * * * * ** *
57165466 TTGAAGTTACAATGG-GTCGGATTAAATATATCATAGTTAACCT-TATCTCC
1 CTGAAGTTGCAGTGGAGT-AGATTGAAGCTA-CA-A---ATCCTATA-CTCC
* *
57165516 CTGAAGTTGCAGTGGAGCAGATTGACGCTACAAATCCTATAC-CC
1 CTGAAGTTGCAGTGGAGTAGATTGAAGCTACAAATCCTATACTCC
* * * * * *
57165560 TTGAAGTTGTAGTGG-GTCGGATTAAATCTACCATAGCAAACCT-TATCTCC
1 CTGAAGTTGCAGTGGAGT-AGATTGAAGCTA-C--A--AATCCTATA-CTCC
* * * *
57165610 CTGAAGTTGCAATGGAGCAGATTGAAGCTACGAATCTTAT-CTCC
1 CTGAAGTTGCAGTGGAGTAGATTGAAGCTACAAATCCTATACTCC
* * * * **
57165654 CTGAAGTTGTAGTGGAGCAAATTGAAGCTACAATTCCTATAC-GA
1 CTGAAGTTGCAGTGGAGTAGATTGAAGCTACAAATCCTATACTCC
* * *
57165698 CTGAAGTTACAGTGGATTAGAATGAAGCTACAA
1 CTGAAGTTGCAGTGGAGTAGATTGAAGCTACAA
57165731 CAACAAATCT
Statistics
Matches: 231, Mismatches: 54, Indels: 48
0.69 0.16 0.14
Matches are distributed among these distances:
42 2 0.01
43 6 0.03
44 139 0.60
45 14 0.06
46 4 0.02
47 1 0.00
48 5 0.02
49 14 0.06
50 44 0.19
51 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (45 bp):
CTGAAGTTGCAGTGGAGTAGATTGAAGCTACAAATCCTATACTCC
Found at i:57165659 original size:94 final size:94
Alignment explanation
Indices: 57165416--57165668 Score: 364
Period size: 94 Copynumber: 2.7 Consensus size: 94
57165406 TACGAATATC
* * ** *
57165416 ATCTCCCTAAAGTTGCAATGGAGTAGATTGAAGCTACAAATCCTATACCCTTGAAGTTACAATGG
1 ATCTCCCTGAAGTTGCAATGGAGCAGATTGAAGCTACAAATCCTATACCCTTGAAGTTGTAGTGG
* **
57165481 GTCGGATTAAATATATCATAGTTAACCTT
66 GTCGGATTAAATATACCATAGCAAACCTT
* *
57165510 ATCTCCCTGAAGTTGCAGTGGAGCAGATTGACGCTACAAATCCTATACCCTTGAAGTTGTAGTGG
1 ATCTCCCTGAAGTTGCAATGGAGCAGATTGAAGCTACAAATCCTATACCCTTGAAGTTGTAGTGG
*
57165575 GTCGGATTAAATCTACCATAGCAAACCTT
66 GTCGGATTAAATATACCATAGCAAACCTT
* * *
57165604 ATCTCCCTGAAGTTGCAATGGAGCAGATTGAAGCTACGAATCTTAT-CTCCCTGAAGTTGTAGTG
1 ATCTCCCTGAAGTTGCAATGGAGCAGATTGAAGCTACAAATCCTATAC-CCTTGAAGTTGTAGTG
57165668 G
65 G
57165669 AGCAAATTGA
Statistics
Matches: 142, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
93 1 0.01
94 141 0.99
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (94 bp):
ATCTCCCTGAAGTTGCAATGGAGCAGATTGAAGCTACAAATCCTATACCCTTGAAGTTGTAGTGG
GTCGGATTAAATATACCATAGCAAACCTT
Found at i:57165745 original size:232 final size:232
Alignment explanation
Indices: 57165313--57165758 Score: 513
Period size: 232 Copynumber: 1.9 Consensus size: 232
57165303 TAGTAAAACC
* ** * *
57165313 ACAAATCATATACCCCTGAAATTGCAGTGGGTCGAATTGAAGTCACCATAGTGAATCTTATCTCT
1 ACAAATCATATACCCCTGAAATTGCAGTGGGTCGAATTGAAATCACCATAGCAAACCTTATCTCC
* * * *
57165378 CTGAAGTTGCAGTGGAATAGATTAAAGCTACGAATATCATCTCCCTAAAGTTGCAATGGAGTAGA
66 CTGAAGTTGCAATGGAACAGATTAAAGCTACGAATATCATCTCCCTAAAGTTGCAATGGAGCAAA
* * * * * * **
57165443 TTGAAGCTACAAATCCTATACCCTTGAAGTTACAATGGGTCGGATTAAATATATCATAGTTAACC
131 TTGAAGCTACAAATCCTATACACTTGAAGTTACAATGGGTAGAATGAAATACAACATAGCAAACC
57165508 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGACGCT
196 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGACGCT
* * * * *
57165545 ACAAATCCTATACCCTTGAAGTTGTAGTGGGTCGGATT-AAATCTACCATAGCAAACCTTATCTC
1 ACAAATCATATACCCCTGAAATTGCAGTGGGTCGAATTGAAATC-ACCATAGCAAACCTTATCTC
* * * * * * *
57165609 CCTGAAGTTGCAATGGAGCAGATTGAAGCTACGAATCTTATCTCCCTGAAGTTGTAGTGGAGCAA
65 CCTGAAGTTGCAATGGAACAGATTAAAGCTACGAATATCATCTCCCTAAAGTTGCAATGGAGCAA
* * * *
57165674 ATTGAAGCTACAATTCCTATACGAC-TGAAGTTACAGTGGATTAGAATGAAGCTACAACA-A-CA
130 ATTGAAGCTACAAATCCTATAC-ACTTGAAGTTACAATGG-GTAGAATGAA-ATACAACATAGCA
* *
57165736 AATCTTATCTCCTTGAAGTTGCA
192 AACCTTATCTCCCTGAAGTTGCA
57165759 ATAGAGCAAG
Statistics
Matches: 175, Mismatches: 35, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
231 4 0.02
232 158 0.90
233 8 0.05
234 5 0.03
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (232 bp):
ACAAATCATATACCCCTGAAATTGCAGTGGGTCGAATTGAAATCACCATAGCAAACCTTATCTCC
CTGAAGTTGCAATGGAACAGATTAAAGCTACGAATATCATCTCCCTAAAGTTGCAATGGAGCAAA
TTGAAGCTACAAATCCTATACACTTGAAGTTACAATGGGTAGAATGAAATACAACATAGCAAACC
TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGACGCT
Found at i:57165755 original size:138 final size:138
Alignment explanation
Indices: 57165507--57165775 Score: 335
Period size: 138 Copynumber: 1.9 Consensus size: 138
57165497 CATAGTTAAC
* * * **
57165507 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGACGCTACAAATCCTATACCCTTGAAGTTGTAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGCTACAAATCCTATACACTTGAAGTTACAG
* * * * * * * *
57165572 TGGGTCGGATTAAATCTACCATAGCAAACCTTATCTCCCTGAAGTTGCAATGGAGC-AGATTGAA
66 TGGATCAGAATAAAGCTACAACAACAAACCTTATCTCCCTGAAGTTGCAATAGAGCAAGA-TGAA
57165636 GCTACGAAT
130 GCTACGAAT
* *
57165645 CTTATCTCCCTGAAGTTGTAGTGGAGCAAATTGAAGCTACAATTCCTATACGAC-TGAAGTTACA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGCTACAAATCCTATAC-ACTTGAAGTTACA
* * * *
57165709 GTGGATTAGAATGAAGCTACAACAACAAATCTTATCTCCTTGAAGTTGCAATAGAGCAAGATGAA
65 GTGGATCAGAATAAAGCTACAACAACAAACCTTATCTCCCTGAAGTTGCAATAGAGCAAGATGAA
57165774 GC
130 GC
57165776 CATGATACCA
Statistics
Matches: 110, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
138 106 0.96
139 4 0.04
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (138 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGCTACAAATCCTATACACTTGAAGTTACAG
TGGATCAGAATAAAGCTACAACAACAAACCTTATCTCCCTGAAGTTGCAATAGAGCAAGATGAAG
CTACGAAT
Found at i:57168558 original size:16 final size:17
Alignment explanation
Indices: 57168533--57168567 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
57168523 TCTTTCTCTC
*
57168533 TTTTCGTTTCT-TTTTT
1 TTTTCCTTTCTGTTTTT
57168549 TTTTCCTTTCTGTTTTT
1 TTTTCCTTTCTGTTTTT
57168566 TT
1 TT
57168568 ATTAATCGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (17 bp):
TTTTCCTTTCTGTTTTT
Found at i:57171276 original size:30 final size:30
Alignment explanation
Indices: 57171214--57171283 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
57171204 TTGTATATAT
* *
57171214 AAACTTTAATTTGGTGCAATTATACACGTG
1 AAACTTTAATGTGGTGCAAATATACACGTG
* * * *
57171244 AAACTATAATGTGGTTCAAATATATACTTG
1 AAACTTTAATGTGGTGCAAATATACACGTG
57171274 AAACTTTAAT
1 AAACTTTAAT
57171284 TTTGATTTAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (30 bp):
AAACTTTAATGTGGTGCAAATATACACGTG
Found at i:57172157 original size:41 final size:40
Alignment explanation
Indices: 57172112--57172210 Score: 101
Period size: 41 Copynumber: 2.4 Consensus size: 40
57172102 TTATTGTTAC
* *
57172112 TTAGTATTATTGTTAGTAAAAAACTAATATTTTTATTATGG
1 TTAGTATTATTGTTAGTAAAAAACTAA-ATTATTATTATAG
* * * *
57172153 TTAGTTATTA-GGATTAGTAAAAACCTTAATTATTATTTTAG
1 TTAG-TATTATTG-TTAGTAAAAAACTAAATTATTATTATAG
*
57172194 TTAGTATGATTGTTAGT
1 TTAGTATTATTGTTAGT
57172211 TATTATTTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
40 9 0.19
41 20 0.43
42 18 0.38
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.48
Consensus pattern (40 bp):
TTAGTATTATTGTTAGTAAAAAACTAAATTATTATTATAG
Found at i:57172197 original size:28 final size:28
Alignment explanation
Indices: 57172166--57172252 Score: 74
Period size: 28 Copynumber: 3.2 Consensus size: 28
57172156 GTTATTAGGA
57172166 TTAGTAAAAACCTTAATTATTATTTTAG
1 TTAGTAAAAACCTTAATTATTATTTTAG
** *** *
57172194 TTAGTATGATTGTTAGTTATTA-TTT--
1 TTAGTAAAAACCTTAATTATTATTTTAG
*
57172219 TTAGT-AAAACCCTAATTATTATTGTTAG
1 TTAGTAAAAACCTTAATTATTATT-TTAG
57172247 TTAGTA
1 TTAGTA
57172253 TTATTTTGAG
Statistics
Matches: 41, Mismatches: 13, Indels: 9
0.65 0.21 0.14
Matches are distributed among these distances:
24 9 0.22
25 6 0.15
26 2 0.05
27 3 0.07
28 21 0.51
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.49
Consensus pattern (28 bp):
TTAGTAAAAACCTTAATTATTATTTTAG
Found at i:57172210 original size:53 final size:53
Alignment explanation
Indices: 57172152--57172253 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
57172142 TTTTATTATG
*
57172152 GTTAGTTATTAGGATTAGTAAAAACCTTAATTATTATT-TTAGTTAGTATGATT
1 GTTAGTTATTAGGATTAGT-AAAACCCTAATTATTATTGTTAGTTAGTATGATT
***
57172205 GTTAGTTATTATTTTTAGTAAAACCCTAATTATTATTGTTAGTTAGTAT
1 GTTAGTTATTAGGATTAGTAAAACCCTAATTATTATTGTTAGTTAGTAT
57172254 TATTTTGAGT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 17 0.39
53 27 0.61
ACGTcount: A:0.32, C:0.05, G:0.14, T:0.49
Consensus pattern (53 bp):
GTTAGTTATTAGGATTAGTAAAACCCTAATTATTATTGTTAGTTAGTATGATT
Found at i:57172283 original size:39 final size:41
Alignment explanation
Indices: 57172205--57172284 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 41
57172195 TAGTATGATT
* *
57172205 GTTAGTTATTATTTTTAGTAAAACCCTAATTATTATTGTTA
1 GTTAGTTATTATTTTGAGTAAAACACTAATTATTATTGTTA
57172246 GTTAG-TATTATTTTGAGTATAAA-ACT-ATTATTATTGTTA
1 GTTAGTTATTATTTTGAGTA-AAACACTAATTATTATTGTTA
57172285 TTGTGTTAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
39 13 0.36
40 15 0.42
41 8 0.22
ACGTcount: A:0.33, C:0.05, G:0.11, T:0.51
Consensus pattern (41 bp):
GTTAGTTATTATTTTGAGTAAAACACTAATTATTATTGTTA
Found at i:57175355 original size:77 final size:77
Alignment explanation
Indices: 57175192--57175429 Score: 328
Period size: 77 Copynumber: 3.2 Consensus size: 77
57175182 TGTAATGTTG
*
57175192 TAAAAAGTATAATTCATTTGGAATAATTAAAATTATT---C--A-GCTTATGCTTAAATTGTATC
1 TAAAAAGTAAAATTCATTTGGAATAATTAAAATTATTCAGCTTATGCTTATGCTTAAATTGTATC
57175251 CAAATTAAGGTA
66 CAAATTAAGGTA
* **
57175263 TTAAAAA-CATGATTCATTTGGAATAATTAAAATTATTCAGCTTATGCTTATGCTTAAATTGTAT
1 -TAAAAAGTAAAATTCATTTGGAATAATTAAAATTATTCAGCTTATGCTTATGCTTAAATTGTAT
*
57175327 CCAAATTAAGTTA
65 CCAAATTAAGGTA
* *
57175340 TAAAAAGTAAAATTCATTTGGAATAATTAAACTTATTCAGCTTATGCTTATGCTTCAATTGTATC
1 TAAAAAGTAAAATTCATTTGGAATAATTAAAATTATTCAGCTTATGCTTATGCTTAAATTGTATC
*
