Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009462.1 Hibiscus syriacus cultivar Beakdansim tig00113725_pilon, whole genome shotgun sequence
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: 20687664
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 91
Found at i:3570880 original size:2 final size:2
Alignment explanation
Indices: 3570864--3570943 Score: 123
Period size: 2 Copynumber: 42.0 Consensus size: 2
3570854 TTCAAAAATC
3570864 AT AT AT -T AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3570904 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT A- AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3570944 TTATTTTCAA
Statistics
Matches: 72, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
1 4 0.06
2 68 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3570964 original size:42 final size:43
Alignment explanation
Indices: 3570918--3571015 Score: 110
Period size: 42 Copynumber: 2.3 Consensus size: 43
3570908 ATATATATAT
** * *
3570918 ATATATATATATATTTAATTATATATTTATTTT-CAAACTACA
1 ATATATATATATATTTAAAAATATATTTATTTTGAAAAATACA
* * **
3570960 ATATATATGTGT-TTTAAAAATATATTTATTTTGAAAAATATT
1 ATATATATATATATTTAAAAATATATTTATTTTGAAAAATACA
3571002 ATATATATATATAT
1 ATATATATATATAT
3571016 ATATTCCAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
41 18 0.41
42 25 0.57
43 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (43 bp):
ATATATATATATATTTAAAAATATATTTATTTTGAAAAATACA
Found at i:3570983 original size:19 final size:19
Alignment explanation
Indices: 3570959--3571005 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
3570949 TTCAAACTAC
*
3570959 AATATATATGTGTTTT-AAA
1 AATATATAT-TATTTTGAAA
3570978 AATATAT-TTATTTTGAAA
1 AATATATATTATTTTGAAA
3570996 AATATTATAT
1 AATA-TATAT
3571006 ATATATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 5 0.21
18 8 0.33
19 10 0.42
20 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (19 bp):
AATATATATTATTTTGAAA
Found at i:3570984 original size:17 final size:18
Alignment explanation
Indices: 3570962--3571000 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
3570952 AAACTACAAT
*
3570962 ATATATGTGTTTT-AAAA
1 ATATATGTATTTTGAAAA
*
3570979 ATATATTTATTTTGAAAA
1 ATATATGTATTTTGAAAA
3570997 ATAT
1 ATAT
3571001 TATATATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (18 bp):
ATATATGTATTTTGAAAA
Found at i:3571077 original size:67 final size:67
Alignment explanation
Indices: 3570997--3571129 Score: 178
Period size: 68 Copynumber: 2.0 Consensus size: 67
3570987 ATTTTGAAAA
* * *
3570997 ATATTATATATATATATATATATTCCAAAATTATTTGC-AAACTCTATTATATATATAATTTTCA
1 ATATTATATATATATATAT-TATTCC-AAATTATTTGCAAAACTATACTATATATAT-ATTTACA
3571061 AAACT
63 AAACT
* * *
3571066 ATATTATATATATATTTATTTTTCCAAATTATTTTCAAAACTATACTATATATATATTTACAAA
1 ATATTATATATATATATATTATTCCAAATTATTTGCAAAACTATACTATATATATATTTACAAA
3571130 TTATTAAATA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
67 18 0.32
68 21 0.37
69 18 0.32
ACGTcount: A:0.43, C:0.10, G:0.01, T:0.47
Consensus pattern (67 bp):
ATATTATATATATATATATTATTCCAAATTATTTGCAAAACTATACTATATATATATTTACAAAA
CT
Found at i:3571661 original size:88 final size:88
Alignment explanation
Indices: 3571569--3571909 Score: 434
Period size: 88 Copynumber: 3.9 Consensus size: 88
3571559 AAGACGGGTC
* * * * **
3571569 TGCTCTACTACACTTTAGGGAAGATCACACTCGAGGTTGATTTGCTTCATTGCTCATCAGGAAGA
1 TGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGGTTGATTTGCTTCGCTGCTCATCAGGAAGA
* *
3571634 CCAAATTTGAAAGAAGAAGAATC
66 CCAAATTTGAAAAAAGAAGAATA
* * * ** *
3571657 TGCTCCACTACTCTTTAGGGGAGATCAGATTCGAGGTTGATTTTCTTTG-TTTTCATTCAGTAAG
1 TGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGGTTGATTTGCTTCGCTGCTCA-TCAGGAAG
*
3571721 ACTAAATCTT-AAAAAAGAAGAATA
65 ACCAAAT-TTGAAAAAAGAAGAATA
* * *
3571745 TACTCCACTACTCTTTAGAGGAGATCAGACTCGAGGTTGATTTGCTTCGCTGCTCTTCAGGAAGA
1 TGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGGTTGATTTGCTTCGCTGCTCATCAGGAAGA
*
3571810 CCAAATCTGAAAAAAGAAGAATA
66 CCAAATTTGAAAAAAGAAGAATA
* * * *
3571833 TGCTTCACTATTCTTTAGGGGAGATCAAACTCGAGGTTGATTTGCTTCGCTGCTCTTCAGGAAGA
1 TGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGGTTGATTTGCTTCGCTGCTCATCAGGAAGA
*
3571898 CCAAATATGAAA
66 CCAAATTTGAAA
3571910 GATTGACTTC
Statistics
Matches: 218, Mismatches: 31, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
87 5 0.02
88 208 0.95
89 5 0.02
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Consensus pattern (88 bp):
TGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGGTTGATTTGCTTCGCTGCTCATCAGGAAGA
CCAAATTTGAAAAAAGAAGAATA
Found at i:3571943 original size:29 final size:29
Alignment explanation
Indices: 3571910--3571966 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
3571900 AAATATGAAA
* *
3571910 GATTGACTTCTCTTCACGAGGAAGTCAAG
1 GATTGACTCCTCTTCACAAGGAAGTCAAG
*
3571939 GATTGACTCCTCTTTACAAGGAAGTCAA
1 GATTGACTCCTCTTCACAAGGAAGTCAA
3571967 TAATAATAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (29 bp):
GATTGACTCCTCTTCACAAGGAAGTCAAG
Found at i:3571983 original size:67 final size:66
Alignment explanation
Indices: 3571907--3572541 Score: 562
Period size: 67 Copynumber: 9.5 Consensus size: 66
3571897 ACCAAATATG
* **
3571907 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTTACAAGGAAGTCAATAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTT-CAAGGGAGTCAGGAATA
*
3571972 AT
65 AC
* * * * * *
3571974 AAGGATTGACTTCTCTTCACGAGAAAGTTAAGGATTAACTACT-TTTCGTAAGGGAGTCAAGAAT
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTTC--AAGGGAGTCAGGAAT
*
3572038 AAA
64 AAC
* * * **
3572041 AAAGATTGACTTCTTTTTACGAGGAAGTCAAGGATTGACTCCTC-TTCGAGAGGAAGTTGGGAAT
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTTC-A-AGGGAGTCAGGAAT
3572105 AAC
64 AAC
* ** ** * *
3572108 AAAGATAGACTTCTCTTCACGAATAAGTCAAGGATTGACTCCTCTACGCGAGGGAGTCAGGAAAA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCT-TTCAAGGGAGTCAGGAATA
3572173 AC
65 AC
* * * * * *
3572175 AAAGATTGACTTCTTTTTACAAGAAAGTCAAGGATTGACTCCTC-TTCGTGAGGGAGTTAGGAAT
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTTC--AAGGGAGTCAGGAAT
*
3572239 AAA
64 AAC
* * * * *
3572242 AAAGATTGAATTCTCTTCACGAGGAAATCAATGATTGACACCTCTTCTTGAA-GGAGTCAGGAAT
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTC-T-TTCAAGGGAGTCAGGAAT
3572306 AAC
64 AAC
* * * * * * *
3572309 AAAGATTGAATTCTTTTTACGAGAAAGTCAAGGATTGACTCCTC-TTCACGAGGGATTTATGAAT
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTTCA--AGGGAGTCAGGAAT
3572373 AAC
64 AAC
* * * *
3572376 AAAGATTGACTTCTCTTCATGAGGAAATCAAGGATTGACTCATCTTCGTGAA-GGAGTCAGGAAT
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTT--TCAAGGGAGTCAGGAAT
*
3572440 ATC
64 AAC
* * * * * * * * * **
3572443 AAAGTTTGATTTCTCTTCATGAAGAAATCAATGATTGACACCTCTTCGCAAGAGAGTCAATAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTT-TCAAGGGAGTCAGGAATA
3572508 AC
65 AC
*
3572510 AAAGATTGACTTCTCTTCATGAGGAAGTCAAG
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAG
3572542 TTAAAGCTTC
Statistics
Matches: 454, Mismatches: 96, Indels: 36
0.77 0.16 0.06
Matches are distributed among these distances:
64 3 0.01
65 2 0.00
66 7 0.02
67 434 0.96
68 3 0.01
69 1 0.00
70 4 0.01
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (66 bp):
AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTTCAAGGGAGTCAGGAATAA
C
Found at i:3572162 original size:134 final size:134
Alignment explanation
Indices: 3571907--3572528 Score: 648
Period size: 134 Copynumber: 4.6 Consensus size: 134
3571897 ACCAAATATG
* * * **
3571907 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTTAC-A-AGGAAGTCAATAA
1 AAAGATTGACTTCTTTTTACGAGGAAGTCAAGGATTGACTCCTC-TT-CGAGAGGAAGTTAGGAA
* * * * * *
3571970 TAATAAGGATTGACTTCTCTTCACG-AGAAAGTTAAGGATTAACTACTTTTCGT-AAGGGAGTCA
64 TAACAAAGATTGACTTCTCTTCACGAAGAAA-TCAAGGATTGACTCCTCTTCGTGAA-GGAGTCA
*
3572033 AGAATAAA
127 GGAATAAA
*
3572041 AAAGATTGACTTCTTTTTACGAGGAAGTCAAGGATTGACTCCTCTTCGAGAGGAAGTTGGGAATA
1 AAAGATTGACTTCTTTTTACGAGGAAGTCAAGGATTGACTCCTCTTCGAGAGGAAGTTAGGAATA
* * * * * *
3572106 ACAAAGATAGACTTCTCTTCACGAATAAGTCAAGGATTGACTCCTCTACGCGAGGGAGTCAGGAA
66 ACAAAGATTGACTTCTCTTCACGAAGAAATCAAGGATTGACTCCTCTTCGTGAAGGAGTCAGGAA
3572171 -AAA
131 TAAA
* * * *
3572174 CAAAGATTGACTTCTTTTTACAAGAAAGTCAAGGATTGACTCCTCTTCGTGAGGGAGTTAGGAAT
1 -AAAGATTGACTTCTTTTTACGAGGAAGTCAAGGATTGACTCCTCTTCGAGAGGAAGTTAGGAAT
* * * * * *
3572239 AAAAAAGATTGAATTCTCTTCACGAGGAAATCAATGATTGACACCTCTTCTTGAAGGAGTCAGGA
65 AACAAAGATTGACTTCTCTTCACGAAGAAATCAAGGATTGACTCCTCTTCGTGAAGGAGTCAGGA
*
3572304 ATAAC
130 ATAAA
* * * * *
3572309 AAAGATTGAATTCTTTTTACGAGAAAGTCAAGGATTGACTCCTCTTC-ACGAGGGATTTATGAAT
1 AAAGATTGACTTCTTTTTACGAGGAAGTCAAGGATTGACTCCTCTTCGA-GAGGAAGTTAGGAAT
* * *
3572373 AACAAAGATTGACTTCTCTTCATGAGGAAATCAAGGATTGACTCATCTTCGTGAAGGAGTCAGGA
65 AACAAAGATTGACTTCTCTTCACGAAGAAATCAAGGATTGACTCCTCTTCGTGAAGGAGTCAGGA
**
3572438 ATATC
130 ATAAA
* * * * * * * * * * **
3572443 AAAGTTTGATTTCTCTTCATGAAGAAATCAATGATTGACACCTCTTCGCA-A-GAGAGTCAATAA
1 AAAGATTGACTTCTTTTTACGAGGAAGTCAAGGATTGACTCCTCTTCG-AGAGGA-AGTTAGGAA
3572506 TAACAAAGATTGACTTCTCTTCA
64 TAACAAAGATTGACTTCTCTTCA
3572529 TGAGGAAGTC
Statistics
Matches: 413, Mismatches: 65, Indels: 20
0.83 0.13 0.04
Matches are distributed among these distances:
132 1 0.00
133 7 0.02
134 398 0.96
135 6 0.01
136 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (134 bp):
AAAGATTGACTTCTTTTTACGAGGAAGTCAAGGATTGACTCCTCTTCGAGAGGAAGTTAGGAATA
ACAAAGATTGACTTCTCTTCACGAAGAAATCAAGGATTGACTCCTCTTCGTGAAGGAGTCAGGAA
TAAA
Found at i:3572266 original size:201 final size:198
Alignment explanation
Indices: 3571907--3572528 Score: 715
Period size: 201 Copynumber: 3.1 Consensus size: 198
3571897 ACCAAATATG
* * * * *
3571907 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTTACAAGGAAGTCAATAATA
1 AAAGATTGACTTCTCTTCACGA-AAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAAGAATA
* * * * * * * * *
3571972 ATAAGGATTGACTTCTCTTCACGAGAAAGTTAAGGATTAACTACTTTTCGTAAGGGAGTCAAGAA
65 ACAAAGATTGACTTCTCTTCACAAGAAAGTCAAGGATTGACTCCTCTTCGTGAGGGAGTCAGGAA
* * * * * * **
