Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008356.1 Hibiscus syriacus cultivar Beakdansim tig00111095_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: 12862612
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 56
Found at i:3374322 original size:31 final size:31
Alignment explanation
Indices: 3374284--3374386 Score: 93
Period size: 30 Copynumber: 3.3 Consensus size: 31
3374274 TAAGACGACC
3374284 CTTGGGTAGGCTCCGAAGCCCCGAGATCTTT
1 CTTGGGTAGGCTCCGAAGCCCCGAGATCTTT
** * *
3374315 CTTGGGTA-G-TCCTGCGGCCCTGAGATCATT
1 CTTGGGTAGGCTCC-GAAGCCCCGAGATCTTT
* * * *
3374345 CTTGAGTAGGCCCCGTAGCCCCGAGTAACTTT
1 CTTGGGTAGGCTCCGAAGCCCCGAG-ATCTTT
*
3374377 CTAGGGTAGG
1 CTTGGGTAGG
3374387 TTTTGGGCCC
Statistics
Matches: 55, Mismatches: 13, Indels: 7
0.73 0.17 0.09
Matches are distributed among these distances:
29 3 0.05
30 21 0.38
31 17 0.31
32 14 0.25
ACGTcount: A:0.17, C:0.27, G:0.30, T:0.26
Consensus pattern (31 bp):
CTTGGGTAGGCTCCGAAGCCCCGAGATCTTT
Found at i:3377521 original size:30 final size:30
Alignment explanation
Indices: 3377460--3377523 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
3377450 AAGAACACAA
* *
3377460 TCTTCTTCCATGGCTTGAAGGGATTGAAAT
1 TCTTCTTCCAGGGCTTGAAGGCATTGAAAT
* *
3377490 TCTTCTTCCAGGGCTTGAAGGCCTTGGAAT
1 TCTTCTTCCAGGGCTTGAAGGCATTGAAAT
3377520 TCTT
1 TCTT
3377524 GTTGTTAGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (30 bp):
TCTTCTTCCAGGGCTTGAAGGCATTGAAAT
Found at i:3382005 original size:2 final size:2
Alignment explanation
Indices: 3381998--3382080 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
3381988 TTCAATAAAT
3381998 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
3382040 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3382081 TCGTCTTGTT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3382111 original size:3 final size:3
Alignment explanation
Indices: 3382097--3382166 Score: 104
Period size: 3 Copynumber: 23.3 Consensus size: 3
3382087 TGTTCGGGTT
* * **
3382097 TTA TTT TTA TTA TTA TTA ATA TTA AAA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3382145 TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA T
3382167 ATTTTTGTTA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:3385257 original size:21 final size:21
Alignment explanation
Indices: 3385231--3385273 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
3385221 TGTGAAACAC
3385231 TCACACGCTAAGTCGATGACT
1 TCACACGCTAAGTCGATGACT
3385252 TCACACGCTAAGTCGATGACT
1 TCACACGCTAAGTCGATGACT
3385273 T
1 T
3385274 AGTGAGACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (21 bp):
TCACACGCTAAGTCGATGACT
Found at i:3385822 original size:23 final size:23
Alignment explanation
Indices: 3385796--3385864 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
3385786 CACCACAGCT
*
3385796 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
3385819 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
3385842 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
3385865 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:3386051 original size:103 final size:103
Alignment explanation
Indices: 3385880--3386092 Score: 399
Period size: 103 Copynumber: 2.1 Consensus size: 103
3385870 TAATGTCCAT
* *
3385880 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
3385945 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
3385983 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
3386048 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
3386086 AAGGACC
1 AAGGACC
3386093 GCGTAGACCC
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:3396019 original size:2 final size:2
Alignment explanation
Indices: 3396012--3396046 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3396002 TCTTAAAGAT
3396012 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3396047 TAAAAATTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3400249 original size:21 final size:21
Alignment explanation
Indices: 3400222--3400271 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
3400212 GGTTCTTGAT
*
3400222 CTGGCTCTGGTGTAGGTTCTG
1 CTGGCTCTGGTGTAGATTCTG
*
3400243 TTGGCTCTGGTGTAGATTCTG
1 CTGGCTCTGGTGTAGATTCTG
3400264 CTGGCTCT
1 CTGGCTCT
3400272 TGATCTGGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.06, C:0.20, G:0.34, T:0.40
Consensus pattern (21 bp):
CTGGCTCTGGTGTAGATTCTG
Found at i:3407982 original size:11 final size:11
Alignment explanation
Indices: 3407966--3407997 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
3407956 GTAATTTTTC
3407966 TTTCTTTCCTT
1 TTTCTTTCCTT
3407977 TTTCTTTCCTT
1 TTTCTTTCCTT
*
3407988 TTTCTCTCCT
1 TTTCTTTCCT
3407998 CCCCTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTCTTTCCTT
Found at i:3408384 original size:4 final size:4
Alignment explanation
Indices: 3408359--3408404 Score: 56
Period size: 4 Copynumber: 11.0 Consensus size: 4
3408349 ACCTTTCTTC
* *
3408359 TTTA TCTTA TCTTA TCTA TTTA TTTA TTTA TTTA ATTA TTTA TTTA
1 TTTA T-TTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
3408405 GTTTTTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
4 28 0.76
5 9 0.24
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:3411317 original size:2 final size:2
Alignment explanation
Indices: 3411306--3411346 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
3411296 ATCAATTAAA
3411306 AT AT -T AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3411345 AT
1 AT
3411347 TACAGTTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 33 0.92
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:3411334 original size:9 final size:9
Alignment explanation
Indices: 3411312--3411346 Score: 61
Period size: 9 Copynumber: 3.8 Consensus size: 9
3411302 TAAAATATTA
3411312 TATATATAT
1 TATATATAT
3411321 ATATATATAT
1 -TATATATAT
3411331 TATATATAT
1 TATATATAT
3411340 TATATAT
1 TATATAT
3411347 TACAGTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 16 0.64
10 9 0.36
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
TATATATAT
Found at i:3413438 original size:27 final size:27
Alignment explanation
Indices: 3413408--3413491 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 27
3413398 TTATTCATCA
3413408 ACATATGATGAATTCCATGGGTTGCAC
1 ACATATGATGAATTCCATGGGTTGCAC
** * ** * *
3413435 ACATAGTGCCGAA-ACGGT-TGTT-CAT
1 ACATA-TGATGAATTCCATGGGTTGCAC
3413460 ACATATGATGAATTCCATGGGTTGCAC
1 ACATATGATGAATTCCATGGGTTGCAC
3413487 ACATA
1 ACATA
3413492 GTACCGAAAC
Statistics
Matches: 39, Mismatches: 14, Indels: 8
0.64 0.23 0.13
Matches are distributed among these distances:
24 5 0.13
25 9 0.23
26 6 0.15
27 14 0.36
28 5 0.13
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (27 bp):
ACATATGATGAATTCCATGGGTTGCAC
Found at i:3413438 original size:54 final size:54
Alignment explanation
Indices: 3413322--3413658 Score: 372
Period size: 54 Copynumber: 6.3 Consensus size: 54
3413312 TTCGTTGAGA
* * ** * * * * ** *
3413322 TGCACACGTAGTGCCAATACGGTCATTCATAAACATATTACGAGTTCTGTGGTT
1 TGCACACATAGTGCCAAAACGGTTGTTCATCAACATATGATGAATTCCATGGGT
* * * *
3413376 TGCTCACATAGTGCCTAAACAGTTATTCATCAACATATGATGAATTCCATGGGT
1 TGCACACATAGTGCCAAAACGGTTGTTCATCAACATATGATGAATTCCATGGGT
*
3413430 TGCACACATAGTGCCGAAACGGTTGTTCAT--ACATATGATGAATTCCATGGGT
1 TGCACACATAGTGCCAAAACGGTTGTTCATCAACATATGATGAATTCCATGGGT
* * * *
3413482 TGCACACATAGTACCGAAACGGTTGTTCATCAACTTATGATGAATTCCGTGGGT
1 TGCACACATAGTGCCAAAACGGTTGTTCATCAACATATGATGAATTCCATGGGT
* * ** * *
3413536 TACACATATAGTGCCAAAACGGTTGTTCATCAATTTATGATGAATTTCGTGGGT
1 TGCACACATAGTGCCAAAACGGTTGTTCATCAACATATGATGAATTCCATGGGT
* * *
3413590 TGCACACATAGTACCAAAATGGTTGTTCATCAACTTATGATGAATTCCATGGGT
1 TGCACACATAGTGCCAAAACGGTTGTTCATCAACATATGATGAATTCCATGGGT
* * *
3413644 TACACATAAAGTGCC
1 TGCACACATAGTGCC
3413659 TAAAGTACAC
Statistics
Matches: 244, Mismatches: 37, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
52 51 0.21
54 193 0.79
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (54 bp):
TGCACACATAGTGCCAAAACGGTTGTTCATCAACATATGATGAATTCCATGGGT
Found at i:3420394 original size:54 final size:54
Alignment explanation
Indices: 3420325--3420463 Score: 174
Period size: 54 Copynumber: 2.6 Consensus size: 54
3420315 ATATATTACG
*
3420325 ATTTACGTGGTTTGTACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGA
1 ATTT-CGTGGGTTGTACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGA
* * *
3420380 A-TTCTGTGGGTTGTACACATTGT-TCTGAAATGGTTGTTCATCAACATATGATGA
1 ATTTC-GTGGGTTGTACACATAGTGCCT-AAACGGTTGTTCATCAACATATGATGA
** *
3420434 ATTTCGTGGGTTACACATATAGTGCCTAAA
1 ATTTCGTGGGTTGTACACATAGTGCCTAAA
3420464 GTACACATAG
Statistics
Matches: 71, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
53 3 0.04
54 62 0.87
55 6 0.08
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (54 bp):
ATTTCGTGGGTTGTACACATAGTGCCTAAACGGTTGTTCATCAACATATGATGA
Found at i:3420951 original size:94 final size:95
Alignment explanation
Indices: 3420809--3420986 Score: 261
Period size: 94 Copynumber: 1.9 Consensus size: 95
3420799 CCCTACCATG
* * *
3420809 GTATCGATACTTCTATACTGTGGTATCGATACTCCCCTTCAGTATCGATACCATTTCTACATTCT
1 GTATCGATACTTCTATACTATGGTACCGATACTCCCATTCAGTATCGATACCATTTCTACATTCT
3420874 G-AATCAATGGTATCGATGTCTGTCTCTTA
66 GAAATCAATGGTATCGATGTCTGTCTCTTA
* * * *
3420903 GTATCGATACTTCTATACTATGGTACCGATACT-CTATTACCGTGTCGATACCATTTCTGCATTC
1 GTATCGATACTTCTATACTATGGTACCGATACTCCCATT-CAGTATCGATACCATTTCTACATTC
3420967 TGTAAATCAATGGTATCGAT
65 TG-AAATCAATGGTATCGAT
3420987 ACCCACCTAA
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
93 3 0.04
94 55 0.74
96 16 0.22
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (95 bp):
GTATCGATACTTCTATACTATGGTACCGATACTCCCATTCAGTATCGATACCATTTCTACATTCT
GAAATCAATGGTATCGATGTCTGTCTCTTA
Found at i:3421007 original size:94 final size:94
Alignment explanation
Indices: 3420809--3421007 Score: 224
Period size: 94 Copynumber: 2.1 Consensus size: 94
3420799 CCCTACCATG
* * *
3420809 GTATCGATACTTCTATACTGTGGTATCGATACTCCCCTTCAGTATCGATACCATTTCTACATTCT
1 GTATCGATACTTCTATACTATGGTACCGATACTCCCATTCAGTATCGATACCATTTCTACATTCT
* *** *
3420874 GAATCAATGGTATCGATGTCTGTCTCTTA
66 GAATCAATGGTATCGATGACCCACTCTAA
* * * *
3420903 GTATCGATACTTCTATACTATGGTACCGATACT-CTATTACCGTGTCGATACCATTTCTGCATTC
1 GTATCGATACTTCTATACTATGGTACCGATACTCCCATT-CAGTATCGATACCATTTCTACATTC
3420967 TGTAAATCAATGGTATCGAT-ACCCAC-CTAA
65 TG--AATCAATGGTATCGATGACCCACTCTAA
* *
3420997 TTATCAATACT
1 GTATCGATACT
3421008 AATTGCATCT