57175405 CAAATCAAGGTA
66 CAAATTAAGGTA
* *
57175417 TTAAAAGTGAAAT
1 TAAAAAGTAAAAT
57175430 AAATTAAGTA
Statistics
Matches: 147, Mismatches: 12, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
71 28 0.19
72 6 0.04
74 1 0.01
76 7 0.05
77 105 0.71
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (77 bp):
TAAAAAGTAAAATTCATTTGGAATAATTAAAATTATTCAGCTTATGCTTATGCTTAAATTGTATC
CAAATTAAGGTA
Found at i:57177928 original size:152 final size:152
Alignment explanation
Indices: 57177466--57178222 Score: 846
Period size: 154 Copynumber: 5.0 Consensus size: 152
57177456 AAAAATTAGT
* * * *
57177466 AAAAAACCA-TTATTTCGGTCATTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTAAAAAAAT
1 AAAAAAACACTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTAAAAATAT
*
57177530 ATCATATTTTCTAATTTTATTATTTTACATTATTTTATTACATTATGTTTGAAATTTAAATAAAT
66 A-C-TATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTT-AATAAAT
*
57177595 TTAGTGTATTTTTTAAATAAATTTA
128 TTAGTGTATTTTTTAAATAAATTAA
* * *
57177620 AAGAAACCA-TTATTTCGGCCCTTTGCTCGTATTTTTTTCCCGAATTTTATTACTTTCAATAAAA
1 AAAAAAACACTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTAC-TT---TAAAA
* * * * * *
57177684 ATATATTATTTT-GATATTTTATTATTTTACTTTATCTTAGTACATTATGTTTGAAATGT-ATTA
62 ATATACTATTTTCTA-ATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTAATAA
* * * * *
57177747 ATTAATTCTATTTTTT---TAATTTAG
126 ATTTAGTGTATTTTTTAAATAAATTAA
* *
57177771 TAAAAAACACTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAAATTTATTACTTTAAAAATAT
1 AAAAAAACACTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTAAAAATAT
57177836 ACTATTTT-TAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTAAATAAATTT
66 ACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTT-AATAAATTT
*
57177900 AGTGTGTTTTTTAAATAAATT-A
130 AGTGTATTTTTTAAATAAATTAA
* * *
57177922 AAAAAAACCCTTATTTCGGCCCTTTGCTCGTATTTTTTTCCCGATTTTTATTACTTTCAATAAAA
1 AAAAAAACACTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTAC-TT---TAAAA
* * * *
57177987 ATATATTATTTTCGT-ATTTTATTATTTTA-ATTTATCTTAGTACATTATGTTTGAAATGTATTA
62 ATATACTATTTTC-TAATTTTATTATTTTACA-TTATTTTAGTACATTATGTTTGAAATTTAATA
* * * *
57178050 ATTATTT-CTGT-TTTTTT--TTAATTTAG
125 A--ATTTAGTGTATTTTTTAAATAAATTAA
* * * * *
57178076 TAAAAAACCCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTACTTTAAAAA-A
1 AAAAAAACACTTATTTCGGCCCTTTGTTCGTATTTTTTTC-CCGAATTTTATTACTTTAAAAATA
*
57178140 TATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTT-ATTAAT
65 TA-C-TATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTAATAAAT
*
57178204 TTAGTGTGTTTTTTAAATA
128 TTAGTGTATTTTTTAAATA
57178223 TACAATTTTT
Statistics
Matches: 512, Mismatches: 61, Indels: 61
0.81 0.10 0.10
Matches are distributed among these distances:
147 41 0.08
148 17 0.03
149 19 0.04
150 6 0.01
151 77 0.15
152 96 0.19
153 8 0.02
154 103 0.20
155 42 0.08
156 89 0.17
157 5 0.01
158 9 0.02
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (152 bp):
AAAAAAACACTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTAAAAATAT
ACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTAATAAATTTA
GTGTATTTTTTAAATAAATTAA
Found at i:57178011 original size:303 final size:305
Alignment explanation
Indices: 57177461--57178222 Score: 1268
Period size: 303 Copynumber: 2.5 Consensus size: 305
57177451 TCAAAAAAAA
*
57177461 TTAGTAAAAAACCATTATTTCGGTCATTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTAAAA
1 TTAGTAAAAAACC-TTATTTCGGCCATTTGTTCGTATTTTTTTCCCGAATTTTATTACTTT-AAA
*
57177526 AAATATCATATTTTCTAATTTTATTATTTTACATTATTTTATTACATTATGTTTGAAATTTAAAT
64 AAATATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTAAAT
* * *
57177591 AAATTTAGTGTATTTTTTAAATAAATTTAAAGAAACCATTATTTCGGCCCTTTGCTCGTATTTTT
129 AAATTTAGTGTGTTTTTTAAATAAATTAAAAAAAACCATTATTTCGGCCCTTTGCTCGTATTTTT
*
57177656 TTCCCGAATTTTATTACTTTCAATAAAAATATATTATTTTGATATTTTATTATTTTACTTTATCT
194 TTCCCGAATTTTATTACTTTCAATAAAAATATATTATTTTGATATTTTATTATTTTAATTTATCT
57177721 TAGTACATTATGTTTGAAATGTATTAATTAATTC-TATTTTTTTAAT
259 TAGTACATTATGTTTGAAATGTATTAATTAATTCGTATTTTTTTAAT
* *
57177767 TTAGTAAAAAACACTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAAATTTATTACTTT-AAA
1 TTAGTAAAAAAC-CTTATTTCGGCCATTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTAAAA
57177831 AATAT-ACTATTTT-TAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTAAAT
65 AATATCA-TATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTAAAT
*
57177894 AAATTTAGTGTGTTTTTTAAATAAATTAAAAAAAACCCTTATTTCGGCCCTTTGCTCGTATTTTT
129 AAATTTAGTGTGTTTTTTAAATAAATTAAAAAAAACCATTATTTCGGCCCTTTGCTCGTATTTTT
*
57177959 TTCCCGATTTTTATTACTTTCAATAAAAATATATTATTTTCG-TATTTTATTATTTTAATTTATC
194 TTCCCGAATTTTATTACTTTCAATAAAAATATATTATTTT-GATATTTTATTATTTTAATTTATC
* *
57178023 TTAGTACATTATGTTTGAAATGTATTAATTATTTCTGTTTTTTTTTAAT
258 TTAGTACATTATGTTTGAAATGTATTAATTAATTC-GTATTTTTTTAAT
* *
57178072 TTAGTAAAAAACCCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTACTTTAAA
1 TTAGTAAAAAA-CCTTATTTCGGCCATTTGTTCGTATTTTTTTC-CCGAATTTTATTACTTTAAA
57178137 AAATATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTT--AT
64 AAATATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTAAAT
*
57178200 TAATTTAGTGTGTTTTTTAAATA
129 AAATTTAGTGTGTTTTTTAAATA
57178223 TACAATTTTT
Statistics
Matches: 429, Mismatches: 17, Indels: 20
0.92 0.04 0.04
Matches are distributed among these distances:
303 205 0.48
304 15 0.03
305 51 0.12
306 96 0.22
307 15 0.03
308 47 0.11
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (305 bp):
TTAGTAAAAAACCTTATTTCGGCCATTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTAAAAA
ATATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTAAATAA
ATTTAGTGTGTTTTTTAAATAAATTAAAAAAAACCATTATTTCGGCCCTTTGCTCGTATTTTTTT
CCCGAATTTTATTACTTTCAATAAAAATATATTATTTTGATATTTTATTATTTTAATTTATCTTA
GTACATTATGTTTGAAATGTATTAATTAATTCGTATTTTTTTAAT
Found at i:57178879 original size:11 final size:11
Alignment explanation
Indices: 57178857--57178889 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
57178847 AACTAATCCT
57178857 CTCTCAAATTTC
1 CTCTC-AATTTC
57178869 CTCTCAATTTC
1 CTCTCAATTTC
57178880 CTCTCAATTT
1 CTCTCAATTT
57178890 TGGTGTTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.21, C:0.33, G:0.00, T:0.45
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:57178994 original size:27 final size:26
Alignment explanation
Indices: 57178964--57179014 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
57178954 ACTAAAGCGT
* *
57178964 ATTGACGATAAAGTTAAAAATAAATAA
1 ATTGA-GAGAAAGTTAAAAAAAAATAA
*
57178991 ATTGAGAGAAATTTAAAAAAAAAT
1 ATTGAGAGAAAGTTAAAAAAAAAT
57179015 TAGAGTCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.61, C:0.02, G:0.12, T:0.25
Consensus pattern (26 bp):
ATTGAGAGAAAGTTAAAAAAAAATAA
Found at i:57179535 original size:14 final size:14
Alignment explanation
Indices: 57179518--57179544 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
57179508 AGTGTTTTGG
57179518 TGCTGTTATTTTTC
1 TGCTGTTATTTTTC
57179532 TGCTGTTATTTTT
1 TGCTGTTATTTTT
57179545 GTTATTTTTG
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:0.07, C:0.11, G:0.15, T:0.67
Consensus pattern (14 bp):
TGCTGTTATTTTTC
Found at i:57179911 original size:14 final size:14
Alignment explanation
Indices: 57179865--57179963 Score: 64
Period size: 14 Copynumber: 7.1 Consensus size: 14
57179855 TTGACCCTTC
*
57179865 TTCTTCCCTTTT-T
1 TTCTTTCCTTTTCT
*
57179878 TT-TTTTC-TTTCT
1 TTCTTTCCTTTTCT
57179890 TCTCCTTTCCTTTTCT
1 T-T-CTTTCCTTTTCT
*
57179906 TTCTTTCTTTTTCT
1 TTCTTTCCTTTTCT
* *
57179920 TTCTCCTCCTTTCTTT
1 TTCT-TTCCTTT-TCT
57179936 TTCTTT-C-TTTCT
1 TTCTTTCCTTTTCT
*
57179948 TTCCTCTCCTTTTCT
1 TT-CTTTCCTTTTCT
57179963 T
1 T
57179964 CTCCACCCAC
Statistics
Matches: 66, Mismatches: 10, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
11 3 0.05
12 9 0.14
13 8 0.12
14 17 0.26
15 17 0.26
16 12 0.18
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (14 bp):
TTCTTTCCTTTTCT
Found at i:57179917 original size:34 final size:34
Alignment explanation
Indices: 57179872--57179949 Score: 124
Period size: 34 Copynumber: 2.4 Consensus size: 34
57179862 TTCTTCTTCC
*
57179872 CTTT-TTT-TTTTTCTTTCTTCTCCTTTCCTTTT
1 CTTTCTTTCTTTTTCTTTCTCCTCCTTTCCTTTT
*
57179904 CTTTCTTTCTTTTTCTTTCTCCTCCTTTCTTTTT
1 CTTTCTTTCTTTTTCTTTCTCCTCCTTTCCTTTT
57179938 CTTTCTTTCTTT
1 CTTTCTTTCTTT
57179950 CCTCTCCTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
32 4 0.10
33 3 0.07
34 35 0.83
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (34 bp):
CTTTCTTTCTTTTTCTTTCTCCTCCTTTCCTTTT
Found at i:57179922 original size:24 final size:24
Alignment explanation
Indices: 57179865--57179914 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
57179855 TTGACCCTTC
*
57179865 TTCTTC-CCTTT--TTTTTTTTCT
1 TTCTTCTCCTTTCCTTTTCTTTCT
57179886 TTCTTCTCCTTTCCTTTTCTTTCT
1 TTCTTCTCCTTTCCTTTTCTTTCT
57179910 TTCTT
1 TTCTT
57179915 TTTCTTTCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 6 0.24
22 5 0.20
24 14 0.56
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (24 bp):
TTCTTCTCCTTTCCTTTTCTTTCT
Found at i:57180309 original size:24 final size:22
Alignment explanation
Indices: 57180257--57180309 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 22
57180247 CTCGTATTTA
57180257 ATTTTT-TTCTCACATTATAGT
1 ATTTTTATTCTCACATTATAGT
*
57180278 ATTGTTATTCTCACTATTACT-GTT
1 ATTTTTATTCTCAC-ATTA-TAG-T
57180302 ATTTTTAT
1 ATTTTTAT
57180310 ATTAATCACA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 5 0.19
22 7 0.27
23 5 0.19
24 9 0.35
ACGTcount: A:0.23, C:0.13, G:0.06, T:0.58
Consensus pattern (22 bp):