3572037 TAAAAAAGATTGACTTCTTTTTACGAGGAAGTCAAGGATTGACTCCTCTTCGAGAGGAAGTTGGG
130 TAAAAAAGATTGAATTCTCTTCACGAGGAAATCAATGATTGACACCTCTTCGA-AGG-AGTCAGG
3572102 AATAAC
193 AATAAC
* * * * *
3572108 AAAGATAGACTTCTCTTCACGAATAAGTCAAGGATTGACTCCTCTACGCGAGGGAGTCAGGAAAA
1 AAAGATTGACTTCTCTTCACGAA-AAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAAGAATA
* * *
3572173 ACAAAGATTGACTTCTTTTTACAAGAAAGTCAAGGATTGACTCCTCTTCGTGAGGGAGTTAGGAA
65 ACAAAGATTGACTTCTCTTCACAAGAAAGTCAAGGATTGACTCCTCTTCGTGAGGGAGTCAGGAA
3572238 TAAAAAAGATTGAATTCTCTTCACGAGGAAATCAATGATTGACACCTCTTCTTGAAGGAGTCAGG
130 TAAAAAAGATTGAATTCTCTTCACGAGGAAATCAATGATTGACACCTCTTC--GAAGGAGTCAGG
3572303 AATAAC
193 AATAAC
* * * * * *
3572309 AAAGATTGAATTCTTTTTACGAGAAAGTCAAGGATTGACTCCTCTTCACGAGGGATTTATGAATA
1 AAAGATTGACTTCTCTTCACGA-AAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAAGAATA
* * * *
3572374 ACAAAGATTGACTTCTCTTCATGAGGAAA-TCAAGGATTGACTCATCTTCGTGAAGGAGTCAGGA
65 ACAAAGATTGACTTCTCTTCA-CAAGAAAGTCAAGGATTGACTCCTCTTCGTGAGGGAGTCAGGA
** * * * * *
3572438 ATATCAAAGTTTGATTTCTCTTCATGAAGAAATCAATGATTGACACCTCTTCGCAAGAGAGTCAA
129 ATAAAAAAGATTGAATTCTCTTCACGAGGAAATCAATGATTGACACCTCTTCG-AAG-GAGTCAG
*
3572503 TAATAAC
192 GAATAAC
3572510 AAAGATTGACTTCTCTTCA
1 AAAGATTGACTTCTCTTCA
3572529 TGAGGAAGTC
Statistics
Matches: 356, Mismatches: 58, Indels: 14
0.83 0.14 0.03
Matches are distributed among these distances:
199 1 0.00
200 3 0.01
201 341 0.96
202 9 0.03
203 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (198 bp):
AAAGATTGACTTCTCTTCACGAAAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAAGAATAA
CAAAGATTGACTTCTCTTCACAAGAAAGTCAAGGATTGACTCCTCTTCGTGAGGGAGTCAGGAAT
AAAAAAGATTGAATTCTCTTCACGAGGAAATCAATGATTGACACCTCTTCGAAGGAGTCAGGAAT
AAC
Found at i:3573843 original size:43 final size:43
Alignment explanation
Indices: 3573722--3573909 Score: 148
Period size: 43 Copynumber: 4.4 Consensus size: 43
3573712 TGATATGAAT
* * * ** *
3573722 CTTC-AAAATG-CCCAACATTAAAACTTATGGATGATATGGAT
1 CTTCAAAAATGCCCCAACATTAATACTTCTGAATGATACAGAC
** *
3573763 CTTCAAATGTTCCCCAACATTAATACTTCTGAATGATACAGAC
1 CTTCAAAAATGCCCCAACATTAATACTTCTGAATGATACAGAC
* * * *
3573806 GTTCAAAAATGCCCCAACATTAATACTTCT-AGTTGATACGGGC
1 CTTCAAAAATGCCCCAACATTAATACTTCTGA-ATGATACAGAC
* * * * * *
3573849 CTTCAAAAGTGCCCTAACATTAATTCTTATGGATGATACATAC
1 CTTCAAAAATGCCCCAACATTAATACTTCTGAATGATACAGAC
* *
3573892 CTTTAAAAGATGTCCCAA
1 CTTCAAAA-ATGCCCCAA
3573910 TATGAGTACT
Statistics
Matches: 112, Mismatches: 30, Indels: 7
0.75 0.20 0.05
Matches are distributed among these distances:
41 4 0.04
42 4 0.04
43 98 0.88
44 6 0.05
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.30
Consensus pattern (43 bp):
CTTCAAAAATGCCCCAACATTAATACTTCTGAATGATACAGAC
Found at i:3573853 original size:86 final size:85
Alignment explanation
Indices: 3573726--3573888 Score: 200
Period size: 86 Copynumber: 1.9 Consensus size: 85
3573716 ATGAATCTTC
* * * * *
3573726 AAAATGCCCAACATTAAAACTTATGGATGATATGGATCTTCAAATGTTCCCCAACATTAATACTT
1 AAAATGCCCAACATTAAAACTTATAGATGATACGGACCTTCAAAAGTGCCCCAACATTAATACTT
*
3573791 CTGAATGATACAGACGTTCA
66 ATGAATGATACAGACGTTCA
* * * * * *
3573811 AAAATGCCCCAACATTAATACTTCTAGTTGATACGGGCCTTCAAAAGTGCCCTAACATTAATTCT
1 AAAATG-CCCAACATTAAAACTTATAGATGATACGGACCTTCAAAAGTGCCCCAACATTAATACT
*
3573876 TATGGATGATACA
65 TATGAATGATACA
3573889 TACCTTTAAA
Statistics
Matches: 64, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
85 6 0.09
86 58 0.91
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.29
Consensus pattern (85 bp):
AAAATGCCCAACATTAAAACTTATAGATGATACGGACCTTCAAAAGTGCCCCAACATTAATACTT
ATGAATGATACAGACGTTCA
Found at i:3577000 original size:19 final size:19
Alignment explanation
Indices: 3576952--3576989 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3576942 GTCCTCGTAC
3576952 AAGATCTTCATAATCATCT
1 AAGATCTTCATAATCATCT
3576971 AAGATCTTCATAATCATCT
1 AAGATCTTCATAATCATCT
3576990 GCAATCTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (19 bp):
AAGATCTTCATAATCATCT
Found at i:3577623 original size:21 final size:19
Alignment explanation
Indices: 3577585--3577630 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
3577575 AATTAATCCT
3577585 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
3577605 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
3577626 A-TAAT
1 ACTAAT
3577631 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:3583620 original size:93 final size:85
Alignment explanation
Indices: 3583503--3583685 Score: 215
Period size: 87 Copynumber: 2.1 Consensus size: 85
3583493 AATACTATAT
* *
3583503 TTATTTTCAAACTACATTATATATATGTGTTCTAAAAAGATATTTATTTTGAAAAATATTA-TAT
1 TTATTTTCAAACTACATTATATATATAT-TT-T-AAAA-A-A-TTATTTTCAAAAATA-TACTAT
*
3583567 ATATATATATATATATGTATTTTCCAAAA
59 ATATATATATATATATATA-TTTCC-AAA
* ** *
3583596 TTATTTTCAAACTATATTATATATATATTTTCCAAAATTATTTTCAAAACTATACTATATATATA
1 TTATTTTCAAACTACATTATATATATATTTTAAAAAATTATTTTCAAAAATATACTATATATATA
3583661 TATATATATATATTTCCAAA
66 TATATATATATATTTCCAAA
3583681 TTATT
1 TTATT
3583686 AAATATATAA
Statistics
Matches: 82, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
85 8 0.10
86 7 0.09
87 34 0.41
88 1 0.01
89 1 0.01
90 2 0.02
91 1 0.01
92 2 0.02
93 26 0.32
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.48
Consensus pattern (85 bp):
TTATTTTCAAACTACATTATATATATATTTTAAAAAATTATTTTCAAAAATATACTATATATATA
TATATATATATATTTCCAAA
Found at i:3583646 original size:38 final size:37
Alignment explanation
Indices: 3583570--3583661 Score: 148
Period size: 37 Copynumber: 2.4 Consensus size: 37
3583560 ATTATATATA
*
3583570 TATATATATATATGTATTTTCCAAAATTATTTTCAAAC
1 TATAT-TATATATATATTTTCCAAAATTATTTTCAAAC
3583608 TATATTATATATATATTTTCCAAAATTATTTTCAAAAC
1 TATATTATATATATATTTTCCAAAATTATTTTC-AAAC
*
3583646 TATACTATATATATAT
1 TATATTATATATATAT
3583662 ATATATATAT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
37 27 0.53
38 24 0.47
ACGTcount: A:0.41, C:0.10, G:0.01, T:0.48
Consensus pattern (37 bp):
TATATTATATATATATTTTCCAAAATTATTTTCAAAC
Found at i:3584207 original size:88 final size:88
Alignment explanation
Indices: 3584113--3584362 Score: 313
Period size: 88 Copynumber: 2.8 Consensus size: 88
3584103 AGACAGGTCT
** * * * * * *
3584113 GCTCCACTACTCTTTAGGAAAGATCAGACTGGAGGCTGATTTTCATCGCTGCTCTTCAGGAAGAC
1 GCTCCACTACTCTTTAGGGGAGATTAGACTCGAGGTTGATTTTCTTCGCTGCTATTAAGGAAGAC
3584178 CAAATCTGAAAGAAGAAGAATCA
66 CAAATCTGAAAGAAGAAGAATCA
* * * * * *
3584201 GCTCCACTATTCTTTAGGGGAGATTAGACTCGAGGTTTAATTGCTTCGCTGCTATTGAGGACGAC
1 GCTCCACTACTCTTTAGGGGAGATTAGACTCGAGGTTGATTTTCTTCGCTGCTATTAAGGAAGAC
* *
3584266 CAAATCTGAAAGAAGAAGCATCT
66 CAAATCTGAAAGAAGAAGAATCA
* * *
3584289 GCTTCACTACTCTTTAGGGGAGATTAGACTCGAGGTTGATTTAT-TTTGCTTCTATTAAGGAAGA
1 GCTCCACTACTCTTTAGGGGAGATTAGACTCGAGGTTGATTT-TCTTCGCTGCTATTAAGGAAGA
3584353 CCAAATCTGA
65 CCAAATCTGA
3584363 CTTGATTTGC
Statistics
Matches: 137, Mismatches: 24, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
88 137 1.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (88 bp):
GCTCCACTACTCTTTAGGGGAGATTAGACTCGAGGTTGATTTTCTTCGCTGCTATTAAGGAAGAC
CAAATCTGAAAGAAGAAGAATCA
Found at i:3584487 original size:67 final size:67
Alignment explanation
Indices: 3584402--3584768 Score: 358
Period size: 67 Copynumber: 5.5 Consensus size: 67
3584392 ACCAAATCTG
* * * * * * *
3584402 AAAGGTTGACCTCTCTTCACAAGGAAGTCAAGGATTTACTCCTCTTTACGAGGAAATCAAGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAATCAAGGATTGACTCCTCTTCACGAGGAAATCAGGAATA
*
3584467 AT
66 AC
* * * *
3584469 AAAGATTGACTTCTCTTCACGAGGAAATCAATGATTGACACCTCTTCGA-GGGGGAATCAGGAAT
1 AAAGATTGACTTCTCTTCACGAGGAAATCAAGGATTGACTCCTCTTC-ACGAGGAAATCAGGAAT
3584533 AAC
65 AAC
* * * * * * * * *
3584536 AAAGATTGACTTCTTTTTATGAGGAAGTCAAGGATCGACTCCTATTCACGAAGAAGTGAGGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAATCAAGGATTGACTCCTCTTCACGAGGAAATCAGGAATA
3584601 AC
66 AC
* * * *
3584603 AAAGATTGACTTCTCTCCACGAGGAAATCAATGATTGACTCCTCTTCACGAGGGAGTCAGGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAATCAAGGATTGACTCCTCTTCACGAGGAAATCAGGAATA
*
3584668 AT
66 AC
* * * * ** * * ***
3584670 AAAGATTGACTTCTCTTCATGATGAAATCAATGATTGGCAACTATTCACAAGGGTGTCAGGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAATCAAGGATTGACTCCTCTTCACGAGGAAATCAGGAATA
3584735 AC
66 AC
* * *
3584737 AAAGATTGACTTCTCTACACAAGGAAGTCAAG
1 AAAGATTGACTTCTCTTCACGAGGAAATCAAG
3584769 TTAAAGCTTC
Statistics
Matches: 245, Mismatches: 53, Indels: 4
0.81 0.18 0.01
Matches are distributed among these distances:
66 1 0.00
67 243 0.99
68 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.26
Consensus pattern (67 bp):
AAAGATTGACTTCTCTTCACGAGGAAATCAAGGATTGACTCCTCTTCACGAGGAAATCAGGAATA
AC
Found at i:3584600 original size:134 final size:134
Alignment explanation
Indices: 3584402--3584767 Score: 414
Period size: 134 Copynumber: 2.7 Consensus size: 134
3584392 ACCAAATCTG
* * ** * * * * * * *
3584402 AAAGGTTGACCTCTCTTCACAAGGAAGTCAAGGATTTACTCCTCTTTACGAGGAAATCAAGAATA
1 AAAGATTGACTTCTCTTCATGAGGAAGTCAAGGATTGACTCCTATTCACGAAGAAGTGAGGAATA
* * *
3584467 ATAAAGATTGACTTCTCTTCACGAGGAAATCAATGATTGACACCTCTTCGA-GGGGGAATCAGGA
66 ACAAAGATTGACTTCTCTACACGAGGAAATCAATGATTGACACCTCTTC-ACGAGGGAATCAGGA
3584531 ATAAC
130 ATAAC
* * *
3584536 AAAGATTGACTTCTTTTTATGAGGAAGTCAAGGATCGACTCCTATTCACGAAGAAGTGAGGAATA
1 AAAGATTGACTTCTCTTCATGAGGAAGTCAAGGATTGACTCCTATTCACGAAGAAGTGAGGAATA
* * *
3584601 ACAAAGATTGACTTCTCTCCACGAGGAAATCAATGATTGACTCCTCTTCACGAGGGAGTCAGGAA
66 ACAAAGATTGACTTCTCTACACGAGGAAATCAATGATTGACACCTCTTCACGAGGGAATCAGGAA
*
3584666 TAAT
131 TAAC
* * * * ** *
3584670 AAAGATTGACTTCTCTTCATGATGAAATCAATGATTGGCAACTATTCAC-AAG-GGTGTCAGGAA
1 AAAGATTGACTTCTCTTCATGAGGAAGTCAAGGATTGACTCCTATTCACGAAGAAGTG--AGGAA
* *
3584733 TAACAAAGATTGACTTCTCTACACAAGGAAGTCAA
64 TAACAAAGATTGACTTCTCTACACGAGGAAATCAA
3584768 GTTAAAGCTT
Statistics
Matches: 196, Mismatches: 33, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
132 3 0.02
133 4 0.02
134 189 0.96
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (134 bp):
AAAGATTGACTTCTCTTCATGAGGAAGTCAAGGATTGACTCCTATTCACGAAGAAGTGAGGAATA
