Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 94 of 295
Found at i:27725199 original size:16 final size:17
Alignment explanation
Indices: 27725169--27725201 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
27725159 CCTTTTGTAT
*
27725169 ATGCTAACAATTTTAAA
1 ATGCTAACAAGTTTAAA
27725186 ATGC-AACAAGTTTAAA
1 ATGCTAACAAGTTTAAA
27725202 GGATCTCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.30
Consensus pattern (17 bp):
ATGCTAACAAGTTTAAA
Found at i:27729572 original size:16 final size:15
Alignment explanation
Indices: 27729555--27729609 Score: 51
Period size: 16 Copynumber: 3.7 Consensus size: 15
27729545 TATAAAATAT
27729555 ATTATATTAATTAT-
1 ATTATATTAATTATA
* *
27729569 A-TATGTTAAATAATA
1 ATTATATT-AATTATA
*
27729584 ATTATATATATTTATA
1 ATTATAT-TAATTATA
27729600 ATTATATTAA
1 ATTATATTAA
27729610 ATCACTAGCC
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
13 5 0.16
14 6 0.19
15 3 0.10
16 16 0.52
17 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
ATTATATTAATTATA
Found at i:27729801 original size:15 final size:16
Alignment explanation
Indices: 27729770--27729803 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
27729760 TTAGTGTATT
27729770 ATATTTTGTAAAAAAA
1 ATATTTTGTAAAAAAA
27729786 ATATTTT-TAAATAAAA
1 ATATTTTGTAAA-AAAA
27729802 AT
1 AT
27729804 TATGTAACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
ATATTTTGTAAAAAAA
Found at i:27733470 original size:5 final size:5
Alignment explanation
Indices: 27733455--27733504 Score: 55
Period size: 6 Copynumber: 9.2 Consensus size: 5
27733445 GGAAGATGAG
*
27733455 TATTT TGTTT TATTT TATTT TATTTT TATTTT TATTTT TATTTT TATTT
1 TATTT TATTT TATTT TATTT TA-TTT TA-TTT TA-TTT TA-TTT TATTT
27733504 T
1 T
27733505 TAATTAACTA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
5 19 0.45
6 23 0.55
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.82
Consensus pattern (5 bp):
TATTT
Found at i:27733483 original size:6 final size:6
Alignment explanation
Indices: 27733462--27733506 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
27733452 GAGTATTTTG
27733462 TTTTA- TTTTA- TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTA
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTA
27733507 ATTAACTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
5 10 0.26
6 29 0.74
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTAT
Found at i:27741117 original size:5 final size:5
Alignment explanation
Indices: 27741110--27741141 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
27741100 AGGGAAGAGG
*
27741110 GAGAG GAGAA GAGAA GAGAA GAGAA GAGAA GA
1 GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA GA
27741142 ACGTGAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (5 bp):
GAGAA
Found at i:27741182 original size:7 final size:7
Alignment explanation
Indices: 27741172--27741217 Score: 60
Period size: 7 Copynumber: 6.6 Consensus size: 7
27741162 AAAAGAGAAA
27741172 AATAAAT
1 AATAAAT
27741179 AATAAAT
1 AATAAAT
27741186 AATAAAT
1 AATAAAT
27741193 AATAAA-
1 AATAAAT
27741199 AATAATAT
1 AATAA-AT
27741207 CAAT-AAT
1 -AATAAAT
27741214 AATA
1 AATA
27741218 TGTTAAAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
6 8 0.23
7 23 0.66
8 1 0.03
9 3 0.09
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (7 bp):
AATAAAT
Found at i:27741949 original size:12 final size:12
Alignment explanation
Indices: 27741932--27741960 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
27741922 ACACGGGGTA
27741932 GGACATGGGCTG
1 GGACATGGGCTG
27741944 GGACATGGGCTG
1 GGACATGGGCTG
27741956 GGACA
1 GGACA
27741961 CGACTGTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.21, C:0.17, G:0.48, T:0.14
Consensus pattern (12 bp):
GGACATGGGCTG
Found at i:27748084 original size:25 final size:25
Alignment explanation
Indices: 27748050--27748099 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
27748040 ATTGAGAAAA
27748050 CATATCTTGTCTGTTCTAAGATGTT
1 CATATCTTGTCTGTTCTAAGATGTT
27748075 CATATCTTGTCTGTTCTAAGATGTT
1 CATATCTTGTCTGTTCTAAGATGTT
27748100 TCTTTATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (25 bp):
CATATCTTGTCTGTTCTAAGATGTT
Found at i:27751637 original size:36 final size:33
Alignment explanation
Indices: 27751581--27751666 Score: 84
Period size: 36 Copynumber: 2.5 Consensus size: 33
27751571 GAGACTTTGA
* *
27751581 TGAATTACTTTTGTATTCCTACTTCAATTTGAAATT
1 TGAATTA-TTTTCTTTTCCTACTTCAA-TTGAAA-T
* *
27751617 TG-ATTATTCTTTCTTTTCCTATTTCCATTGAAAT
1 TGAATTA-T-TTTCTTTTCCTACTTCAATTGAAAT
27751651 TGAATTATTTTCTTTT
1 TGAATTATTTTCTTTT
27751667 ATCTTTCAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
33 8 0.19
34 4 0.09
35 15 0.35
36 16 0.37
ACGTcount: A:0.23, C:0.14, G:0.07, T:0.56
Consensus pattern (33 bp):
TGAATTATTTTCTTTTCCTACTTCAATTGAAAT
Found at i:27752082 original size:15 final size:14
Alignment explanation
Indices: 27752056--27752141 Score: 61
Period size: 15 Copynumber: 6.0 Consensus size: 14
27752046 TATTCTAATA
*
27752056 CTATTATTATTTAT
1 CTATTTTTATTTAT
27752070 CTAATTTTTATTTAT
1 CT-ATTTTTATTTAT
* *
27752085 CTATTTATATTTCT
1 CTATTTTTATTTAT
*
27752099 ACTATTATTATATT-T
1 -CTATTTTTAT-TTAT
27752114 CTATTTATTATATT-T
1 CTATTT-TTAT-TTAT
*
27752129 -TATTTCTATTTAT
1 CTATTTTTATTTAT
27752142 ATACTAATAT
Statistics
Matches: 60, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
12 2 0.03
13 4 0.07
14 22 0.37
15 30 0.50
16 2 0.03