ATTTTTATTCTCACATTATAGT
Found at i:57185722 original size:14 final size:14
Alignment explanation
Indices: 57185683--57185722 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
57185673 TTATAAACAA
*
57185683 TAAACTTTAAACCT
1 TAAACTTTAAATCT
* *
57185697 TAAATTTTAAATGT
1 TAAACTTTAAATCT
57185711 TAAACTTTAAAT
1 TAAACTTTAAAT
57185723 ACTAAAATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (14 bp):
TAAACTTTAAATCT
Found at i:57185728 original size:21 final size:21
Alignment explanation
Indices: 57185689--57185728 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
57185679 ACAATAAACT
**
57185689 TTAAACCTTAAATTTTAAATG
1 TTAAACCTTAAATACTAAATG
*
57185710 TTAAACTTTAAATACTAAA
1 TTAAACCTTAAATACTAAA
57185729 ATTTACATTT
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:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (21 bp):
TTAAACCTTAAATACTAAATG
Found at i:57185755 original size:20 final size:21
Alignment explanation
Indices: 57185716--57185756 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
57185706 AATGTTAAAC
57185716 TTTAAATACTAAAATTTACAT
1 TTTAAATACTAAAATTTACAT
* *
57185737 TTTAAATCCT-AACTTTACAT
1 TTTAAATACTAAAATTTACAT
57185757 CTAAAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (21 bp):
TTTAAATACTAAAATTTACAT
Found at i:57185791 original size:7 final size:7
Alignment explanation
Indices: 57185777--57185846 Score: 51
Period size: 7 Copynumber: 10.4 Consensus size: 7
57185767 CTAACAGCTA
57185777 AAAT-TT
1 AAATATT
57185783 AAATATT
1 AAATATT
*
57185790 AAATACT
1 AAATATT
57185797 AAAT-TCT
1 AAATAT-T
57185804 AAAT-TCT
1 AAATAT-T
*
57185811 AAATCTT
1 AAATATT
57185818 AAATATT
1 AAATATT
57185825 -AAT-TT
1 AAATATT
*
57185830 AAATACT
1 AAATATT
*
57185837 AAATAAT
1 AAATATT
57185844 AAA
1 AAA
57185847 CCATAAATAA
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
5 2 0.04
6 10 0.19
7 41 0.76
8 1 0.02
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (7 bp):
AAATATT
Found at i:57185798 original size:21 final size:20
Alignment explanation
Indices: 57185774--57185839 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
57185764 AATCTAACAG
57185774 CTAAAATTTAAATATTAAATA
1 CTAAAATTTAAAT-TTAAATA
57185795 CT-AAATTCTAAATTCTAAAT-
1 CTAAAATT-TAAATT-TAAATA
*
57185815 CTTAAATATT-AATTTAAATA
1 CTAAAAT-TTAAATTTAAATA
57185835 CTAAA
1 CTAAA
57185840 TAATAAACCA
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
19 5 0.13
20 16 0.41
21 17 0.44
22 1 0.03
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (20 bp):
CTAAAATTTAAATTTAAATA
Found at i:57185799 original size:14 final size:13
Alignment explanation
Indices: 57185782--57185840 Score: 66
Period size: 14 Copynumber: 4.4 Consensus size: 13
57185772 AGCTAAAATT
57185782 TAAATATTAAATAC
1 TAAAT-TTAAATAC
*
57185796 TAAATTCTAAATTC
1 TAAATT-TAAATAC
57185810 TAAATCTTAAATA-
1 TAAAT-TTAAATAC
*
57185823 TTAATTTAAATAC
1 TAAATTTAAATAC
57185836 TAAAT
1 TAAAT
57185841 AATAAACCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
12 7 0.18
13 9 0.24
14 21 0.55
15 1 0.03
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (13 bp):
TAAATTTAAATAC
Found at i:57185839 original size:33 final size:33
Alignment explanation
Indices: 57185777--57185881 Score: 104
Period size: 33 Copynumber: 3.1 Consensus size: 33
57185767 CTAACAGCTA
* *
57185777 AAAT-TTAAATATTAAATACTAAATTCTAAATTCT
1 AAATCTTAAATATT-AAT-TTAAATACTAAATTCT
**
57185811 AAATCTTAAATATTAATTTAAATACTAAATAAT
1 AAATCTTAAATATTAATTTAAATACTAAATTCT
* * * *
57185844 AAACCATAAATAATAATTTAAAATACTAAACTCT
1 AAATCTTAAATATTAATTT-AAATACTAAATTCT
57185878 AAAT
1 AAAT
57185882 TATAAAGAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
33 28 0.48
34 21 0.36
35 9 0.16
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (33 bp):
AAATCTTAAATATTAATTTAAATACTAAATTCT
Found at i:57186860 original size:16 final size:16
Alignment explanation
Indices: 57186825--57186873 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
57186815 CTAAAATTAT
*
57186825 ATAAGTTTTC-TTTAA
1 ATAAATTTTCATTTAA
*
57186840 TTAAATTTTCATTTAA
1 ATAAATTTTCATTTAA
**
57186856 ATAAATTTAAATTTAA
1 ATAAATTTTCATTTAA
57186872 AT
1 AT
57186874 CACCTTCTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 8 0.29
16 20 0.71
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (16 bp):
ATAAATTTTCATTTAA
Found at i:57196838 original size:33 final size:33
Alignment explanation
Indices: 57196801--57196868 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 33
57196791 TTGCTGCTAT
*
57196801 TTTTGCTGAGTAAATGACGCATCTGTATGCACA
1 TTTTGCTGAGTAAATGACGCATATGTATGCACA
* * * *
57196834 TTTTGTTGAGTAAATGTCGTATATGTGTGCACA
1 TTTTGCTGAGTAAATGACGCATATGTATGCACA
57196867 TT
1 TT
57196869 CTACTGTTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.40
Consensus pattern (33 bp):
TTTTGCTGAGTAAATGACGCATATGTATGCACA
Found at i:57202283 original size:43 final size:43
Alignment explanation
Indices: 57202222--57202421 Score: 258
Period size: 43 Copynumber: 4.7 Consensus size: 43
57202212 AAAAGTATTT
*
57202222 GCGGCGCTTTGCTCACAAACGCCGCTAAAGACCAAGACCTTTA
1 GCGGCGCTTTTCTCACAAACGCCGCTAAAGACCAAGACCTTTA
* * * *
57202265 GCGGCGCTTATCCCACAAACGCCGGTAAAGATCAAGACCTTTA
1 GCGGCGCTTTTCTCACAAACGCCGCTAAAGACCAAGACCTTTA
** * **
57202308 GCGGCATTTTTCTCACAAATGCCGCT-AAGGTCAAGACCTTTA
1 GCGGCGCTTTTCTCACAAACGCCGCTAAAGACCAAGACCTTTA
* * *
57202350 GCGGCACTTTTTTTACAAACGCCGCTAAAGACCAAGACCTTTA
1 GCGGCGCTTTTCTCACAAACGCCGCTAAAGACCAAGACCTTTA
* *
57202393 GCGACGCTTTTCTCACAAACACCGCTAAA
1 GCGGCGCTTTTCTCACAAACGCCGCTAAA
57202422 AACATGACTT
Statistics
Matches: 133, Mismatches: 23, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
42 37 0.28
43 96 0.72
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (43 bp):
GCGGCGCTTTTCTCACAAACGCCGCTAAAGACCAAGACCTTTA
Found at i:57202368 original size:85 final size:85
Alignment explanation
Indices: 57202228--57202420 Score: 242
Period size: 85 Copynumber: 2.3 Consensus size: 85
57202218 ATTTGCGGCG
* * *
57202228 CTTTGCTCACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTATCCCACAAACGCCGGTAA
1 CTTTTCTCACAAACGCCGCT-AAGACCAAGACCTTTAGCGGCACTTATCCCACAAACGCCGCTAA
* *
57202293 AGATCAAGACCTTTAGCGGCA
65 AGACCAAGACCTTTAGCGACA
* * ** * ***
57202314 TTTTTCTCACAAATGCCGCTAAGGTCAAGACCTTTAGCGGCACTTTTTTTACAAACGCCGCTAAA
1 CTTTTCTCACAAACGCCGCTAAGACCAAGACCTTTAGCGGCACTTATCCCACAAACGCCGCTAAA
*
57202379 GACCAAGACCTTTAGCGACG
66 GACCAAGACCTTTAGCGACA
*
57202399 CTTTTCTCACAAACACCGCTAA
1 CTTTTCTCACAAACGCCGCTAA
57202421 AAACATGACT
Statistics
Matches: 90, Mismatches: 17, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
85 73 0.81
86 17 0.19
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (85 bp):
CTTTTCTCACAAACGCCGCTAAGACCAAGACCTTTAGCGGCACTTATCCCACAAACGCCGCTAAA
GACCAAGACCTTTAGCGACA
Found at i:57206201 original size:41 final size:41
Alignment explanation
Indices: 57206120--57206437 Score: 401
Period size: 41 Copynumber: 7.8 Consensus size: 41
57206110 CAAAATATTT
* * * *
57206120 TTAGCGGCGCTTCTCCAAAAACGCCGCTACAGACCTCAGCA
1 TTAGCGGCGCTTTTACAAAAACGCCGCTAAAGACCCCAGCA
* *
57206161 TTAGTGGCG-TTTTACCAAAAACGCCGCTAAAGATCCCAGCA
1 TTAGCGGCGCTTTTA-CAAAAACGCCGCTAAAGACCCCAGCA
* *
57206202 CTAGCGGCGC-TTTATTAAAAACGCCGCTAAAGACCCCAGCA
1 TTAGCGGCGCTTTTA-CAAAAACGCCGCTAAAGACCCCAGCA
* *
57206243 TTAGCGGCGCTTCTACACAAACGCCGCTAAAGACCCCAGCA
1 TTAGCGGCGCTTTTACAAAAACGCCGCTAAAGACCCCAGCA
* *
57206284 CTAGCGGCGC-TTTATTAAAAACGCCGCTAAAGACCCCAGCA
1 TTAGCGGCGCTTTTA-CAAAAACGCCGCTAAAGACCCCAGCA
* * *
57206325 TTAGCGGCGCTTCTACACAAACGCCGCTAAATACCCCAGCA
1 TTAGCGGCGCTTTTACAAAAACGCCGCTAAAGACCCCAGCA
* *
57206366 TTAGCGGCGCTTTT-CAAAAAATGCCGCTAAAGATCCCAGCA
1 TTAGCGGCGCTTTTAC-AAAAACGCCGCTAAAGACCCCAGCA
* *
57206407 TTAGCGGCGCTTCTACAGAAACGCCGCTAAA
1 TTAGCGGCGCTTTTACAAAAACGCCGCTAAA
57206438 TCCCCCAAAG
Statistics
Matches: 238, Mismatches: 32, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
40 7 0.03
41 224 0.94
42 7 0.03
ACGTcount: A:0.30, C:0.32, G:0.19, T:0.18
Consensus pattern (41 bp):
TTAGCGGCGCTTTTACAAAAACGCCGCTAAAGACCCCAGCA
Found at i:57206444 original size:82 final size:82
Alignment explanation
Indices: 57206136--57206437 Score: 464
Period size: 82 Copynumber: 3.7 Consensus size: 82
57206126 GCGCTTCTCC
* * * * * *
57206136 AAAAACGCCGCTACAGACCTCAGCATTAGTGGCG-TTTTACCAAAAACGCCGCTAAAGATCCCAG
1 AAAAACGCCGCTAAAGACCCCAGCATTAGCGGCGCTTCTA-CACAAACGCCGCTAAAGACCCCAG
57206200 CACTAGCGGCGCTTTATT
65 CACTAGCGGCGCTTTATT
57206218 AAAAACGCCGCTAAAGACCCCAGCATTAGCGGCGCTTCTACACAAACGCCGCTAAAGACCCCAGC
1 AAAAACGCCGCTAAAGACCCCAGCATTAGCGGCGCTTCTACACAAACGCCGCTAAAGACCCCAGC
57206283 ACTAGCGGCGCTTTATT
66 ACTAGCGGCGCTTTATT
*
57206300 AAAAACGCCGCTAAAGACCCCAGCATTAGCGGCGCTTCTACACAAACGCCGCTAAATACCCCAGC
1 AAAAACGCCGCTAAAGACCCCAGCATTAGCGGCGCTTCTACACAAACGCCGCTAAAGACCCCAGC
* *
57206365 ATTAGCGGCGCTTT-TCA
66 ACTAGCGGCGCTTTAT-T
* * *
57206382 AAAAATGCCGCTAAAGATCCCAGCATTAGCGGCGCTTCTACAGAAACGCCGCTAAA
1 AAAAACGCCGCTAAAGACCCCAGCATTAGCGGCGCTTCTACACAAACGCCGCTAAA
57206438 TCCCCCAAAG
Statistics
Matches: 206, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
81 1 0.00
82 201 0.98
83 4 0.02
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (82 bp):
AAAAACGCCGCTAAAGACCCCAGCATTAGCGGCGCTTCTACACAAACGCCGCTAAAGACCCCAGC
ACTAGCGGCGCTTTATT
Found at i:57207430 original size:3 final size:3
Alignment explanation
Indices: 57207424--57207470 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
57207414 ATTATGTGAC
57207424 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
57207471 TCACCAAACC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:57211018 original size:16 final size:18