ACAAAGATTGACTTCTCTACACGAGGAAATCAATGATTGACACCTCTTCACGAGGGAATCAGGAA
TAAC
Found at i:3585293 original size:43 final size:43
Alignment explanation
Indices: 3585233--3585421 Score: 247
Period size: 43 Copynumber: 4.4 Consensus size: 43
3585223 TGTTATGAAT
* *
3585233 CTTCAAAA-TGCCCCAACATTAATACTTTTGGATGATATGGAC
1 CTTCAAAAGTGCCCCAACATTAATACTTATGGATGATACGGAC
3585275 CTTCAAAAGTGCCCCAACATTAATACTTATGGATGATACGGAC
1 CTTCAAAAGTGCCCCAACATTAATACTTATGGATGATACGGAC
* * * *
3585318 CTT-AGAAAGTGCCCCAATATTAATACTTCTCGATGATACAGAC
1 CTTCA-AAAGTGCCCCAACATTAATACTTATGGATGATACGGAC
*** *
3585361 CTTCAAAAGTGCATAAACATTAATACTTATAGATGATACGGAC
1 CTTCAAAAGTGCCCCAACATTAATACTTATGGATGATACGGAC
*
3585404 CTTCAAAAGATGTCCCAA
1 CTTCAAAAG-TGCCCCAA
3585422 TATGAGTACT
Statistics
Matches: 126, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
42 9 0.07
43 112 0.89
44 5 0.04
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.28
Consensus pattern (43 bp):
CTTCAAAAGTGCCCCAACATTAATACTTATGGATGATACGGAC
Found at i:3588693 original size:14 final size:15
Alignment explanation
Indices: 3588676--3588712 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
3588666 TTAATAACAT
3588676 AAAATTTTTAAATAA
1 AAAATTTTTAAATAA
*
3588691 AAAATATTTAAAT-A
1 AAAATTTTTAAATAA
3588705 AAAATTTT
1 AAAATTTT
3588713 AGATGGATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAATTTTTAAATAA
Found at i:3588768 original size:37 final size:36
Alignment explanation
Indices: 3588725--3588832 Score: 162
Period size: 37 Copynumber: 2.9 Consensus size: 36
3588715 ATGGATGTCA
*
3588725 TTCGTAAAATAAATAATTAATTAAAGAAAATTAAAGT
1 TTCGTAAAATAAATAATTAATCAAA-AAAATTAAAGT
*
3588762 TTCGTAAAATAAATAATTAATCAAAAAATATTAAATT
1 TTCGTAAAATAAATAATTAATCAAAAAA-ATTAAAGT
* *
3588799 TTCATAAAATAAATAATTAATCAAAAAAACTAAA
1 TTCGTAAAATAAATAATTAATCAAAAAAATTAAA
3588833 ATTCAAAATA
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
36 8 0.12
37 58 0.88
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (36 bp):
TTCGTAAAATAAATAATTAATCAAAAAAATTAAAGT
Found at i:3588791 original size:19 final size:19
Alignment explanation
Indices: 3588767--3588826 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
3588757 AAAGTTTCGT
3588767 AAAATAAATAATTAATCAA
1 AAAATAAATAATTAATCAA
* * *
3588786 AAAAT-ATTAAATT-TTCAT
1 AAAATAAAT-AATTAATCAA
3588804 AAAATAAATAATTAATCAA
1 AAAATAAATAATTAATCAA
3588823 AAAA
1 AAAA
3588827 ACTAAAATTC
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
18 14 0.44
19 18 0.56
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAATAAATAATTAATCAA
Found at i:3588816 original size:18 final size:18
Alignment explanation
Indices: 3588761--3588816 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
3588751 AAAATTAAAG
*
3588761 TTTCGTAAAATAAATAAT
1 TTTCATAAAATAAATAAT
* * *
3588779 TAATCAAAAAAT-ATTAAAT
1 T-TTCATAAAATAAAT-AAT
3588798 TTTCATAAAATAAATAAT
1 TTTCATAAAATAAATAAT
3588816 T
1 T
3588817 AATCAAAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 6
0.68 0.17 0.15
Matches are distributed among these distances:
18 15 0.54
19 13 0.46
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (18 bp):
TTTCATAAAATAAATAAT
Found at i:3588825 original size:18 final size:18
Alignment explanation
Indices: 3588767--3588825 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
3588757 AAAGTTTCGT
3588767 AAAATAAATAATTAATCA
1 AAAATAAATAATTAATCA
* *
3588785 AAAA-ATATTAAATT-TTCA
1 AAAATA-AAT-AATTAATCA
3588803 TAAAATAAATAATTAATCA
1 -AAAATAAATAATTAATCA
3588822 AAAA
1 AAAA
3588826 AACTAAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
17 1 0.03
18 17 0.53
19 13 0.41
20 1 0.03
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAATAAATAATTAATCA
Found at i:3588855 original size:20 final size:20
Alignment explanation
Indices: 3588830--3588874 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
3588820 CAAAAAAACT
*
3588830 AAAATTCAAAATAGACACGA
1 AAAATTCAAAATAGACACAA
* *
3588850 AAAATTCATAATGGACACAA
1 AAAATTCAAAATAGACACAA
3588870 AAAAT
1 AAAAT
3588875 AAAATAACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.60, C:0.13, G:0.09, T:0.18
Consensus pattern (20 bp):
AAAATTCAAAATAGACACAA
Found at i:3590904 original size:20 final size:20
Alignment explanation
Indices: 3590879--3590921 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
3590869 AAGTTGTACA
3590879 TGGACTTGGACGACCCAAAC
1 TGGACTTGGACGACCCAAAC
*
3590899 TGGACTTGGACGACCCGAAC
1 TGGACTTGGACGACCCAAAC
3590919 TGG
1 TGG
3590922 CCCCTTCCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.28, G:0.30, T:0.16
Consensus pattern (20 bp):
TGGACTTGGACGACCCAAAC
Found at i:3591499 original size:88 final size:87
Alignment explanation
Indices: 3591407--3591726 Score: 325
Period size: 88 Copynumber: 3.7 Consensus size: 87
3591397 GGGTTTGCTC
*
3591407 CACTACTCATTAGGGAAGATCAGACTCGAGGTTGATTTGCTTCGCTGCTCTTCAGGAAGACCAAA
1 CACTACTC-TTAGGGGAGATCAGACTCGAGGTTGATTTGCTTCGCTGCTCTTCAGGAAGACCAAA
* *
3591472 TCTAAAAGAAGAAGAATCT-ACTA
65 TATAAAAGAAGAAGAATATGA-TA
* * *
3591495 CACTACTCTTTAGGGGAGATCAGACTCGATGTTGATTTGGTTTGCTGCTCTTCAGGAAGACCAAA
1 CACTACTC-TTAGGGGAGATCAGACTCGAGGTTGATTTGCTTCGCTGCTCTTCAGGAAGACCAAA
* *
3591560 TATGAAAGAAGAAGAATATGATC
65 TATAAAAGAAGAAGAATATGATA
* * ** * **
3591583 CACTACTCTTCAGGGGAGATCAGACTCGAGGTTGATTTGCTTCGTTTCTAGTCAGGAATATAAAA
1 CACTACTCTT-AGGGGAGATCAGACTCGAGGTTGATTTGCTTCGCTGCTCTTCAGGAAGACCAAA
* * * * *
3591648 TCTGAAAGAAAAAGAATCTGATT
65 TATAAAAGAAGAAGAATATGATA
* * * *
3591671 CACAACTCTT--------TCAGACTCGAGGTTTATTTTCTTCGCTGCTCTTTAGGAAGACCAAA
1 CACTACTCTTAGGGGAGATCAGACTCGAGGTTGATTTGCTTCGCTGCTCTTCAGGAAGACCAAA
3591727 CCTGACTTGA
Statistics
Matches: 196, Mismatches: 34, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
79 36 0.18
87 2 0.01
88 157 0.80
89 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.29
Consensus pattern (87 bp):
CACTACTCTTAGGGGAGATCAGACTCGAGGTTGATTTGCTTCGCTGCTCTTCAGGAAGACCAAAT
ATAAAAGAAGAAGAATATGATA
Found at i:3591816 original size:29 final size:29
Alignment explanation
Indices: 3591774--3591829 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
3591764 AAATCTAAAA
3591774 GATTGACCTCTCTTCACGAGGAAGTCAAG
1 GATTGACCTCTCTTCACGAGGAAGTCAAG
*
3591803 GATTGA-CTCATCTTTACGAGGAAGTCA
1 GATTGACCTC-TCTTCACGAGGAAGTCA
3591830 GGAATAACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (29 bp):
GATTGACCTCTCTTCACGAGGAAGTCAAG
Found at i:3591862 original size:67 final size:66
Alignment explanation
Indices: 3591771--3592338 Score: 625
Period size: 67 Copynumber: 8.5 Consensus size: 66
3591761 ACCAAATCTA
* * *
3591771 AAAGATTGACCTCTCTTCACGAGGAAGTCAAGGATTGACTCATCTTTACGAGGAAGTCAGGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTC-TCTTCACGAGGGAGTCAGGAATA
3591836 AC
65 AC
* * * *
3591838 AAGGATTGTCTTCTCTTCACGAGGAAGTCAAGGATTGACTCCCATTCATGAGGGAG-CTAGGAAT
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTC-TTCACGAGGGAGTC-AGGAAT
3591902 AAC
64 AAC
* * * *
3591905 AAAGATTGACTTCTTTTGACGAGGAAGTCAAGGATTGACTTCTCTTTATGAGGGAGTCAGGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGAC-TCTCTTCACGAGGGAGTCAGGAATA
3591970 AC
65 AC
* * ** *
3591972 AAAGATTGACTTCTCTTTACGAGGAAGTTAAGGATTGACTCCTCTTCGTGAGGGAGTCATGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACT-CTCTTCACGAGGGAGTCAGGAATA
**
3592037 GT
65 AC
* * * * * * *
3592039 AAAGATTGACTTCTTTTTACAAGGAAGTCAAGGATTGACTCGTCTTCAAGAGAGAGTCAAGATTA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTC-TCTTCACGAGGGAGTCAGGAATA
*
3592104 AT
65 AC
* * * * * * *
3592106 AAAAATTTACTTCTCGTCATGAGGAAATCAATGATTGACTCCTCTTCGCGAGGGAGTCAGGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACT-CTCTTCACGAGGGAGTCAGGAATA
*
3592171 AT
65 AC
* * * * *
3592173 AAAGATTGACTTCTTTTTACGAGGGAGTCAAGGATTGACTCCCTTTCGCGAGGGAGTCAGGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTC-TTCACGAGGGAGTCAGGAATA
3592238 AC
65 AC
* * * * * * *
3592240 AAAGATTGACTTCTCTTCACGAAGAAATCAATGATTGACACCTCTTCGCAAGGGAGTCAAGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGAC-TCTCTTCACGAGGGAGTCAGGAATA
3592305 AC
65 AC
*
3592307 AAAGATTGATTTCTCTTCACGAGGAAGTCAAG
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAG
3592339 TTAAAGCTTC
Statistics
Matches: 423, Mismatches: 69, Indels: 18
0.83 0.14 0.04
Matches are distributed among these distances:
66 6 0.01
67 410 0.97
68 7 0.02
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.27
Consensus pattern (66 bp):
AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTCTTCACGAGGGAGTCAGGAATAA
C
Found at i:3591957 original size:29 final size:29
Alignment explanation
Indices: 3591908--3592017 Score: 87
Period size: 29 Copynumber: 3.5 Consensus size: 29
3591898 GAATAACAAA
3591908 GATTGACTTCT-TTTGACGAGGAAGTCAAG
1 GATTGACTTCTCTTT-ACGAGGAAGTCAAG
* *
3591937 GATTGACTTCTCTTTATGAGGGAGTCAGGAATAACAAA
1 GATTGACTTCTCTTTACGA-GGA---A-G--T--CAAG
*
3591975 GATTGACTTCTCTTTACGAGGAAGTTAAG
1 GATTGACTTCTCTTTACGAGGAAGTCAAG
*
3592004 GATTGACTCCTCTT
1 GATTGACTTCTCTT
3592018 CGTGAGGGAG
Statistics
Matches: 65, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
29 29 0.45
30 6 0.09
31 1 0.02
33 2 0.03
34 2 0.03
36 1 0.02
37 3 0.05
38 21 0.32
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (29 bp):
GATTGACTTCTCTTTACGAGGAAGTCAAG
Found at i:3592180 original size:38 final size:37
Alignment explanation
Indices: 3592138--3592336 Score: 99
Period size: 38 Copynumber: 5.7 Consensus size: 37
3592128 GGAAATCAAT
3592138 GATTGACTCCTCTTCGCGAGGGAGTCAGGAATAATAAA
1 GATTGACTCCTCTTCGCGAGGGAGTCAGGAATAA-AAA
* * ** *
3592176 GATTGACTTCTTTTTACGAGGGAGTC--------AAG
1 GATTGACTCCTCTTCGCGAGGGAGTCAGGAATAAAAA
3592205 GATTGACTCC-CTTTCGCGAGGGAGTCAGGAATAACAAA
1 GATTGACTCCTC-TTCGCGAGGGAGTCAGGAATAA-AAA
* * * *
3592243 GATTGACTTCTCTTCACGA---AG--A--AAT-CAAT
1 GATTGACTCCTCTTCGCGAGGGAGTCAGGAATAAAAA
* * *
3592272 GATTGACACCTCTTCGCAAGGGAGTCAAGAATAACAAA
1 GATTGACTCCTCTTCGCGAGGGAGTCAGGAATAA-AAA
* * * *
3592310 GATTGATTTCTCTTCACGAGGAAGTCA
1 GATTGACTCCTCTTCGCGAGGGAGTCA
3592337 AGTTAAAGCT
Statistics
Matches: 115, Mismatches: 26, Indels: 40
0.64 0.14 0.22
Matches are distributed among these distances:
29 40 0.35
31 3 0.03
32 2 0.02
33 1 0.01