Statistics
Matches: 88, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
93 3 0.03
94 67 0.76
95 2 0.02
96 16 0.18
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.37
Consensus pattern (94 bp):
GTATCGATACTTCTATACTATGGTACCGATACTCCCATTCAGTATCGATACCATTTCTACATTCT
GAATCAATGGTATCGATGACCCACTCTAA
Found at i:3421916 original size:13 final size:13
Alignment explanation
Indices: 3421882--3421916 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
3421872 CACATTACCC
3421882 TTTTAATTTAATT
1 TTTTAATTTAATT
*
3421895 TTTAAATTTAATT
1 TTTTAATTTAATT
*
3421908 TTTTTATTT
1 TTTTAATTT
3421917 TTAATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTAATTTAATT
Found at i:3423893 original size:16 final size:16
Alignment explanation
Indices: 3423872--3423913 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
3423862 CTTGAACTTA
3423872 TTTTTGGGGCCCCTAT
1 TTTTTGGGGCCCCTAT
*
3423888 TTTTTGGGGGCCCTAT
1 TTTTTGGGGCCCCTAT
3423904 TTTTTGGGGC
1 TTTTTGGGGC
3423914 TTCTTAATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.05, C:0.19, G:0.31, T:0.45
Consensus pattern (16 bp):
TTTTTGGGGCCCCTAT
Found at i:3423982 original size:73 final size:73
Alignment explanation
Indices: 3423885--3424047 Score: 256
Period size: 73 Copynumber: 2.2 Consensus size: 73
3423875 TTGGGGCCCC
* *
3423885 TATTTTTTGGGGGCCCTATTTTTTGGGGCTTCTTAATGGAAACAACTGATAGATATACTCAATTT
1 TATTTTTT-GGGGCCCTATTTTTTGGAGCTTCTTAATGGAAACAACTAATAGATATACTCAATTT
3423950 CGGGGGCCT-
65 C-GGGGCCTA
* * *
3423959 TATTTTTTGGGTCCCTATTTTTTGGAGCTTCTTAATGGCAACAACTAATAGATATACTCGATTTC
1 TATTTTTTGGGGCCCTATTTTTTGGAGCTTCTTAATGGAAACAACTAATAGATATACTCAATTTC
3424024 GGGGCCTA
66 GGGGCCTA
3424032 TATTTTTTGGGGCCCT
1 TATTTTTTGGGGCCCT
3424048 GTGCCGTTGC
Statistics
Matches: 82, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
72 7 0.09
73 67 0.82
74 8 0.10
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (73 bp):
TATTTTTTGGGGCCCTATTTTTTGGAGCTTCTTAATGGAAACAACTAATAGATATACTCAATTTC
GGGGCCTA
Found at i:3428892 original size:2 final size:2
Alignment explanation
Indices: 3428885--3428916 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3428875 GACCCGACTC
3428885 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
3428917 TGCAGCCCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3429659 original size:14 final size:14
Alignment explanation
Indices: 3429640--3429681 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
3429630 AGGAGGAGGA
3429640 GAGAGGAAAGGGAT
1 GAGAGGAAAGGGAT
3429654 GAGAGGAAAGGGAT
1 GAGAGGAAAGGGAT
*
3429668 GGGAGGAAATGGGA
1 GAGAGGAAA-GGGA
3429682 AAGGAGGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 22 0.85
15 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.52, T:0.07
Consensus pattern (14 bp):
GAGAGGAAAGGGAT
Found at i:3429687 original size:15 final size:14
Alignment explanation
Indices: 3429642--3429697 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
3429632 GAGGAGGAGA
*
3429642 GAGGAAAGGG-ATG
1 GAGGAAAGGGAAAG
**
3429655 AGAGGAAAGGGATGG
1 -GAGGAAAGGGAAAG
3429670 GAGGAAATGGGAAAG
1 GAGGAAA-GGGAAAG
*
3429685 GAGGTAAGGGAAA
1 GAGGAAAGGGAAA
3429698 ACCGGCAAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
14 23 0.66
15 12 0.34
ACGTcount: A:0.43, C:0.00, G:0.50, T:0.07
Consensus pattern (14 bp):
GAGGAAAGGGAAAG
Found at i:3431324 original size:185 final size:185
Alignment explanation
Indices: 3430927--3431382 Score: 587
Period size: 185 Copynumber: 2.5 Consensus size: 185
3430917 TTAGGTTGTA
* * * *
3430927 CCTAAAATGTTACCAGAGTTTAAGCTGATGAGACTTTAAATATTCTCACGATAACAAAATAAATT
1 CCTAAAATGTTACCAGAGTTTAAGCTGATGAGGCATTAGACATTCTCACGATAACAAAATAAATT
* *
3430992 AAAAGT-TAGAAATATTATGAATATATATAAGAAATCCAGTTGCGCCCAAGAATGATATGGTTCA
66 AAAA-TCTA-AAATATTATGAATATATATAAGAAATCCAGTTGCACCCAAGAATGATATAGTTCA
* * *
3431056 CGAAGGAATATGTTGCAATCTAAAATGTTAATTTTCTTTATAATAAAATCGATTACG
129 CGAAGAAATAGGTTGCAATATAAAATGTTAATTTTCTTTATAATAAAATCGATTACG
* * * * * * *
3431113 CCTAAAATGTCACTAGAGTTTAAGCTGATGGGGCATTAGTA-ATTCACACAATAATAAAATAATT
1 CCTAAAATGTTACCAGAGTTTAAGCTGATGAGGCATTAG-ACATTCTCACGATAACAAAATAAAT
* * *
3431177 TAAAATCTGAAAATGTTATGAATATTTATAAGAAATCCAGTTGCACCCAAGAATGTTATAGTTC-
65 TAAAATCT-AAAATATTATGAATATATATAAGAAATCCAGTTGCACCCAAGAATGATATAGTTCA
* * * *
3431241 C-AAGAAAGTAGGTTGCAATATGAAATGTTAATTTTCTTTGTAATAAAATCGGTTGCG
129 CGAAGAAA-TAGGTTGCAATATAAAATGTTAATTTTCTTTATAATAAAATCGATTACG
* *
3431298 CCTAAAATGTTACCAGAGTTTAAGCTGATGAGGCCTTAGACATTCTCACGATAACAAAATAAGTT
1 CCTAAAATGTTACCAGAGTTTAAGCTGATGAGGCATTAGACATTCTCACGATAACAAAATAAATT
* *
3431363 AAAAGCTAAAAATTTTATGA
66 AAAATCT-AAAATATTATGA
3431383 TAGTCGATAC
Statistics
Matches: 232, Mismatches: 33, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
184 6 0.03
185 117 0.50
186 107 0.46
187 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (185 bp):
CCTAAAATGTTACCAGAGTTTAAGCTGATGAGGCATTAGACATTCTCACGATAACAAAATAAATT
AAAATCTAAAATATTATGAATATATATAAGAAATCCAGTTGCACCCAAGAATGATATAGTTCACG
AAGAAATAGGTTGCAATATAAAATGTTAATTTTCTTTATAATAAAATCGATTACG
Found at i:3431636 original size:72 final size:70
Alignment explanation
Indices: 3431496--3431745 Score: 276
Period size: 72 Copynumber: 3.6 Consensus size: 70
3431486 CTTATGATAT
* * * * * **
3431496 GATAATTGTGGAAAAAT-TTGATACTTTGCAGCGTTCTCATTTTACAT-TTTTTT-AATTTTAAA
1 GATATTTGTGGAAAAATATCGAAACTTTGCAGCCTTCTCATTTTTCATGTTTTTTAAATTCGAAA
3431558 GTATC
66 GTATC
* *
3431563 GATATTTGTGGAAAAGTATCGAAACTTTACAGCCTTCTCATTTTTCATGTTTAGTTTAAATTCGA
1 GATATTTGTGGAAAAATATCGAAACTTTGCAGCCTTCTCATTTTTCATGTTT--TTTAAATTCGA
3431628 AAGTATC
64 AAGTATC
* *
3431635 GATATTTAT-GAAAAATATC-AATACTTTGCAGCCTTCTCATTTTTTTATGTTTTCTTAAATTCG
1 GATATTTGTGGAAAAATATCGAA-ACTTTGCAGCCTTCTCA-TTTTTCATGTTTT-TTAAATTCG
* *
3431698 GAACTATC
63 AAAGTATC
* * *
3431706 GATATTTGTGAAAAAATATCGACACTTTTCAGCCTTCTCA
1 GATATTTGTGGAAAAATATCGAAACTTTGCAGCCTTCTCA
3431746 ATATATAAAA
Statistics
Matches: 154, Mismatches: 19, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
67 15 0.10
68 25 0.16
69 3 0.02
70 3 0.02
71 51 0.33
72 56 0.36
73 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.42
Consensus pattern (70 bp):
GATATTTGTGGAAAAATATCGAAACTTTGCAGCCTTCTCATTTTTCATGTTTTTTAAATTCGAAA
GTATC
Found at i:3431850 original size:21 final size:21
Alignment explanation
Indices: 3431826--3431877 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
3431816 TAATATTTAA
3431826 AAGTATCGATCATTATCGCAT
1 AAGTATCGATCATTATCGCAT
*
3431847 AAGTATCGATCATTATCGGAT
1 AAGTATCGATCATTATCGCAT
3431868 AAGTATCGAT
1 AAGTATCGAT
3431878 ATTTAACTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (21 bp):
AAGTATCGATCATTATCGCAT
Found at i:3431878 original size:10 final size:10
Alignment explanation
Indices: 3431826--3431878 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
3431816 TAATATTTAA
3431826 AAGTATCGAT
1 AAGTATCGAT
* *
3431836 CATTATCGCAT
1 AAGTATCG-AT
3431847 AAGTATCGAT
1 AAGTATCGAT
* *
3431857 CATTATCGGAT
1 AAGTATC-GAT
3431868 AAGTATCGAT
1 AAGTATCGAT
3431878 A
1 A
3431879 TTTAACTTTT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
10 17 0.52
11 16 0.48
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (10 bp):
AAGTATCGAT
Found at i:3431914 original size:93 final size:93
Alignment explanation
Indices: 3431754--3431927 Score: 217
Period size: 93 Copynumber: 1.9 Consensus size: 93
3431744 CAATATATAA
* * * *
3431754 AAGTATCGATCATCATTGCATAAGTATCAATATTTTAAATTTCGATCTTTTTATCATTTTTTTAA
1 AAGTATCGATCATCATCGCATAAGTATCAATATTTTAAATTTCGATCTTTCTATCACTTTTTCAA
*
3431819 TATTTAAAAGTATCGATCATTATCGCAT
66 TATTTAAAAATATCGATCATTATCGCAT
* * * * **
3431847 AAGTATCGATCATTATCGGATAAGTATCGATA-TTTAACTTTTTATCTTATCT-TCAACTTTTTC
1 AAGTATCGATCATCATCGCATAAGTATCAATATTTTAAATTTCGATCTT-TCTATC-ACTTTTTC
3431910 AATATTTAAAAATATCGA
64 AATATTTAAAAATATCGA
3431928 CCATCATATA
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
92 15 0.22
93 53 0.78
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.44
Consensus pattern (93 bp):
AAGTATCGATCATCATCGCATAAGTATCAATATTTTAAATTTCGATCTTTCTATCACTTTTTCAA
TATTTAAAAATATCGATCATTATCGCAT
Found at i:3431943 original size:93 final size:93
Alignment explanation
Indices: 3431754--3431949 Score: 209
Period size: 93 Copynumber: 2.1 Consensus size: 93
3431744 CAATATATAA
* * * *
3431754 AAGTATCGATCATCATTGCATAAGTATCAATATTTTAAATTTCGATCTTTTTATCATTTTTTTAA
1 AAGTATCGATCATCATCGCATAAGTATCAATATTTTAAATTTCGATCTTTCTATCACTTTTTCAA
* * * *
3431819 TATTTAAAAGTATCGATCATTATCGCAT
66 TATTTAAAAATATCGACCATCATCACAT
* * * * **
3431847 AAGTATCGATCATTATCGGATAAGTATCGATA-TTTAACTTTTTATCTTATCT-TCAACTTTTTC
1 AAGTATCGATCATCATCGCATAAGTATCAATATTTTAAATTTCGATCTT-TCTATC-ACTTTTTC
*
3431910 AATATTTAAAAATATCGACCATCAT-ATATT
64 AATATTTAAAAATATCGACCATCATCACA-T
3431940 AAGTATCGAT
1 AAGTATCGAT
3431950 ATTTAAAATT
Statistics
Matches: 85, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
92 16 0.19
93 69 0.81
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (93 bp):
AAGTATCGATCATCATCGCATAAGTATCAATATTTTAAATTTCGATCTTTCTATCACTTTTTCAA
TATTTAAAAATATCGACCATCATCACAT
Found at i:3434446 original size:196 final size:195
Alignment explanation
Indices: 3434107--3434484 Score: 562
Period size: 196 Copynumber: 1.9 Consensus size: 195
3434097 TGTGCATTTT
*
3434107 GACATACTTTGTGTATGATTGTTATCGATCGATTTTTTTAATTCATATGTTGAATTTTCGTATCA
1 GACATACTTTGTGTATGATTGTTATCGATCGATTTTTTTAATGCATATGTTGAATTTTCGTATCA
* * * *
3434172 ATACTATATGTACTTTAGGCATTATGTCTGCATTAATGGAATTCATAATAAGTTTGTGAATTACC
66 ATACTATATGTACTTTAGACACTATGTATGCATCAATGGAATTCATAATAAGTTTGTGAATTACC
* * *
3434237 ATTTCAGCACTATGTGTGGATCCATGGAATTAATAATGAGTTTGTGAATTACGATATCAACACTC
131 ATTTCAGCACTATGTATGCATCCATGAAATTAATAATGAGTTTGTGAATTACGATATCAACACTC
* *
3434302 GACATACTTTGTGTATGA-TGATTATTGATCGATTTTGTTTAATGCATATGTTGCATTTTCGTAT
1 GACATACTTTGTGTATGATTG-TTATCGATCGATTTT-TTTAATGCATATGTTGAATTTTCGTAT
* * * * * *
3434366 TAGTGCTATATGTACTTTCGACACTATGTATGTATCCATGGAATTCATAATAAGTTTGTGAATTA
64 CAATACTATATGTACTTTAGACACTATGTATGCATCAATGGAATTCATAATAAGTTTGTGAATTA
*
3434431 CCATTTC-GACACTATGTATGCATCCATGAAATTCATAATGAGTTTGTGAATTAC
129 CCATTTCAG-CACTATGTATGCATCCATGAAATTAATAATGAGTTTGTGAATTAC
3434485 CATTTTGACA
Statistics
Matches: 163, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
194 2 0.01
195 33 0.20
196 128 0.79
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (195 bp):
GACATACTTTGTGTATGATTGTTATCGATCGATTTTTTTAATGCATATGTTGAATTTTCGTATCA