Alignment explanation
Indices: 57210991--57211023 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
57210981 TAGAATTGGG
57210991 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
57211008 TTGAG-AAATTAATTTA
1 TTGAGAAAATTAATTTA
57211024 TTTAACTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:57213313 original size:49 final size:49
Alignment explanation
Indices: 57213257--57213352 Score: 183
Period size: 49 Copynumber: 2.0 Consensus size: 49
57213247 TAGTAAAGAA
*
57213257 CAAAGTAGAAAAATAATGAACAACTAATATGTTTACACAGTTCGATTCC
1 CAAAGTAGAAAAACAATGAACAACTAATATGTTTACACAGTTCGATTCC
57213306 CAAAGTAGAAAAACAATGAACAACTAATATGTTTACACAGTTCGATT
1 CAAAGTAGAAAAACAATGAACAACTAATATGTTTACACAGTTCGATT
57213353 TCCCTACGTT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.26
Consensus pattern (49 bp):
CAAAGTAGAAAAACAATGAACAACTAATATGTTTACACAGTTCGATTCC
Found at i:57216024 original size:255 final size:255
Alignment explanation
Indices: 57215573--57216083 Score: 1004
Period size: 255 Copynumber: 2.0 Consensus size: 255
57215563 AGAGAGTGGG
57215573 AAGTGGGAGAGATAATTTGGGATAATTTCAAAACTACCTATATCCCACTAAATCCCATTAACTAA
1 AAGTGGGAGAGATAATTTGGGATAATTTCAAAACTACCTATATCCCACTAAATCCCATTAACTAA
57215638 TCACCTATCGGATTCCTCTCAGAGTTCAAAACAAAAACAATTCCCACTTTGCACACACAAGATTT
66 TCACCTATCGGATTCCTCTCAGAGTTCAAAACAAAAACAATTCCCACTTTGCACACACAAGATTT
57215703 GAACACAAGACCAAAGAGTAAGTTGAAGCCTTGCCACTGAACCAACAAACTCATCATTATCATCA
131 GAACACAAGACCAAAGAGTAAGTTGAAGCCTTGCCACTGAACCAACAAACTCATCATTATCATCA
57215768 ATTGAGTGAAATTAATATATAAACTAGGTCTTTAAAGTCAAAGGTTGAAACAAAAATTGA
196 ATTGAGTGAAATTAATATATAAACTAGGTCTTTAAAGTCAAAGGTTGAAACAAAAATTGA
*
57215828 AAGTGGGAGAGATCATTTGGGATAATTTCAAAACTACCTATATCCCACTAAATCCCATTAACTAA
1 AAGTGGGAGAGATAATTTGGGATAATTTCAAAACTACCTATATCCCACTAAATCCCATTAACTAA
57215893 TCACCTATCGGATTCCTCTCAGAGTTCAAAACAAAAACAATTCCCACTTTGCACACACAAGATTT
66 TCACCTATCGGATTCCTCTCAGAGTTCAAAACAAAAACAATTCCCACTTTGCACACACAAGATTT
*
57215958 GAACACAAGACCAAAGGGTAAGTTGAAGCCTTGCCACTGAACCAACAAACTCATCATTATCATCA
131 GAACACAAGACCAAAGAGTAAGTTGAAGCCTTGCCACTGAACCAACAAACTCATCATTATCATCA
57216023 ATTGAGTGAAATTAATATATAAACTAGGTCTTTAAAGTCAAAGGTTGAAACAAAAATTGA
196 ATTGAGTGAAATTAATATATAAACTAGGTCTTTAAAGTCAAAGGTTGAAACAAAAATTGA
57216083 A
1 A
57216084 GGAAAGGGAT
Statistics
Matches: 254, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
255 254 1.00
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.25
Consensus pattern (255 bp):
AAGTGGGAGAGATAATTTGGGATAATTTCAAAACTACCTATATCCCACTAAATCCCATTAACTAA
TCACCTATCGGATTCCTCTCAGAGTTCAAAACAAAAACAATTCCCACTTTGCACACACAAGATTT
GAACACAAGACCAAAGAGTAAGTTGAAGCCTTGCCACTGAACCAACAAACTCATCATTATCATCA
ATTGAGTGAAATTAATATATAAACTAGGTCTTTAAAGTCAAAGGTTGAAACAAAAATTGA
Found at i:57220992 original size:3 final size:3
Alignment explanation
Indices: 57220968--57221007 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
57220958 ATTAATTAAT
* *
57220968 TAA T-A TAA TGA TAA TGA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
57221008 TTTAAAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:57221091 original size:19 final size:21
Alignment explanation
Indices: 57221057--57221106 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
57221047 AAAATGTATT
*
57221057 TTAAATATTATATAATT-ATA
1 TTAAATATTTTATAATTCATA
57221077 TTAAA-ATTTTATAATTCATA
1 TTAAATATTTTATAATTCATA
*
57221097 ATAAATATTT
1 TTAAATATTT
57221107 ATGTTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 10 0.38
20 12 0.46
21 4 0.15
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAAATATTTTATAATTCATA
Found at i:57228166 original size:22 final size:23
Alignment explanation
Indices: 57228125--57228167 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
57228115 TATAATTTCT
* *
57228125 TTTTCGGTTTTGGGGGTTTTTTG
1 TTTTCGGTTTTAGGGATTTTTTG
57228148 TTTTC-GTTTTAGGGATTTTT
1 TTTTCGGTTTTAGGGATTTTT
57228168 AATTTGGGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.05, C:0.05, G:0.28, T:0.63
Consensus pattern (23 bp):
TTTTCGGTTTTAGGGATTTTTTG
Found at i:57231518 original size:24 final size:24
Alignment explanation
Indices: 57231487--57231534 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
57231477 ATTTGCACAT
57231487 CATTAAATTTATTAATAATATATA
1 CATTAAATTTATTAATAATATATA
*
57231511 CATTAAATTTATTGATAATATATA
1 CATTAAATTTATTAATAATATATA
57231535 TAATTTTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (24 bp):
CATTAAATTTATTAATAATATATA
Found at i:57240150 original size:4 final size:4
Alignment explanation
Indices: 57240141--57240165 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
57240131 ATACTCCATG
57240141 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
57240166 TAAAAAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:57241658 original size:20 final size:20
Alignment explanation
Indices: 57241635--57241673 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
57241625 AGAGACAAAA
*
57241635 TTAATACAACAGA-GCGTATG
1 TTAATAAAAC-GATGCGTATG
57241655 TTAATAAAACGATGCGTAT
1 TTAATAAAACGATGCGTAT
57241674 TATTGGGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (20 bp):
TTAATAAAACGATGCGTATG
Found at i:57242541 original size:8 final size:8
Alignment explanation
Indices: 57242521--57242561 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
57242511 CCACCTCCAC
57242521 CTCCACCGA
1 CTCCA-CGA
57242530 -TCCACGA
1 CTCCACGA
57242537 CTCCACGA
1 CTCCACGA
57242545 --CCACGA
1 CTCCACGA
57242551 CTCCACGA
1 CTCCACGA
57242559 CTC
1 CTC
57242562 GACAGTGCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
6 6 0.21
7 3 0.10
8 20 0.69
ACGTcount: A:0.24, C:0.51, G:0.12, T:0.12
Consensus pattern (8 bp):
CTCCACGA
Found at i:57242542 original size:22 final size:22
Alignment explanation
Indices: 57242515--57242561 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
57242505 GGAAATCCAC
*
57242515 CTCCACCTCCACCGA-TCCACGA
1 CTCCACCACCA-CGACTCCACGA
*
57242537 CTCCACGACCACGACTCCACGA
1 CTCCACCACCACGACTCCACGA
57242559 CTC
1 CTC
57242562 GACAGTGCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.23, C:0.53, G:0.11, T:0.13
Consensus pattern (22 bp):
CTCCACCACCACGACTCCACGA
Found at i:57242548 original size:14 final size:14
Alignment explanation
Indices: 57242521--57242559 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 14
57242511 CCACCTCCAC
57242521 CTCCACCGATCCACGA
1 CTCCA-CGA-CCACGA
57242537 CTCCACGACCACGA
1 CTCCACGACCACGA
57242551 CTCCACGAC
1 CTCCACGAC
57242560 TCGACAGTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 15 0.65
15 3 0.13
16 5 0.22
ACGTcount: A:0.26, C:0.51, G:0.13, T:0.10
Consensus pattern (14 bp):
CTCCACGACCACGA
Found at i:57242745 original size:17 final size:17
Alignment explanation
Indices: 57242723--57242757 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
57242713 ACAAACAGTA
57242723 GATGTATAATTTCGTTT
1 GATGTATAATTTCGTTT
*
57242740 GATGTATAATTTCTTTT
1 GATGTATAATTTCGTTT
57242757 G
1 G
57242758 GTTGGATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.23, C:0.06, G:0.17, T:0.54
Consensus pattern (17 bp):
GATGTATAATTTCGTTT
Found at i:57242791 original size:37 final size:37
Alignment explanation
Indices: 57242732--57242826 Score: 172
Period size: 37 Copynumber: 2.6 Consensus size: 37
57242722 AGATGTATAA
*
57242732 TTTCGTTTGATGTATAATTTCTTTTGGTTGGATTATT
1 TTTCATTTGATGTATAATTTCTTTTGGTTGGATTATT
*
57242769 TTTCATTTTATGTATAATTTCTTTTGGTTGGATTATT
1 TTTCATTTGATGTATAATTTCTTTTGGTTGGATTATT
57242806 TTTCATTTGATGTATAATTTC
1 TTTCATTTGATGTATAATTTC
57242827 AGATATTTGT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.19, C:0.06, G:0.15, T:0.60
Consensus pattern (37 bp):
TTTCATTTGATGTATAATTTCTTTTGGTTGGATTATT
Found at i:57242814 original size:20 final size:20
Alignment explanation
Indices: 57242749--57242814 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 20
57242739 TGATGTATAA
*
57242749 TTTCTTTTGGTTGGATTATT
1 TTTCATTTGGTTGGATTATT
* *
57242769 TTTCATTT--TATGTA-TA-A
1 TTTCATTTGGT-TGGATTATT
*
57242786 TTTCTTTTGGTTGGATTATT
1 TTTCATTTGGTTGGATTATT
57242806 TTTCATTTG
1 TTTCATTTG
57242815 ATGTATAATT
Statistics
Matches: 34, Mismatches: 7, Indels: 10
0.67 0.14 0.20
Matches are distributed among these distances:
17 7 0.21
18 6 0.18
19 6 0.18
20 15 0.44
ACGTcount: A:0.15, C:0.06, G:0.15, T:0.64
Consensus pattern (20 bp):
TTTCATTTGGTTGGATTATT
Found at i:57243189 original size:16 final size:16
Alignment explanation
Indices: 57243168--57243201 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
57243158 ATATAAATTC
*
57243168 AATAACATTTAATTTT
1 AATAACAATTAATTTT
*
57243184 AATAACAATTAGTTTT
1 AATAACAATTAATTTT
57243200 AA
1 AA
57243202 CTTTTAAGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (16 bp):
AATAACAATTAATTTT
Found at i:57243862 original size:24 final size:24
Alignment explanation
Indices: 57243835--57243883 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
57243825 TTATCTTTAG
57243835 TAAATTTGATGTATTAT-ATATTTT
1 TAAATTTGATGTA-TATGATATTTT
* *
57243859 TAAATTTGTTTTATATGATATTTT
1 TAAATTTGATGTATATGATATTTT
57243883 T
1 T
57243884 TTAAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (24 bp):
TAAATTTGATGTATATGATATTTT
Found at i:57244213 original size:26 final size:24
Alignment explanation
Indices: 57244166--57244214 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
57244156 TTTAATTTGG
*
57244166 TAAATTTTAATTTCTATACTTTTT
1 TAAATTTTAATTTCAATACTTTTT
*
57244190 TAAATTTTAAAATTTCAATCCTTTT
1 TAAATTTT--AATTTCAATACTTTT
57244215 CAAATGACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.38