34 1 0.01
35 2 0.02
36 3 0.03
38 62 0.54
39 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (37 bp):
GATTGACTCCTCTTCGCGAGGGAGTCAGGAATAAAAA
Found at i:3593534 original size:42 final size:42
Alignment explanation
Indices: 3593481--3593686 Score: 214
Period size: 43 Copynumber: 4.8 Consensus size: 42
3593471 CTTAATAAAA
* * ** * * *
3593481 AAAATGTCCCAACATTTATTTTTCTTGCTGATATAAATCTTC
1 AAAATGCCCCAACATTAATACTTCTGGATGATATAAACCTTC
*
3593523 AAAATGCCCCAACATTAATACTTCTGGATGATATGAACCTTC
1 AAAATGCCCCAACATTAATACTTCTGGATGATATAAACCTTC
* * * * *
3593565 AAAAGTGCCCCAATAATAATACTTTTGGATGTTATAGACCTTC
1 AAAA-TGCCCCAACATTAATACTTCTGGATGATATAAACCTTC
* *** *
3593608 AAAAGTGCCCCAACATTAATACTTCTGGATGCTACGGACCTTT
1 AAAA-TGCCCCAACATTAATACTTCTGGATGATATAAACCTTC
*
3593651 AAAAGTGCCCCAACATTAATACTTATGGATGATATA
1 AAAA-TGCCCCAACATTAATACTTCTGGATGATATA
3593687 TACCATCATA
Statistics
Matches: 138, Mismatches: 25, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
42 38 0.28
43 100 0.72
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (42 bp):
AAAATGCCCCAACATTAATACTTCTGGATGATATAAACCTTC
Found at i:3593586 original size:43 final size:43
Alignment explanation
Indices: 3593509--3593685 Score: 232
Period size: 43 Copynumber: 4.1 Consensus size: 43
3593499 TTTTTCTTGC
* *
3593509 TGATATAAATCTTCAAAA-TGCCCCAACATTAATACTTCTGGA
1 TGATATGAACCTTCAAAAGTGCCCCAACATTAATACTTCTGGA
* * *
3593551 TGATATGAACCTTCAAAAGTGCCCCAATAATAATACTTTTGGA
1 TGATATGAACCTTCAAAAGTGCCCCAACATTAATACTTCTGGA
*
3593594 TGTTAT-AGACCTTCAAAAGTGCCCCAACATTAATACTTCTGGA
1 TGATATGA-ACCTTCAAAAGTGCCCCAACATTAATACTTCTGGA
* * * * *
3593637 TGCTACGGACCTTTAAAAGTGCCCCAACATTAATACTTATGGA
1 TGATATGAACCTTCAAAAGTGCCCCAACATTAATACTTCTGGA
3593680 TGATAT
1 TGATAT
3593686 ATACCATCAT
Statistics
Matches: 116, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
42 17 0.15
43 99 0.85
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.31
Consensus pattern (43 bp):
TGATATGAACCTTCAAAAGTGCCCCAACATTAATACTTCTGGA
Found at i:3593626 original size:86 final size:85
Alignment explanation
Indices: 3593509--3593686 Score: 257
Period size: 86 Copynumber: 2.1 Consensus size: 85
3593499 TTTTTCTTGC
* * *
3593509 TGATATAAATCTTCAAAATGCCCCAACATTAATACTTCTGGATGATATGAACCTTCAAAAGTGCC
1 TGATATAGACCTTCAAAATGCCCCAACATTAATACTTCTGGATGATACGAACCTTCAAAAGTGCC
* *
3593574 CCAATAATAATACTTTTGGA
66 CCAACAATAATACTTATGGA
* * * *
3593594 TGTTATAGACCTTCAAAAGTGCCCCAACATTAATACTTCTGGATGCTACGGACCTTTAAAAGTGC
1 TGATATAGACCTTCAAAA-TGCCCCAACATTAATACTTCTGGATGATACGAACCTTCAAAAGTGC
*
3593659 CCCAACATTAATACTTATGGA
65 CCCAACAATAATACTTATGGA
3593680 TGATATA
1 TGATATA
3593687 TACCATCATA
Statistics
Matches: 81, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
85 15 0.19
86 66 0.81
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.30
Consensus pattern (85 bp):
TGATATAGACCTTCAAAATGCCCCAACATTAATACTTCTGGATGATACGAACCTTCAAAAGTGCC
CCAACAATAATACTTATGGA
Found at i:3595813 original size:32 final size:33
Alignment explanation
Indices: 3595776--3595843 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 33
3595766 CCTATACCCG
3595776 AAAAGGTAAAAATATGAATTTGGCA-TCTC-GAA
1 AAAAGGTAAAAATATGAATTTGG-AGTCTCAGAA
** *
3595808 AAAAGGTAAAGGTATGACTTTGGAGTCTCAGAA
1 AAAAGGTAAAAATATGAATTTGGAGTCTCAGAA
3595841 AAA
1 AAA
3595844 TCGAGTAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 1 0.03
32 24 0.77
33 6 0.19
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.24
Consensus pattern (33 bp):
AAAAGGTAAAAATATGAATTTGGAGTCTCAGAA
Found at i:3603159 original size:8 final size:8
Alignment explanation
Indices: 3603146--3603172 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
3603136 CCAAAACGTC
3603146 CTTTCATT
1 CTTTCATT
3603154 CTTTCATT
1 CTTTCATT
3603162 CTTTCATT
1 CTTTCATT
3603170 CTT
1 CTT
3603173 ACTAATGGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.00, T:0.63
Consensus pattern (8 bp):
CTTTCATT
Found at i:3603584 original size:3 final size:3
Alignment explanation
Indices: 3603576--3603626 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
3603566 AATAAATATA
* * * * *
3603576 AAT AAT AAT AAT AAT AAT AAT AAC AAC AAC AAC AAC AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3603624 AAT
1 AAT
3603627 TTATAAACTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.24
Consensus pattern (3 bp):
AAT
Found at i:3603784 original size:13 final size:13
Alignment explanation
Indices: 3603752--3603858 Score: 57
Period size: 12 Copynumber: 8.4 Consensus size: 13
3603742 TACATTATAT
3603752 ATATATTTTCCAAA
1 ATATATTTT-CAAA
3603766 AT-TATTTTCAAA
1 ATATATTTTCAAA
* * *
3603778 CTATATTAT--AT
1 ATATATTTTCAAA
3603789 ATATATATTTCAAA
1 ATATAT-TTTCAAA
3603803 AT-TATTTTCAAA
1 ATATATTTTCAAA
* * *
3603815 ACTATACTAT--AT
1 A-TATATTTTCAAA
*
3603827 ATATATTTTTCCAA
1 ATATA-TTTTCAAA
3603841 AT-TATTTTCAAA
1 ATATATTTTCAAA
3603853 ACTATA
1 A-TATA
3603859 CTATATATAT
Statistics
Matches: 69, Mismatches: 13, Indels: 22
0.66 0.12 0.21
Matches are distributed among these distances:
11 10 0.14
12 27 0.39
13 18 0.26
14 14 0.20
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (13 bp):
ATATATTTTCAAA
Found at i:3603826 original size:38 final size:37
Alignment explanation
Indices: 3603729--3603882 Score: 204
Period size: 38 Copynumber: 4.1 Consensus size: 37
3603719 AAAAATATAT
* * * *
3603729 TTATTTTGAAAAATACATTATATATATATTTTCCAAAA
1 TTATTTTCAAAACTATACTATATATATATTTT-CAAAA
*
3603767 TTATTTTC-AAACTATATTATATATATATATTTCAAAA
1 TTATTTTCAAAACTATACTATATATATAT-TTTCAAAA
*
3603804 TTATTTTCAAAACTATACTATATATATATTTTTCCAAA
1 TTATTTTCAAAACTATACTATATATATA-TTTTCAAAA
*
3603842 TTATTTTCAAAACTATACTATATATAT-TTTTCTAAA
1 TTATTTTCAAAACTATACTATATATATATTTTCAAAA
3603878 TTATT
1 TTATT
3603883 AAATATATAA
Statistics
Matches: 107, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
36 13 0.12
37 31 0.29
38 62 0.58
39 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.01, T:0.49
Consensus pattern (37 bp):
TTATTTTCAAAACTATACTATATATATATTTTCAAAA
Found at i:3603847 original size:75 final size:74
Alignment explanation
Indices: 3603729--3603882 Score: 213
Period size: 75 Copynumber: 2.1 Consensus size: 74
3603719 AAAAATATAT
* * *
3603729 TTATTTTGAAAAATACATTATATATATATTTTCCAAAATTATTTTC-AAACTATATTATATATAT
1 TTATTTTCAAAAATACACTATATATATATTTTCCAAAATTATTTTCAAAACTATACTATATATAT
3603793 ATATTTCAAAA
66 -T-TTTCAAAA
* *
3603804 TTATTTTCAAAACTATACTATATATATATTTTTCC-AAATTATTTTCAAAACTATACTATATATA
1 TTATTTTCAAAAATACACTATATATATA-TTTTCCAAAATTATTTTCAAAACTATACTATATATA
*
3603868 TTTTTCTAAA
65 TTTTTCAAAA
3603878 TTATT
1 TTATT
3603883 AAATATATAA
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
74 12 0.17
75 36 0.51
76 23 0.32
ACGTcount: A:0.41, C:0.10, G:0.01, T:0.49
Consensus pattern (74 bp):
TTATTTTCAAAAATACACTATATATATATTTTCCAAAATTATTTTCAAAACTATACTATATATAT
TTTTCAAAA
Found at i:3607384 original size:13 final size:13
Alignment explanation
Indices: 3607342--3607384 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
3607332 ACTTTGTGAA
3607342 TTGTATCTCAAAG
1 TTGTATCTCAAAG
* * *
3607355 TTATCTCTCAAAA
1 TTGTATCTCAAAG
*
3607368 TTGTTTCTCAAAG
1 TTGTATCTCAAAG
3607381 TTGT
1 TTGT
3607385 GTCTAAGATT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (13 bp):
TTGTATCTCAAAG
Found at i:3607585 original size:35 final size:35
Alignment explanation
Indices: 3607537--3607608 Score: 99
Period size: 35 Copynumber: 2.1 Consensus size: 35
3607527 TAAACTAAAA
* * * *
3607537 AATAAGTCAATTCATCAAGTGATATGACTTATTAT
1 AATAAGTCAATTCACCAAGTGACATGAATTATAAT
*
3607572 AATAAGTCTATTCACCAAGTGACATGAATTATAAT
1 AATAAGTCAATTCACCAAGTGACATGAATTATAAT
3607607 AA
1 AA
3607609 ATAGCATCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.33
Consensus pattern (35 bp):
AATAAGTCAATTCACCAAGTGACATGAATTATAAT
Found at i:3609563 original size:21 final size:21
Alignment explanation
Indices: 3609537--3609629 Score: 91
Period size: 21 Copynumber: 4.3 Consensus size: 21
3609527 ACCAAAAGTG
**
3609537 CCACATAAATGTCCCGAATGA
1 CCACATATTTGTCCCGAATGA
3609558 CCACATAGGTTTG-CACCGAAGTG-
1 CCACATA--TTTGTC-CCGAA-TGA
* *
3609581 CCACATATTTGTGCCGAAGGA
1 CCACATATTTGTCCCGAATGA
*
3609602 CAACATATTTGTCCCGAATGA
1 CCACATATTTGTCCCGAATGA
3609623 CCACATA
1 CCACATA
3609630 GAACCCTCGA
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
20 1 0.02
21 40 0.69
22 1 0.02
23 14 0.24
24 2 0.03
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (21 bp):
CCACATATTTGTCCCGAATGA
Found at i:3618124 original size:24 final size:22
Alignment explanation
Indices: 3618083--3618129 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
3618073 ACCGATACTA
*
3618083 TATATAGTATCAACACTACTTAG
1 TATATAGTACCAACACTA-TTAG
*
3618106 TATAGTAGTACCAATACTATTAG
1 TATA-TAGTACCAACACTATTAG
3618129 T
1 T
3618130 GGAGGTATCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (22 bp):
TATATAGTACCAACACTATTAG
Found at i:3624460 original size:3 final size:3
Alignment explanation
Indices: 3624448--3624504 Score: 50
Period size: 3 Copynumber: 19.7 Consensus size: 3
3624438 GCAATATTTG
**
3624448 TAA T-A TAA TAA TAA TAA TAA TTTT TAA TAA T-A TATA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TA-A TAA TAA TAA
3624492 TAA TAA -AA TAA TA
1 TAA TAA TAA TAA TA
3624505 GCACTAAGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
2 8 0.18
3 32 0.73
4 4 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:3631247 original size:13 final size:13
Alignment explanation
Indices: 3631229--3631253 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3631219 AATGAATTTT
3631229 AAGATTTTCCAAA
1 AAGATTTTCCAAA
3631242 AAGATTTTCCAA
1 AAGATTTTCCAA
3631254 GTATATTCGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (13 bp):
AAGATTTTCCAAA
Found at i:3632682 original size:5 final size:5
Alignment explanation
Indices: 3632672--3632696 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3632662 AAATTAATTT
3632672 TTCAA TTCAA TTCAA TTCAA TTCAA
1 TTCAA TTCAA TTCAA TTCAA TTCAA
3632697 AGGACTCAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
TTCAA
Found at i:3633725 original size:119 final size:118