ATACTATATGTACTTTAGACACTATGTATGCATCAATGGAATTCATAATAAGTTTGTGAATTACC
ATTTCAGCACTATGTATGCATCCATGAAATTAATAATGAGTTTGTGAATTACGATATCAACACTC
Found at i:3434464 original size:53 final size:53
Alignment explanation
Indices: 3434381--3434496 Score: 196
Period size: 53 Copynumber: 2.2 Consensus size: 53
3434371 CTATATGTAC
* *
3434381 TTTCGACACTATGTATGTATCCATGGAATTCATAATAAGTTTGTGAATTACCA
1 TTTCGACACTATGTATGCATCCATGAAATTCATAATAAGTTTGTGAATTACCA
*
3434434 TTTCGACACTATGTATGCATCCATGAAATTCATAATGAGTTTGTGAATTACCA
1 TTTCGACACTATGTATGCATCCATGAAATTCATAATAAGTTTGTGAATTACCA
*
3434487 TTTTGACACT
1 TTTCGACACT
3434497 TAGGTGGAAC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 59 1.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (53 bp):
TTTCGACACTATGTATGCATCCATGAAATTCATAATAAGTTTGTGAATTACCA
Found at i:3435058 original size:13 final size:13
Alignment explanation
Indices: 3435040--3435065 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3435030 ATATATATGT
3435040 GTGTGTTTGTGTG
1 GTGTGTTTGTGTG
3435053 GTGTGTTTGTGTG
1 GTGTGTTTGTGTG
3435066 TGTATTTGAA
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:0.00, C:0.00, G:0.46, T:0.54
Consensus pattern (13 bp):
GTGTGTTTGTGTG
Found at i:3443765 original size:37 final size:37
Alignment explanation
Indices: 3443693--3443766 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
3443683 TACTCAATAA
**
3443693 TTCATTTTCATTTTCAGTTATGTACATATGTATATAT
1 TTCATTTTCATTTTCAGTTATGTACATATACATATAT
* *
3443730 TTCATTTTCATTTTTAGTTATGTACATGTACATATAT
1 TTCATTTTCATTTTCAGTTATGTACATATACATATAT
3443767 ATATATACAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.27, C:0.11, G:0.08, T:0.54
Consensus pattern (37 bp):
TTCATTTTCATTTTCAGTTATGTACATATACATATAT
Found at i:3446216 original size:17 final size:18
Alignment explanation
Indices: 3446189--3446223 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3446179 TTTTTAGTTG
*
3446189 TTATCTTAAAACATTATT
1 TTATCTTAAAAAATTATT
3446207 TTAT-TTAAAAAATTATT
1 TTATCTTAAAAAATTATT
3446224 AATTTACCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATCTTAAAAAATTATT
Found at i:3446599 original size:30 final size:31
Alignment explanation
Indices: 3446565--3446623 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
3446555 CGAGTTGAGT
3446565 AACAAA-TTTCTGAACGAGCACGAGTCGAAC
1 AACAAATTTTCTGAACGAGCACGAGTCGAAC
* *
3446595 AACAAATTTTCTTAACGAGCATGAGTCGA
1 AACAAATTTTCTGAACGAGCACGAGTCGA
3446624 GCAAAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 6 0.23
31 20 0.77
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (31 bp):
AACAAATTTTCTGAACGAGCACGAGTCGAAC
Found at i:3448423 original size:22 final size:21
Alignment explanation
Indices: 3448363--3448495 Score: 95
Period size: 22 Copynumber: 5.8 Consensus size: 21
3448353 ATATGATAAT
*
3448363 ATATAATATATAGTTTTGTCAAA
1 ATAT-ATATATAGTTTT-TGAAA
* * *
3448386 AAATAATTTATGGTTTTTGAAA
1 ATAT-ATATATAGTTTTTGAAA
*
3448408 ATATATAGTCTAGTTTTTGAAA
1 ATATATA-TATAGTTTTTGAAA
* *
3448430 ACATATTATATAGTTTTTTAAAAAAA
1 ATATA-TATATAG-TTTTT---GAAA
3448456 CATATAATATATAGTTTTTGAAA
1 -ATAT-ATATATAGTTTTTGAAA
3448479 ATATATAGTATAGTTTT
1 ATATATA-TATAGTTTT
3448496 CAAAAAACAT
Statistics
Matches: 88, Mismatches: 13, Indels: 19
0.73 0.11 0.16
Matches are distributed among these distances:
21 5 0.06
22 40 0.45
23 24 0.27
26 8 0.09
27 10 0.11
28 1 0.01
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (21 bp):
ATATATATATAGTTTTTGAAA
Found at i:3448455 original size:25 final size:26
Alignment explanation
Indices: 3448427--3448479 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
3448417 CTAGTTTTTG
*
3448427 AAAACATAT-TATATAGTTTTTTAAA
1 AAAACATATATATATAGTTTTTGAAA
3448452 AAAACATATAATATATAGTTTTTGAAA
1 AAAACATAT-ATATATAGTTTTTGAAA
3448479 A
1 A
3448480 TATATAGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 9 0.36
27 16 0.64
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.40
Consensus pattern (26 bp):
AAAACATATATATATAGTTTTTGAAA
Found at i:3448471 original size:49 final size:48
Alignment explanation
Indices: 3448418--3448568 Score: 155
Period size: 47 Copynumber: 3.0 Consensus size: 48
3448408 ATATATAGTC
3448418 TAGTTTTTGAAAACATATTATATAGTTTTTTAAAAAAACATA-TAATATA
1 TAGTTTTTGAAAACATATTATATAG-TTTTT-AAAAAACATAGTAATATA
* * * ** *
3448467 TAGTTTTTGAAAATATA-TAGTATAGTTTTCAAAAAACATATTGTTGTA
1 TAGTTTTTGAAAACATATTA-TATAGTTTTTAAAAAACATAGTAATATA
3448515 TAG-TTTTGAAAACATATAATATACATAGTTTTTAAAAAACATAAGTAATATA
1 TAGTTTTTGAAAACATAT--TAT--ATAGTTTTTAAAAAACAT-AGTAATATA
3448567 TA
1 TA
3448569 TATATATATT
Statistics
Matches: 83, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
47 22 0.27
48 13 0.16
49 22 0.27
50 2 0.02
51 17 0.20
52 7 0.08
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.41
Consensus pattern (48 bp):
TAGTTTTTGAAAACATATTATATAGTTTTTAAAAAACATAGTAATATA
Found at i:3448527 original size:71 final size:67
Alignment explanation
Indices: 3448369--3448552 Score: 174
Period size: 71 Copynumber: 2.6 Consensus size: 67
3448359 TAATATATAA
* * * **
3448369 TATATAGTTTTGTCAAAA-A-ATAATTTATGGTTTTTGAAAATATATAGTCTAGTTTTTGAAAAC
1 TATATAGTTTTG--AAAACATATAATATATAGTTTTTGAAAATATATAGTATAGTTTTAAAAAAC
3448432 ATAT
64 ATAT
*
3448436 TATATAGTTTTTTAAAAAAACATATAATATATAGTTTTTGAAAATATATAGTATAGTTTTCAAAA
1 TATATAG--TTTT--GAAAACATATAATATATAGTTTTTGAAAATATATAGTATAGTTTT-AAAA
3448501 AACATATTGT
61 AACATA---T
* *
3448511 TGTATAGTTTTGAAAACATATAATATACATAGTTTTTAAAAA
1 TATATAGTTTTGAAAACATATAATAT--ATAGTTTTTGAAAA
3448553 ACATAAGTAA
Statistics
Matches: 96, Mismatches: 9, Indels: 18
0.78 0.07 0.15
Matches are distributed among these distances:
67 7 0.07
69 8 0.08
70 1 0.01
71 48 0.50
72 8 0.08
73 17 0.18
75 7 0.07
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (67 bp):
TATATAGTTTTGAAAACATATAATATATAGTTTTTGAAAATATATAGTATAGTTTTAAAAAACAT
AT
Found at i:3448558 original size:25 final size:24
Alignment explanation
Indices: 3448363--3448557 Score: 104
Period size: 25 Copynumber: 8.1 Consensus size: 24
3448353 ATATGATAAT
*
3448363 ATATAATATATAGTTTTGTCAAAAA-
1 ATAT-ATATATAGTTTT-TAAAAAAC
* * *
3448388 ATA-ATTTATGGTTTTT--GAAA-
1 ATATATATATAGTTTTTAAAAAAC
* *
3448408 ATATATAGTCTAGTTTTT-GAAAAC
1 ATATATA-TATAGTTTTTAAAAAAC
3448432 ATAT-TATATAGTTTTTTAAAAAAAC
1 ATATATATATAG-TTTTT-AAAAAAC
*
3448457 ATATAATATATAGTTTTT--GAAA-
1 ATAT-ATATATAGTTTTTAAAAAAC
*
3448479 ATATATAGTATAGTTTTCAAAAAAC
1 ATATATA-TATAGTTTTTAAAAAAC
* * * * *
3448504 ATATTGTTGTATAGTTTTGAAAACAT
1 ATA-T-ATATATAGTTTTTAAAAAAC
*
3448530 ATAATATACATAGTTTTTAAAAAAC
1 AT-ATATATATAGTTTTTAAAAAAC
3448555 ATA
1 ATA
3448558 AGTAATATAT
Statistics
Matches: 131, Mismatches: 23, Indels: 33
0.70 0.12 0.18
Matches are distributed among these distances:
20 6 0.05
21 5 0.04
22 26 0.20
23 23 0.18
24 8 0.06
25 31 0.24
26 23 0.18
27 9 0.07
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (24 bp):
ATATATATATAGTTTTTAAAAAAC
Found at i:3448613 original size:21 final size:20
Alignment explanation
Indices: 3448561--3448619 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
3448551 AAACATAAGT
3448561 AATATATATATATATATTGAA
1 AATATA-ATATATATATTGAA
* ** *
3448582 AACATGTTATATGATTTTGAA
1 AATATAATATAT-ATATTGAA
3448603 AATATAATATATTATAT
1 AATATAATATA-TATAT
3448620 AGTCTTTTTA
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
20 5 0.18
21 22 0.79
22 1 0.04
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (20 bp):
AATATAATATATATATTGAA
Found at i:3448620 original size:28 final size:31
Alignment explanation
Indices: 3448589--3448651 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 31
3448579 GAAAACATGT
3448589 TATATG-ATTTTGAAAATATA-ATATAT-TA
1 TATATGTATTTTGAAAATATATATATATATA
* * *
3448617 TATA-GTCTTTTTAATATATATATATATATA
1 TATATGTATTTTGAAAATATATATATATATA
3448647 TATAT
1 TATAT
3448652 ATATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 1 0.04
28 15 0.54
29 6 0.21
30 6 0.21
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (31 bp):
TATATGTATTTTGAAAATATATATATATATA
Found at i:3448635 original size:2 final size:2
Alignment explanation
Indices: 3448630--3448674 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3448620 AGTCTTTTTA
3448630 AT AT AT 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 AT AT AT
3448672 AT A
1 AT A
3448675 GCTTATAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3449839 original size:14 final size:15
Alignment explanation
Indices: 3449822--3449855 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3449812 ATCCTTTTAA
3449822 TTTA-AAATTTTCTT
1 TTTATAAATTTTCTT
*
3449836 TTTATTAATTTTCTT
1 TTTATAAATTTTCTT
3449851 TTTAT
1 TTTAT
3449856 TTTATTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTATAAATTTTCTT
Found at i:3449847 original size:15 final size:15
Alignment explanation
Indices: 3449827--3449856 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3449817 TTTAATTTAA
3449827 AATTTTCTTTTTATT
1 AATTTTCTTTTTATT
3449842 AATTTTCTTTTTATT
1 AATTTTCTTTTTATT
3449857 TTATTATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (15 bp):
AATTTTCTTTTTATT
Found at i:3450822 original size:9 final size:9
Alignment explanation
Indices: 3450808--3450849 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
3450798 GTGGGGTAGG
3450808 ATTTTTTTT
1 ATTTTTTTT
3450817 ATTTTTTTT
1 ATTTTTTTT
*
3450826 ATTTTTAATT
1 ATTTTT-TTT
*
3450836 ATTTTTTCT
1 ATTTTTTTT
3450845 ATTTT
1 ATTTT
3450850 ACTAACTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
9 21 0.72
10 8 0.28
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:3452287 original size:24 final size:24
Alignment explanation
Indices: 3452259--3452327 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 24
3452249 AAGGGGACTA
3452259 ATCTACTGCAAAAACACAAGCTTC
1 ATCTACTGCAAAAACACAAGCTTC
* * *
3452283 ATCTACTGTAAAAAAATAAGCTTC
1 ATCTACTGCAAAAACACAAGCTTC
* * *
3452307 GTTTACTGCAAAAGCACAAGC
1 ATCTACTGCAAAAACACAAGC
3452328 CTCTGTAACC
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.42, C:0.23, G:0.12, T:0.23
Consensus pattern (24 bp):
ATCTACTGCAAAAACACAAGCTTC
Found at i:3461849 original size:34 final size:34
Alignment explanation
Indices: 3461803--3461919 Score: 90
Period size: 34 Copynumber: 3.1 Consensus size: 34
3461793 AGCTGAAATA
*
3461803 CATATGGATGCATTATCGACATAAAAGAATAATG
1 CATATGGGTGCATTATCGACATAAAAGAATAATG
* * *
3461837 CATATGGGTGCATTTTTGGCATGAAAGAATGCCATAGCTGAAATG
1 CATATGGGTGCATTATCGACAT--AA-AA-G--A-A--T--AATG
*