26 13 0.62
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (24 bp):
TAAATTTTAATTTCAATACTTTTT
Found at i:57244852 original size:23 final size:24
Alignment explanation
Indices: 57244826--57244881 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 24
57244816 CACTTAGCCG
57244826 AAATTCCCCCCAAATTAT-CCCCA
1 AAATTCCCCCCAAATTATCCCCCA
*
57244849 AAATT-CCCCCAAATTTTCCCCCA
1 AAATTCCCCCCAAATTATCCCCCA
*
57244872 AAAATCCCCC
1 AAATTCCCCC
57244882 AATTCTAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 11 0.38
23 14 0.48
24 4 0.14
ACGTcount: A:0.34, C:0.45, G:0.00, T:0.21
Consensus pattern (24 bp):
AAATTCCCCCCAAATTATCCCCCA
Found at i:57244879 original size:11 final size:11
Alignment explanation
Indices: 57244826--57244883 Score: 62
Period size: 11 Copynumber: 5.1 Consensus size: 11
57244816 CACTTAGCCG
*
57244826 AAATTCCCCCC
1 AAATTCCCCCA
*
57244837 AAATTATCCCCA
1 AAATT-CCCCCA
57244849 AAATTCCCCCA
1 AAATTCCCCCA
*
57244860 AATTTTCCCCCA
1 AA-ATTCCCCCA
*
57244872 AAAATCCCCCA
1 AAATTCCCCCA
57244883 A
1 A
57244884 TTCTAGAACC
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
11 20 0.51
12 19 0.49
ACGTcount: A:0.36, C:0.43, G:0.00, T:0.21
Consensus pattern (11 bp):
AAATTCCCCCA
Found at i:57244881 original size:12 final size:12
Alignment explanation
Indices: 57244826--57244883 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 12
57244816 CACTTAGCCG
*
57244826 AAATTCCCCC-C
1 AAATTCCCCCAA
*
57244837 AAATTATCCCC-A
1 AAATT-CCCCCAA
57244849 AAATTCCCCCAA
1 AAATTCCCCCAA
**
57244861 ATTTTCCCCCAA
1 AAATTCCCCCAA
57244873 AAA-TCCCCCAA
1 AAATTCCCCCAA
57244884 TTCTAGAACC
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
11 17 0.45
12 21 0.55
ACGTcount: A:0.36, C:0.43, G:0.00, T:0.21
Consensus pattern (12 bp):
AAATTCCCCCAA
Found at i:57246941 original size:70 final size:69
Alignment explanation
Indices: 57246858--57247069 Score: 345
Period size: 69 Copynumber: 3.1 Consensus size: 69
57246848 CTATATTTAA
* * *
57246858 ATATTGTTAATAATAAATTTTATATTTTTA-AAACTAATTGTACATGTTATTTTTCTAAATATTA
1 ATATTTTTAATAATAAATTTTATAATTTTAGAAA-TAATTGTAAATGTTA-TTTTCTAAATATTA
57246922 ACATCT
64 ACATCT
57246928 ATATTTTTAATAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAAC
1 ATATTTTTAATAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAAC
57246993 ATCT
66 ATCT
* * *
57246997 ATATTTTCAATAATAAATTTTATAATTTTAGAAAGAATTGTAAATGTTATTTTCCAAATATTAAC
1 ATATTTTTAATAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAAC
57247062 ATCT
66 ATCT
57247066 ATAT
1 ATAT
57247070 CGCGAGAGAT
Statistics
Matches: 135, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
69 90 0.67
70 42 0.31
71 3 0.02
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.48
Consensus pattern (69 bp):
ATATTTTTAATAATAAATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAAC
ATCT
Found at i:57249779 original size:44 final size:43
Alignment explanation
Indices: 57249731--57249857 Score: 137
Period size: 44 Copynumber: 2.9 Consensus size: 43
57249721 GCGTTTTTAT
*
57249731 GAAAAGCGTCGCTAAAAGTCAAGGTCTTTTCGCGGCGTTTATGA
1 GAAAAGCGCCGCTAAAAGTCAAGGTCTTTT-GCGGCGTTTATGA
** * * * *
57249775 GAAAAGCGCCGCTAAAACCCAATGCCTTTTAGCGGCATTTGTGA
1 GAAAAGCGCCGCTAAAAGTCAAGGTCTTTT-GCGGCGTTTATGA
** * *
57249819 TCAAAGCGCCGCTAAAGGTCAAGGTATTTTGCGGCGTTT
1 GAAAAGCGCCGCTAAAAGTCAAGGTCTTTTGCGGCGTTT
57249858 GTAGTGGAAG
Statistics
Matches: 66, Mismatches: 17, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
43 8 0.12
44 58 0.88
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (43 bp):
GAAAAGCGCCGCTAAAAGTCAAGGTCTTTTGCGGCGTTTATGA
Found at i:57251235 original size:14 final size:14
Alignment explanation
Indices: 57251212--57251258 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
57251202 TTCTTTTTCT
57251212 TTTTAGTTTATATA
1 TTTTAGTTTATATA
*
57251226 TTTTAATTTA-ATCAA
1 TTTTAGTTTATAT--A
*
57251241 TTTTAGTTTTTATA
1 TTTTAGTTTATATA
57251255 TTTT
1 TTTT
57251259 TCGAATTCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
13 2 0.07
14 14 0.52
15 9 0.33
16 2 0.07
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (14 bp):
TTTTAGTTTATATA
Found at i:57252844 original size:19 final size:19
Alignment explanation
Indices: 57252784--57252844 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 19
57252774 AACTTTTTTT
*
57252784 TTTTAAAAATCAATTAAAATA
1 TTTTAAAAAT--ATAAAAATA
*
57252805 -TTTAAAAATTTAAAAATTA
1 TTTTAAAAATATAAAAA-TA
57252824 TTTTAAAAA-ATAAATAATA
1 TTTTAAAAATATAAA-AATA
57252843 TT
1 TT
57252845 ATAGAAAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
18 5 0.15
19 10 0.29
20 19 0.56
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
TTTTAAAAATATAAAAATA
Found at i:57254196 original size:31 final size:32
Alignment explanation
Indices: 57254137--57254201 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
57254127 GGCAAATTAC
57254137 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
57254169 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
57254200 AA
1 AA
57254202 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:57256961 original size:12 final size:11
Alignment explanation
Indices: 57256944--57257097 Score: 65
Period size: 12 Copynumber: 14.3 Consensus size: 11
57256934 GGTAGGCAAC
57256944 TTTTTTTTGCGT
1 TTTTTTTTGC-T
57256956 TTTTTTTTGCT
1 TTTTTTTTGCT
**
57256967 TTTTTTGCGCT
1 TTTTTTTTGCT
* *
57256978 TTTTACTCT-CT
1 TTTT-TTTTGCT
**
57256989 CTTTTTTGCGCTT
1 -TTTTTTTTGC-T
57257002 TTTTTTTTGCT
1 TTTTTTTTGCT
*
57257013 TTTTTTTGGC-
1 TTTTTTTTGCT
** *
57257023 -GCTTTTTACT
1 TTTTTTTTGCT
*
57257033 CTCTTTTTTGC-
1 -TTTTTTTTGCT
**
57257044 GCTTTTTTGC-
1 TTTTTTTTGCT
57257054 -TTTTTTTG-T
1 TTTTTTTTGCT
57257063 TTTTTTTTGC-
1 TTTTTTTTGCT
*
57257073 -TGTTTTTGCT
1 TTTTTTTTGCT
57257083 GTTTTTTTTGCT
1 -TTTTTTTTGCT
57257095 TTT
1 TTT
57257098 ATTTAAAGAA
Statistics
Matches: 107, Mismatches: 22, Indels: 27
0.69 0.14 0.17
Matches are distributed among these distances:
9 20 0.19
10 17 0.16
11 30 0.28
12 39 0.36
13 1 0.01
ACGTcount: A:0.01, C:0.14, G:0.13, T:0.71
Consensus pattern (11 bp):
TTTTTTTTGCT
Found at i:57257006 original size:13 final size:13
Alignment explanation
Indices: 57256990--57257029 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
57256980 TTACTCTCTC
57256990 TTTTTTGCGCTTT
1 TTTTTTGCGCTTT
*
57257003 TTTTTT-TGCTTT
1 TTTTTTGCGCTTT
*
57257015 TTTTTGGCGCTTT
1 TTTTTTGCGCTTT
57257028 TT
1 TT
57257030 ACTCTCTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.00, C:0.12, G:0.15, T:0.72
Consensus pattern (13 bp):
TTTTTTGCGCTTT
Found at i:57257010 original size:46 final size:46
Alignment explanation
Indices: 57256946--57257051 Score: 166
Period size: 46 Copynumber: 2.3 Consensus size: 46
57256936 TAGGCAACTT
57256946 TTTTTTGCG--TTTTTTTTTGC-TTTTTTT-GCGCTTTTTACTCTCTC
1 TTTTTTGCGCTTTTTTTTTTGCTTTTTTTTGGCGCTTTTTA--CTCTC
57256990 TTTTTTGCGCTTTTTTTTTTGCTTTTTTTTGGCGCTTTTTACTCTC
1 TTTTTTGCGCTTTTTTTTTTGCTTTTTTTTGGCGCTTTTTACTCTC
57257036 TTTTTTGCGCTTTTTT
1 TTTTTTGCGCTTTTTT
57257052 GCTTTTTTTG
Statistics
Matches: 58, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
44 9 0.16
46 32 0.55
47 7 0.12
48 10 0.17
ACGTcount: A:0.02, C:0.17, G:0.12, T:0.69
Consensus pattern (46 bp):
TTTTTTGCGCTTTTTTTTTTGCTTTTTTTTGGCGCTTTTTACTCTC
Found at i:57257015 original size:10 final size:10
Alignment explanation
Indices: 57257002--57257097 Score: 63
Period size: 10 Copynumber: 9.4 Consensus size: 10
57256992 TTTTGCGCTT
57257002 TTTTTTTTGC
1 TTTTTTTTGC
57257012 TTTTTTTTGGCGC
1 TTTTTTTT---GC
**
57257025 TTTTTACT-C
1 TTTTTTTTGC
*
57257034 TCTTTTTTGC
1 TTTTTTTTGC
**
57257044 GCTTTTTTGC
1 TTTTTTTTGC
*
57257054 -TTTTTTTGT
1 TTTTTTTTGC
57257063 TTTTTTTTGC
1 TTTTTTTTGC
*
57257073 -TGTTTTTGC
1 TTTTTTTTGC
57257082 TGTTTTTTTTGC
1 --TTTTTTTTGC
57257094 TTTT
1 TTTT
57257098 ATTTAAAGAA
Statistics
Matches: 67, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
9 21 0.31
10 30 0.45
12 8 0.12
13 8 0.12
ACGTcount: A:0.01, C:0.12, G:0.14, T:0.73
Consensus pattern (10 bp):
TTTTTTTTGC
Found at i:57257066 original size:48 final size:47
Alignment explanation
Indices: 57256955--57257067 Score: 149
Period size: 48 Copynumber: 2.3 Consensus size: 47
57256945 TTTTTTTGCG
*
57256955 TTTTTTTTTGCTTTTTTTGCGCTTTTTACTCTCTCTTTTTTGCGCTTTT
1 TTTTTTTTTG-TTTTTTGGCGCTTTTTAC-CTCTCTTTTTTGCGCTTTT
*
57257004 TTTTTTGCTT-TTTTTTGGCGCTTTTTA-CTCTCTTTTTTGCGCTTTT
1 TTTTTT-TTTGTTTTTTGGCGCTTTTTACCTCTCTTTTTTGCGCTTTT
57257050 TTGCTTTTTTTGTTTTTT
1 TT--TTTTTTTGTTTTTT
57257068 TTTGCTGTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
46 21 0.37
47 2 0.04
48 26 0.46
49 6 0.11
50 2 0.04
ACGTcount: A:0.02, C:0.16, G:0.12, T:0.71
Consensus pattern (47 bp):
TTTTTTTTTGTTTTTTGGCGCTTTTTACCTCTCTTTTTTGCGCTTTT
Found at i:57257697 original size:31 final size:32
Alignment explanation
Indices: 57257638--57257702 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
57257628 GGCAAATTAC
57257638 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
57257670 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
57257701 AA
1 AA
57257703 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:57259900 original size:22 final size:22
Alignment explanation
Indices: 57259870--57259941 Score: 85
Period size: 22 Copynumber: 3.3 Consensus size: 22
57259860 AGCTCAACCC
*
57259870 ATATTAAATATATATATTTAAT
1 ATATAAAATATATATATTTAAT
*
57259892 ATATAAAATATATATATTTGAT
1 ATATAAAATATATATATTTAAT
*
57259914 -TA-AAAGTAAATATATATTTAAT
1 ATATAAA--ATATATATATTTAAT
57259936 ATATAA
1 ATATAA