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (14 bp):
CTATTTTTATTTAT
Found at i:27752095 original size:14 final size:15
Alignment explanation
Indices: 27752063--27752096 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
27752053 ATACTATTAT
*
27752063 TATTTATCTAATTTT
1 TATTTATCTAATTTA
27752078 TATTTATCT-ATTTA
1 TATTTATCTAATTTA
27752092 TATTT
1 TATTT
27752097 CTACTATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTTATCTAATTTA
Found at i:27752095 original size:29 final size:29
Alignment explanation
Indices: 27752063--27752121 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 29
27752053 ATACTATTAT
*
27752063 TATTTAT-CTAATTTTTAT-TTATCTATTTA
1 TATTTATACT-ATTATTATATT-TCTATTTA
*
27752092 TATTTCTACTATTATTATATTTCTATTTA
1 TATTTATACTATTATTATATTTCTATTTA
27752121 T
1 T
27752122 TATATTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.64
Consensus pattern (29 bp):
TATTTATACTATTATTATATTTCTATTTA
Found at i:27752132 original size:20 final size:20
Alignment explanation
Indices: 27752073--27752141 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
27752063 TATTTATCTA
*
27752073 ATTTTTATTTATCTAT-TTAT
1 ATTTCTATTTAT-TATATTAT
*
27752093 ATTTCTA-CTA-T-TATTAT
1 ATTTCTATTTATTATATTAT
*
27752110 ATTTCTATTTATTATATTTT
1 ATTTCTATTTATTATATTAT
27752130 ATTTCTATTTAT
1 ATTTCTATTTAT
27752142 ATACTAATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
16 1 0.02
17 12 0.29
18 2 0.05
19 3 0.07
20 23 0.56
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTTCTATTTATTATATTAT
Found at i:27752133 original size:14 final size:15
Alignment explanation
Indices: 27752089--27752133 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
27752079 ATTTATCTAT
27752089 TTATATTTCTACTATTA
1 TTATATTTCTA-T-TTA
27752106 TTATATTTCTATTTA
1 TTATATTTCTATTTA
27752121 TTATATTT-TATTT
1 TTATATTTCTATTT
27752134 CTATTTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.18
15 11 0.39
16 1 0.04
17 11 0.39
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATATTTCTATTTA
Found at i:27752143 original size:17 final size:16
Alignment explanation
Indices: 27752089--27752143 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
27752079 ATTTATCTAT
*
27752089 TTATATTTCTACTATTA
1 TTATATTTCTA-TTTTA
27752106 TTATATTTCTA-TTTA
1 TTATATTTCTATTTTA
27752121 TTATATTT-TATTTCTA
1 TTATATTTCTATTT-TA
27752137 TTTATAT
1 -TTATAT
27752144 ACTAATATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
14 2 0.06
15 13 0.38
16 2 0.06
17 17 0.50
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATATTTCTATTTTA
Found at i:27752152 original size:20 final size:20
Alignment explanation
Indices: 27752073--27752152 Score: 62
Period size: 20 Copynumber: 4.2 Consensus size: 20
27752063 TATTTATCTA
* *
27752073 ATTTTTATTTATCTAT-TTAT
1 ATTTCTATTTAT-TATATAAT
*
27752093 ATTTCTA-CTATTAT-T-AT
1 ATTTCTATTTATTATATAAT
**
27752110 ATTTCTATTTATTATATTTT
1 ATTTCTATTTATTATATAAT
27752130 ATTTCTATTTA-TATACTAAT
1 ATTTCTATTTATTATA-TAAT
27752150 ATT
1 ATT
27752153 ATTTTCATTA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
17 9 0.18
18 10 0.20
19 8 0.16
20 23 0.46
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (20 bp):
ATTTCTATTTATTATATAAT
Found at i:27752324 original size:25 final size:24
Alignment explanation
Indices: 27752263--27752324 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
27752253 TATAATGCTC
* * *
27752263 ATTTCAAATTTTTATACATTATTT
1 ATTTCAAATTTTCATAAATTATGT
27752287 ACTTT-AATATTTTCATAAATTATGT
1 A-TTTCAA-ATTTTCATAAATTATGT
27752312 ATTTCAAACTTTT
1 ATTTCAAA-TTTT
27752325 TTTTCACACA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
24 7 0.23
25 24 0.77
ACGTcount: A:0.34, C:0.10, G:0.02, T:0.55
Consensus pattern (24 bp):
ATTTCAAATTTTCATAAATTATGT
Found at i:27755008 original size:18 final size:18
Alignment explanation
Indices: 27754985--27755020 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
27754975 TAAGAATGTT
27754985 TACATTGCGAGAAAGACA
1 TACATTGCGAGAAAGACA
*
27755003 TACATTGTGAGAAAGACA
1 TACATTGCGAGAAAGACA
27755021 ACTTACTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.19
Consensus pattern (18 bp):
TACATTGCGAGAAAGACA
Found at i:27755247 original size:23 final size:22
Alignment explanation
Indices: 27755217--27755260 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
27755207 TACATTAGAC
27755217 TGGACCCA-AGATGAATTAATTT
1 TGGACCCATAG-TGAATTAATTT
*
27755239 TGGATCCCATTGTGAATTAATT
1 TGGA-CCCATAGTGAATTAATT
27755261 CACTGCTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 14 0.74
24 1 0.05
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (22 bp):
TGGACCCATAGTGAATTAATTT
Found at i:27755654 original size:19 final size:19
Alignment explanation
Indices: 27755607--27755664 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
27755597 AAAATGATAA
27755607 AATCAAGTTAAAATGGTTTC
1 AATCAAGTTAAAAT-GTTTC
**
27755627 AATTGAGTTAAACAT-TTTC
1 AATCAAGTTAAA-ATGTTTC
27755646 AATCAAGTTAAAATTGTTT
1 AATCAAGTTAAAA-TGTTT
27755665 TAAAACAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
18 1 0.03
19 15 0.48
20 13 0.42
21 2 0.06
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.40
Consensus pattern (19 bp):
AATCAAGTTAAAATGTTTC
Found at i:27761461 original size:12 final size:12
Alignment explanation
Indices: 27761441--27761473 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
27761431 AGTGTCATCG
27761441 CACATGGCCTAC
1 CACATGGCCTAC
*
27761453 CACACGGCCTAC