3461882 CATATGGGTGCATTATCGACATAAAAGAATAATT
1 CATATGGGTGCATTATCGACATAAAAGAATAATG
3461916 CATA
1 CATA
3461920 GGGGCGTGAA
Statistics
Matches: 64, Mismatches: 8, Indels: 22
0.68 0.09 0.23
Matches are distributed among these distances:
34 25 0.39
36 3 0.05
37 2 0.03
38 2 0.03
39 1 0.02
40 1 0.02
41 2 0.03
42 2 0.03
43 3 0.05
45 23 0.36
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (34 bp):
CATATGGGTGCATTATCGACATAAAAGAATAATG
Found at i:3461875 original size:79 final size:79
Alignment explanation
Indices: 3461744--3461919 Score: 280
Period size: 79 Copynumber: 2.2 Consensus size: 79
3461734 GAACGAATGA
* *
3461744 ATAAAAGAATAATGCATATAGGTTCATTATTGGCATCAAAGGATGCCATAGCTGAAATACATATG
1 ATAAAAGAATAATGCATATAGGTGCATTATTGGCATCAAAGAATGCCATAGCTGAAATACATATG
3461809 GATGCATTATCGAC
66 GATGCATTATCGAC
* * * *
3461823 ATAAAAGAATAATGCATATGGGTGCATTTTTGGCATGAAAGAATGCCATAGCTGAAATGCATATG
1 ATAAAAGAATAATGCATATAGGTGCATTATTGGCATCAAAGAATGCCATAGCTGAAATACATATG
*
3461888 GGTGCATTATCGAC
66 GATGCATTATCGAC
*
3461902 ATAAAAGAATAATTCATA
1 ATAAAAGAATAATGCATA
3461920 GGGGCGTGAA
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 89 1.00
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATAGGTGCATTATTGGCATCAAAGAATGCCATAGCTGAAATACATATG
GATGCATTATCGAC
Found at i:3465333 original size:27 final size:27
Alignment explanation
Indices: 3465303--3465367 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
3465293 ATTTAAAGAA
3465303 ATGGGTTTTTAAATGACATATTGATAT
1 ATGGGTTTTTAAATGACATATTGATAT
3465330 ATGGGTTTTTAAATGACATATTGATAT
1 ATGGGTTTTTAAATGACATATTGATAT
*
3465357 ATGTGTTTTTA
1 ATGGGTTTTTA
3465368 TTGATGTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.31, C:0.03, G:0.18, T:0.48
Consensus pattern (27 bp):
ATGGGTTTTTAAATGACATATTGATAT
Found at i:3466277 original size:45 final size:42
Alignment explanation
Indices: 3466213--3466678 Score: 266
Period size: 45 Copynumber: 11.6 Consensus size: 42
3466203 AATAAAAAAT
*
3466213 AATGCATATAGGTGCATTATTGGCATGAAAGGATGCCATAGTTGA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GATG-CATAG-TGA
* * *
3466258 AATGCATATAGTTGTATTATTGGCAT-AAA-A-G-A-A-T--
1 AATGCATATGGGTGCATTATTGGCATGAAAGATGCATAGTGA
*
3466292 AATGCATATGGGTGCATTATTGGCATGAAATGATGTCATAGCCGA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GATG-CATAG-TGA
* *
3466337 AATGCATATGGGTGTATTATCGGCAT-AAA-A-G-A-A-T--
1 AATGCATATGGGTGCATTATTGGCATGAAAGATGCATAGTGA
**
3466371 AATGCATATGGTGTATTATTGGCA-T-G-A--AAAGATGCCATAGCTGA
1 AATGCATATGG-GT-GCATT---ATTGGCATGAAAGATG-CATAG-TGA
3466415 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GATG-CATAG-TGA
*
3466460 AATGCATATGGGTGCATTATCGGCAT-AAA-A-G-A-A-T--
1 AATGCATATGGGTGCATTATTGGCATGAAAGATGCATAGTGA
*
3466494 AATGCATATGGGTGCATTATTGGCATGGAAGGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCAT-GAAAGATG-CATAG-TGA
* * *
3466539 AATGAATATGGGTGTATTATCGGCAT-AAA-A-G-A-A-T--
1 AATGCATATGGGTGCATTATTGGCATGAAAGATGCATAGTGA
* *
3466573 AATGCATATGAGTGCATTATTGGTATGAAAGGATGTCATAGTTGA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GATG-CATAG-TGA
*
3466618 AATGCATATGGGTGCATTATTGACAT-AAA-A-G-A-A-T--
1 AATGCATATGGGTGCATTATTGGCATGAAAGATGCATAGTGA
3466652 AATGCATATGGGTGCATTATTGGCATG
1 AATGCATATGGGTGCATTATTGGCATG
3466679 TAAGGGTGCC
Statistics
Matches: 337, Mismatches: 30, Indels: 118
0.69 0.06 0.24
Matches are distributed among these distances:
34 105 0.31
35 11 0.03
36 12 0.04
37 5 0.01
38 8 0.02
39 8 0.02
40 5 0.01
41 9 0.03
42 10 0.03
43 6 0.02
44 26 0.08
45 132 0.39
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.30
Consensus pattern (42 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGATGCATAGTGA
Found at i:3466306 original size:79 final size:78
Alignment explanation
Indices: 3466204--3466445 Score: 360
Period size: 79 Copynumber: 3.1 Consensus size: 78
3466194 GAACGAATGA
* * *
3466204 ATAAAA-AATAATGCATATAGGTGCATTATTGGCATGAAAGGATGCCATAGTTGAAATGCATATA
1 ATAAAAGAATAATGCATAT-GGTGCATTATTGGCATGAAAAGATGCCATAGCTGAAATGCATATG
*
3466268 GTTGTATTATTGGC
65 GGTGTATTATTGGC
* * *
3466282 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAATGATGTCATAGCCGAAATGCATATG
1 ATAAAAGAATAATGCATAT-GGTGCATTATTGGCATGAAAAGATGCCATAGCTGAAATGCATATG
*
3466347 GGTGTATTATCGGC
65 GGTGTATTATTGGC
*
3466361 ATAAAAGAATAATGCATATGGTGTATTATTGGCATGAAAAGATGCCATAGCTGAAATGCATATGG
1 ATAAAAGAATAATGCATATGGTGCATTATTGGCATGAAAAGATGCCATAGCTGAAATGCATATGG
*
3466426 GTGCATTATTGGC
66 GTGTATTATTGGC
*
3466439 ATGAAAG
1 ATAAAAG
3466446 GATGTCATAG
Statistics
Matches: 148, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
78 65 0.44
79 83 0.56
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (78 bp):
ATAAAAGAATAATGCATATGGTGCATTATTGGCATGAAAAGATGCCATAGCTGAAATGCATATGG
GTGTATTATTGGC
Found at i:3466435 original size:123 final size:124
Alignment explanation
Indices: 3466292--3466569 Score: 459
Period size: 123 Copynumber: 2.2 Consensus size: 124
3466282 ATAAAAGAAT
* *
3466292 AATGCATATGGGTGCATTATTGGCATGAAATGATGTCATAGCCGAAATGCATATGGGTGTATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCCGAAATGCATATGGGTGCATTAT
*
3466357 CGGCATAAAAGAATAATGCATAT-GGTGTATTATTGGCATGAAAAGATGCCATAGCTGA
66 CGGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAAGATGCCATAGCTGA
*
3466415 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCCGAAATGCATATGGGTGCATTAT
* *
3466480 CGGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGGAAGGATGCCATAGCTGA
66 CGGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAAGATGCCATAGCTGA
* * * *
3466539 AATGAATATGGGTGTATTATCGGCATAAAAG
1 AATGCATATGGGTGCATTATTGGCATGAAAG
3466570 AATAATGCAT
Statistics
Matches: 144, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
123 85 0.59
124 59 0.41
ACGTcount: A:0.34, C:0.11, G:0.27, T:0.28
Consensus pattern (124 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCCGAAATGCATATGGGTGCATTAT
CGGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAAGATGCCATAGCTGA
Found at i:3466511 original size:79 final size:79
Alignment explanation
Indices: 3466415--3466683 Score: 448
Period size: 79 Copynumber: 3.4 Consensus size: 79
3466405 CCATAGCTGA
3466415 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATGGGTGCATTAT
3466480 CGGCATAAAAGAAT
66 CGGCATAAAAGAAT
* * * *
3466494 AATGCATATGGGTGCATTATTGGCATGGAAGGATGCCATAGCTGAAATGAATATGGGTGTATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATGGGTGCATTAT
3466559 CGGCATAAAAGAAT
66 CGGCATAAAAGAAT
* * *
3466573 AATGCATATGAGTGCATTATTGGTATGAAAGGATGTCATAGTTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATGGGTGCATTAT
* *
3466638 TGACATAAAAGAAT
66 CGGCATAAAAGAAT
*
3466652 AATGCATATGGGTGCATTATTGGCATGTAAGG
1 AATGCATATGGGTGCATTATTGGCATGAAAGG
3466684 GTGCCATAAA
Statistics
Matches: 174, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 174 1.00
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (79 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATGGGTGCATTAT
CGGCATAAAAGAAT
Found at i:3466559 original size:202 final size:203
Alignment explanation
Indices: 3466213--3466648 Score: 694
Period size: 202 Copynumber: 2.2 Consensus size: 203
3466203 AATAAAAAAT
* * * *
3466213 AATGCATATAGGTGCATTATTGGCATGAAAGGATGCCATAGTTGAAATGCATATAGTTGTATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATAGGTGCATTAT
* * * *
3466278 TGGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAATGATGTCATAGCCGAAATGCA
66 CGGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCCGAAATGAA
*
3466343 TATGGGTGTATTATCGGCATAAAAGAATAATGCATATG-GTGTATTATTGGCATGAAAAGATGCC
131 TATGGGTGTATTATCGGCATAAAAGAATAATGCATATGAGTGCATTATTGGCATGAAAAGATGCC
3466407 ATAGCTGA
196 ATAGCTGA
* *
3466415 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATAGGTGCATTAT
* *
3466480 CGGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGGAAGGATGCCATAGCTGAAATGAA
66 CGGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCCGAAATGAA
* * *
3466545 TATGGGTGTATTATCGGCATAAAAGAATAATGCATATGAGTGCATTATTGGTATGAAAGGATGTC
131 TATGGGTGTATTATCGGCATAAAAGAATAATGCATATGAGTGCATTATTGGCATGAAAAGATGCC
*
3466610 ATAGTTGA
196 ATAGCTGA
* *
3466618 AATGCATATGGGTGCATTATTGACATAAAAG
1 AATGCATATGGGTGCATTATTGGCATGAAAG
3466649 AATAATGCAT
Statistics
Matches: 214, Mismatches: 19, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
202 156 0.73
203 58 0.27
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (203 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATAGGTGCATTAT
CGGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCCGAAATGAA
TATGGGTGTATTATCGGCATAAAAGAATAATGCATATGAGTGCATTATTGGCATGAAAAGATGCC
ATAGCTGA
Found at i:3466725 original size:20 final size:20
Alignment explanation
Indices: 3466700--3466773 Score: 67
Period size: 20 Copynumber: 3.4 Consensus size: 20
3466690 TAAATAAAAT
*
3466700 GCATGAAATGATGCAATAAG
1 GCATGAAAGGATGCAATAAG
*
3466720 GCATGAAAGGATGTCATAAATAAAAT
1 GCATGAAAGGATG-C---AAT--AAG
*
3466746 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCAATAAG
3466766 GCATGAAA
1 GCATGAAA
3466774 AATGCCATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
20 22 0.50
21 1 0.02
22 2 0.05
24 3 0.07
25 1 0.02
26 15 0.34
ACGTcount: A:0.46, C:0.09, G:0.24, T:0.20
Consensus pattern (20 bp):
GCATGAAAGGATGCAATAAG
Found at i:3466738 original size:46 final size:46
Alignment explanation
Indices: 3466673--3466791 Score: 168
Period size: 46 Copynumber: 2.6 Consensus size: 46
3466663 GTGCATTATT
* * *
3466673 GGCATGTAAGGGTGCCATAAATAAAATGCATGAAATGATGCAATAA
1 GGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCAATAA
* *
3466719 GGCATGAAAGGATGTCATAAATAAAATGCATGAAAGGATGCATTAA
1 GGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCAATAA
* *
3466765 GGCATGAAA-AATGCCATAATTAAAATG
1 GGCATGAAAGGATGCCATAAATAAAATG
3466792 AAATTTAATG
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
45 15 0.23
46 50 0.77
ACGTcount: A:0.45, C:0.10, G:0.23, T:0.22
Consensus pattern (46 bp):
GGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCAATAA
Found at i:3466750 original size:26 final size:25
Alignment explanation
Indices: 3466674--3466761 Score: 87
Period size: 26 Copynumber: 3.6 Consensus size: 25
3466664 TGCATTATTG
* *
3466674 GCATGTAAGGGTGCCATAAATAAAAT
1 GCATGAAAGGATG-CATAAATAAAAT
* *
3466700 GCATGAAATGATGC---AAT--AAG
1 GCATGAAAGGATGCATAAATAAAAT
3466720 GCATGAAAGGATGTCATAAATAAAAT
1 GCATGAAAGGATG-CATAAATAAAAT
3466746 GCATGAAAGGATGCAT
1 GCATGAAAGGATGCAT
3466762 TAAGGCATGA
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