57259942 TTCGAGCTGG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
20 3 0.07
21 2 0.05
22 33 0.79
23 2 0.05
24 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (22 bp):
ATATAAAATATATATATTTAAT
Found at i:57260532 original size:2 final size:2
Alignment explanation
Indices: 57260525--57260553 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
57260515 CAAATGAGGA
57260525 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
57260554 AGAAAGCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:57261614 original size:15 final size:16
Alignment explanation
Indices: 57261594--57261644 Score: 50
Period size: 17 Copynumber: 3.2 Consensus size: 16
57261584 ACACTATAAA
57261594 ATATTTAT-TATTAAT
1 ATATTTATATATTAAT
*
57261609 ATATTTATAATTTTAAT
1 ATATTTAT-ATATTAAT
* * *
57261626 ATATTAAAACATTAAT
1 ATATTTATATATTAAT
57261642 ATA
1 ATA
57261645 AATATTTTCC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
15 8 0.28
16 9 0.31
17 12 0.41
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATTTATATATTAAT
Found at i:57261732 original size:7 final size:7
Alignment explanation
Indices: 57261675--57261718 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
57261665 GAATAATATT
*
57261675 ATTTGAA
1 ATTTAAA
57261682 ATTTAAA
1 ATTTAAA
57261689 ATTTAAA
1 ATTTAAA
**
57261696 A-TTATT
1 ATTTAAA
57261702 ATTTAAA
1 ATTTAAA
57261709 ATTTAAA
1 ATTTAAA
57261716 ATT
1 ATT
57261719 ATTATTTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
6 4 0.13
7 27 0.87
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (7 bp):
ATTTAAA
Found at i:57261739 original size:20 final size:20
Alignment explanation
Indices: 57261682--57261733 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
57261672 ATTATTTGAA
57261682 ATTTAAAATTTAAAATTATT
1 ATTTAAAATTTAAAATTATT
57261702 ATTTAAAATTTAAAATTATT
1 ATTTAAAATTTAAAATTATT
*
57261722 ATTTTAAATTTA
1 ATTTAAAATTTA
57261734 TTATTAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTTAAAATTTAAAATTATT
Found at i:57261747 original size:31 final size:30
Alignment explanation
Indices: 57261688--57261776 Score: 90
Period size: 31 Copynumber: 2.8 Consensus size: 30
57261678 TGAAATTTAA
*
57261688 AATTTAAAATTATTATTTAAAATTTAAAATTATT
1 AATTTTAAATTATTA-TTAAAA--TAAAATT-TT
57261722 -ATTTTAAATTTATTATTAAAATAAAATTTT
1 AATTTTAAA-TTATTATTAAAATAAAATTTT
* *
57261752 AATATTAAATAATTTATTAAAATAA
1 AATTTTAAATTA-TTATTAAAATAA
57261777 TAATATGTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
30 4 0.08
31 26 0.53
33 13 0.27
34 6 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
AATTTTAAATTATTATTAAAATAAAATTTT
Found at i:57277351 original size:6 final size:6
Alignment explanation
Indices: 57277340--57277366 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
57277330 TAGTTTAGGA
57277340 TCCGAC TCCGAC TCCGAC TCCGAC TCC
1 TCCGAC TCCGAC TCCGAC TCCGAC TCC
57277367 TAATCTGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.52, G:0.15, T:0.19
Consensus pattern (6 bp):
TCCGAC
Found at i:57279656 original size:32 final size:33
Alignment explanation
Indices: 57279587--57279659 Score: 105
Period size: 33 Copynumber: 2.3 Consensus size: 33
57279577 TCAAAAGAAC
* **
57279587 AAAT-TTTGTAAATGTTTTGTTAGTAGCTTTAG
1 AAATATTTGTAAATGATTCATTAGTAGCTTTAG
57279619 AAATATTTGTAAATGATTCATTAGTAGC-TTAG
1 AAATATTTGTAAATGATTCATTAGTAGCTTTAG
57279651 AAATATTTG
1 AAATATTTG
57279660 CCTTAATATT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 17 0.46
33 20 0.54
ACGTcount: A:0.34, C:0.04, G:0.16, T:0.45
Consensus pattern (33 bp):
AAATATTTGTAAATGATTCATTAGTAGCTTTAG
Found at i:57284471 original size:8 final size:8
Alignment explanation
Indices: 57284460--57284517 Score: 53
Period size: 9 Copynumber: 6.6 Consensus size: 8
57284450 AAAATCATAA
57284460 AAAAATAT
1 AAAAATAT
57284468 AAAAATTTAT
1 AAAAA--TAT
57284478 AAAAATAT
1 AAAAATAT
*
57284486 AAAAAATTT
1 -AAAAATAT
57284495 AAAATATAT
1 AAAA-ATAT
*
57284504 AGAAATAT
1 AAAAATAT
57284512 GAAAAA
1 -AAAAA
57284518 AAATTATAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
8 16 0.39
9 17 0.41
10 8 0.20
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (8 bp):
AAAAATAT
Found at i:57284471 original size:18 final size:18
Alignment explanation
Indices: 57284449--57284519 Score: 63
Period size: 18 Copynumber: 3.8 Consensus size: 18
57284439 AAAAATTAGG
57284449 AAAAATCATAAAAAAATAT
1 AAAAAT-ATAAAAAAATAT
* *
57284468 AAAAATTTATAAAAATAT
1 AAAAATATAAAAAAATAT
* *
57284486 AAAAA-ATTTAAAATATAT
1 AAAAATA-TAAAAAAATAT
*
57284504 AGAAATATGAAAAAAA
1 AAAAATAT-AAAAAAA
57284520 ATTATAAAAT
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
18 28 0.70
19 12 0.30
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.25
Consensus pattern (18 bp):
AAAAATATAAAAAAATAT
Found at i:57284528 original size:10 final size:10
Alignment explanation
Indices: 57284439--57284528 Score: 62
Period size: 10 Copynumber: 9.3 Consensus size: 10
57284429 TTAAAATATT
**
57284439 AAAAATTAGG
1 AAAAATTATA
*
57284449 AAAAATCATA
1 AAAAATTATA
*
57284459 AAAAAATATA
1 AAAAATTATA
*
57284469 AAAATTTAT-
1 AAAAATTATA
57284478 AAAAA-TATA
1 AAAAATTATA
57284487 AAAAATT-TA
1 AAAAATTATA
*
57284496 AAATA-TATA
1 AAAAATTATA
* * *
57284505 GAAATATGAAA
1 -AAAAATTATA
57284516 AAAAATTATA
1 AAAAATTATA
57284526 AAA
1 AAA
57284529 TTTTATAAAG
Statistics
Matches: 61, Mismatches: 14, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
8 4 0.07
9 17 0.28
10 38 0.62
11 2 0.03
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.26
Consensus pattern (10 bp):
AAAAATTATA
Found at i:57284795 original size:10 final size:10
Alignment explanation
Indices: 57284782--57284849 Score: 56
Period size: 9 Copynumber: 7.3 Consensus size: 10
57284772 TTTTGATGCA
57284782 TTTTATAATT
1 TTTTATAATT
*
57284792 TTTT-TTATT
1 TTTTATAATT
**
57284801 TTTTA-CGTT
1 TTTTATAATT
57284810 TTTTATAATT
1 TTTTATAATT
*
57284820 TTTAATAA-T
1 TTTTATAATT
*
57284829 TTTTA-ATTT
1 TTTTATAATT
57284838 TTTTAT-ATT
1 TTTTATAATT
57284847 TTT
1 TTT
57284850 ATTAAAATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 9
0.71 0.14 0.14
Matches are distributed among these distances:
8 1 0.02
9 31 0.69
10 13 0.29
ACGTcount: A:0.24, C:0.01, G:0.01, T:0.74
Consensus pattern (10 bp):
TTTTATAATT
Found at i:57284813 original size:28 final size:28
Alignment explanation
Indices: 57284782--57284850 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
57284772 TTTTGATGCA
** * *
57284782 TTTTATAATTTTTTTTATTTTTTACGTT
1 TTTTATAATTTTTAATAATTTTTAAGTT
*
57284810 TTTTATAATTTTTAATAATTTTTAATTT
1 TTTTATAATTTTTAATAATTTTTAAGTT
57284838 TTTTAT-ATTTTTA
1 TTTTATAATTTTTA
57284851 TTAAAATTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 7 0.19
28 29 0.81
ACGTcount: A:0.25, C:0.01, G:0.01, T:0.72
Consensus pattern (28 bp):
TTTTATAATTTTTAATAATTTTTAAGTT
Found at i:57284840 original size:37 final size:38
Alignment explanation
Indices: 57284781--57284867 Score: 92
Period size: 37 Copynumber: 2.3 Consensus size: 38
57284771 TTTTTGATGC
**
57284781 ATTTT-ATAATTTTTTTTATTTTTTACGT-TTTTTA-TAA
1 ATTTTAATAATTTTTAATATTTTTTA--TATTTTTATTAA
*
57284818 TTTTTAATAATTTTTAAT-TTTTTTATATTTTTATTAA
1 ATTTTAATAATTTTTAATATTTTTTATATTTTTATTAA
*
57284855 AATTTAATAATTT
1 ATTTTAATAATTT
57284868 ACCTAAAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
35 1 0.02
36 6 0.14
37 25 0.60
38 10 0.24
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.68
Consensus pattern (38 bp):
ATTTTAATAATTTTTAATATTTTTTATATTTTTATTAA
Found at i:57284860 original size:27 final size:28
Alignment explanation
Indices: 57284808--57284862 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
57284798 ATTTTTTACG
**
57284808 TTTTTTATAATTTTTAATAATTTTTAAT
1 TTTTTTATAATTTTTAATAAAATTTAAT
*
57284836 TTTTTTAT-ATTTTTATTAAAATTTAAT
1 TTTTTTATAATTTTTAATAAAATTTAAT
57284863 AATTTACCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (28 bp):
TTTTTTATAATTTTTAATAAAATTTAAT
Found at i:57285079 original size:90 final size:86
Alignment explanation
Indices: 57284919--57285107 Score: 200
Period size: 90 Copynumber: 2.2 Consensus size: 86
57284909 ATAAGAGCAG
* * * * **
57284919 GGGCTTAATTGCTTTTTTGAAGAATTTGAGAGTCTTTTTGATGCATTTTGAATGTTCAAGTACCC
1 GGGCTTAATTGCTTTTTTGAAAAATTTGAAAGCCTTTTTGATGCATTTTAAAAATTCAAGTACCC
*
57284984 AATTGAGTGCAACAAAAAAATAA
66 AATTGAGCGCAA-AAAAAAA-AA
* * * * *
57285007 GGGCTTAATTGATTTTTTTGAAAAAGTTTGAAAGCCTTTTTTATGTATTTTAAAAATTTAAGTGC
1 GGGCTTAATTG-CTTTTTTGAAAAA-TTTGAAAGCCTTTTTGATGCATTTTAAAAATTCAAGTAC
* *
57285072 TCGATTGAGCGCAAAAAAAAAAA
64 CCAATTGAGCGCAAAAAAAAAAA
*
57285095 -GACTTAATTGCTT
1 GGGCTTAATTGCTT
57285108 CTTCTTTTTT
Statistics
Matches: 83, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
86 2 0.02
87 9 0.11
88 13 0.16
89 18 0.22
90 41 0.49
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (86 bp):
GGGCTTAATTGCTTTTTTGAAAAATTTGAAAGCCTTTTTGATGCATTTTAAAAATTCAAGTACCC
AATTGAGCGCAAAAAAAAAAA
Found at i:57285186 original size:22 final size:22
Alignment explanation
Indices: 57285161--57285209 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
57285151 AATATATATT
57285161 ATAAATTAAAAATATAT-TTAAA
1 ATAAATT-AAAATATATGTTAAA
57285183 AT-AATTAAAATATATGTTAAA
1 ATAAATTAAAATATATGTTAAA
*
57285204 TTAAAT
1 ATAAAT
57285210 CGATTTTTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 9 0.38
21 10 0.42
22 5 0.21
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
ATAAATTAAAATATATGTTAAA
Found at i:57285192 original size:20 final size:22
Alignment explanation
Indices: 57285164--57285203 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
57285154 ATATATTATA