Alignment explanation
Indices: 3633491--3633727 Score: 361
Period size: 117 Copynumber: 2.0 Consensus size: 118
3633481 CTTAGGCCCC
* * * *
3633491 CCAATTTTTTTACATTTATAATTAAGTCCCCTGATTTTTATAATTTCATAAAATTTTTAGTTTTT
1 CCAATTTTTTTACATGTATAATTAAGGCCCCTAATTTTTATAATTTCATAAAATGTTTAGTTTTT
*
3633556 GACTATTTTTTCCATTTCTCTTATTAATTCATTCAATTTTGAATTAAATTTAA
66 GACTATTTTTTCCATTTCTCTTATTAATTCATTCAACTTTGAATTAAATTTAA
* *
3633609 CCAA-TTTTTTATATGTATAATTAGGGCCCCTAATTTTTATAATTTCATAAAATGTTTAGTTTTT
1 CCAATTTTTTTACATGTATAATTAAGGCCCCTAATTTTTATAATTTCATAAAATGTTTAG-TTTT
*
3633673 TGACCT-TGTTTTTCCATTTCTCTTATTTATTCATTCAACTTTGAATTAAATTTAA
65 TGA-CTAT-TTTTTCCATTTCTCTTATTAATTCATTCAACTTTGAATTAAATTTAA
3633728 TCATGTTTTT
Statistics
Matches: 108, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
117 49 0.45
118 12 0.11
119 47 0.44
ACGTcount: A:0.29, C:0.13, G:0.06, T:0.52
Consensus pattern (118 bp):
CCAATTTTTTTACATGTATAATTAAGGCCCCTAATTTTTATAATTTCATAAAATGTTTAGTTTTT
GACTATTTTTTCCATTTCTCTTATTAATTCATTCAACTTTGAATTAAATTTAA
Found at i:3647442 original size:36 final size:36
Alignment explanation
Indices: 3647395--3647506 Score: 179
Period size: 36 Copynumber: 3.1 Consensus size: 36
3647385 AGTTTGAAAT
*
3647395 ACTTCACTACTCTTCCGTGAAAGTTGAAAATGACTG
1 ACTTCACTACTCTTCCGTGAAAGTTGAAAATGATTG
**
3647431 ACTTCACTACTCTTTTGTGAAAGTTGAAAATGATTG
1 ACTTCACTACTCTTCCGTGAAAGTTGAAAATGATTG
* *
3647467 ACTTCACTACTCTTCCATGAAGGTTGAAAATGATTG
1 ACTTCACTACTCTTCCGTGAAAGTTGAAAATGATTG
3647503 ACTT
1 ACTT
3647507 GAGAAGAATA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 69 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (36 bp):
ACTTCACTACTCTTCCGTGAAAGTTGAAAATGATTG
Found at i:3647760 original size:20 final size:20
Alignment explanation
Indices: 3647724--3647882 Score: 153
Period size: 20 Copynumber: 8.0 Consensus size: 20
3647714 CTGACAGATG
* *
3647724 ACCC-AAGGATTTGCAAATT
1 ACCCGAAGGCTTTACAAATT
*
3647743 ACCCGAAGGTTTTACAAATT
1 ACCCGAAGGCTTTACAAATT
*
3647763 ACCCGAAGGCTTTACAAATA
1 ACCCGAAGGCTTTACAAATT
*
3647783 ACCCGAAGGCTTTACAAATG
1 ACCCGAAGGCTTTACAAATT
* *
3647803 ACAC-ATAGACTTTACAAATGT
1 ACCCGA-AGGCTTTACAAAT-T
* * *
3647824 -CCCGGAGGTTTTACAAATG
1 ACCCGAAGGCTTTACAAATT
* *
3647843 ACCCGGAGGCTTTACAAATG
1 ACCCGAAGGCTTTACAAATT
* *
3647863 ACCCGGAGACTTTACAAATT
1 ACCCGAAGGCTTTACAAATT
3647883 CGTGGGAAAT
Statistics
Matches: 119, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
19 5 0.04
20 114 0.96
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.25
Consensus pattern (20 bp):
ACCCGAAGGCTTTACAAATT
Found at i:3647797 original size:40 final size:39
Alignment explanation
Indices: 3647721--3647881 Score: 169
Period size: 40 Copynumber: 4.1 Consensus size: 39
3647711 AGACTGACAG
* * * *
3647721 ATGACCCAAGGATTTGCAAATTACCCGAAGGTTTTACAA
1 ATGACCCAAGGCTTTACAAATGACCCGAAGGCTTTACAA
* *
3647760 ATTACCCGAAGGCTTTACAAATAACCCGAAGGCTTTACAA
1 ATGACCC-AAGGCTTTACAAATGACCCGAAGGCTTTACAA
* * * * *
3647800 ATGACACATAGACTTTACAAATGTCCCGGAGGTTTTACAA
1 ATGACCCA-AGGCTTTACAAATGACCCGAAGGCTTTACAA
* * *
3647840 ATGACCCGGAGGCTTTACAAATGACCCGGAGACTTTACAA
1 ATGACCC-AAGGCTTTACAAATGACCCGAAGGCTTTACAA
3647880 AT
1 AT
3647882 TCGTGGGAAA
Statistics
Matches: 101, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
39 7 0.07
40 94 0.93
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (39 bp):
ATGACCCAAGGCTTTACAAATGACCCGAAGGCTTTACAA
Found at i:3647837 original size:60 final size:60
Alignment explanation
Indices: 3647753--3647882 Score: 181
Period size: 60 Copynumber: 2.2 Consensus size: 60
3647743 ACCCGAAGGT
*
3647753 TTTACAAATTACCCGAAGGCTTTACAAATAACCCGAAGGCTTTACAAATGACACATAGAC
1 TTTACAAATTACCCGAAGGCTTTACAAATAACCCGAAGGCTTTACAAATGACACAGAGAC
* * * * * *
3647813 TTTACAAATGT-CCCGGAGGTTTTACAAATGACCCGGAGGCTTTACAAATGACCCGGAGAC
1 TTTACAAAT-TACCCGAAGGCTTTACAAATAACCCGAAGGCTTTACAAATGACACAGAGAC
3647873 TTTACAAATT
1 TTTACAAATT
3647883 CGTGGGAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
59 1 0.02
60 60 0.97
61 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.25
Consensus pattern (60 bp):
TTTACAAATTACCCGAAGGCTTTACAAATAACCCGAAGGCTTTACAAATGACACAGAGAC
Found at i:3657573 original size:12 final size:12
Alignment explanation
Indices: 3657558--3657585 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3657548 ATAGTGACAA
3657558 ATGACATGACGG
1 ATGACATGACGG
3657570 ATGACATGACGG
1 ATGACATGACGG
3657582 ATGA
1 ATGA
3657586 GCTAAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.14, G:0.32, T:0.18
Consensus pattern (12 bp):
ATGACATGACGG
Found at i:3657675 original size:23 final size:22
Alignment explanation
Indices: 3657649--3657713 Score: 67
Period size: 24 Copynumber: 2.8 Consensus size: 22
3657639 AATTAAAGGC
**
3657649 TTATTTATTTTTAAAAATAAAAA
1 TTATTTAAATTTAAAAAT-AAAA
*
3657672 TTATTTTAAATTTAAATATAAAA
1 TTA-TTTAAATTTAAAAATAAAA
3657695 TTATTTAAATATTCAAAAA
1 TTATTTAAAT-TT-AAAAA
3657714 ATTAACATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 7 0.20
23 12 0.34
24 16 0.46
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
TTATTTAAATTTAAAAATAAAA
Found at i:3657679 original size:24 final size:23
Alignment explanation
Indices: 3657658--3657713 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 23
3657648 CTTATTTATT
3657658 TTTAAAAATAAAAATTATTTTAAA
1 TTTAAAAAT-AAAATTATTTTAAA
*
3657682 TTTAAATATAAAATTA-TTTAAA
1 TTTAAAAATAAAATTATTTTAAA
3657704 TATTCAAAAA
1 T-TT-AAAAA
3657714 ATTAACATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 7 0.25
23 9 0.32
24 12 0.43
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
TTTAAAAATAAAATTATTTTAAA
Found at i:3657701 original size:22 final size:22
Alignment explanation
Indices: 3657663--3657704 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
3657653 TTATTTTTAA
3657663 AAATAAAAATTATTTTAAATTT
1 AAATAAAAATTATTTTAAATTT
3657685 AAATATAAAATTA-TTTAAAT
1 AAATA-AAAATTATTTTAAAT
3657705 ATTCAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AAATAAAAATTATTTTAAATTT
Found at i:3658264 original size:2 final size:2
Alignment explanation
Indices: 3658257--3658341 Score: 170
Period size: 2 Copynumber: 42.5 Consensus size: 2
3658247 TTTAATAACT
3658257 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3658299 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3658341 T
1 T
3658342 CCTTTTACAA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3658523 original size:8 final size:8
Alignment explanation
Indices: 3658512--3658553 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
3658502 TATTTAATTT
3658512 TTTGAATA
1 TTTGAATA
3658520 TTTGAATA
1 TTTGAATA
3658528 TTTGAATGA
1 TTTGAAT-A
*
3658537 TTT-TATA
1 TTTGAATA
3658544 TTT-AATA
1 TTTGAATA
3658551 TTT
1 TTT
3658554 AAAATAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
7 10 0.32
8 17 0.55
9 4 0.13
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (8 bp):
TTTGAATA
Found at i:3658531 original size:16 final size:15
Alignment explanation
Indices: 3658502--3658555 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
3658492 TTTATTTTTT
*
3658502 TATTTAATTTTTTGAA
1 TATTTAA-TATTTGAA
3658518 TATTTGAATATTTGAA
1 TATTT-AATATTTGAA
*
3658534 TGATTTTATATTT-AA
1 T-ATTTAATATTTGAA
3658549 TATTTAA
1 TATTTAA
3658556 AATAATTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
14 5 0.15
15 3 0.09
16 19 0.58
17 6 0.18
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (15 bp):
TATTTAATATTTGAA
Found at i:3658563 original size:24 final size:24
Alignment explanation
Indices: 3658517--3658564 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
3658507 AATTTTTTGA
* *
3658517 ATATTTGAATATTTGAATGATTTT
1 ATATTTGAATATTTAAATAATTTT
3658541 ATATTT-AATATTTAAAATAATTTT
1 ATATTTGAATATTT-AAATAATTTT
3658565 TGTTTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (24 bp):
ATATTTGAATATTTAAATAATTTT
Found at i:3660317 original size:24 final size:24
Alignment explanation
Indices: 3660289--3660350 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
3660279 ACTTGAACTG
3660289 TTGACTTTGACCTGCCCATTGAAT
1 TTGACTTTGACCTGCCCATTGAAT
* * * *
3660313 TTGACTTTGACATTCCCGTTGACT
1 TTGACTTTGACCTGCCCATTGAAT
*
3660337 TTGACCGTTGACCT
1 TTGA-CTTTGACCT
3660351 TTGACTTTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
24 24 0.77
25 7 0.23
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.39
Consensus pattern (24 bp):
TTGACTTTGACCTGCCCATTGAAT
Found at i:3660356 original size:20 final size:20
Alignment explanation
Indices: 3660331--3660382 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
3660321 GACATTCCCG
3660331 TTGACTTTGACCGTTGACCT
1 TTGACTTTGACCGTTGACCT
**
3660351 TTGACTTTGACCGTTGATTT
1 TTGACTTTGACCGTTGACCT
3660371 TTGACTTTGACC
1 TTGACTTTGACC
3660383 AAACTTCCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.44
Consensus pattern (20 bp):
TTGACTTTGACCGTTGACCT
Found at i:3667698 original size:17 final size:17
Alignment explanation
Indices: 3667676--3667708 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3667666 TTTCTCTAGG
3667676 GAAATTTCTTGTAGGAT
1 GAAATTTCTTGTAGGAT
3667693 GAAATTTCTTGTAGGA
1 GAAATTTCTTGTAGGA
3667709 GGCGAGAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.06, G:0.24, T:0.39
Consensus pattern (17 bp):
GAAATTTCTTGTAGGAT
Found at i:3669166 original size:20 final size:20
Alignment explanation
Indices: 3669126--3669171 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
3669116 AGTGAGGGTG
*
3669126 TTGATATTGAAAGGTCGGTA
1 TTGATATTGAAAGGTCAGTA
3669146 TTGATATTGAAA-GTCTAGTA
1 TTGATATTGAAAGGTC-AGTA
*
3669166 TCGATA
1 TTGATA
3669172 CCAAGGTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.37
Consensus pattern (20 bp):
TTGATATTGAAAGGTCAGTA
Found at i:3674095 original size:97 final size:97
Alignment explanation
Indices: 3673890--3674107 Score: 235
Period size: 97 Copynumber: 2.2 Consensus size: 97
3673880 AAAACATAAA
* *
3673890 ATCATAGTTCATAAACCAGTAAATTTCATGATTCCATAAATCAAGAATAATTCATATTTTCCAGT
1 ATCATAGTTCATAAACCAGTAAATTCCATGATTCCATAAATCAAGAACAATTCATATTTTCCAGT
* **
3673955 GAAAACAAAAAACTCGATAACACATTTCAGGT
66 GAAAACAAAAAACTCAATAACACATACCAGGT
* * ** *