20 14 0.28
21 1 0.02
22 3 0.06
24 3 0.06
25 4 0.08
26 25 0.50
ACGTcount: A:0.44, C:0.10, G:0.24, T:0.22
Consensus pattern (25 bp):
GCATGAAAGGATGCATAAATAAAAT
Found at i:3468183 original size:23 final size:22
Alignment explanation
Indices: 3468154--3468241 Score: 117
Period size: 22 Copynumber: 4.0 Consensus size: 22
3468144 ATGATAATAT
3468154 ATAATATATAGTTTTGTGAAAAA
1 ATAATATATAGTTTT-TGAAAAA
3468177 ATAATATATAGTTTTT-AAAAA
1 ATAATATATAGTTTTTGAAAAA
*
3468198 CAT-ATAGTATAGTTTTTGAAAAC
1 -ATAATA-TATAGTTTTTGAAAAA
*
3468221 ATATTATATAGTTTTTGAAAA
1 ATAATATATAGTTTTTGAAAA
3468242 TATATAGTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
21 8 0.14
22 30 0.51
23 21 0.36
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.42
Consensus pattern (22 bp):
ATAATATATAGTTTTTGAAAAA
Found at i:3468229 original size:44 final size:45
Alignment explanation
Indices: 3468160--3468249 Score: 137
Period size: 44 Copynumber: 2.0 Consensus size: 45
3468150 ATATATAATA
3468160 TATAGTTTTGTGAAAAAATAATATATAGTTTTTAAAAACATATAG
1 TATAGTTTTGTGAAAAAATAATATATAGTTTTTAAAAACATATAG
* * * *
3468205 TATAGTTTT-TGAAAACATATTATATAGTTTTTGAAAATATATAG
1 TATAGTTTTGTGAAAAAATAATATATAGTTTTTAAAAACATATAG
3468249 T
1 T
3468250 TTTTGAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 32 0.78
45 9 0.22
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.43
Consensus pattern (45 bp):
TATAGTTTTGTGAAAAAATAATATATAGTTTTTAAAAACATATAG
Found at i:3468261 original size:15 final size:17
Alignment explanation
Indices: 3468225--3468266 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
3468215 GAAAACATAT
3468225 TATATAGTTTTTGAAAA
1 TATATAGTTTTTGAAAA
3468242 TATATAGTTTTTGAAAA
1 TATATAGTTTTTGAAAA
3468259 TATATAGT
1 TATATAGT
3468267 ATATATGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (17 bp):
TATATAGTTTTTGAAAA
Found at i:3468263 original size:2 final size:2
Alignment explanation
Indices: 3468258--3468370 Score: 53
Period size: 2 Copynumber: 57.5 Consensus size: 2
3468248 GTTTTTGAAA
* *
3468258 AT AT AT AGT AT AT AT GT A- AT AT AT AT AT AT AT AT AT AT TT GA-
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
* * *
3468300 AA AT AT AT -T AT AT GAT -T TT GA- AA AT AT ACT AT AT -T AT AT
1 AT AT AT AT AT AT AT -AT AT AT -AT AT AT AT A-T AT AT AT AT AT
* *
3468339 AGT -T TT TT A- AT AT AT AT AT AT AT AT AT AT AT A
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3468371 ATTAAGTTTA
Statistics
Matches: 89, Mismatches: 8, Indels: 28
0.71 0.06 0.22
Matches are distributed among these distances:
1 8 0.09
2 74 0.83
3 7 0.08
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3468284 original size:39 final size:40
Alignment explanation
Indices: 3468157--3468286 Score: 97
Period size: 39 Copynumber: 3.2 Consensus size: 40
3468147 ATAATATATA
* * * * *
3468157 ATATATAGTTTTGTGAAAAAATAATATATAGTTTTTAAAAACAT
1 ATATATAGTTTT-TGAAAACATATTATATAGTATGT--GAA-AT
* *
3468201 ATAGTATAGTTTTTGAAAACATATTATATAGTTTTTGAAA-
1 ATA-TATAGTTTTTGAAAACATATTATATAGTATGTGAAAT
*
3468241 ATATATAGTTTTTGAAAATATA-TAGTATA-TATGT-AATAT
1 ATATATAGTTTTTGAAAACATATTA-TATAGTATGTGAA-AT
3468280 ATATATA
1 ATATATA
3468287 TATATATATT
Statistics
Matches: 76, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
37 2 0.03
38 6 0.08
39 29 0.38
40 3 0.04
41 1 0.01
42 2 0.03
44 24 0.32
45 9 0.12
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.44
Consensus pattern (40 bp):
ATATATAGTTTTTGAAAACATATTATATAGTATGTGAAAT
Found at i:3468299 original size:61 final size:61
Alignment explanation
Indices: 3468179--3468307 Score: 156
Period size: 61 Copynumber: 2.1 Consensus size: 61
3468169 GTGAAAAAAT
* * *
3468179 AATATATAGTTTTTAAAAACATATAGTATAGTTTTTGAAAACATATTATATAGTTTTTGAA
1 AATATATAGTTTTTAAAAACATATAGTATAGTATGTGAAAACATATTATATAGTATTTGAA
* * *
3468240 AATATATAGTTTTTGAAAATATATAGTATA-TATGT-AATATATATATATATATA-TATTTGAA
1 AATATATAGTTTTTAAAAACATATAGTATAGTATGTGAA-A-ACATAT-TATATAGTATTTGAA
3468301 AATATAT
1 AATATAT
3468308 TATATGATTT
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
59 2 0.03
60 4 0.07
61 47 0.80
62 6 0.10
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.45
Consensus pattern (61 bp):
AATATATAGTTTTTAAAAACATATAGTATAGTATGTGAAAACATATTATATAGTATTTGAA
Found at i:3468353 original size:27 final size:26
Alignment explanation
Indices: 3468275--3468366 Score: 79
Period size: 27 Copynumber: 3.7 Consensus size: 26
3468265 GTATATATGT
*
3468275 AATATATATA-TATATATATATTTG--
1 AATATATATATTATATAGAT-TTTGAA
3468299 AA-A-ATATATTATAT-GATTTTGAA
1 AATATATATATTATATAGATTTTGAA
* *
3468322 AATATACTATATTATATAGTTTTTTAA
1 AATATA-TATATTATATAGATTTTGAA
*
3468349 TATATATATATATATATA
1 AATATATATAT-TATATA
3468367 TATAATTAAG
Statistics
Matches: 56, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
21 4 0.07
22 7 0.12
23 8 0.14
24 3 0.05
25 1 0.02
26 15 0.27
27 18 0.32
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (26 bp):
AATATATATATTATATAGATTTTGAA
Found at i:3475425 original size:30 final size:29
Alignment explanation
Indices: 3475387--3475532 Score: 123
Period size: 30 Copynumber: 4.9 Consensus size: 29
3475377 GTTAATACCA
*
3475387 ATTTAGTCCTTTAATTTTCTATTTTTTCT
1 ATTTAGTCCTTTAATTTTCTATTTTTGCT
*
3475416 ATTTCAGTCCTTT-ATGTTTCTATTTTTGCC
1 ATTT-AGTCCTTTAAT-TTTCTATTTTTGCT
** * *
3475446 ATTTTAGTCCTTCGAGTTTCTGTTTTTGCT
1 A-TTTAGTCCTTTAATTTTCTATTTTTGCT
* * *
3475476 ATTTTGATCCTTTAACTTTCTATTTTTGAT
1 ATTTAG-TCCTTTAATTTTCTATTTTTGCT
* * * *
3475506 ATTTTAATCTTTTAAGTTTCTGTTTTT
1 A-TTTAGTCCTTTAATTTTCTATTTTT
3475533 TGTCCTTCAA
Statistics
Matches: 94, Mismatches: 17, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
29 10 0.11
30 77 0.82
31 7 0.07
ACGTcount: A:0.16, C:0.14, G:0.09, T:0.61
Consensus pattern (29 bp):
ATTTAGTCCTTTAATTTTCTATTTTTGCT
Found at i:3475452 original size:60 final size:60
Alignment explanation
Indices: 3475388--3475533 Score: 168
Period size: 60 Copynumber: 2.4 Consensus size: 60
3475378 TTAATACCAA
* * ** *
3475388 TTTAGTCCTTTAATTTTCTATTTTTTCTATTTCAG-TCCTTTATGTTTCTATTTTTGCCAT
1 TTTAGTCCTTTAAGTTTCTGTTTTTTCTATTT-AGATCCTTTAACTTTCTATTTTTGACAT
** * * *
3475448 TTTAGTCCTTCGAGTTTCTGTTTTTGCTATTTTGATCCTTTAACTTTCTATTTTTGATAT
1 TTTAGTCCTTTAAGTTTCTGTTTTTTCTATTTAGATCCTTTAACTTTCTATTTTTGACAT
* *
3475508 TTTAATCTTTTAAGTTTCTGTTTTTT
1 TTTAGTCCTTTAAGTTTCTGTTTTTT
3475534 GTCCTTCAAG
Statistics
Matches: 70, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
59 1 0.01
60 69 0.99
ACGTcount: A:0.15, C:0.14, G:0.09, T:0.62
Consensus pattern (60 bp):
TTTAGTCCTTTAAGTTTCTGTTTTTTCTATTTAGATCCTTTAACTTTCTATTTTTGACAT
Found at i:3479281 original size:16 final size:16
Alignment explanation
Indices: 3479228--3479283 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
3479218 GAGAAAAGAA
*
3479228 AAAACAAAGAAACAAAG
1 AAAA-AAAGAATCAAAG
3479245 -AAAAAA-AATCAAA-
1 AAAAAAAGAATCAAAG
*
3479258 AAACAAAAGAATGAAAG
1 AAA-AAAAGAATCAAAG
3479275 AAAAAAAGA
1 AAAAAAAGA
3479284 CAAGAAGCAC
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
14 8 0.24
15 7 0.21
16 15 0.45
17 3 0.09
ACGTcount: A:0.79, C:0.07, G:0.11, T:0.04
Consensus pattern (16 bp):
AAAAAAAGAATCAAAG
Found at i:3480502 original size:15 final size:15
Alignment explanation
Indices: 3480478--3480507 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3480468 CCCGAATTTT
*
3480478 GTCTCTCTTGAGACA
1 GTCTCCCTTGAGACA
3480493 GTCTCCCTTGAGACA
1 GTCTCCCTTGAGACA
3480508 TTATCCCTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (15 bp):
GTCTCCCTTGAGACA
Found at i:3480716 original size:40 final size:41
Alignment explanation
Indices: 3480533--3480716 Score: 108
Period size: 40 Copynumber: 4.3 Consensus size: 41
3480523 GCTTGCCGTT
* *
3480533 CTCATCATGTAGGAGTTGTGTCATCCCCT-GACCAGACC-TC
1 CTCATCACGTAGGAATTGTGTCAT-CCCTAGACCAGACCATC
* ** *
3480573 CTCATCACGTAGGAGTCATGTCA-CCCTAGATAACCAG-CCGTC
1 CTCATCACGTAGGAATTGTGTCATCCCTAG---ACCAGACCATC
* * * ** *
3480615 CTCATCACATAGGAACTGTGTTATCATTCCTAAAGATGGTATACCATC
1 CTCATCACGTAGGAA-T-TG-TGTCATCCCT--AGA--CCAGACCATC
* *
3480663 CTCATCAAGTAGGAATTGTGTCATCCCTCGACCAGACC-TC
1 CTCATCACGTAGGAATTGTGTCATCCCTAGACCAGACCATC
3480703 CTCATCACGTAGGA
1 CTCATCACGTAGGA
3480717 GCCCTATCAC
Statistics
Matches: 108, Mismatches: 22, Indels: 28
0.68 0.14 0.18
Matches are distributed among these distances:
38 4 0.04
39 1 0.01
40 35 0.32
41 6 0.06
42 20 0.19
43 3 0.03
45 13 0.12
46 5 0.05
47 2 0.02
48 19 0.18
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (41 bp):
CTCATCACGTAGGAATTGTGTCATCCCTAGACCAGACCATC
Found at i:3480790 original size:130 final size:128
Alignment explanation
Indices: 3480533--3480772 Score: 365
Period size: 130 Copynumber: 1.9 Consensus size: 128
3480523 GCTTGCCGTT
* * * *
3480533 CTCATCATGTAGGAGTTGTGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGTCATGTCACC
1 CTCATCAAGTAGGAATTGTGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGCCATATCACC
* *
3480598 CTAGATAACCAGCCGTCCTCATCACATAGGAACTGTGTTATCATTCCTAAAGATGGTATACCATC
66 CTAAATAACCAGCCGTCCTCATCACATAGGAACCGTGTTATCATTCCTAAAGA--GTATACCATC
*
3480663 CTCATCAAGTAGGAATTGTGTCAT-CCCTCGACCAGACCTCCTCATCACGTAGGAGCCCTATCAC
1 CTCATCAAGTAGGAATTGTGTCATCCCCT-GACCAGACCTCCTCATCACGTAGGAGCCATATCA-
*
3480727 CCCTAAATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCAT
64 CCCTAAATAACCAGCCGTCCTCATCACATAGGAACCGTGTTATCAT
3480773 CATTCCTAAA
Statistics
Matches: 100, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
129 4 0.04
130 53 0.53
131 43 0.43
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.25
Consensus pattern (128 bp):
CTCATCAAGTAGGAATTGTGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGCCATATCACC
CTAAATAACCAGCCGTCCTCATCACATAGGAACCGTGTTATCATTCCTAAAGAGTATACCATC
Found at i:3480874 original size:134 final size:128
Alignment explanation
Indices: 3480533--3480890 Score: 398
Period size: 134 Copynumber: 2.7 Consensus size: 128
3480523 GCTTGCCGTT
*
3480533 CTCATCATGTAGGAGTTGTGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGTCATGTCACC
1 CTCATCAAGTAGGAGTTGTGTCATCCCC-GACCAGACCTCCTCATCACGTAGGAGTCATGTCACC
* * * **
3480598 CTAGATAACCAGCCGTCCTCATCACATAGGAACTGTGTTATCATTCCTAAAGATGGTATACCATC
65 CTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCATTCCTAAAGAT-GTACAAAATC
* * * *
3480663 CTCATCAAGTAGGAATTGTGTCATCCCTCGACCAGACCTCCTCATCACGTAGGAGCCCTATCACC
1 CTCATCAAGTAGGAGTTGTGTCATCCC-CGACCAGACCTCCTCATCACGTAGGAGTCATGTCA-C
*