1 CACATGGCCTAC
27761465 CACATGGCC
1 CACATGGCC
27761474 GTGTGGCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.24, C:0.45, G:0.18, T:0.12
Consensus pattern (12 bp):
CACATGGCCTAC
Found at i:27767008 original size:23 final size:21
Alignment explanation
Indices: 27766982--27767028 Score: 51
Period size: 23 Copynumber: 2.1 Consensus size: 21
27766972 TAATGTTTTT
27766982 ATAA-CTATATACAGTATTTCAGA
1 ATAATCTATATA-AGT-TTT-AGA
*
27767005 ATAATCTATTTAAGTTTTAGA
1 ATAATCTATATAAGTTTTAGA
27767026 ATA
1 ATA
27767029 CTTATAGGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 6 0.27
22 3 0.14
23 7 0.32
24 6 0.27
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.40
Consensus pattern (21 bp):
ATAATCTATATAAGTTTTAGA
Found at i:27768924 original size:43 final size:43
Alignment explanation
Indices: 27768877--27768992 Score: 146
Period size: 43 Copynumber: 2.7 Consensus size: 43
27768867 TGTGATTACA
* *
27768877 TGTAAGACCATGTCTGGGATATTTGGCATTG-TA-TTGGATTATG
1 TGTAAGACCATGTCTGGGACA-TTGGCATCGTTAGTT-GATTATG
* *
27768920 TGTAAGACCATGTCTGAGACATTGGCATCGTTAGTTGATTTTG
1 TGTAAGACCATGTCTGGGACATTGGCATCGTTAGTTGATTATG
* *
27768963 TGTAAGACCTTGTCTGGGACAATGGCATCG
1 TGTAAGACCATGTCTGGGACATTGGCATCG
27768993 ATGTGTGATA
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
42 8 0.12
43 54 0.84
44 2 0.03
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.35
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATTGGCATCGTTAGTTGATTATG
Found at i:27769010 original size:43 final size:43
Alignment explanation
Indices: 27768867--27769032 Score: 142
Period size: 43 Copynumber: 3.9 Consensus size: 43
27768857 GTTATCGAGA
* *
27768867 TGTGATTACATGTAAGACCATGTCTGGGATATTTGGCATTGTAT-
1 TGTGATTACATGTAAGACCATGTCTGGGACA-TTGGCATCG-ATG
** * *
27768911 TG-GATTATGTGTAAGACCATGTCTGAGACATTGGCATCGTTAG
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGAT-G
*** * *
27768954 T-TGATTTTGTGTAAGACCTTGTCTGGGACAATGGCATCGATG
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGATG
* * * *
27768996 TGTGATAACATGTAAGGCCATATCTGGGATA-TGGCAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCAT
27769033 TGTACGAGCT
Statistics
Matches: 99, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
41 1 0.01
42 16 0.16
43 80 0.81
44 2 0.02
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.34
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGATG
Found at i:27773565 original size:19 final size:19
Alignment explanation
Indices: 27773518--27773566 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
27773508 AAAATGATAA
27773518 AATCAAGTTAAAATGGTTTC
1 AATCAAGTTAAAAT-GTTTC
**
27773538 AATTGAGTTAAACAT-TTTC
1 AATCAAGTTAAA-ATGTTTC
27773557 AATCAAGTTA
1 AATCAAGTTA
27773567 CTGTTTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 12 0.50
20 10 0.42
21 2 0.08
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (19 bp):
AATCAAGTTAAAATGTTTC
Found at i:27792708 original size:17 final size:16
Alignment explanation
Indices: 27792668--27792704 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
27792658 CTCAGATCTT
*
27792668 AAAAACAAAACATTAA
1 AAAAATAAAACATTAA
27792684 AAAAATAAAACATTAA
1 AAAAATAAAACATTAA
27792700 AAAAA
1 AAAAA
27792705 ATAACAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.78, C:0.08, G:0.00, T:0.14
Consensus pattern (16 bp):
AAAAATAAAACATTAA
Found at i:27792710 original size:15 final size:14
Alignment explanation
Indices: 27792666--27792710 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 14
27792656 ACCTCAGATC
*
27792666 TTAAAAACAAAACA
1 TTAAAAAAAAAACA
27792680 TTAAAAAAATAAAACA
1 TT-AAAAAA-AAAACA
27792696 TTAAAAAAAATAACA
1 TTAAAAAAAA-AACA
27792711 AAACACTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 4 0.15
15 15 0.56
16 8 0.30
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (14 bp):
TTAAAAAAAAAACA
Found at i:27792713 original size:20 final size:20
Alignment explanation
Indices: 27792671--27792723 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
27792661 AGATCTTAAA
27792671 AACAAAACATT-AAAAAAAT
1 AACAAAACATTAAAAAAAAT
27792690 ---AAAACATTAAAAAAAAT
1 AACAAAACATTAAAAAAAAT
*
27792707 AACAAAACACTAAAAAA
1 AACAAAACATTAAAAAA
27792724 TAAAGTGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 8 0.28
17 8 0.28
20 13 0.45
ACGTcount: A:0.75, C:0.11, G:0.00, T:0.13
Consensus pattern (20 bp):
AACAAAACATTAAAAAAAAT
Found at i:27793681 original size:13 final size:13
Alignment explanation
Indices: 27793663--27793689 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
27793653 AAAGTTGTGA
27793663 TCCATGATAAATT
1 TCCATGATAAATT
27793676 TCCATGATAAATT
1 TCCATGATAAATT
27793689 T
1 T
27793690 AAAAGTTGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (13 bp):
TCCATGATAAATT
Found at i:27798896 original size:17 final size:18
Alignment explanation
Indices: 27798874--27798918 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
27798864 TTATGAATTA
27798874 AAAAATAATTATA-AAAG
1 AAAAATAATTATACAAAG
*
27798891 AAAAATAGTTATACTAAAG
1 AAAAATAATTATAC-AAAG
*
27798910 ATAAATAAT
1 AAAAATAAT
27798919 ATGAAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 12 0.52
19 11 0.48
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (18 bp):
AAAAATAATTATACAAAG
Found at i:27802679 original size:46 final size:46
Alignment explanation
Indices: 27802611--27802713 Score: 188
Period size: 46 Copynumber: 2.2 Consensus size: 46
27802601 TATGTGCATG