3673987 ACCATAATTCATAAACCAGTAAATTCCATGATTCCATAAATCATTAACAATTCATAGTTTTCTA-
1 ATCATAGTTCATAAACCAGTAAATTCCATGATTCCATAAATCAAGAACAATTCATA-TTTTCCAG
** * *
3674051 TGAAAAC-CGAAA-TCAAATATCACATACCATGTT
65 TGAAAACAAAAAACTC-AATAACACATACCA-GGT
* * *
3674084 GTCATGGTTCATAAACCATTAAAT
1 ATCATAGTTCATAAACCAGTAAAT
3674108 CAATACTTTC
Statistics
Matches: 99, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
95 2 0.02
96 13 0.13
97 78 0.79
98 6 0.06
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (97 bp):
ATCATAGTTCATAAACCAGTAAATTCCATGATTCCATAAATCAAGAACAATTCATATTTTCCAGT
GAAAACAAAAAACTCAATAACACATACCAGGT
Found at i:3677098 original size:18 final size:18
Alignment explanation
Indices: 3677075--3677111 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3677065 TTCCTTTCTT
3677075 CTTCCTTGGGTTTTCCTC
1 CTTCCTTGGGTTTTCCTC
3677093 CTTCCTTGGGTTTTCCTC
1 CTTCCTTGGGTTTTCCTC
3677111 C
1 C
3677112 ATTGATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.00, C:0.35, G:0.16, T:0.49
Consensus pattern (18 bp):
CTTCCTTGGGTTTTCCTC
Found at i:3677371 original size:23 final size:23
Alignment explanation
Indices: 3677341--3677389 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
3677331 TGGTGGTTGG
*
3677341 TTTAATGG-ATGTTTAGACTTTAT
1 TTTAATGGTATATTTA-ACTTTAT
*
3677364 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
3677387 TTT
1 TTT
3677390 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:3690333 original size:31 final size:31
Alignment explanation
Indices: 3690275--3690333 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
3690265 CTACGGATGC
* * * *
3690275 TTGAACTTTGATCTTTGCTTTGCTTGTTTAA
1 TTGAACTTGGATATTTGCATTACTTGTTTAA
*
3690306 TTGAACTTGGATATTTGCATTATTTGTT
1 TTGAACTTGGATATTTGCATTACTTGTT
3690334 AAAACATTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.19, C:0.10, G:0.17, T:0.54
Consensus pattern (31 bp):
TTGAACTTGGATATTTGCATTACTTGTTTAA
Found at i:3696938 original size:23 final size:23
Alignment explanation
Indices: 3696908--3696956 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
3696898 TGGTGGTTGG
*
3696908 TTTAATGG-ATGTTTAGACTTTAT
1 TTTAATGGTATATTTA-ACTTTAT
*
3696931 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
3696954 TTT
1 TTT
3696957 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:3703812 original size:18 final size:17
Alignment explanation
Indices: 3703798--3703842 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
3703788 ATTAACTTGA
3703798 TTTATTGAATGAACTAG
1 TTTATTGAATGAACTAG
*
3703815 TTTAATGAATGAACTAG
1 TTTATTGAATGAACTAG
3703832 CTTTATTGAAT
1 -TTTATTGAAT
3703843 AAAGAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 16 0.64
18 9 0.36
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.42
Consensus pattern (17 bp):
TTTATTGAATGAACTAG
Found at i:3703823 original size:17 final size:18
Alignment explanation
Indices: 3703783--3703842 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 18
3703773 GCTTCAATTC
* *
3703783 AATGAATTAACTTGATTT
1 AATGAATGAACTAGATTT
*
3703801 ATTGAATGAACTAG-TTT
1 AATGAATGAACTAGATTT
*
3703818 AATGAATGAACTAGCTTT
1 AATGAATGAACTAGATTT
*
3703836 ATTGAAT
1 AATGAAT
3703843 AAAGAATATA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
17 16 0.44
18 20 0.56
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (18 bp):
AATGAATGAACTAGATTT
Found at i:3718275 original size:23 final size:23
Alignment explanation
Indices: 3718232--3718275 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3718222 CTGAAAAAGG
* *
3718232 TAAACAAAAATAACAAGTAAATA
1 TAAACAAAAAGAACAAATAAATA
*
3718255 TAAACAAAAAGAAGAAATAAA
1 TAAACAAAAAGAACAAATAAA
3718276 ATAGTGTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.73, C:0.07, G:0.07, T:0.14
Consensus pattern (23 bp):
TAAACAAAAAGAACAAATAAATA
Found at i:3739758 original size:24 final size:24
Alignment explanation
Indices: 3739721--3739768 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3739711 ACAGATGAGT
*
3739721 ACCATTATCGTAGGTTCAAGGAGA
1 ACCATTATCATAGGTTCAAGGAGA
* *
3739745 ACCATTGTCATAGGTTCATGGAGA
1 ACCATTATCATAGGTTCAAGGAGA
3739769 GACTACACCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (24 bp):
ACCATTATCATAGGTTCAAGGAGA
Found at i:3750542 original size:22 final size:22
Alignment explanation
Indices: 3750514--3750562 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
3750504 GTGTTTTATT
3750514 GCTTTCGAATAGAAAAATAATA
1 GCTTTCGAATAGAAAAATAATA
* *
3750536 GCTTTCGCATAGGAAAATAATA
1 GCTTTCGAATAGAAAAATAATA
3750558 GCTTT
1 GCTTT
3750563 TGAAAACGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (22 bp):
GCTTTCGAATAGAAAAATAATA
Found at i:3751667 original size:41 final size:42
Alignment explanation
Indices: 3751562--3751669 Score: 114
Period size: 41 Copynumber: 2.6 Consensus size: 42
3751552 AAACTACCGC
* *
3751562 AATAG-GTTCATCCATAGTGGCGTTTTTATAACAAACGTCGT
1 AATAGAGTTCATCTATAGTGGCGTTTTTATAACAAACGCCGT
* * * * *
3751603 TATAGAGTAC-TGCTTTAGCGGCGTTTTTAT-ATAAACGCCGT
1 AATAGAGTTCAT-CTATAGTGGCGTTTTTATAACAAACGCCGT
*
3751644 AATATAGTTCATCTATAGTGGCGTTT
1 AATAGAGTTCATCTATAGTGGCGTTT
3751670 ACAACAAACT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
41 33 0.63
42 19 0.37
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (42 bp):
AATAGAGTTCATCTATAGTGGCGTTTTTATAACAAACGCCGT
Found at i:3751704 original size:81 final size:82
Alignment explanation
Indices: 3751567--3751723 Score: 210
Period size: 81 Copynumber: 1.9 Consensus size: 82
3751557 ACCGCAATAG
* * * * *
3751567 GTTCATCCATAGTGGCGTTTTTATAACAAACGTCGTTATAGAGTACTGCTTTAGCGGCGTTTTTA
1 GTTCATCCATAGTGGCG-TTTTACAACAAACGTCGATATAGAATACTACATTAGCGGCGTTTTTA
*
3751632 TATAAACGCCGTAATATA
65 TACAAACGCCGTAATATA
* *
3751650 GTTCATCTATAGTGGCG-TTTACAACAAAC-TCCGATATAGAATAGTACATTAGCGGCGTTTTTA
1 GTTCATCCATAGTGGCGTTTTACAACAAACGT-CGATATAGAATACTACATTAGCGGCGTTTTTA
3751713 TACAAACGCCG
65 TACAAACGCCG
3751724 CAGTAGATGT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
80 1 0.02
81 48 0.74
83 16 0.25
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Consensus pattern (82 bp):
GTTCATCCATAGTGGCGTTTTACAACAAACGTCGATATAGAATACTACATTAGCGGCGTTTTTAT
ACAAACGCCGTAATATA
Found at i:3753752 original size:16 final size:16
Alignment explanation
Indices: 3753721--3753754 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3753711 CTTGCTCCCA
3753721 TAAAATTTTATCAATT
1 TAAAATTTTATCAATT
3753737 TAAAAGTTTTAT-AATT
1 TAAAA-TTTTATCAATT
3753753 TA
1 TA
3753755 GGAGTGATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (16 bp):
TAAAATTTTATCAATT
Found at i:3759221 original size:21 final size:21
Alignment explanation
Indices: 3759205--3759244 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3759195 ATGAAGCGAG
*
3759205 GGAAGCAGAGAGAGAAGCAAC
1 GGAAGCACAGAGAGAAGCAAC
*
3759226 GGAAGCACATAGAGAAGCA
1 GGAAGCACAGAGAGAAGCA
3759245 GCATATCAGC
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:0.47, C:0.15, G:0.35, T:0.03
Consensus pattern (21 bp):
GGAAGCACAGAGAGAAGCAAC
Found at i:3759694 original size:43 final size:42
Alignment explanation
Indices: 3759647--3759765 Score: 139
Period size: 43 Copynumber: 2.7 Consensus size: 42
3759637 AGTTTAGCTA
3759647 TTTTGTGGCGTTTGTATCGAAAAACGTCGCTATATACCAGACC
1 TTTTGTGGCGTTTGTATCGAAAAACG-CGCTATATACCAGACC
* * * *
3759690 TTTTGTGGTGTTTGTATCAAAAAACGCTGCTATATACCATATC
1 TTTTGTGGCGTTTGTATCGAAAAACGC-GCTATATACCAGACC
* * *
3759733 TTTTGCGACGTTTGTATCCGACAAACGCCGCTA
1 TTTTGTGGCGTTTGTAT-CGAAAAACG-CGCTA
3759766 AATATCTTAA
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
42 1 0.02
43 51 0.80
44 11 0.17
45 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.34
Consensus pattern (42 bp):
TTTTGTGGCGTTTGTATCGAAAAACGCGCTATATACCAGACC
Found at i:3762078 original size:14 final size:12
Alignment explanation
Indices: 3762050--3762074 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3762040 TGAATAATAG
3762050 TTTAAAAAAAAC
1 TTTAAAAAAAAC
3762062 TTTAAAAAAAAC
1 TTTAAAAAAAAC
3762074 T
1 T
3762075 CTTTGATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (12 bp):
TTTAAAAAAAAC
Found at i:3762629 original size:9 final size:9
Alignment explanation
Indices: 3762617--3762648 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
3762607 TCTTCTTTAC
3762617 TTTTTTATTT
1 TTTTTTA-TT
3762627 TTTTTTATT
1 TTTTTTATT
3762636 TTTTTTATT
1 TTTTTTATT
3762645 TTTT
1 TTTT
3762649 GAATGGTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 15 0.68
10 7 0.32
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (9 bp):
TTTTTTATT
Found at i:3762632 original size:10 final size:10
Alignment explanation
Indices: 3762617--3762648 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
3762607 TCTTCTTTAC
3762617 TTTTTTATTT
1 TTTTTTATTT
3762627 TTTTTTA-TT
1 TTTTTTATTT
3762636 TTTTTTATTT
1 TTTTTTATTT
3762646 TTT
1 TTT
3762649 GAATGGTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTTTTATTT
Found at i:3762717 original size:3 final size:3
Alignment explanation
Indices: 3762709--3762762 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
3762699 TTCAAAAGAA
3762709 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
3762757 CTT CTT
1 CTT CTT
3762763 TACTTTTTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:3764884 original size:33 final size:34
Alignment explanation
Indices: 3764844--3764938 Score: 167
Period size: 33 Copynumber: 2.9 Consensus size: 34
3764834 TGTTCAAAGT
*
3764844 TTGGCCACCAACCAAGATAAAATTTCCAATAA-G
1 TTGGCCACCAACCAAGATGAAATTTCCAATAAGG
3764877 TTGGCCACCAACCAAGATGAAATTTCCAATAAGG
1 TTGGCCACCAACCAAGATGAAATTTCCAATAAGG
3764911 TT-GCCACCAACCAAGATGAAATTTCCAA
1 TTGGCCACCAACCAAGATGAAATTTCCAA
3764939 CTTGCCAACT
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
33 57 0.95
34 3 0.05
ACGTcount: A:0.40, C:0.25, G:0.14, T:0.21
Consensus pattern (34 bp):
TTGGCCACCAACCAAGATGAAATTTCCAATAAGG
Found at i:3774739 original size:10 final size:11
Alignment explanation
Indices: 3774710--3774739 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
3774700 ACATAAGTAT
3774710 AAGAGATGATA
1 AAGAGATGATA
3774721 AAGAGATGATA
1 AAGAGATGATA
3774732 AAGA-ATGA
1 AAGAGATGA