3480728 CCTAAATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCATCATTCCTAAAGAT-TACCAA
64 CCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTG-T-T-ATCATTCCTAAAGATGTA-CAA
3480792 AACTC
125 AA-TC
* * * * * * * *
3480797 TTCATCACGTATGAGTCGTGTCATCCACCAACCAGATCTCCTCATCACATAGGAGTCGTGTCACC
1 CTCATCAAGTAGGAGTTGTGTCATCC-CCGACCAGACCTCCTCATCACGTAGGAGTCATGTCACC
*
3480862 CTTAGACT-ACCAGGCC-TCTTCATCACGTA
65 C-TAGA-TAACCA-GCCGTCCTCATCACGTA
3480891 TCAGCAATGT
Statistics
Matches: 193, Mismatches: 24, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
130 56 0.29
131 37 0.19
132 3 0.02
133 6 0.03
134 86 0.45
135 5 0.03
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.26
Consensus pattern (128 bp):
CTCATCAAGTAGGAGTTGTGTCATCCCCGACCAGACCTCCTCATCACGTAGGAGTCATGTCACCC
TAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCATTCCTAAAGATGTACAAAATC
Found at i:3481080 original size:3 final size:3
Alignment explanation
Indices: 3481056--3481124 Score: 74
Period size: 3 Copynumber: 23.7 Consensus size: 3
3481046 CTACAAAAAA
* *
3481056 TAT TAT TTT TA- TAT TA- TCT TAT TAT TAT TAT TAT TAT TAT TAT TACT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
3481103 T-T TAT TAT TAAT T-T TAT TAT TA
1 TAT TAT TAT T-AT TAT TAT TAT TA
3481125 ATAACTAATA
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
2 7 0.12
3 44 0.79
4 5 0.09
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3488462 original size:23 final size:22
Alignment explanation
Indices: 3488428--3488487 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 22
3488418 CATCTTATAT
3488428 GGCACTACGGTGCAATTCTACGC
1 GGCACTA-GGTGCAATTCTACGC
*
3488451 GGCACTTAGGTGCAATTCTACGT
1 GGCAC-TAGGTGCAATTCTACGC
*
3488474 GGCACATCGGTGCA
1 GGCAC-TAGGTGCA
3488488 TTTATTTGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 31 0.94
24 2 0.06
ACGTcount: A:0.22, C:0.27, G:0.28, T:0.23
Consensus pattern (22 bp):
GGCACTAGGTGCAATTCTACGC
Found at i:3495041 original size:21 final size:21
Alignment explanation
Indices: 3495017--3495056 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3495007 TTCTTCCAAA
*
3495017 TAAAATTCATAATTATTTTTT
1 TAAAATTAATAATTATTTTTT
*
3495038 TAAACTTAATAATTATTTT
1 TAAAATTAATAATTATTTT
3495057 CAAAAAAAAA
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:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
TAAAATTAATAATTATTTTTT
Found at i:3500355 original size:21 final size:21
Alignment explanation
Indices: 3500320--3500359 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
3500310 AGTAAGTTCT
3500320 TTATCTGCTTGGATGCAAACAG
1 TTATCTGCTTGGATG-AAACAG
3500342 TTATCTGC-TGGATGAAAC
1 TTATCTGCTTGGATGAAAC
3500360 TTTCTTGGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 6 0.33
22 8 0.44
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.33
Consensus pattern (21 bp):
TTATCTGCTTGGATGAAACAG
Found at i:3504661 original size:24 final size:23
Alignment explanation
Indices: 3504617--3504661 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
3504607 TTTCAGTTAG
* *
3504617 TATTTTTTTTAAAATAGTTATTA
1 TATTTTTATTAAAATAATTATTA
*
3504640 TATTTTATATTAATATAATTAT
1 TATTTT-TATTAAAATAATTAT
3504662 ATAAATATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 6 0.33
24 12 0.67
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
TATTTTTATTAAAATAATTATTA
Found at i:3504675 original size:30 final size:32
Alignment explanation
Indices: 3504640--3504715 Score: 88
Period size: 33 Copynumber: 2.5 Consensus size: 32
3504630 ATAGTTATTA
3504640 TATTTTATATT-AAT-ATAATTATATAAATAT
1 TATTTTATATTAAATAATAATTATATAAATAT
* * *
3504670 TATTTTTTATTAAAATAATATTTATATAATTAT
1 TATTTTATATT-AAATAATAATTATATAAATAT
3504703 TA-TTTAT-TTAAAT
1 TATTTTATATTAAAT
3504716 TTATTAATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
30 14 0.36
31 2 0.05
32 7 0.18
33 16 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (32 bp):
TATTTTATATTAAATAATAATTATATAAATAT
Found at i:3504678 original size:32 final size:32
Alignment explanation
Indices: 3504635--3504725 Score: 87
Period size: 32 Copynumber: 2.8 Consensus size: 32
3504625 TTAAAATAGT
*
3504635 TATTATATTTTATATTAATATAATTATATAAA
1 TATTATTTTTTATATTAATATAATTATATAAA
* * *
3504667 TATTATTTTTTAT-TAAAATAATATTTATATAAT
1 TATTATTTTTTATAT-TAAT-ATAATTATATAAA
* *
3504700 TATTATTTATTTAAATTTAT-TAATTA
1 TATTATTT-TTTATATTAATATAATTA
3504726 ATTATTTTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
31 1 0.02
32 20 0.43
33 19 0.40
34 6 0.13
35 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (32 bp):
TATTATTTTTTATATTAATATAATTATATAAA
Found at i:3507070 original size:34 final size:34
Alignment explanation
Indices: 3507027--3507133 Score: 160
Period size: 34 Copynumber: 3.1 Consensus size: 34
3507017 ATTAATGTTT
3507027 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
* * *
3507061 TTAAAATACAAATAATATTATTCGAAATTTAAAT
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
* * *
3507095 TTAAAATATAAATTATAGTATTTGAAATTTAACA
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
3507129 TTAAA
1 TTAAA
3507134 TTCAACTTAA
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 64 1.00
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (34 bp):
TTAAAATACAAATTATAGTATTCGAAATTTAAAA
Found at i:3513621 original size:20 final size:20
Alignment explanation
Indices: 3513592--3513634 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
3513582 ACTCTACCAC
3513592 ATGCAACTATATG-ATCCTAA
1 ATGCAACTATATGTA-CCTAA
*
3513612 ATGCATCTATATGTACCTAA
1 ATGCAACTATATGTACCTAA
3513632 ATG
1 ATG
3513635 TGCCTTAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGTACCTAA
Found at i:3522011 original size:31 final size:31
Alignment explanation
Indices: 3521969--3522039 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
3521959 AGTGACCTTT
*
3521969 TTTTTTTACAAATCGATAACATTAGTGACCA
1 TTTTGTTACAAATCGATAACATTAGTGACCA
* *
3522000 TTTTGTTACAAATCTATAACGTTAGTGACCA
1 TTTTGTTACAAATCGATAACATTAGTGACCA
*
3522031 ATTTGTTAC
1 TTTTGTTAC
3522040 TTTTGATACT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.41
Consensus pattern (31 bp):
TTTTGTTACAAATCGATAACATTAGTGACCA
Found at i:3522322 original size:20 final size:21
Alignment explanation
Indices: 3522297--3522336 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3522287 TTAGGGGGGG
3522297 TTTGAAT-AGTTATTGAGAAT
1 TTTGAATAAGTTATTGAGAAT
*
3522317 TTTGAATAAGTTTTTGAGAA
1 TTTGAATAAGTTATTGAGAA
3522337 ATTGTTGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.45
Consensus pattern (21 bp):
TTTGAATAAGTTATTGAGAAT
Found at i:3522740 original size:8 final size:8
Alignment explanation
Indices: 3522727--3522768 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
3522717 CATATTGTTG
3522727 TTATAATT
1 TTATAATT
3522735 TTATAATT
1 TTATAATT
3522743 TTAT-ATT
1 TTATAATT
*
3522750 TT-TATTT
1 TTATAATT
*
3522757 TTATATTT
1 TTATAATT
3522765 TTAT
1 TTAT
3522769 TATAGTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
6 1 0.03
7 9 0.29
8 21 0.68
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (8 bp):
TTATAATT
Found at i:3522760 original size:14 final size:14
Alignment explanation
Indices: 3522727--3522769 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 14
3522717 CATATTGTTG
*
3522727 TTATAATTTTATAATT
1 TTAT-ATTTT-TATTT
3522743 TTATATTTTTATTT
1 TTATATTTTTATTT
3522757 TTATATTTTTATT
1 TTATATTTTTATT
3522770 ATAGTTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 17 0.65
15 5 0.19
16 4 0.15
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTATATTTTTATTT
Found at i:3523649 original size:27 final size:28
Alignment explanation
Indices: 3523600--3523652 Score: 99
Period size: 27 Copynumber: 1.9 Consensus size: 28
3523590 ATTGAAATTA
3523600 TTGTTTTATCTGTTAAAATTTTATAAAC
1 TTGTTTTATCTGTTAAAATTTTATAAAC
3523628 TTGTTTTATCT-TTAAAATTTTATAA
1 TTGTTTTATCTGTTAAAATTTTATAA
3523653 GTTCAACTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 14 0.56
28 11 0.44
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.57
Consensus pattern (28 bp):
TTGTTTTATCTGTTAAAATTTTATAAAC
Found at i:3526508 original size:53 final size:53
Alignment explanation
Indices: 3526435--3526651 Score: 292
Period size: 53 Copynumber: 4.1 Consensus size: 53
3526425 ACTTATAATC
* * *
3526435 ACCTCAGACTATTTTAAAAAAATAATAATGATGCGTACTTATATAATTTTTTTC
1 ACCTCAAACTA-TTTAAAAAAATAATAATGACGCGTACTTATATAATTTTTTTG
* * * *
3526489 ACTTTAGACTATTT-AAAAAATCAATAATGACCCGTACTTATATAATTTTTTTG
1 ACCTCAAACTATTTAAAAAAAT-AATAATGACGCGTACTTATATAATTTTTTTG
* *
3526542 ACCTCAAACTATTTAAAAAATTAATAATGACGCGCACTTATATAATTTTTTTG
1 ACCTCAAACTATTTAAAAAAATAATAATGACGCGTACTTATATAATTTTTTTG
* * *
3526595 ACCTCAAAGTATTTAAAAAATTAATAATGATGCGTACTTATATAATTTTTTTAG
1 ACCTCAAACTATTTAAAAAAATAATAATGACGCGTACTTATATAATTTTTTT-G
3526649 ACC
1 ACC
3526652 GTTCACCAAT
Statistics
Matches: 146, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
52 7 0.05
53 120 0.82
54 19 0.13
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (53 bp):
ACCTCAAACTATTTAAAAAAATAATAATGACGCGTACTTATATAATTTTTTTG
Found at i:3527167 original size:42 final size:42
Alignment explanation
Indices: 3527109--3527396 Score: 312
Period size: 42 Copynumber: 6.7 Consensus size: 42
3527099 TCCCTTATTT
*
3527109 TACCTTTATAATTGAGGCCCCTAATTTTGTAATCTCACTTTC
1 TACCTTTATAATTGAGGCCCCTAATTTTTTAATCTCACTTTC
*
3527151 TACCTTT-TCAATTGAGGCCCCTAAGTTTTTTCAATCTCAATTTC
1 TACCTTTAT-AATTGAGGCCCCTAA-TTTTTT-AATCTCACTTTC
* * *
3527195 TACTTTTATAATTAAGGCCCCTAATTTTTTAATCTCACTTTT
1 TACCTTTATAATTGAGGCCCCTAATTTTTTAATCTCACTTTC
* *
3527237 TAACTTTATAATTGAGGCCCTTAAGTTTTTTTAATCTCACTTTC
1 TACCTTTATAATTGAGGCCCCTAA--TTTTTTAATCTCACTTTC
* * * ** * *
3527281 TAACTTTCTAATTGAGGTCCCTAAGTTTTTCCGATCTCA-ATTA
1 TACCTTTATAATTGAGGCCCCTAA-TTTTT-TAATCTCACTTTC
* *
3527324 TACCTTTATAATTGAGGGCCCTATTTTTTTAATCTCGA-TTTC
1 TACCTTTATAATTGAGGCCCCTAATTTTTTAATCTC-ACTTTC
* * *
3527366 TATCTTTATAATTAAGGCCTCTAATTTTTTA
1 TACCTTTATAATTGAGGCCCCTAATTTTTTA
3527397 CAATTTCATA
Statistics
Matches: 206, Mismatches: 32, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
41 6 0.03
42 86 0.42
43 38 0.18
44 75 0.36
45 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.09, T:0.46
Consensus pattern (42 bp):
TACCTTTATAATTGAGGCCCCTAATTTTTTAATCTCACTTTC
Found at i:3527207 original size:86 final size:85
Alignment explanation
Indices: 3527051--3527394 Score: 315
Period size: 86 Copynumber: 4.0 Consensus size: 85
3527041 ACTATTATTC
* * * * * * * * * *