*
27802611 TGAATTTAAGTTGGTGTTTAAGTGCTTCTGAACTAGGCAAAATGGAT
1 TGAATTT-GGTTGGTGTTTAAGTGCTTCTGAACTAGGCAAAATGGAT
27802658 TGAATTTGGTTGGTGTTTAAGTGCTTCTGAACTAGGCAAAATGGAT
1 TGAATTTGGTTGGTGTTTAAGTGCTTCTGAACTAGGCAAAATGGAT
27802704 TGAATTTGGT
1 TGAATTTGGT
27802714 AGGTTTATAA
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 48 0.87
47 7 0.13
ACGTcount: A:0.27, C:0.08, G:0.27, T:0.38
Consensus pattern (46 bp):
TGAATTTGGTTGGTGTTTAAGTGCTTCTGAACTAGGCAAAATGGAT
Found at i:27812134 original size:32 final size:32
Alignment explanation
Indices: 27812098--27812160 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
27812088 CACATCTAAG
27812098 ATGAACTTGGAGAAATAGTTG-TCCAAGTTCAA
1 ATGAACTTGGAGAAATAGTTGCT-CAAGTTCAA
*
27812130 ATGAACTTGGATAAATAGTTGCTCAAGTTCA
1 ATGAACTTGGAGAAATAGTTGCTCAAGTTCA
27812161 TCTTAAACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 28 0.97
33 1 0.03
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.30
Consensus pattern (32 bp):
ATGAACTTGGAGAAATAGTTGCTCAAGTTCAA
Found at i:27812217 original size:21 final size:22
Alignment explanation
Indices: 27812176--27812217 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
27812166 AACATAGTCT
*
27812176 TTTAAATAATTATATAAAATTA
1 TTTAAATAATTATAGAAAATTA
*
27812198 TTTAAA-AATTATAGAGAATT
1 TTTAAATAATTATAGAAAATT
27812218 GTATGTGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (22 bp):
TTTAAATAATTATAGAAAATTA
Found at i:27812745 original size:6 final size:6
Alignment explanation
Indices: 27812736--27812774 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
27812726 AAGTAAAATG
27812736 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATA
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATA
27812775 GTTTTAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (6 bp):
ATATGT
Found at i:27812899 original size:18 final size:17
Alignment explanation
Indices: 27812849--27812917 Score: 61
Period size: 18 Copynumber: 3.9 Consensus size: 17
27812839 CATTTTCAAC
* *
27812849 ATTATTTTTAAATAACTT
1 ATTA-TTTTATATAATTT
27812867 ATTAATATTTA-ATAATATT
1 ATT-AT-TTTATATAAT-TT
27812886 ATTATTTTATATAATTT
1 ATTATTTTATATAATTT
*
27812903 TTTATTTT-TATAATT
1 ATTATTTTATATAATT
27812918 ATTTCAAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
16 7 0.16
17 13 0.29
18 15 0.33
19 10 0.22
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTATTTTATATAATTT
Found at i:27823698 original size:46 final size:46
Alignment explanation
Indices: 27823631--27823723 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
27823621 CAAAAGTAAC
27823631 AAACAACATTGGCAATTGGATTGCATCTTGCTTAAATCCTTTTCTT
1 AAACAACATTGGCAATTGGATTGCATCTTGCTTAAATCCTTTTCTT
27823677 AAACAACATTGGCAATTGGATTGCATCTTGCTTAAATCCTTTTCTT
1 AAACAACATTGGCAATTGGATTGCATCTTGCTTAAATCCTTTTCTT
27823723 A
1 A
27823724 GGTTAGAACC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (46 bp):
AAACAACATTGGCAATTGGATTGCATCTTGCTTAAATCCTTTTCTT
Found at i:27835682 original size:17 final size:19
Alignment explanation
Indices: 27835649--27835683 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
27835639 GAATAGAATA
27835649 GAAAATAGTGTAAATTGAT
1 GAAAATAGTGTAAATTGAT
27835668 GAAAATA-TG-AAATTGA
1 GAAAATAGTGTAAATTGA
27835684 CTTTGAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 2 0.12
19 7 0.44
ACGTcount: A:0.51, C:0.00, G:0.20, T:0.29
Consensus pattern (19 bp):
GAAAATAGTGTAAATTGAT
Found at i:27836469 original size:35 final size:35
Alignment explanation
Indices: 27836423--27836502 Score: 126
Period size: 35 Copynumber: 2.3 Consensus size: 35
27836413 GGCTCATGCC
*
27836423 CACGTCTAAGGCGA-CTTTAAAAAGGTTGGAATAGA
1 CACGTCTAAGGCAACCTTT-AAAAGGTTGGAATAGA
*
27836458 CCCGTCTAAGGCAACCTTTAAAAGGTTGGAATAGA
1 CACGTCTAAGGCAACCTTTAAAAGGTTGGAATAGA
27836493 CACGTCTAAG
1 CACGTCTAAG
27836503 ACAAAATATT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 37 0.90
36 4 0.10
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.23
Consensus pattern (35 bp):
CACGTCTAAGGCAACCTTTAAAAGGTTGGAATAGA
Found at i:27838770 original size:13 final size:13
Alignment explanation
Indices: 27838749--27838822 Score: 103
Period size: 13 Copynumber: 5.7 Consensus size: 13
27838739 CTTAAATTTT
27838749 TCAAAAGCACTTC
1 TCAAAAGCACTTC
*
27838762 TCTAAAGCACTTC
1 TCAAAAGCACTTC
* *
27838775 TTAAAAGCACTTT
1 TCAAAAGCACTTC
* *
27838788 TCCACAGCACTTC
1 TCAAAAGCACTTC
27838801 TCAAAAGCACTTC
1 TCAAAAGCACTTC
27838814 TCAAAAGCA
1 TCAAAAGCA
27838823 TTGCCAAACT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 51 1.00
ACGTcount: A:0.36, C:0.30, G:0.08, T:0.26
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:27839410 original size:37 final size:37
Alignment explanation
Indices: 27839369--27839464 Score: 95
Period size: 41 Copynumber: 2.5 Consensus size: 37
27839359 TAATAAAAAA
* *
27839369 AGTGTAAGATAATATTTTTGGTACTAAAAAAATAGAT
1 AGTGTAAGATAATATTTTGGGCACTAAAAAAATAGAT
* *
27839406 AGTGTAA-ATTTAATGAAATTTTGGGCATTAAACAAATAGAT
1 AGTGTAAGA--TAAT---ATTTTGGGCACTAAAAAAATAGAT
*
27839447 AGTGTAAGATTATATTTT
1 AGTGTAAGATAATATTTT
27839465 ATCTAATTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
36 1 0.02
37 12 0.25
38 4 0.08
40 3 0.06
41 27 0.56
42 1 0.02
ACGTcount: A:0.43, C:0.03, G:0.17, T:0.38
Consensus pattern (37 bp):
AGTGTAAGATAATATTTTGGGCACTAAAAAAATAGAT
Found at i:27840018 original size:126 final size:126
Alignment explanation
Indices: 27839793--27840044 Score: 396