57285164 AATTAAAAATATAT-TTAAAAT
1 AATTAAAAATATATGTTAAAAT
57285185 AATT-AAAATATATGTTAAA
1 AATTAAAAATATATGTTAAA
57285204 TTAAATCGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (22 bp):
AATTAAAAATATATGTTAAAAT
Found at i:57285204 original size:20 final size:20
Alignment explanation
Indices: 57285151--57285204 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
57285141 CCTTAAGCCT
*
57285151 AATATATATTATA-AATTAAA
1 AATATAT-TTAAATAATTAAA
57285171 AATATATTTAAAATAATT-AA
1 AATATATTT-AAATAATTAAA
57285191 AATATATGTTAAAT
1 AATATAT-TTAAAT
57285205 TAAATCGATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.07
20 22 0.73
21 6 0.20
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
AATATATTTAAATAATTAAA
Found at i:57290316 original size:32 final size:33
Alignment explanation
Indices: 57290258--57290325 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 33
57290248 AAATTTCAAT
*
57290258 AAATAAAAAATATATACAATTATT-AAATATTA
1 AAATAAAAAATATATACAATTATTAAAAAATTA
* * *
57290290 AAATAAAATAA-ATATATATTTTTTAAAAAATTA
1 AAATAAAA-AATATATACAATTATTAAAAAATTA
57290323 AAA
1 AAA
57290326 ACTAATATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
32 18 0.60
33 12 0.40
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (33 bp):
AAATAAAAAATATATACAATTATTAAAAAATTA
Found at i:57291196 original size:20 final size:21
Alignment explanation
Indices: 57291161--57291201 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
57291151 ACTCAATTGG
*
57291161 AACATAAATTGACATT-TTCA
1 AACATAAATGGACATTATTCA
*
57291181 AACATAAATGGCCATTATTCA
1 AACATAAATGGACATTATTCA
57291202 TTTAAATCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.32
Consensus pattern (21 bp):
AACATAAATGGACATTATTCA
Found at i:57292086 original size:24 final size:25
Alignment explanation
Indices: 57292036--57292087 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
57292026 TCTTTTTGAA
**
57292036 TTTTTAGAAAACTTTTTATGTTTAT
1 TTTTTAGAAAACTTTTTATGTGCAT
57292061 TTTTTA-AAAA-TTTTTGATGTGCAT
1 TTTTTAGAAAACTTTTT-ATGTGCAT
57292085 TTT
1 TTT
57292088 CCATTGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 5 0.21
24 13 0.54
25 6 0.25
ACGTcount: A:0.27, C:0.04, G:0.10, T:0.60
Consensus pattern (25 bp):
TTTTTAGAAAACTTTTTATGTGCAT
Found at i:57303072 original size:13 final size:13
Alignment explanation
Indices: 57303024--57303073 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
57303014 CTTAATGGAG
*
57303024 TAAAATGTTTTAAA
1 TAAAAT-TTTTTAA
**
57303038 TAAAATAATTTAA
1 TAAAATTTTTTAA
*
57303051 TAAATTTTTTTAA
1 TAAAATTTTTTAA
57303064 TAAAATTTTT
1 TAAAATTTTT
57303074 AACTATCTGT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
13 23 0.79
14 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (13 bp):
TAAAATTTTTTAA
Found at i:57303767 original size:13 final size:13
Alignment explanation
Indices: 57303719--57303768 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
57303709 CTTAATGGAG
*
57303719 TAAAATGTTTTAAA
1 TAAAAT-TTTTTAA
**
57303733 TAAAATAATTTAA
1 TAAAATTTTTTAA
*
57303746 TAAATTTTTTTAA
1 TAAAATTTTTTAA
57303759 TAAAATTTTT
1 TAAAATTTTT
57303769 AACTATCTGT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
13 23 0.79
14 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (13 bp):
TAAAATTTTTTAA
Found at i:57314305 original size:44 final size:44
Alignment explanation
Indices: 57314257--57314596 Score: 174
Period size: 44 Copynumber: 7.7 Consensus size: 44
57314247 AGCCACCAGC
* *
57314257 CTTAT-TTCCCTGAGGTAGCAAAGGAGTAGGCTGAAGATTGTAGT
1 CTTATCTT-CCTGAGGTAGCAAAGGAGCAGGCTGAAGATTGAAGT
** *
57314301 CTTATCTTTTTGAGGTAGC-AAGGAGGCAGACTGAAGATTGAAGAT
1 CTTATCTTCCTGAGGTAGCAAAGGA-GCAGGCTGAAGATTGAAG-T
* ** * * * *
57314346 CTTATC-TCTCTGAGATAGCAGTGGAGTA-GATCGAATA-TGACAAAT
1 CTTATCTTC-CTGAGGTAGCAAAGGAGCAGGCT-GAAGATTG--AAGT
* * ** ** ***** *
57314391 CTTATCTTCCCGAGGTAGCAGAGGAGCAGATTTTAGCCACCAGC
1 CTTATCTTCCTGAGGTAGCAAAGGAGCAGGCTGAAGATTGAAGT
* * * *
57314435 CTTAT-TTCCCTGAGGTAGCAAGGGAGTAGGCTAAAGATTGCAGT
1 CTTATCTT-CCTGAGGTAGCAAAGGAGCAGGCTGAAGATTGAAGT
* * *
57314479 CTTATCTTTCTGAGGTAGCAAAGGAACAGACTGAAGATTGAAGAT
1 CTTATCTTCCTGAGGTAGCAAAGGAGCAGGCTGAAGATTGAAG-T
* * * * * * *
57314524 CTTGTATTCCTGAAGCAGCATA-GAGCAGGCTGAGGATTGTAGAT
1 CTTATCTTCCTGAGGTAGCAAAGGAGCAGGCTGAAGATTGAAG-T
*
57314568 CTTATCTTCATGAGGTAGCAATA-GAGCAG
1 CTTATCTTCCTGAGGTAGCAA-AGGAGCAG
57314597 ATCGAAGATG
Statistics
Matches: 215, Mismatches: 66, Indels: 29
0.69 0.21 0.09
Matches are distributed among these distances:
43 7 0.03
44 128 0.60
45 72 0.33
46 8 0.04
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (44 bp):
CTTATCTTCCTGAGGTAGCAAAGGAGCAGGCTGAAGATTGAAGT
Found at i:57314372 original size:89 final size:86
Alignment explanation
Indices: 57314265--57314605 Score: 210
Period size: 89 Copynumber: 3.8 Consensus size: 86
57314255 GCCTTATTTC
* ** **
57314265 CCTGAGGTAGCAAAGGAGTAGGCTGAAGATTGTAGTCTTATCTTTTTGAGGTAGCAAGGAGGCAG
1 CCTGAGATAGCAGTGGAGTAGGCTGAAGATTGTAGTCTTATCTTCCTGAGGTAGCAAGGA-GCAG
57314330 ACTGAAGATTGAAGATCTTATCT
65 ACTGAAGATTGAAGATCTTAT-T
* * * * *
57314353 CTCTGAGATAGCAGTGGAGTA-GATCGAATA-TGACAAATCTTATCTTCCCGAGGTAGCAGAGGA
1 C-CTGAGATAGCAGTGGAGTAGGCT-GAAGATTG--TAGTCTTATCTTCCTGAGGTAGCA-AGGA
* ** ***** *
57314416 GCAGATTTTAGCCACCAG-CCTTATTT
61 GCAGACTGAAGATTGAAGATCTTA-TT
* * * * *
57314442 CCCTGAGGTAGCAAG-GGAGTAGGCTAAAGATTGCAGTCTTATCTTTCTGAGGTAGCAAAGGAAC
1 -CCTGAGATAGC-AGTGGAGTAGGCTGAAGATTGTAGTCTTATCTTCCTGAGGTAGC-AAGGAGC
57314506 AGACTGAAGATTGAAGATCTTGTATT
63 AGACTGAAGATTGAAGATC-T-TATT
* * * * * *
57314532 CCTGA-AGCAGCA-TAGAGCAGGCTGAGGATTGTAGATCTTATCTTCATGAGGTAGCAATAGAGC
1 CCTGAGA-TAGCAGTGGAGTAGGCTGAAGATTGTAG-TCTTATCTTCCTGAGGTAGCAA-GGAGC
57314595 AGA-TCGAAGAT
63 AGACT-GAAGAT
57314606 GGCGAATCTT
Statistics
Matches: 186, Mismatches: 48, Indels: 37
0.69 0.18 0.14
Matches are distributed among these distances:
88 57 0.31
89 83 0.45
90 40 0.22
91 6 0.03
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.26
Consensus pattern (86 bp):
CCTGAGATAGCAGTGGAGTAGGCTGAAGATTGTAGTCTTATCTTCCTGAGGTAGCAAGGAGCAGA
CTGAAGATTGAAGATCTTATT
Found at i:57314682 original size:44 final size:43
Alignment explanation
Indices: 57314634--57315089 Score: 164
Period size: 44 Copynumber: 10.3 Consensus size: 43
57314624 AAGGTAGCAA
*
57314634 TGGAGCAGATTTAAGCCACCAGCCTTATCTCCCTGAAGTTGCAG
1 TGGAGCAGATTGAAG-CACCAGCCTTATCTCCCTGAAGTTGCAG
* * ** * * *
57314678 TGGAGCAGGTCGAAATTACAAACCTTATCTCCCTG-AGTTGCAT
1 TGGAGCAGATTG-AAGCACCAGCCTTATCTCCCTGAAGTTGCAG
* * * * ** * *
57314721 TGGAGTAGACTGAAGATAGCAAATCTTATTTCCCTGAAGATGCAG
1 TGGAGCAGATTGAAG-CA-CCAGCCTTATCTCCCTGAAGTTGCAG
* * * *
57314766 TGGAACAGATTGAAGCTATAAATAAACAGATCTTATCTCTCTGAA-TTGCAG
1 TGGAGCAGATTGAAGC--------ACCAG-CCTTATCTCCCTGAAGTTGCAG
* * * *
57314817 TAGAGCAGA-TCATAGCA--AACTTTATCTCCCTGAAGTTGCAG
1 TGGAGCAGATTGA-AGCACCAGCCTTATCTCCCTGAAGTTGCAG
* * * * * * *
57314858 TGGAGCAGGTTGAAGTAACAGGTCTTATCTCCTTGAGGTAGCAG
1 TGGAGCAGATTGAAGCACCA-GCCTTATCTCCCTGAAGTTGCAG
* * *
57314902 -GGAAGAAGATTTAAGCCACCAGCCTTATCT-CCTGAA-TTACAG
1 TGG-AGCAGATTGAAG-CACCAGCCTTATCTCCCTGAAGTTGCAG
** * * *
57314944 TGGAGCA-AGTTGACATTACCAATCCTTATCTCCCTAAAGTTGTAG
1 TGGAGCAGA-TTGA-AGCACC-AGCCTTATCTCCCTGAAGTTGCAG
* * * * *
57314989 TGGAGCAAGAAAAT-AA-AACGAGTCTTATCT-CCTGAAGTTGTAG
1 TGGAGC-AG--ATTGAAGCACCAGCCTTATCTCCCTGAAGTTGCAG
* * *
57315032 TGGAGCA-AGTTGAAGTCACGAACCTTATCTCCCTGAAGTTGTAG
1 TGGAGCAGA-TTGAAG-CACCAGCCTTATCTCCCTGAAGTTGCAG
*
57315076 TGGAGCAGGTTGAA
1 TGGAGCAGATTGAA
57315090 ATTATCAATT
Statistics
Matches: 302, Mismatches: 73, Indels: 74
0.67 0.16 0.16
Matches are distributed among these distances:
39 1 0.00
40 13 0.04
41 20 0.07
42 18 0.06
43 66 0.22
44 112 0.37
45 35 0.12
46 2 0.01
47 1 0.00
48 1 0.00
49 1 0.00
50 2 0.01
51 16 0.05
52 14 0.05
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.27
Consensus pattern (43 bp):
TGGAGCAGATTGAAGCACCAGCCTTATCTCCCTGAAGTTGCAG
Found at i:57315059 original size:43 final size:43
Alignment explanation
Indices: 57314924--57315089 Score: 160
Period size: 43 Copynumber: 3.8 Consensus size: 43
57314914 AAGCCACCAG
** * *
57314924 CCTTATCT-CCTGAA-TTACAGTGGAGCAAGTTGACATTACCAA
1 CCTTATCTCCCTGAAGTTGTAGTGGAGCAAGTTGA-ATAACGAA
* ** *
57314966 TCCTTATCTCCCTAAAGTTGTAGTGGAGCAAG-AAAATAAAACGAG
1 -CCTTATCTCCCTGAAGTTGTAGTGGAGCAAGTTGAAT--AACGAA
* *
57315011 TCTTATCT-CCTGAAGTTGTAGTGGAGCAAGTTGAAGTCACGAA
1 CCTTATCTCCCTGAAGTTGTAGTGGAGCAAGTTGAA-TAACGAA
*
57315054 CCTTATCTCCCTGAAGTTGTAGTGGAGCAGGTTGAA
1 CCTTATCTCCCTGAAGTTGTAGTGGAGCAAGTTGAA
57315090 ATTATCAATT
Statistics
Matches: 100, Mismatches: 16, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
43 42 0.42
44 41 0.41
45 17 0.17
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (43 bp):
CCTTATCTCCCTGAAGTTGTAGTGGAGCAAGTTGAATAACGAA
Found at i:57315555 original size:19 final size:19
Alignment explanation
Indices: 57315531--57315585 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
57315521 AGGAAGATAA
* * *
57315531 TTATTTGTTTTTGTTTTAT
1 TTATTTATTTTTATTTCAT
57315550 TTATTTATTTTTATTTCAT
1 TTATTTATTTTTATTTCAT
*
57315569 TTCATTTATTTTAATTT
1 TT-ATTTATTTTTATTT
57315586 ATTAAATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.58
20 13 0.42
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.75
Consensus pattern (19 bp):
TTATTTATTTTTATTTCAT
Found at i:57316146 original size:14 final size:13
Alignment explanation
Indices: 57316106--57316202 Score: 74
Period size: 14 Copynumber: 7.1 Consensus size: 13
57316096 TTATTATGTT
57316106 TCTATTTTATTCTAA
1 TCTATTTTATT-T-A
57316121 TACTATTATTATTTA