3774740 GGTTCTGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.21
11 15 0.79
ACGTcount: A:0.57, C:0.00, G:0.27, T:0.17
Consensus pattern (11 bp):
AAGAGATGATA
Found at i:3777078 original size:31 final size:31
Alignment explanation
Indices: 3777038--3777111 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
3777028 AAGAGTCGAG
* *
3777038 GGTTACCTATGTCCTTC-AGGACATATAGATA
1 GGTTACCTATGTACTTCGA-GACATATAGACA
* * *
3777069 GTTTACCTATTTACTTCGAGACATATGGACA
1 GGTTACCTATGTACTTCGAGACATATAGACA
3777100 GGTTACCTATGT
1 GGTTACCTATGT
3777112 TCTTTGGAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
31 34 0.97
32 1 0.03
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (31 bp):
GGTTACCTATGTACTTCGAGACATATAGACA
Found at i:3786369 original size:11 final size:11
Alignment explanation
Indices: 3786343--3786384 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
3786333 TGAAGGTACT
*
3786343 GGTTCAATCG-
1 GGTTCAACCGC
3786353 GGTTCAACCGC
1 GGTTCAACCGC
3786364 GGTTCAACCGC
1 GGTTCAACCGC
3786375 GGTTCAACCG
1 GGTTCAACCG
3786385 GATTTTATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
10 9 0.30
11 21 0.70
ACGTcount: A:0.19, C:0.31, G:0.29, T:0.21
Consensus pattern (11 bp):
GGTTCAACCGC
Found at i:3787524 original size:16 final size:16
Alignment explanation
Indices: 3787503--3787536 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3787493 CACTCTTAAA
3787503 ATTTTAAAGT-TTTTAT
1 ATTTTAAA-TATTTTAT
3787519 ATTTTAAATATTTTAT
1 ATTTTAAATATTTTAT
3787535 AT
1 AT
3787537 AAATTATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 16 0.94
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
ATTTTAAATATTTTAT
Found at i:3787552 original size:35 final size:33
Alignment explanation
Indices: 3787513--3787580 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 33
3787503 ATTTTAAAGT
*
3787513 TTTTATATTT-TAAATATTTTATATAAATTATTTAA
1 TTTTATATTTCTAAAT-TTTAATAT-AATT-TTTAA
3787548 TTTTATATTTCTAAATTTTAATATAATTTTTAA
1 TTTTATATTTCTAAATTTTAATATAATTTTTAA
3787581 AATTTACGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 5 0.16
34 4 0.13
35 17 0.55
36 5 0.16
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (33 bp):
TTTTATATTTCTAAATTTTAATATAATTTTTAA
Found at i:3787585 original size:35 final size:36
Alignment explanation
Indices: 3787499--3787585 Score: 92
Period size: 35 Copynumber: 2.4 Consensus size: 36
3787489 CTTCCACTCT
* * *
3787499 TAAAATTTTAAAGTTTTTATATTTTAAATATTTTATA
1 TAAATTTTTAAA-ATTTTATATTTTAAATATTTAATA
3787536 TAAATTATTT--AATTTTATATTTCTAAAT-TTTAATA
1 TAAATT-TTTAAAATTTTATATTT-TAAATATTTAATA
3787571 T-AATTTTTAAAATTT
1 TAAATTTTTAAAATTT
3787586 ACGTCTCTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
33 3 0.07
34 4 0.09
35 22 0.51
36 6 0.14
37 5 0.12
38 3 0.07
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (36 bp):
TAAATTTTTAAAATTTTATATTTTAAATATTTAATA
Found at i:3788893 original size:30 final size:30
Alignment explanation
Indices: 3788792--3788898 Score: 92
Period size: 30 Copynumber: 3.6 Consensus size: 30
3788782 TACTTTTATC
* **
3788792 TAAGTACCTAAAGTTTTTTTTTTATCAAAA
1 TAAGTACCTAAAGTATTTTTTTGGTCAAAA
* * * *
3788822 CAAGTATCTAAA-CATACTTTTTGGTCAAAA
1 TAAGTACCTAAAGTAT-TTTTTTGGTCAAAA
* *
3788852 TAGGTTA-CTAAAGTATTTTTTTGGTTAAAA
1 TAAG-TACCTAAAGTATTTTTTTGGTCAAAA
*
3788882 TAAGTACCTAAATTATT
1 TAAGTACCTAAAGTATT
3788899 CATTTATTCA
Statistics
Matches: 59, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
29 3 0.05
30 52 0.88
31 4 0.07
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.42
Consensus pattern (30 bp):
TAAGTACCTAAAGTATTTTTTTGGTCAAAA
Found at i:3789032 original size:28 final size:28
Alignment explanation
Indices: 3788974--3789032 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
3788964 TAAAAAAATT
* **
3788974 AAATACTCTAAGTATCTATTTTGACTGA
1 AAATACTCTAAGTACCTATTTTGACCAA
* *
3789002 AAATACTTTTAGTACCTATTTTGACCAA
1 AAATACTCTAAGTACCTATTTTGACCAA
3789030 AAA
1 AAA
3789033 AATAAGTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.37
Consensus pattern (28 bp):
AAATACTCTAAGTACCTATTTTGACCAA
Found at i:3789584 original size:24 final size:24
Alignment explanation
Indices: 3789557--3789660 Score: 97
Period size: 24 Copynumber: 4.2 Consensus size: 24
3789547 ATATATATAT
*
3789557 ATATATATATATATTAACTT-TAAA
1 ATATAT-TTTATATTAACTTATAAA
*
3789581 ATATATTTTTATATTAACTTATTAA
1 ATATA-TTTTATATTAACTTATAAA
3789606 ATATATTTTATTATTAACTTAATTTAAA
1 ATATATTTTA-TATTAACTT-A--TAAA
* *
3789634 ATAT-TTTTATTTTAATTTA-AAA
1 ATATATTTTATATTAACTTATAAA
3789656 ATATA
1 ATATA
3789661 CATTTTATGT
Statistics
Matches: 68, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
22 7 0.10
24 22 0.32
25 19 0.28
26 8 0.12
27 5 0.07
28 7 0.10
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (24 bp):
ATATATTTTATATTAACTTATAAA
Found at i:3789586 original size:2 final size:2
Alignment explanation
Indices: 3789535--3789570 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3789525 TAAATTCATA
3789535 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3789571 TAACTTTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3789648 original size:21 final size:21
Alignment explanation
Indices: 3789624--3789681 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
3789614 TATTATTAAC
*
3789624 TTAATTTAAAATATTTTTATT
1 TTAATTTAAAATATTTTCATT
* *
3789645 TTAATTTAAAA-ATATACATT
1 TTAATTTAAAATATTTTCATT
3789665 TT-ATGTTAAAATATTTT
1 TTAAT-TTAAAATATTTT
3789682 GAAGTTAAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.07
20 14 0.47
21 14 0.47
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (21 bp):
TTAATTTAAAATATTTTCATT
Found at i:3789897 original size:28 final size:28
Alignment explanation
Indices: 3789862--3789958 Score: 106
Period size: 28 Copynumber: 3.4 Consensus size: 28
3789852 TAAAAAAATT
3789862 AAATATTTTAATTACCTATTTTGACTAA
1 AAATATTTTAATTACCTATTTTGACTAA
* *
3789890 AAATATTTTAAGTACCTATTTTGACCAAA
1 AAATATTTTAATTACCTATTTTGA-CTAA
* * *
3789919 AAATAAGTTT-ATATACTTAGTTTGACTAA
1 AAAT-ATTTTAAT-TACCTATTTTGACTAA
3789948 AACATATTTTA
1 AA-ATATTTTA
3789959 GGTACTTCAA
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
28 23 0.41
29 17 0.30
30 16 0.29
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.42
Consensus pattern (28 bp):
AAATATTTTAATTACCTATTTTGACTAA
Found at i:3790462 original size:24 final size:25
Alignment explanation
Indices: 3790435--3790489 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
3790425 ATATATATAT
*
3790435 ATATATATATATATTAACTT-TAAA
1 ATATATATATAAATTAACTTATAAA
* * *
3790459 ATATATTTTTAAATTAACTTATTAA
1 ATATATATATAAATTAACTTATAAA
3790484 ATATAT
1 ATATAT
3790490 TTTATTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 17 0.65
25 9 0.35
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (25 bp):
ATATATATATAAATTAACTTATAAA
Found at i:3790464 original size:2 final size:2
Alignment explanation
Indices: 3790416--3790448 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3790406 TAAATTCATA
3790416 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3790449 TAACTTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3790533 original size:20 final size:20
Alignment explanation
Indices: 3790505--3790559 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
3790495 TTTTAACTTA
*
3790505 ATTTAAAAAAAATTTATTTT
1 ATTTTAAAAAAATTTATTTT
** *
3790525 ATTTTAAAAATGTATATTTT
1 ATTTTAAAAAAATTTATTTT
* *
3790545 ATGTTAAAATAATTT
1 ATTTTAAAAAAATTT
3790560 GAAGTTAAGG
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (20 bp):
ATTTTAAAAAAATTTATTTT
Found at i:3790737 original size:2 final size:2
Alignment explanation
Indices: 3790695--3790720 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3790685 GATAAGAATA
3790695 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3790721 TAAATAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3790786 original size:26 final size:25
Alignment explanation
Indices: 3790721--3790815 Score: 88
Period size: 25 Copynumber: 3.7 Consensus size: 25
3790711 ATATATATAT
3790721 TAAATA-AAAAAATATATTTTTAAA
1 TAAATATAAAAAATATATTTTTAAA
* * *
3790745 TAAGTTAGTAGTAAAATATATTTAATAAA
1 TAA-ATA-TA-AAAAATATATTT-TTAAA
3790774 TAAATATAAAAAATAT-TTTTTAAA
1 TAAATATAAAAAATATATTTTTAAA
*
3790798 TTTAATATAAAAAA-ATAT
1 -TAAATATAAAAAATATAT
3790816 GAATTTAAGT
Statistics
Matches: 57, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
24 9 0.16
25 18 0.32
26 7 0.12
27 3 0.05
28 13 0.23
29 7 0.12
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (25 bp):
TAAATATAAAAAATATATTTTTAAA
Found at i:3790789 original size:24 final size:25
Alignment explanation
Indices: 3790756--3790811 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
3790746 AAGTTAGTAG
*
3790756 TAAAATATATTTAATAAA-TAAATA
1 TAAAAAATATTTAATAAATTAAATA
** *
3790780 TAAAAAATATTTTTTAAATTTAATA
1 TAAAAAATATTTAATAAATTAAATA
3790805 TAAAAAA
1 TAAAAAA
3790812 ATATGAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 15 0.56
25 12 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
TAAAAAATATTTAATAAATTAAATA
Found at i:3790822 original size:27 final size:25
Alignment explanation
Indices: 3790776--3790828 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
3790766 TTAATAAATA
**
3790776 AATATAAAAAATATTTTTTAAATTT
1 AATATAAAAAATATAATTTAAATTT
*
3790801 AATATAAAAAAATATGAATTTAAGTTT
1 AATAT-AAAAAATAT-AATTTAAATTT
3790828 A
1 A
3790829 GAGACCAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 5 0.22
26 9 0.39
27 9 0.39
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (25 bp):
AATATAAAAAATATAATTTAAATTT
Found at i:3792371 original size:30 final size:30
Alignment explanation
Indices: 3792336--3792396 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
3792326 TTCATATATA
3792336 TATTTTAATTAGATCCTTTAACAACACTTT
1 TATTTTAATTAGATCCTTTAACAACACTTT
3792366 TATTTTAATTAGATCCTTTAACAACACTTT
1 TATTTTAATTAGATCCTTTAACAACACTTT
3792396 T
1 T
3792397 GTTTAGAAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.33, C:0.16, G:0.03, T:0.48
Consensus pattern (30 bp):
TATTTTAATTAGATCCTTTAACAACACTTT
Found at i:3803452 original size:233 final size:228