Period size: 126 Copynumber: 2.0 Consensus size: 126
27839783 TATAAAAAAA
* * * *
27839793 GTCGGCATGGTGTTGAACAAAACTGACTCTTATTTAAGCGTTGCCTTAGGCATACATATCCCGAC
1 GTCGGCATAGTGTTGAACAAAACTGACTCTTATGTAAGCGCTGCCTTAGGCATACATATCCCAAC
* *
27839858 TCTTATACAAAGAGTTGGCCAAAGAGTATGTTGGCAAGTCTATCCCAACACTTAGGAAAGT
66 CCTTATACAAAGAGTTGGCCAAAGAGTATGTTGGCAAGTCTATCCCAACACTTAAGAAAGT
* * *
27839919 GTCGGCATAGTGTTGGACAAAGCTGACTCTTATGTAAGCGCTGCCTTAGGCATCCATATCCCAAC
1 GTCGGCATAGTGTTGAACAAAACTGACTCTTATGTAAGCGCTGCCTTAGGCATACATATCCCAAC
* **
27839984 CCTTATACAAAGAGTTGGCTAAAGCTTATGTTGGCAAGTCTATCCCAACACTTAAGAAAGT
66 CCTTATACAAAGAGTTGGCCAAAGAGTATGTTGGCAAGTCTATCCCAACACTTAAGAAAGT
27840045 ATTAGCCCAA
Statistics
Matches: 114, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
126 114 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (126 bp):
GTCGGCATAGTGTTGAACAAAACTGACTCTTATGTAAGCGCTGCCTTAGGCATACATATCCCAAC
CCTTATACAAAGAGTTGGCCAAAGAGTATGTTGGCAAGTCTATCCCAACACTTAAGAAAGT
Found at i:27845556 original size:13 final size:13
Alignment explanation
Indices: 27845538--27845566 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
27845528 AGGAGCAATC
27845538 GTTGATCCATAGG
1 GTTGATCCATAGG
27845551 GTTGATCCATAGG
1 GTTGATCCATAGG
27845564 GTT
1 GTT
27845567 AAAGTCAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.14, G:0.31, T:0.34
Consensus pattern (13 bp):
GTTGATCCATAGG
Found at i:27852076 original size:22 final size:21
Alignment explanation
Indices: 27852006--27852077 Score: 67
Period size: 22 Copynumber: 3.4 Consensus size: 21
27851996 TTTGCATTTT
* *
27852006 GTAGGTATAGAATAAAAGTAAC
1 GTAGATATAGGATAAAAGT-AC
* *
27852028 ATAGATAT-GAGATAAAA-TAA
1 GTAGATATAG-GATAAAAGTAC
27852048 GTAGATATAGGATAAAAGTATC
1 GTAGATATAGGATAAAAGTA-C
27852070 GTAGATAT
1 GTAGATAT
27852078 TTTTGTAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
20 15 0.38
21 5 0.12
22 20 0.50
ACGTcount: A:0.50, C:0.03, G:0.21, T:0.26
Consensus pattern (21 bp):
GTAGATATAGGATAAAAGTAC
Found at i:27862131 original size:22 final size:22
Alignment explanation
Indices: 27862100--27862142 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
27862090 TGTATGTCAC
*
27862100 CTTTTGGACTCACACTGAGCTT
1 CTTTTAGACTCACACTGAGCTT
27862122 CTTTTAGACTCACACTGAGCT
1 CTTTTAGACTCACACTGAGCT
27862143 CATGTAGCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.28, G:0.16, T:0.35
Consensus pattern (22 bp):
CTTTTAGACTCACACTGAGCTT
Found at i:27865105 original size:13 final size:13
Alignment explanation
Indices: 27865087--27865112 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27865077 TAGTGGACGG
27865087 TTAGTGCATTCTC
1 TTAGTGCATTCTC
27865100 TTAGTGCATTCTC
1 TTAGTGCATTCTC
27865113 CCATTATTTT
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:0.15, C:0.23, G:0.15, T:0.46
Consensus pattern (13 bp):
TTAGTGCATTCTC
Found at i:27869418 original size:47 final size:47
Alignment explanation
Indices: 27869364--27869465 Score: 195
Period size: 47 Copynumber: 2.2 Consensus size: 47
27869354 AAATTAATAA
*
27869364 AATTACCTTTAAAAAAATTCATCTCCAATTAGATAGTAAACACTTCG
1 AATTACCTTTAAAAAAATACATCTCCAATTAGATAGTAAACACTTCG
27869411 AATTACCTTTAAAAAAATACATCTCCAATTAGATAGTAAACACTTCG
1 AATTACCTTTAAAAAAATACATCTCCAATTAGATAGTAAACACTTCG
27869458 AATTACCT
1 AATTACCT
27869466 AACTTGAGTA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.31
Consensus pattern (47 bp):
AATTACCTTTAAAAAAATACATCTCCAATTAGATAGTAAACACTTCG
Found at i:27869567 original size:54 final size:54
Alignment explanation
Indices: 27869500--27869602 Score: 129
Period size: 54 Copynumber: 1.9 Consensus size: 54
27869490 TACTTAATTC
* *
27869500 AAATTGTAATTAATG-GTAAAAAAGATGTTT-TTTCTTCTCAAATAACAATGAATA
1 AAATAGTAATTAATGAG-AAAAAAGAT-TTTCTTTCTTATCAAATAACAATGAATA
** *
27869554 AAATAGTAATTAATGAGCGAAAATATTTTCTTTCTTATCAAATAACAAT
1 AAATAGTAATTAATGAGAAAAAAGATTTTCTTTCTTATCAAATAACAAT
27869603 TAACAATTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
53 3 0.07
54 38 0.90
55 1 0.02
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.37
Consensus pattern (54 bp):
AAATAGTAATTAATGAGAAAAAAGATTTTCTTTCTTATCAAATAACAATGAATA
Found at i:27877918 original size:20 final size:20
Alignment explanation
Indices: 27877893--27877932 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
27877883 TTTTTTTTAC
27877893 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
27877913 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
27877933 TTTAAATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATATTAATAAATTTATAT
Found at i:27877937 original size:16 final size:18
Alignment explanation
Indices: 27877888--27877932 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
27877878 AAAAGTTTTT
* *
27877888 TTTACATATATTAATAAA
1 TTTATATATTTTAATAAA
27877906 TTTATATATATATTAATAAA
1 TTTATATAT-T-TTAATAAA
27877926 TTTATAT
1 TTTATAT
27877933 TTTAAATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.35
20 15 0.65
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTATATATTTTAATAAA
Found at i:27880196 original size:15 final size:15
Alignment explanation
Indices: 27880151--27880258 Score: 87
Period size: 15 Copynumber: 7.2 Consensus size: 15
27880141 CCAATATCTC
27880151 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
27880166 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
27880181 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
27880196 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