1 T-CTATT-TTATTTA
57316136 TCTAATTTTATTTA
1 TCT-ATTTTATTTA
*
57316150 TCTATTTATATTTC
1 TCTATTT-TATTTA
57316164 TACTA-TTTATATT-
1 T-CTATTTTAT-TTA
*
57316177 TCTATTTTATAT-
1 TCTATTTTATTTA
*
57316189 TCTATTGTATTTA
1 TCTATTTTATTTA
57316202 T
1 T
57316203 ATACTAATAT
Statistics
Matches: 70, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
12 14 0.20
13 14 0.20
14 22 0.31
15 9 0.13
16 6 0.09
17 5 0.07
ACGTcount: A:0.27, C:0.09, G:0.01, T:0.63
Consensus pattern (13 bp):
TCTATTTTATTTA
Found at i:57316171 original size:15 final size:15
Alignment explanation
Indices: 57316151--57316189 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
57316141 TTTTATTTAT
57316151 CTATTTATATTTCTA
1 CTATTTATATTTCTA
57316166 CTATTTATATTTCTA
1 CTATTTATATTTCTA
57316181 -T-TTTATATT
1 CTATTTATATT
57316190 CTATTGTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 8 0.33
14 1 0.04
15 15 0.62
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (15 bp):
CTATTTATATTTCTA
Found at i:57316208 original size:40 final size:39
Alignment explanation
Indices: 57316105--57316224 Score: 104
Period size: 40 Copynumber: 2.9 Consensus size: 39
57316095 ATTATTATGT
*
57316105 TTCTATTTTATTCTA-ATACTATTATTATTTATCTAATTTTATT
1 TTCTA-TTTATT-TATATACTATTATTA-TT-TCT-ATTTTATA
*
57316148 TATCTATTTATATT-TCTACTATT-TATATTTCTATTTTATA
1 T-TCTATTTAT-TTATATACTATTAT-TATTTCTATTTTATA
*
57316188 TTCTATTGTATTTATATACTAATATTATTTC-ATTTTA
1 TTCTATT-TATTTATATACTATTATTATTTCTATTTTA
57316225 GTTTCTTATA
Statistics
Matches: 66, Mismatches: 4, Indels: 18
0.75 0.05 0.20
Matches are distributed among these distances:
39 14 0.21
40 24 0.36
41 4 0.06
42 3 0.05
43 16 0.24
44 5 0.08
ACGTcount: A:0.28, C:0.09, G:0.01, T:0.62
Consensus pattern (39 bp):
TTCTATTTATTTATATACTATTATTATTTCTATTTTATA
Found at i:57316339 original size:3 final size:3
Alignment explanation
Indices: 57316331--57316482 Score: 145
Period size: 3 Copynumber: 51.0 Consensus size: 3
57316321 ACTATTATAC
57316331 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT
* * *
57316377 ATAT ATAT GTAT CAA TAT CAT TAT T-T TAT T-T TAT T-T TAT TAT ATAT
1 -TAT -TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
* * * *
57316423 TAT TAT TAT CAT TAT TAT TA- TAC TAT TAG TAC TAT TAT TAT T-T T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
57316468 TAT TAT TAT TTT TAT
1 TAT TAT TAT TAT TAT
57316483 ATTTATTTAT
Statistics
Matches: 126, Mismatches: 15, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
2 12 0.10
3 98 0.78
4 16 0.13
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:57316464 original size:58 final size:59
Alignment explanation
Indices: 57316323--57316476 Score: 187
Period size: 58 Copynumber: 2.6 Consensus size: 59
57316313 GATTTAAAAC
*
57316323 TATTATACTATTAT-TATTATTATTATTATTATTATTATATATTATTATTATTATATATA
1 TATTATACTATTATATATTATTATT-TTATTATTATTATATATTATTATTATCATATATA
* *
57316382 TATGTATCAATATCAT-TATT-TTATTTTATT-TTATTATATATTATTATTATCAT-TAT-
1 TAT-TAT-ACTATTATATATTATTATTTTATTATTATTATATATTATTATTATCATATATA
57316438 TATTATACTATTAGTACTATTATTATTTT-TTATTATTAT
1 TATTATACTATTA-TA-TATTATTATTTTATTATTATTAT
57316477 TTTTATATTT
Statistics
Matches: 83, Mismatches: 5, Indels: 15
0.81 0.05 0.15
Matches are distributed among these distances:
54 5 0.06
55 4 0.05
56 3 0.04
57 9 0.11
58 36 0.43
59 8 0.10
60 8 0.10
61 10 0.12
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.61
Consensus pattern (59 bp):
TATTATACTATTATATATTATTATTTTATTATTATTATATATTATTATTATCATATATA
Found at i:57317917 original size:35 final size:34
Alignment explanation
Indices: 57317878--57317961 Score: 143
Period size: 35 Copynumber: 2.5 Consensus size: 34
57317868 AGCCCTCCAA
*
57317878 AAAAAACCTAACCCCCCCACCCCCCCCAAAAAAAG
1 AAAAAACCTAACCCCCCC-CCCCCCCAAAAAAAAG
57317913 AAAAAACCTAACCCCCCCCCCCCCCAAAAAAAAG
1 AAAAAACCTAACCCCCCCCCCCCCCAAAAAAAAG
57317947 -AAAAACCTAACCCCC
1 AAAAAACCTAACCCCC
57317962 AAAAAAAAAC
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
33 15 0.31
34 15 0.31
35 18 0.38
ACGTcount: A:0.46, C:0.48, G:0.02, T:0.04
Consensus pattern (34 bp):
AAAAAACCTAACCCCCCCCCCCCCCAAAAAAAAG
Found at i:57317934 original size:33 final size:33
Alignment explanation
Indices: 57317876--57317961 Score: 138
Period size: 33 Copynumber: 2.5 Consensus size: 33
57317866 TAAGCCCTCC
57317876 AAAAAAAACCTAACCCCCCCACCCCCCCCAAAAA
1 AAAAAAAACCTAA-CCCCCCACCCCCCCCAAAAA
57317910 AAGAAAAAACCTAACCCCCC-CCCCCCCCAAAAA
1 AA-AAAAAACCTAACCCCCCACCCCCCCCAAAAA
57317943 AAAGAAAAACCTAACCCCC
1 AAA-AAAAACCTAACCCCC
57317962 AAAAAAAAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
32 1 0.02
33 30 0.60
34 8 0.16
35 11 0.22
ACGTcount: A:0.48, C:0.47, G:0.02, T:0.03
Consensus pattern (33 bp):
AAAAAAAACCTAACCCCCCACCCCCCCCAAAAA
Found at i:57318213 original size:15 final size:14
Alignment explanation
Indices: 57318186--57318219 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
57318176 CTAAAGGTGA
57318186 TTTATCTTCTTTAT
1 TTTATCTTCTTTAT
*
57318200 TTTACTCTTTTTTAT
1 TTTA-TCTTCTTTAT
57318215 TTTAT
1 TTTAT
57318220 TTTTATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATCTTCTTTAT
Found at i:57331082 original size:74 final size:74
Alignment explanation
Indices: 57330980--57331616 Score: 907
Period size: 72 Copynumber: 8.7 Consensus size: 74
57330970 TGATGTTTTT
* *
57330980 ATTTCTG-TTTCAAAAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGAACACGCTG
1 ATTTCTGTTTTC--AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
57331044 AGGTAATTTCA
64 AGGTAATTTCA
* * *
57331055 ATTTCTGTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGAGACGCTGAG
1 ATTTCTGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
57331120 GTAATTTCA
66 GTAATTTCA
* *
57331129 ATTTCTGTTTT--AAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGACACGCTGAG
1 ATTTCTGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
57331192 GTAATTTCA
66 GTAATTTCA
* * ** * *
57331201 ATTTCTGTTTTC--AAAATTCAACTCCTATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
1 ATTTCTGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
* *
57331264 GTATTTTTA
66 GTAATTTCA
* *
57331273 ATTTTTGTCTTTCAAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
1 ATTTCTGT-TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
57331338 GGTAATTTCA
65 GGTAATTTCA
**
57331348 ATTTCTGTTGTT-AAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGA
1 ATTTCTGTT-TTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
57331412 GGTAATTTCA
65 GGTAATTTCA
* ** * *
57331422 ATTTCTGTTTTC--AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAG
1 ATTTCTGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
*
57331485 GTATTTTCA
66 GTAATTTCA
* *
57331494 ATTTTTTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTG
1 A-TTTCTG-TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
57331559 AGGTAATTTCA
64 AGGTAATTTCA
57331570 ATTTCTGTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 ATTTCTGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
57331617 TTCAAATCAC
Statistics
Matches: 506, Mismatches: 45, Indels: 25
0.88 0.08 0.04
Matches are distributed among these distances:
72 219 0.43
73 11 0.02
74 147 0.29
75 72 0.14
76 57 0.11
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (74 bp):
ATTTCTGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
GTAATTTCA
Found at i:57332513 original size:26 final size:25
Alignment explanation
Indices: 57332473--57332546 Score: 123
Period size: 25 Copynumber: 3.0 Consensus size: 25
57332463 AGCCCTCCAA
57332473 AAAAAACCTAACCCCCAAAAAAAAG
1 AAAAAACCTAACCCCCAAAAAAAAG
57332498 AAAAAACCTAACCCCCCAAAAAAAAG
1 AAAAAACCTAA-CCCCCAAAAAAAAG
*
57332524 -AAAAACCTAACCCCAAAAAAAAA
1 AAAAAACCTAACCCCCAAAAAAAA
57332547 CCAAGAAACT
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
24 12 0.26
25 21 0.45
26 14 0.30
ACGTcount: A:0.65, C:0.28, G:0.03, T:0.04
Consensus pattern (25 bp):
AAAAAACCTAACCCCCAAAAAAAAG
Found at i:57332779 original size:14 final size:13
Alignment explanation
Indices: 57332760--57332806 Score: 51
Period size: 15 Copynumber: 3.4 Consensus size: 13
57332750 CCTAAAGGTG
57332760 ATTTTATCTTCTTT
1 ATTTTATCTT-TTT
57332774 ATTTTACTCTTTTTT
1 ATTTTA-TC-TTTTT
57332789 ATTTTTAT-TTTTT
1 A-TTTTATCTTTTT
57332802 ATTTT
1 ATTTT
57332807 TTTCCTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
12 4 0.13
13 6 0.20
14 6 0.20
15 7 0.23
16 7 0.23
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.77
Consensus pattern (13 bp):
ATTTTATCTTTTT
Found at i:57332789 original size:15 final size:14
Alignment explanation
Indices: 57332760--57332806 Score: 60
Period size: 13 Copynumber: 3.4 Consensus size: 14
57332750 CCTAAAGGTG
*
57332760 ATTTTATCTTCTTT
1 ATTTTATCTTTTTT
57332774 ATTTTACTCTTTTTT
1 ATTTTA-TCTTTTTT
*
57332789 ATTTT-TATTTTTT
1 ATTTTATCTTTTTT
57332802 ATTTT
1 ATTTT
57332807 TTTCCTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
13 12 0.40
14 6 0.20
15 12 0.40
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.77
Consensus pattern (14 bp):
ATTTTATCTTTTTT
Found at i:57332815 original size:28 final size:30
Alignment explanation
Indices: 57332761--57332816 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 30
57332751 CTAAAGGTGA
*
57332761 TTTTATCTTCTTTATTTTACTCTTTTTTAT
1 TTTTATCTTCTTTATTTTACTCCTTTTTAT
**
57332791 TTTTAT-TT-TTTATTTTTTTCCTTTTT
1 TTTTATCTTCTTTATTTTACTCCTTTTT
57332817 TTGAATCTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 15 0.65
29 2 0.09
30 6 0.26
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (30 bp):
TTTTATCTTCTTTATTTTACTCCTTTTTAT
Done.