Alignment explanation
Indices: 3803091--3803554 Score: 831
Period size: 233 Copynumber: 2.0 Consensus size: 228
3803081 TTCAAAGGTT
* *
3803091 AAAATAAAGTTTTACCCTTTCATTAAACTTTTTTTTTTAATTTTGTAAAAAATATATAAATATTA
1 AAAATAAAATTTTACCCTTCCATTAAACTTTTTTTTTTAATTTTGTAAAAAATATATAAATATTA
*
3803156 TGAATTTAAATTTTTTTTAAAGAAAATATATAAATATTTTTCAACTTGTAATATTATACAAATAT
66 TGAATTTAAATTTTTTTTAAAGAAAATATATAAATATTTTCCAACTTGTAATATTATACAAATAT
3803221 ATAATAAGGACAATTTGGTTAAATATACATTCCAATAATCTTTTATTCCTTTAACCAAACACGGT
131 ATAATAAGGACAATTTGGTTAAATATACATTCCAATAATCTTTTATTCCTTTAACCAAACACGGT
*
3803286 AATCTTACATTCATGCTAAGCGAACCAAACACA
196 AATCTTACATTCATGCTAAGCCAACCAAACACA
3803319 AAAATAAAATTTTACCCTTCCATTAAACTTTTATTTTTATTTTTAATTTTGTAAAAAATATATAA
1 AAAATAAAATTTTACCCTTCCATTAAAC-----TTTTT-TTTTTAATTTTGTAAAAAATATATAA
3803384 ATATTATGAATTT-AATTTTTTTTAAAGAAAATATATAAATATTTTCCAACTTGTAATATTATAC
60 ATATTATGAATTTAAATTTTTTTTAAAGAAAATATATAAATATTTTCCAACTTGTAATATTATAC
3803448 AAATATATAATAAGGACAATTTGGTTAAATATACATTCCAATAATCTTTTATTCCTTTAACCAAA
125 AAATATATAATAAGGACAATTTGGTTAAATATACATTCCAATAATCTTTTATTCCTTTAACCAAA
3803513 CACGGTAATCTTACATTCATGCTAAGCCAACCAAACACA
190 CACGGTAATCTTACATTCATGCTAAGCCAACCAAACACA
3803552 AAA
1 AAA
3803555 TACAACATTC
Statistics
Matches: 226, Mismatches: 4, Indels: 7
0.95 0.02 0.03
Matches are distributed among these distances:
228 26 0.12
233 161 0.71
234 39 0.17
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.40
Consensus pattern (228 bp):
AAAATAAAATTTTACCCTTCCATTAAACTTTTTTTTTTAATTTTGTAAAAAATATATAAATATTA
TGAATTTAAATTTTTTTTAAAGAAAATATATAAATATTTTCCAACTTGTAATATTATACAAATAT
ATAATAAGGACAATTTGGTTAAATATACATTCCAATAATCTTTTATTCCTTTAACCAAACACGGT
AATCTTACATTCATGCTAAGCCAACCAAACACA
Found at i:3803606 original size:20 final size:20
Alignment explanation
Indices: 3803581--3803618 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3803571 ATCCTATTAT
3803581 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
3803601 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
3803619 GTGAACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:3804019 original size:15 final size:15
Alignment explanation
Indices: 3803982--3804043 Score: 63
Period size: 16 Copynumber: 4.0 Consensus size: 15
3803972 TTCTATGCAC
*
3803982 TGTTTTTATTATTAAT
1 TGTTTTTATT-TTATT
*
3803998 TATTTTTATGTTTATT
1 TGTTTTTAT-TTTATT
3804014 TGTTTTTATTTTATT
1 TGTTTTTATTTTATT
*
3804029 T-TTTATTTTTTTATT
1 TGTTT-TTATTTTATT
3804044 AACCACTAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
14 3 0.08
15 16 0.40
16 20 0.50
17 1 0.03
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (15 bp):
TGTTTTTATTTTATT
Found at i:3804027 original size:21 final size:21
Alignment explanation
Indices: 3804001--3804040 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3803991 TATTAATTAT
3804001 TTTTA-TGTTTATTTGTTTTTA
1 TTTTATTGTTTATTT-TTTTTA
*
3804022 TTTTATTTTTTATTTTTTT
1 TTTTATTGTTTATTTTTTT
3804041 ATTAACCACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.12, C:0.00, G:0.05, T:0.82
Consensus pattern (21 bp):
TTTTATTGTTTATTTTTTTTA
Found at i:3805464 original size:18 final size:18
Alignment explanation
Indices: 3805429--3805465 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3805419 TAATTTCTCA
*
3805429 TCAATGTAGATCCGACTC
1 TCAATGTAGATCCAACTC
*
3805447 TCAATGTAGATCTAACTC
1 TCAATGTAGATCCAACTC
3805465 T
1 T
3805466 TAATTTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (18 bp):
TCAATGTAGATCCAACTC
Found at i:3806325 original size:3 final size:3
Alignment explanation
Indices: 3806317--3806348 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3806307 CATCTAACAC
3806317 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3806349 ATAACCTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3807112 original size:21 final size:22
Alignment explanation
Indices: 3807076--3807116 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3807066 TTAAAAATTA
*
3807076 TAAAGGAAGTATCGATACTCAT
1 TAAAGGAAGTACCGATACTCAT
3807098 TAAAGG-AGTACCGATACTC
1 TAAAGGAAGTACCGATACTC
3807117 CATGTCCTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (22 bp):
TAAAGGAAGTACCGATACTCAT
Found at i:3811072 original size:20 final size:20
Alignment explanation
Indices: 3811043--3811099 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 20
3811033 AGAAAAGGAT
3811043 AAAACTATTTTCTTTTAAACA
1 AAAAC-ATTTTCTTTTAAACA
3811064 AAAACATTTTTTTCTTTTAAACA
1 AAAACA---TTTTCTTTTAAACA
* *
3811087 AAACCTTTTTCTT
1 AAAACATTTTCTT
3811100 ATATTGTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
20 8 0.26
21 5 0.16
23 18 0.58
ACGTcount: A:0.37, C:0.16, G:0.00, T:0.47
Consensus pattern (20 bp):
AAAACATTTTCTTTTAAACA
Found at i:3811731 original size:36 final size:36
Alignment explanation
Indices: 3811622--3811753 Score: 178
Period size: 35 Copynumber: 3.7 Consensus size: 36
3811612 AACACAATCA
3811622 TCAATTACATTCTAAACCCCAAATT-CAAAAATGCT
1 TCAATTACATTCTAAACCCCAAATTCCAAAAATGCT
*
3811657 TCAATTACATTTTAAACCCCAAATTCC-AAAATGCT
1 TCAATTACATTCTAAACCCCAAATTCCAAAAATGCT
* * *
3811692 TCAATTACATTCTAAACCTCTAATTCCAAAAATACT
1 TCAATTACATTCTAAACCCCAAATTCCAAAAATGCT
* ** *
3811728 TCAATTATATTCCCAACTCCAAATTC
1 TCAATTACATTCTAAACCCCAAATTC
3811754 ATAATCCATT
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
35 56 0.67
36 28 0.33
ACGTcount: A:0.40, C:0.27, G:0.02, T:0.32
Consensus pattern (36 bp):
TCAATTACATTCTAAACCCCAAATTCCAAAAATGCT
Found at i:3811752 original size:71 final size:70
Alignment explanation
Indices: 3811622--3811753 Score: 183
Period size: 71 Copynumber: 1.9 Consensus size: 70
3811612 AACACAATCA
* **
3811622 TCAATTACATTCTAAACCCCAAATTCAAAAATGCTTCAATTACATTTTAAACCCCAAATTCCAAA
1 TCAATTACATTCTAAACCCCAAATTCAAAAATACTTCAATTACATTCCAAACCCCAAATTCCAAA
3811687 ATGCT
66 ATGCT
* * * * *
3811692 TCAATTACATTCTAAACCTCTAATTCCAAAAATACTTCAATTATATTCCCAACTCCAAATTC
1 TCAATTACATTCTAAACCCCAAATT-CAAAAATACTTCAATTACATTCCAAACCCCAAATTC
3811754 ATAATCCATT
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
70 23 0.43
71 30 0.57
ACGTcount: A:0.40, C:0.27, G:0.02, T:0.32
Consensus pattern (70 bp):
TCAATTACATTCTAAACCCCAAATTCAAAAATACTTCAATTACATTCCAAACCCCAAATTCCAAA
ATGCT
Found at i:3812508 original size:148 final size:148
Alignment explanation
Indices: 3812236--3812523 Score: 472
Period size: 148 Copynumber: 1.9 Consensus size: 148
3812226 AAACTATTTA
* *
3812236 AATTAGAATCAAATAATATTATAGTATTATAAATATTTATAATTAAATTTAAACAAAAACTCAGA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAAAAACTCAGA
3812301 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAACAGAAAAATTTGTGAGTCAACT
66 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAACAGAAAAATTTGTGAGTCAACT
*
3812366 GTTTTATAAACTGAACTG
131 ATTTTATAAACTGAACTG
* * *
3812384 AATTAGAATCAAATAATATTATAATATGATAACTATTTATAATTAAATTTAAACAGAAACT-TGA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAAAAACTCAG-
* *
3812448 AAATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATC-GAAAACTTTTTGAGTCAA
65 AAATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAA-CAGAAAAATTTGTGAGTCAA
3812512 CTATTTTATAAA
129 CTATTTTATAAA
3812524 TTTAATTGAG
Statistics
Matches: 130, Mismatches: 8, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
147 1 0.01
148 128 0.98
149 1 0.01
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.37
Consensus pattern (148 bp):
AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAAAAACTCAGA
AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAACAGAAAAATTTGTGAGTCAACT
ATTTTATAAACTGAACTG
Found at i:3812747 original size:35 final size:35
Alignment explanation
Indices: 3812708--3812789 Score: 121
Period size: 35 Copynumber: 2.3 Consensus size: 35
3812698 GGGGTTGGAC
*
3812708 ATGTAATTGATGTATTTTGGGA-TTTGAGGTTTAGA
1 ATGTAATTGATGCATTTT-GGATTTTGAGGTTTAGA
* *
3812743 ATGTAATTGAAGCATTTTGGATTTTGGGGTTTAGA
1 ATGTAATTGATGCATTTTGGATTTTGAGGTTTAGA
3812778 ATGTAATTGATG
1 ATGTAATTGATG
3812790 ACTGTGTTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
34 3 0.07
35 39 0.93
ACGTcount: A:0.27, C:0.01, G:0.28, T:0.44
Consensus pattern (35 bp):
ATGTAATTGATGCATTTTGGATTTTGAGGTTTAGA
Found at i:3814983 original size:14 final size:14
Alignment explanation
Indices: 3814964--3815004 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
3814954 CCATAGCTTC
3814964 AAAAAGGTTTTTGG
1 AAAAAGGTTTTTGG
*
3814978 AAAAAGATTTTTGG
1 AAAAAGGTTTTTGG
3814992 AAAAAGGTTTTTG
1 AAAAAGGTTTTTG
3815005 CTGAAGATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (14 bp):
AAAAAGGTTTTTGG
Found at i:3816260 original size:138 final size:138
Alignment explanation
Indices: 3816012--3816265 Score: 382
Period size: 138 Copynumber: 1.8 Consensus size: 138
3816002 CTAAGTGCTG
* * *
3816012 AAATGGAAATTTACAAACTCATTATGAATTCCATGGATGCACCTATAGTGCCGAAAGTACACATA
1 AAATGGAAATTCACAAACTCATTATGAATACCATGGATGCACATATAGTGCCGAAAGTACACATA
* *
3816077 GTACTGATACAAAAATGCATCGTTATACATTAAACAAAATCGATCGATAACTTTTATACATAATT
66 GTACTGATACAAAAATGCACCATTATACATTAAACAAAATCGATCGATAACTTTTATACATAATT
3816142 GTATGTCA
131 GTATGTCA
* * * * *
3816150 AAATGGTAATTCACAAACTCATTATGAATACCTTGGTTGGACATCTAGTGCCGAAAGTACACATA
1 AAATGGAAATTCACAAACTCATTATGAATACCATGGATGCACATATAGTGCCGAAAGTACACATA
* * **
3816215 GTACTGATACGAAAATGCACCATTATGCATTACTCAAAATCGATCGATAAC
66 GTACTGATACAAAAATGCACCATTATACATTAAACAAAATCGATCGATAAC
3816266 CATTACATAC
Statistics
Matches: 102, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
138 102 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.28
Consensus pattern (138 bp):
AAATGGAAATTCACAAACTCATTATGAATACCATGGATGCACATATAGTGCCGAAAGTACACATA
GTACTGATACAAAAATGCACCATTATACATTAAACAAAATCGATCGATAACTTTTATACATAATT
GTATGTCA
Found at i:3820914 original size:16 final size:16
Alignment explanation
Indices: 3820893--3820927 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
3820883 AACATTATCA
3820893 ATGCAAATGACTAAGT
1 ATGCAAATGACTAAGT
3820909 ATGCAAATGACTAAGT
1 ATGCAAATGACTAAGT
3820925 ATG
1 ATG
3820928 AAAAATACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.26
Consensus pattern (16 bp):
ATGCAAATGACTAAGT
Done.