27880211 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
27880226 GACTTTCCAT-TATTT
1 GA-TACCCATATCTTT
27880241 GATACCCATATCTTT
1 GATACCCATATCTTT
27880256 GAT
1 GAT
27880259 TTTCCATAAA
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
14 13 0.19
15 43 0.62
16 13 0.19
ACGTcount: A:0.26, C:0.23, G:0.07, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:27880265 original size:30 final size:30
Alignment explanation
Indices: 27880141--27880264 Score: 212
Period size: 30 Copynumber: 4.1 Consensus size: 30
27880131 TTTTATTATG
*
27880141 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
27880172 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
27880202 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* *
27880232 CCATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
27880262 CCA
1 CCA
27880265 TAAATATGGA
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
30 83 0.92
31 7 0.08
ACGTcount: A:0.26, C:0.25, G:0.06, T:0.43
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:27884889 original size:15 final size:15
Alignment explanation
Indices: 27884844--27884951 Score: 87
Period size: 15 Copynumber: 7.2 Consensus size: 15
27884834 CCAATATCTC
27884844 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
27884859 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
27884874 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
27884889 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
27884904 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
27884919 GACTTTCCAT-TATTT
1 GA-TACCCATATCTTT
27884934 GATACCCATATCTTT
1 GATACCCATATCTTT
27884949 GAT
1 GAT
27884952 TTTCCATAAA
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
14 13 0.19
15 43 0.62
16 13 0.19
ACGTcount: A:0.26, C:0.23, G:0.07, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:27884958 original size:30 final size:30
Alignment explanation
Indices: 27884834--27884957 Score: 212
Period size: 30 Copynumber: 4.1 Consensus size: 30
27884824 TTTTATTATG
*
27884834 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
27884865 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
27884895 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* *
27884925 CCATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
27884955 CCA
1 CCA
27884958 TAAATATAGA
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
30 83 0.92
31 7 0.08
ACGTcount: A:0.26, C:0.25, G:0.06, T:0.43
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:27886086 original size:14 final size:14
Alignment explanation
Indices: 27886067--27886093 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
27886057 AGAAAAACTT
27886067 GAAAAGCTTTTACG
1 GAAAAGCTTTTACG
27886081 GAAAAGCTTTTAC
1 GAAAAGCTTTTAC
27886094 AGGTTACCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (14 bp):
GAAAAGCTTTTACG
Found at i:27892144 original size:39 final size:39
Alignment explanation
Indices: 27892086--27892210 Score: 169
Period size: 39 Copynumber: 3.2 Consensus size: 39
27892076 AACCTGAAAT
* * *
27892086 TATATTACCAGCACAAAGCCTACGGGACTTTAGCTCGAA
1 TATATTTCCAGCACAAAGCCTGCGGGACTTTAGCCCGAA
* *
27892125 TATATTTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGA
1 TATATTTCCAGCACAAAGCCTGCGGGACTTTAGCCCGAA
* * *
27892164 TACATTTCCAGCACAAAGCCTGCGGGACTTTATCCCGGA
1 TATATTTCCAGCACAAAGCCTGCGGGACTTTAGCCCGAA
*
27892203 TACATTTC
1 TATATTTC
27892211 TAGTGTCTTG
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (39 bp):
TATATTTCCAGCACAAAGCCTGCGGGACTTTAGCCCGAA
Found at i:27903415 original size:42 final size:44
Alignment explanation
Indices: 27903350--27903438 Score: 103
Period size: 42 Copynumber: 2.1 Consensus size: 44
27903340 CATCGACTTA
* *
27903350 TGATTTACTTGTAAGACCATGTCTAGGACA-TCGGAATCG-TATT
1 TGATTTACGTGTAAAACCATGTCTAGGACAGT-GGAATCGATATT
* * *
27903393 TGATTT-CGTGTAAAACCCTGTCTGGGACAGTGGCATCGATATT
1 TGATTTACGTGTAAAACCATGTCTAGGACAGTGGAATCGATATT
27903436 TGA
1 TGA
27903439 CTACATGTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
42 25 0.64
43 14 0.36
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.34
Consensus pattern (44 bp):
TGATTTACGTGTAAAACCATGTCTAGGACAGTGGAATCGATATT
Found at i:27903436 original size:43 final size:43
Alignment explanation
Indices: 27903337--27903438 Score: 102
Period size: 42 Copynumber: 2.4 Consensus size: 43
27903327 TCTGGAACGT
* * *
27903337 TGGCATCGACT-TATGATTTACTTGTAAGACCATGTCTAGGACA
1 TGGCATCGA-TATTTGATTTACGTGTAAAACCATGTCTAGGACA
* * *
27903380 TCGGAATCG-TATTTGATTT-CGTGTAAAACCCTGTCTGGGACA
1 T-GGCATCGATATTTGATTTACGTGTAAAACCATGTCTAGGACA
27903422 GTGGCATCGATATTTGA
1 -TGGCATCGATATTTGA
27903439 CTACATGTAA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
42 26 0.54
43 16 0.33
44 6 0.12
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (43 bp):
TGGCATCGATATTTGATTTACGTGTAAAACCATGTCTAGGACA
Found at i:27913313 original size:22 final size:23
Alignment explanation
Indices: 27913263--27913314 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
27913253 ATGTTTTTAC
*
27913263 TTTTATTTTACTTTAGGACTACT
1 TTTTATTTTACTTTAAGACTACT
*
27913286 TTTTATTTTTCTTTAAG-CTTA-T
1 TTTTATTTTACTTTAAGAC-TACT
27913308 TTTTATT
1 TTTTATT
27913315 AGGATTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.19, C:0.10, G:0.06, T:0.65
Consensus pattern (23 bp):
TTTTATTTTACTTTAAGACTACT
Found at i:27917127 original size:44 final size:42
Alignment explanation