3527051 AATCTCACTTTTTATCTTTGTAATTGAAGTCTCTAATTTTCTTTTCAATCCCTTATTT-TACCTT
1 AATCTCACTTTATACCTTTATAATTGAGGCCCCTAAGTTT-TTTT-AATCTC-AATTTCTACTTT
*
3527115 TATAATTGAGGCCCCTAATTTTGT
63 TATAATTAAGGCCCCTAATTTT-T
* *
3527139 AATCTCACTTTCTACCTTT-TCAATTGAGGCCCCTAAGTTTTTTCAATCTCAATTTCTACTTTTA
1 AATCTCACTTTATACCTTTAT-AATTGAGGCCCCTAAGTTTTTTTAATCTCAATTTCTACTTTTA
3527203 TAATTAAGGCCCCTAATTTTTT
65 TAATTAAGGCCCCTAA-TTTTT
* * * * *
3527225 AATCTCACTTTTTAACTTTATAATTGAGGCCCTTAAGTTTTTTTAATCTCACTTTCTAAC-TTTC
1 AATCTCACTTTATACCTTTATAATTGAGGCCCCTAAGTTTTTTTAATCTCAATTTCT-ACTTTTA
* *
3527289 TAATTGAGGTCCCTAAGTTTTT
65 TAATTAAGGCCCCTAA-TTTTT
* * * *
3527311 CCGATCTCA-ATTATACCTTTATAATTGAGGGCCCT-A-TTTTTTTAATCTCGATTTCTA-TCTT
1 --AATCTCACTTTATACCTTTATAATTGAGGCCCCTAAGTTTTTTTAATCTCAATTTCTACT-TT
*
3527372 TATAATTAAGGCCTCTAATTTTT
63 TATAATTAAGGCCCCTAATTTTT
3527395 TACAATTTCA
Statistics
Matches: 215, Mismatches: 32, Indels: 22
0.80 0.12 0.08
Matches are distributed among these distances:
84 6 0.03
85 38 0.18
86 101 0.47
87 32 0.15
88 38 0.18
ACGTcount: A:0.24, C:0.20, G:0.08, T:0.47
Consensus pattern (85 bp):
AATCTCACTTTATACCTTTATAATTGAGGCCCCTAAGTTTTTTTAATCTCAATTTCTACTTTTAT
AATTAAGGCCCCTAATTTTT
Found at i:3527213 original size:44 final size:43
Alignment explanation
Indices: 3527105--3527400 Score: 268
Period size: 44 Copynumber: 6.9 Consensus size: 43
3527095 TCAATCCCTT
* *
3527105 ATTT-TACCTTTATAATTGAGGCCCCTAATTTTGT-AATCTCA
1 ATTTCTACTTTTATAATTGAGGCCCCTAATTTTTTCAATCTCA
* *
3527146 CTTTCTACCTTTT-CAATTGAGGCCCCTAAGTTTTTTCAATCTCA
1 ATTTCTA-CTTTTATAATTGAGGCCCCTAA-TTTTTTCAATCTCA
*
3527190 ATTTCTACTTTTATAATTAAGGCCCCTAATTTTTT-AATCTCA
1 ATTTCTACTTTTATAATTGAGGCCCCTAATTTTTTCAATCTCA
* * * *
3527232 CTTTTTAAC-TTTATAATTGAGGCCCTTAAGTTTTTTTAATCTCA
1 ATTTCT-ACTTTTATAATTGAGGCCCCTAA-TTTTTTCAATCTCA
* * * * *
3527276 CTTTCTAAC-TTTCTAATTGAGGTCCCTAAGTTTTTCCGATCTCA
1 ATTTCT-ACTTTTATAATTGAGGCCCCTAA-TTTTTTCAATCTCA
* * * * *
3527320 A-TTATACCTTTATAATTGAGGGCCCT-ATTTTTTTAATCTCG
1 ATTTCTACTTTTATAATTGAGGCCCCTAATTTTTTCAATCTCA
* *
3527361 ATTTCTA-TCTTTATAATTAAGGCCTCTAATTTTTTACAAT
1 ATTTCTACT-TTTATAATTGAGGCCCCTAATTTTTT-CAAT
3527401 TTCATAAAAT
Statistics
Matches: 210, Mismatches: 32, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
41 14 0.07
42 68 0.32
43 54 0.26
44 74 0.35
ACGTcount: A:0.25, C:0.20, G:0.09, T:0.46
Consensus pattern (43 bp):
ATTTCTACTTTTATAATTGAGGCCCCTAATTTTTTCAATCTCA
Found at i:3528327 original size:20 final size:20
Alignment explanation
Indices: 3528302--3528341 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3528292 TTTGGGTTCG
* *
3528302 AATATCGATACTGGATGAAC
1 AATATCAATACTAGATGAAC
3528322 AATATCAATACTAGATGAAC
1 AATATCAATACTAGATGAAC
3528342 TTGGTCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATATCAATACTAGATGAAC
Found at i:3530197 original size:75 final size:79
Alignment explanation
Indices: 3530107--3530262 Score: 176
Period size: 82 Copynumber: 2.0 Consensus size: 79
3530097 CATGCCTGCC
* *
3530107 AATTATCGATTGATTTTTATGTCCG-AAAAAA-G-GGG-AACGAGGAAGGAGATGAAGCTTATGG
1 AATTATCGACTGATTTTTATGTCCGAAAAAAAGGAGGGAAACGAGGAAAGAGATGAAGCTTATGG
*
3530168 CAAAAAGAAAAAAA
66 CAAAAACAAAAAAA
* * ** *
3530182 AATTGTCGACTGATTTTTCTGTTTGAAAAAAAAGGAGGGAAAAAGGAGGAAAGAGATGAAGCTTA
1 AATTATCGACTGATTTTTATGTCCG-AAAAAAAGGAGGG--AAACGAGGAAAGAGATGAAGCTTA
*
3530247 TGGTAAAAACAAAAAA
63 TGGCAAAAACAAAAAA
3530263 GGGTTATTAT
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
75 20 0.31
77 6 0.09
78 1 0.02
79 3 0.05
82 35 0.54
ACGTcount: A:0.46, C:0.07, G:0.25, T:0.22
Consensus pattern (79 bp):
AATTATCGACTGATTTTTATGTCCGAAAAAAAGGAGGGAAACGAGGAAAGAGATGAAGCTTATGG
CAAAAACAAAAAAA
Found at i:3530498 original size:24 final size:24
Alignment explanation
Indices: 3530466--3530513 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
3530456 TTAGCGTTGG
3530466 GGGTAGCCTACTATTATATCTCCC
1 GGGTAGCCTACTATTATATCTCCC
3530490 GGGTAGCCTACTATTATATCTCCC
1 GGGTAGCCTACTATTATATCTCCC
3530514 CCTTACTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (24 bp):
GGGTAGCCTACTATTATATCTCCC
Found at i:3532793 original size:38 final size:38
Alignment explanation
Indices: 3532750--3532829 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
3532740 CAGCAGGGTC
* *
3532750 ATTTAAATA-AATTTCAGGGACTCCTACGAGTACTATAA
1 ATTTAAA-ACAATTTCAGCGACTCCTACGAGTACCATAA
***
3532788 ATTTAAAACAATTTGTTCGACTCCTACGAGTACCATAA
1 ATTTAAAACAATTTCAGCGACTCCTACGAGTACCATAA
3532826 ATTT
1 ATTT
3532830 GACATGATCT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
37 1 0.03
38 35 0.97
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (38 bp):
ATTTAAAACAATTTCAGCGACTCCTACGAGTACCATAA
Found at i:3534125 original size:5 final size:5
Alignment explanation
Indices: 3534115--3534141 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
3534105 TTTCTAATGT
3534115 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
3534142 CGTATATATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:3534182 original size:3 final size:3
Alignment explanation
Indices: 3534174--3534219 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
3534164 TGTGATATGT
3534174 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3534220 TCGGATAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3540905 original size:25 final size:25
Alignment explanation
Indices: 3540871--3540926 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
3540861 GGCACCTATG
* *
3540871 GTGCAATTCTACGATGTACTTTCGA
1 GTGCAATTCTACGAGGCACTTTCGA
*
3540896 GTGCAATTCTATGAGGCACTTTCGA
1 GTGCAATTCTACGAGGCACTTTCGA
3540921 GTGCAA
1 GTGCAA
3540927 ATACATGACT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (25 bp):
GTGCAATTCTACGAGGCACTTTCGA
Found at i:3544766 original size:20 final size:19
Alignment explanation
Indices: 3544750--3544798 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 19
3544740 TATGAAATAA
3544750 GAAATGAAAGAAA-GAAAT
1 GAAATGAAAGAAAGGAAAT
3544768 GAAATGATAAGAAAGGAAAT
1 GAAATGA-AAGAAAGGAAAT
3544788 GGAAATGAAAG
1 -GAAATGAAAG
3544799 GAATTAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.25
19 6 0.21
20 8 0.29
21 7 0.25
ACGTcount: A:0.61, C:0.00, G:0.27, T:0.12
Consensus pattern (19 bp):
GAAATGAAAGAAAGGAAAT
Found at i:3547051 original size:31 final size:32
Alignment explanation
Indices: 3547009--3547090 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 32
3546999 CTAGTCAGGG
* *
3547009 TGTATTTAGATAATGCACAATAT-GCCAGGTT
1 TGTATTCAGATAATGCACAATATGGCCAAGTT
* * *
3547040 TGTATTCAGATAATACACATTATGGTCAAGTT
1 TGTATTCAGATAATGCACAATATGGCCAAGTT
* *
3547072 TGCATTCAAATAATGCACA
1 TGTATTCAGATAATGCACA
3547091 TGAGTATCCG
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 20 0.48
32 22 0.52
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (32 bp):
TGTATTCAGATAATGCACAATATGGCCAAGTT
Found at i:3547644 original size:44 final size:44
Alignment explanation
Indices: 3547595--3547721 Score: 118
Period size: 44 Copynumber: 3.2 Consensus size: 44
3547585 TTAAACATTA
3547595 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAG
1 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAG
***
3547639 TATTTTAAT-TAAATTTTAGG-A---TA--TT--AT---TTTTA-
1 TATTTT-ATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAG
*
3547671 TATTTTATCTTTGGTTTAGGTATTTTAGTTTAAATAGGTTTTAG
1 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAG
3547715 TATTTTA
1 TATTTTA
3547722 ATTAGGATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 28
0.64 0.07 0.29
Matches are distributed among these distances:
31 2 0.03
32 13 0.21
33 6 0.10
36 4 0.06
38 4 0.06
40 4 0.06
43 6 0.10
44 21 0.34
45 2 0.03
ACGTcount: A:0.26, C:0.02, G:0.13, T:0.59
Consensus pattern (44 bp):
TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAG
Found at i:3547663 original size:65 final size:66
Alignment explanation
Indices: 3547593--3547797 Score: 204
Period size: 76 Copynumber: 3.0 Consensus size: 66
3547583 TTTTAAACAT
*
3547593 TATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTA-AATTTTA
1 TATATTTTATCTTTGATTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGAA-TTTA
3547657 GGATATTA
65 -G-----A
* *
3547665 TTTTTATATTTTATCTTTGGTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGAT
1 ----TATATTTTATCTTTGATTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGAAT
3547730 TTAGA
62 TTAGA
* *
3547735 -ATATTATTAT-TATT-ATTTAGGTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTAGGATT
1 TATATT-TTATCT-TTGATTTAGGTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAGAATT
3547796 TA
63 TA
3547798 AGATGTTTTA
Statistics
Matches: 121, Mismatches: 4, Indels: 19
0.84 0.03 0.13
Matches are distributed among these distances:
64 5 0.04
65 47 0.39
66 6 0.05
70 1 0.01
75 1 0.01
76 60 0.50
77 1 0.01
ACGTcount: A:0.29, C:0.01, G:0.14, T:0.57
Consensus pattern (66 bp):
TATATTTTATCTTTGATTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGAATTTAG
A
Found at i:3547683 original size:76 final size:76
Alignment explanation
Indices: 3547591--3547752 Score: 263
Period size: 76 Copynumber: 2.1 Consensus size: 76
3547581 TATTTTAAAC
*
3547591 ATTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTA-AATTT
1 ATTATATTTTATCTTTGGTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGAA-TT
*
3547655 TAGGATATTATT
65 TAGAATATTATT
* *
3547667 TTTATATTTTATCTTTGGTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTT
1 ATTATATTTTATCTTTGGTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGAATTT
3547732 AGAATATTATT
66 AGAATATTATT
3547743 ATTATTATTT
1 ATTA-TATTT
3547753 AGGTATTTTA
Statistics
Matches: 79, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
76 73 0.92
77 6 0.08
ACGTcount: A:0.28, C:0.01, G:0.12, T:0.58
Consensus pattern (76 bp):
ATTATATTTTATCTTTGGTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGAATTT
AGAATATTATT
Found at i:3548398 original size:17 final size:17
Alignment explanation
Indices: 3548373--3548406 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3548363 CTTTATCCCA
*
3548373 ATTTATTTATTTTATTT
1 ATTTATTTATTTAATTT
*
3548390 ATTTGTTTATTTAATTT
1 ATTTATTTATTTAATTT
3548407 TTATCTCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTATTTATTTAATTT
Found at i:3551461 original size:5 final size:5
Alignment explanation
Indices: 3551451--3551485 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
3551441 CATTCTATTA
* *
3551451 ATTTT ATTTT AATTA ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