Indices: 27917077--27917227 Score: 135
Period size: 44 Copynumber: 3.5 Consensus size: 42
27917067 TATGTGTTTT
27917077 CGTGTAAGACCACGTCTGGGACATTGGCATCGACTTATGATTTA
1 CGTGTAAGACCACGTCTGGGACATTGGCATCGA-TT-TGATTTA
* * * *
27917121 CGTGTAATACTATGTCTGGGACATCGGCATCGTATTTGATTT-
1 CGTGTAAGACCACGTCTGGGACATTGGCATCG-ATTTGATTTA
* *** * *
27917163 CGTATAAGACCTTATCTGGGACAGTGGCATCGATATTTGA-CTA
1 CGTGTAAGACCACGTCTGGGACATTGGCATCG--ATTTGATTTA
* *
27917206 CATGTAAGACCACGTTTGGGAC
1 CGTGTAAGACCACGTCTGGGAC
27917228 GTTCGTATTG
Statistics
Matches: 86, Mismatches: 18, Indels: 7
0.77 0.16 0.06
Matches are distributed among these distances:
42 26 0.30
43 29 0.34
44 30 0.35
45 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (42 bp):
CGTGTAAGACCACGTCTGGGACATTGGCATCGATTTGATTTA
Found at i:27917192 original size:42 final size:42
Alignment explanation
Indices: 27917091--27917202 Score: 113
Period size: 42 Copynumber: 2.6 Consensus size: 42
27917081 TAAGACCACG
* * *
27917091 TCTGGGACATTGGCATCG-ACTTATGATTTACGTGTAATACTATG
1 TCTGGGACA-TGGCATCGTA-TT-TGATTTACGTATAAGACTATA
27917135 TCTGGGACATCGGCATCGTATTTGATTT-CGTATAAGACCT-TA
1 TCTGGGACAT-GGCATCGTATTTGATTTACGTATAAGA-CTATA
27917177 TCTGGGACAGTGGCATCGATATTTGA
1 TCTGGGACA-TGGCATCG-TATTTGA
27917203 CTACATGTAA
Statistics
Matches: 60, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
42 24 0.40
43 17 0.28
44 18 0.30
45 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (42 bp):
TCTGGGACATGGCATCGTATTTGATTTACGTATAAGACTATA
Found at i:27917214 original size:43 final size:42
Alignment explanation
Indices: 27917135--27917216 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 42
27917125 TAATACTATG
* * *
27917135 TCTGGGACATCGGCATCGTATTTGATTTCGTATAAGACCTTA
1 TCTGGGACATCGGCATCGTATTTGACTACATATAAGACCTTA
*
27917177 TCTGGGACAGT-GGCATCGATATTTGACTACATGTAAGACC
1 TCTGGGACA-TCGGCATCG-TATTTGACTACATATAAGACC
27917217 ACGTTTGGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
42 16 0.47
43 18 0.53
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.32
Consensus pattern (42 bp):
TCTGGGACATCGGCATCGTATTTGACTACATATAAGACCTTA
Found at i:27925035 original size:17 final size:17
Alignment explanation
Indices: 27924986--27925036 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
27924976 TTTTTAAAAC
27924986 ATGTTATGCTTAAGTAT
1 ATGTTATGCTTAAGTAT
*
27925003 ATG-T-T--TTGA-T-T
1 ATGTTATGCTTAAGTAT
27925014 ATGTTATGCTTAAGTAT
1 ATGTTATGCTTAAGTAT
27925031 ATGTTA
1 ATGTTA
27925037 ATGTTCTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 12
0.65 0.05 0.30
Matches are distributed among these distances:
11 4 0.15
12 2 0.08
13 4 0.15
15 4 0.15
16 2 0.08
17 10 0.38
ACGTcount: A:0.27, C:0.04, G:0.18, T:0.51
Consensus pattern (17 bp):
ATGTTATGCTTAAGTAT
Found at i:27925049 original size:28 final size:28
Alignment explanation
Indices: 27924990--27925049 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
27924980 TAAAACATGT
* *
27924990 TATGCTTAAGTATATGTTTTGATTATGT
1 TATGCTTAAGTATATGTTATGATTATGG
*
27925018 TATGCTTAAGTATATGTTAATG-TTCTGG
1 TATGCTTAAGTATATGTT-ATGATTATGG
27925046 TATG
1 TATG
27925050 TCTGGTAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 26 0.93
29 2 0.07
ACGTcount: A:0.25, C:0.05, G:0.20, T:0.50
Consensus pattern (28 bp):
TATGCTTAAGTATATGTTATGATTATGG
Found at i:27944122 original size:56 final size:56
Alignment explanation
Indices: 27944055--27944181 Score: 164
Period size: 56 Copynumber: 2.3 Consensus size: 56
27944045 GCCCCTATGG
*
27944055 GTATACTGACTTGTGACACACGACCAAGCCACACGCCCATGCCCTAAGTTGTGTGA
1 GTATACTGACTTGTGACACACGACCAAGCCACACGCCCATGCCCTAAGCTGTGTGA
* * * * * **
27944111 GTATACTGACTTGGGTCACACGGCCAAGCTACATGCCCATGTGCTAAGCTGTGTGA
1 GTATACTGACTTGTGACACACGACCAAGCCACACGCCCATGCCCTAAGCTGTGTGA
* *
27944167 GCATTCTGACTTGTG
1 GTATACTGACTTGTG
27944182 CTCTTTAAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
56 60 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (56 bp):
GTATACTGACTTGTGACACACGACCAAGCCACACGCCCATGCCCTAAGCTGTGTGA
Found at i:27945310 original size:25 final size:26
Alignment explanation
Indices: 27945267--27945340 Score: 89
Period size: 25 Copynumber: 2.9 Consensus size: 26
27945257 ATGAGATATA
* *
27945267 AACAGTAAGCTCCTTCGAGCTGAA-T
1 AACAGTAAGCTCATACGAGCTGAAGT
*
27945292 AACAGTAAGCTCATACGAG-TTAAGT
1 AACAGTAAGCTCATACGAGCTGAAGT
* *
27945317 ATCAGTAAGCTCATAAGAGCTGAA
1 AACAGTAAGCTCATACGAGCTGAA
27945341 ATCGTTAACC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
24 3 0.07
25 35 0.85
26 3 0.07
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (26 bp):
AACAGTAAGCTCATACGAGCTGAAGT
Found at i:27945482 original size:20 final size:19
Alignment explanation
Indices: 27945457--27945494 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
27945447 TGGAAATTAC
27945457 TCAATTCACAAACATATAAT
1 TCAATTCA-AAACATATAAT
*
27945477 TCAATTTAAAACATATAA
1 TCAATTCAAAACATATAA
27945495 ATGTACAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.32
Consensus pattern (19 bp):
TCAATTCAAAACATATAAT
Found at i:27950004 original size:48 final size:44
Alignment explanation
Indices: 27949912--27950007 Score: 111
Period size: 48 Copynumber: 2.1 Consensus size: 44
27949902 AAGTGAAAAT
*
27949912 TATTAAATTATTTTTATTTATATTAATTATTTAAAATATATAAA
1 TATTAAATTATTTATATTTATATTAATTATTTAAAATATATAAA
* * * *
27949956 TATTAAATTAATTTATATTTTGTATATAATTATATTACATTATTTAAA
1 TATTAAATT-ATTTATA-TTTATAT-TAATTAT-TTAAAATATATAAA