3551486 TCTGAATAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (5 bp):
ATTTT
Found at i:3551485 original size:15 final size:15
Alignment explanation
Indices: 3551447--3551476 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3551437 ATTTCATTCT
3551447 ATTAATTTTATTTTA
1 ATTAATTTTATTTTA
3551462 ATTAATTTTATTTTA
1 ATTAATTTTATTTTA
3551477 TTTTATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTAATTTTATTTTA
Found at i:3553335 original size:44 final size:43
Alignment explanation
Indices: 3553286--3553413 Score: 100
Period size: 44 Copynumber: 3.2 Consensus size: 43
3553276 TTAAACATTA
3553286 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAG
1 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATA-GTTTTAG
** * *
3553330 TATTTTAAT-TAAGTTTTATG-A---T--CTT--AT--TTTTA-
1 TATTTT-ATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAG
3553362 TATTTTATCTTTGTTTTTAGGTATTTTAGTTTAAATATGTTTTAG
1 TATTTTATCTTTG-TTTTAGGTATTTTAGTTTAAATA-GTTTTAG
3553407 TATTTTA
1 TATTTTA
3553414 ATTACGATTT
Statistics
Matches: 61, Mismatches: 8, Indels: 29
0.62 0.08 0.30
Matches are distributed among these distances:
31 2 0.03
32 8 0.13
33 11 0.18
34 1 0.02
36 2 0.03
37 1 0.02
38 2 0.03
39 2 0.03
40 1 0.02
41 2 0.03
43 1 0.02
44 19 0.31
45 9 0.15
ACGTcount: A:0.24, C:0.02, G:0.12, T:0.62
Consensus pattern (43 bp):
TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAG
Found at i:3553434 original size:77 final size:76
Alignment explanation
Indices: 3553282--3553444 Score: 247
Period size: 77 Copynumber: 2.1 Consensus size: 76
3553272 TATTTTAAAC
*
3553282 ATTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTT
1 ATTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTT
*
3553347 ATGATCTTATT
66 ATGATATTATT
* * *
3553358 TTTATATTTTATCTTTGTTTTTAGGTATTTTAGTTTAAATATGTTTTAGTATTTTAATTACGATT
1 ATTATATTTTATCTTTG-TTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATT
3553423 TA-GAATATTATT
65 TATG-ATATTATT
3553435 ATTATTATTT
1 ATTA-TATTT
3553445 AGGTATTTTA
Statistics
Matches: 78, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
76 17 0.22
77 56 0.72
78 5 0.06
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.60
Consensus pattern (76 bp):
ATTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTT
ATGATATTATT
Found at i:3554080 original size:9 final size:9
Alignment explanation
Indices: 3554066--3554098 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
3554056 TTTATCCTAA
3554066 TTTATTTAT
1 TTTATTTAT
3554075 TTTATTTAT
1 TTTATTTAT
3554084 TTT-TTTAT
1 TTTATTTAT
*
3554092 TTAATTT
1 TTTATTT
3554099 TTATCTCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTATTTAT
Found at i:3554090 original size:17 final size:17
Alignment explanation
Indices: 3554065--3554098 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3554055 CTTTATCCTA
*
3554065 ATTTATTTATTTTATTT
1 ATTTATTTATTTAATTT
*
3554082 ATTTTTTTATTTAATTT
1 ATTTATTTATTTAATTT
3554099 TTATCTCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
ATTTATTTATTTAATTT
Found at i:3554098 original size:13 final size:12
Alignment explanation
Indices: 3554065--3554100 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 12
3554055 CTTTATCCTA
3554065 ATTTATTTATTTT
1 ATTTATTT-TTTT
3554078 ATTTATTTTTTT
1 ATTTATTTTTTT
3554090 ATTTAATTTTT
1 ATTT-ATTTTT
3554101 ATCTCATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
ATTTATTTTTTT
Found at i:3556115 original size:3 final size:3
Alignment explanation
Indices: 3556103--3556149 Score: 69
Period size: 3 Copynumber: 15.3 Consensus size: 3
3556093 AAAAATAAAG
3556103 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATAA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A AT-A ATA ATA
3556149 A
1 A
3556150 AATGTTTTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.79
4 7 0.17
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:3556467 original size:84 final size:84
Alignment explanation
Indices: 3556359--3556543 Score: 248
Period size: 84 Copynumber: 2.2 Consensus size: 84
3556349 AGTAGTTCGA
* *
3556359 AATCAAACTCGTCAA-GTCTTTGGTTGGCAGATAGCCCTTCTCGAC-TTAAGCTATGTTGCAAAT
1 AATCAAACTCG--AAGGTCTTTGGTTGGCAAATAACCCTTCT-GACTTTAAGCTATGTTGCAAAT
*
3556422 GATATGCCTTGGAGCTGAGCGT
63 AATATGCCTTGGAGCTGAGCGT
* * *
3556444 AGTCAAACTCGAAGGTCTTTGGTTGGCAAATAACCCTTCTTACTTTGAGCTATGTTGCAAATAAT
1 AATCAAACTCGAAGGTCTTTGGTTGGCAAATAACCCTTCTGACTTTAAGCTATGTTGCAAATAAT
* *
3556509 GTGCCTTGGAGCTGAGTGT
66 ATGCCTTGGAGCTGAGCGT
*
3556528 AATCGAACTCGAAGGT
1 AATCAAACTCGAAGGT
3556544 TTGGTGTTTC
Statistics
Matches: 88, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
83 4 0.05
84 74 0.84
85 10 0.11
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (84 bp):
AATCAAACTCGAAGGTCTTTGGTTGGCAAATAACCCTTCTGACTTTAAGCTATGTTGCAAATAAT
ATGCCTTGGAGCTGAGCGT
Found at i:3556701 original size:36 final size:37
Alignment explanation
Indices: 3556651--3556815 Score: 190
Period size: 36 Copynumber: 4.4 Consensus size: 37
3556641 CAAAGATTGG
* *
3556651 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAATTT
3556687 TGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAATTT
* ** *
3556723 TGTTTCAAGAGAAATTGTCTCAAGATAGACAAAATATTT
1 TGTTTCAAGGGAAACCGTCTCAAGAGAGAC-AAA-ATTT
* * *
3556762 TGTTTCGAGGGAAACCATCTCAGGAGAGACAAAATCTT
1 TGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAAT-TT
*
3556800 CTGTTTCGAGGGAAAC
1 -TGTTTCAAGGGAAAC
3556816 AATCTCAAAG
Statistics
Matches: 111, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
36 60 0.54
37 5 0.05
38 6 0.05
39 40 0.36
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (37 bp):
TGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAATTT
Found at i:3556732 original size:21 final size:21
Alignment explanation
Indices: 3556670--3556734 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
3556660 AGAAACTGTC
3556670 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
** *
3556691 TCAAG-G-G---AAA-CCGTC
1 TCAAGAGAGACAAAATTTGTT
3556706 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
3556727 TCAAGAGA
1 TCAAGAGA
3556735 AATTGTCTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
15 7 0.22
16 4 0.12
17 1 0.03
19 1 0.03
20 4 0.12
21 15 0.47
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.23
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:3556742 original size:72 final size:75
Alignment explanation
Indices: 3556651--3556796 Score: 226
Period size: 75 Copynumber: 2.0 Consensus size: 75
3556641 CAAAGATTGG
*
3556651 TGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAA-A-TTTGTTTCAAGGGAAACCGTCTCAAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATATTTTGTTTCAAGGGAAACCATCTCAAGAG
3556713 AGACAAAATT
66 AGACAAAATT
* * * *
3556723 TGTTTCAAGAGAAATTGTCTCAAGATAGACAAAATATTTTGTTTCGAGGGAAACCATCTCAGGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATATTTTGTTTCAAGGGAAACCATCTCAAGAG
3556788 AGACAAAAT
66 AGACAAAAT
3556797 CTTCTGTTTC
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
72 28 0.42
73 3 0.05
74 1 0.02
75 34 0.52
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (75 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATATTTTGTTTCAAGGGAAACCATCTCAAGAG
AGACAAAATT
Found at i:3557742 original size:110 final size:109
Alignment explanation
Indices: 3557522--3557822 Score: 396
Period size: 110 Copynumber: 2.8 Consensus size: 109
3557512 GAAATCCAAG
* * *
3557522 CTTGTGTTGTTTCGAGTCCAATATCCTTCGTCGTAAAGTTGAAATTAGCT-T---TGAAACTAGG
1 CTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTAAAGTTGAAATTA-CTCTGAATGAAACT-GA
* * *
3557583 AAA-TTATTTGTTGACAGCCAACCGCCCCTTCACTGTGAAGTTGAG
64 AAAGTTGTTTGTTGACAGTCAACCGCCCCTTCACTGTGAAGTTGAA
* *
3557628 CTTGTGCTGTCTCGAGTCCAATATCCTTCGTTGTAAAGTTGAAATTGACTCTGAATAAAACTGAA
1 CTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTAAAGTTGAAATT-ACTCTGAATGAAACTGAA
**
3557693 AAGTTGTTTGTTGACAGTCAGTCGCCCCTTCACTGTGAAGTTGAA
65 AAGTTGTTTGTTGACAGTCAACCGCCCCTTCACTGTGAAGTTGAA
* * * *
3557738 CTTGTGTTGTCTCGAATCCAATATCCTTCGCTATGAAGTTGAAATTAACTCTGAATGAAACTGAA
1 CTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTAAAGTTGAAATT-ACTCTGAATGAAACTGAA
*
3557803 AAGTTGTTTGTTGATAGTCA
65 AAGTTGTTTGTTGACAGTCA
3557823 CCCCTTCGCT
Statistics
Matches: 171, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
106 45 0.26
107 2 0.01
109 4 0.02
110 120 0.70
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (109 bp):
CTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTAAAGTTGAAATTACTCTGAATGAAACTGAAA
AGTTGTTTGTTGACAGTCAACCGCCCCTTCACTGTGAAGTTGAA
Found at i:3558004 original size:20 final size:20
Alignment explanation
Indices: 3557979--3558019 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3557969 GTCTAAGATG
3557979 TATGCAACATGAATGAGTTA
1 TATGCAACATGAATGAGTTA
3557999 TATGCAACATGAATGAGTTA
1 TATGCAACATGAATGAGTTA
3558019 T
1 T
3558020 GTTTTATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.32
Consensus pattern (20 bp):
TATGCAACATGAATGAGTTA
Found at i:3561475 original size:25 final size:26
Alignment explanation
Indices: 3561429--3561477 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
3561419 TGTCTTTATT
*
3561429 TTCAAAAATTGAAATTTAAATTAAAA
1 TTCAAAAATTGAAATATAAATTAAAA
* *
3561455 TTCAAAAATT-CAATATGAATTAA
1 TTCAAAAATTGAAATATAAATTAA
3561478 TTACCTTTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 10 0.50
26 10 0.50
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (26 bp):
TTCAAAAATTGAAATATAAATTAAAA
Found at i:3561896 original size:21 final size:21
Alignment explanation
Indices: 3561862--3562027 Score: 146
Period size: 21 Copynumber: 7.8 Consensus size: 21
3561852 ATTGCGAGAG
3561862 TCCAAGTTTGCGTTGCGATTTAT
1 TCCAAG-TT-CGTTGCGATTTAT
*
3561885 TCCAAGTTCGTTGCGA--TAG
1 TCCAAGTTCGTTGCGATTTAT
* *
3561904 TCGATGTTCGCATTGCGATTTAT
1 TCCAAGTTCG--TTGCGATTTAT
* *
3561927 TCCAAATTCGTTGCGA--TAG
1 TCCAAGTTCGTTGCGATTTAT
*
3561946 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGATTTAT
*
3561969 TCCAAGTTCGTTGCGA--TAG
1 TCCAAGTTCGTTGCGATTTAT
*
3561988 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGATTTAT
3562011 TCCAAGTTCGTTGCGAT
1 TCCAAGTTCGTTGCGAT
3562028 AGTCCAAAAT
Statistics
Matches: 115, Mismatches: 16, Indels: 26
0.73 0.10 0.17
Matches are distributed among these distances:
19 27 0.23
21 53 0.46
22 2 0.02
23 33 0.29
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.37
Consensus pattern (21 bp):
TCCAAGTTCGTTGCGATTTAT
Done.