27950004 TATT
1 TATT
27950008 TTATGTATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
44 9 0.21
45 6 0.14
46 6 0.14
47 7 0.16
48 15 0.35
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (44 bp):
TATTAAATTATTTATATTTATATTAATTATTTAAAATATATAAA
Found at i:27950021 original size:33 final size:33
Alignment explanation
Indices: 27949947--27950045 Score: 107
Period size: 33 Copynumber: 3.1 Consensus size: 33
27949937 ATTATTTAAA
27949947 ATATATAA--ATATTAAATTAATTT--ATATTTT
1 ATATATAATTATATTAAATT-ATTTAAATATTTT
* *
27949977 GTATATAATTATATTACATTATTTAAATATTTT
1 ATATATAATTATATTAAATTATTTAAATATTTT
* * * *
27950010 ATGTATTATTATGTTAAATTATTTAAATATTAT
1 ATATATAATTATATTAAATTATTTAAATATTTT
27950043 ATA
1 ATA
27950046 ACTTAATTAA
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
30 7 0.12
31 4 0.07
32 9 0.16
33 36 0.64
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (33 bp):
ATATATAATTATATTAAATTATTTAAATATTTT
Found at i:27952391 original size:25 final size:25
Alignment explanation
Indices: 27952363--27952422 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
27952353 AGGTGACTGG
*
27952363 ATGCATAGATCCTAAATACTGCTGC
1 ATGCATAGATCCTAAATACTGCTAC
**
27952388 ATGCATAGATCCTAAATGGTGCTAC
1 ATGCATAGATCCTAAATACTGCTAC
27952413 ATGCATAGAT
1 ATGCATAGAT
27952423 AGTGTTACCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.28
Consensus pattern (25 bp):
ATGCATAGATCCTAAATACTGCTAC
Found at i:27958888 original size:4 final size:4
Alignment explanation
Indices: 27958879--27958903 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
27958869 GTAAATATAA
27958879 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
27958904 CAGTTAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:27960411 original size:23 final size:21
Alignment explanation
Indices: 27960377--27960434 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
27960367 TTATCCAAAC
* *
27960377 AAAAAATATAAATAATAATCCTA
1 AAAAAATTTAAATAAAAAT--TA
*
27960400 AAAAAATTTAAAACAAAAATTA
1 AAAAAATTT-AAATAAAAATTA
27960422 AAAAAATTTAAAT
1 AAAAAATTTAAAT
27960435 CTAACTGTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 3 0.10
22 11 0.37
23 8 0.27
24 8 0.27
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAAAATTTAAATAAAAATTA
Found at i:27961512 original size:38 final size:37
Alignment explanation
Indices: 27961453--27961536 Score: 100
Period size: 38 Copynumber: 2.2 Consensus size: 37
27961443 ATATAATAAT
* **
27961453 AATTTTAATGGATTTATGATAATGACT-ATTATTT-TA
1 AATTTTAATAGATTTATGATAACCA-TAATTATTTATA
27961489 AATTTTAATAGATAATTATGATAACCATAATTATTTATA
1 AATTTTAATAGAT--TTATGATAACCATAATTATTTATA
27961528 AATTTTAAT
1 AATTTTAAT
27961537 TACCCACCAC
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
36 12 0.29
37 1 0.02
38 17 0.41
39 11 0.27
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.48
Consensus pattern (37 bp):
AATTTTAATAGATTTATGATAACCATAATTATTTATA
Found at i:27966373 original size:23 final size:24
Alignment explanation
Indices: 27966347--27966447 Score: 90
Period size: 23 Copynumber: 4.4 Consensus size: 24
27966337 TTGATGAACA
*
27966347 GTAAGCTCTAATGAGCT-AAAATG
1 GTAAGCTCTAATGAGCTGAAAACG
27966370 GTAAGCTCT-ATCGAGCTGAACAA--
1 GTAAGCTCTAAT-GAGCTGAA-AACG
*
27966393 -TAAGCTCATAA-GAGTTG-AAACG
1 GTAAGCTC-TAATGAGCTGAAAACG
* *
27966415 GTAAGCTCCAATGAGCTGAAAACA
1 GTAAGCTCTAATGAGCTGAAAACG
27966439 GTAAGCTCT
1 GTAAGCTCT
27966448 TACGAGTTGA
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
20 2 0.03
21 1 0.02
22 16 0.25
23 27 0.43
24 15 0.24
25 2 0.03
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.23
Consensus pattern (24 bp):
GTAAGCTCTAATGAGCTGAAAACG
Found at i:27966431 original size:45 final size:44
Alignment explanation
Indices: 27966341--27966471 Score: 120
Period size: 45 Copynumber: 2.8 Consensus size: 44
27966331 CCTGAGTTGA
* * * *
27966341 TGAACAGTAAGCTCTAATGAGCTAAAATGGTAAGCTCTATCGAGC
1 TGAACAGTAAGCTCTAA-GAGTTGAAACGGTAAGCTCAATCGAGC
*
27966386 TGAACAATAAGCTCATAAGAGTTGAAACGGTAAGCTCCAAT-GAGC
1 TGAACAGTAAGCTC-TAAGAGTTGAAACGGTAAGCT-CAATCGAGC
*
27966431 TGAAAACAGTAAGCTCTTACGAGTTGATACATCGGTAAGCT
1 TG--AACAGTAAGCTC-TAAGAGTTGA-A-A-CGGTAAGCT
27966472 TATACGAACT
Statistics
Matches: 71, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
45 34 0.48
46 6 0.08
47 20 0.28
48 1 0.01
49 1 0.01
50 9 0.13
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.24
Consensus pattern (44 bp):
TGAACAGTAAGCTCTAAGAGTTGAAACGGTAAGCTCAATCGAGC
Found at i:27976704 original size:33 final size:33
Alignment explanation
Indices: 27976653--27976732 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
27976643 TCACAAGTGT
* *
27976653 TCATCACATGTTAGTCATTTTACAAATGCATGAAA
1 TCATC-CAT-TTATTCATTTTACAAATACATGAAA
27976688 TCATCCATTTATTCATTTTACAAATACATGAAA
1 TCATCCATTTATTCATTTTACAAATACATGAAA
27976721 TCATCCATTTAT
1 TCATCCATTTAT
27976733 ACAATACTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
33 35 0.81
34 3 0.07
35 5 0.12
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.39
Consensus pattern (33 bp):
TCATCCATTTATTCATTTTACAAATACATGAAA
Found at i:27976985 original size:46 final size:48
Alignment explanation
Indices: 27976923--27977014 Score: 134
Period size: 46 Copynumber: 1.9 Consensus size: 48
27976913 AGCTCCTCCT
* **
27976923 GAGCTGATGAACAGTAAGCTCTAATGAGCT-AAAATGGTAAGCTCTATC
1 GAGCTGA-GAACAGTAAGCTCTAATGAGATGAAAACAGTAAGCTCTATC
27976971 GAGCTGA-AACAGTAAGCTCTAATGAGATGAAAACAGTAAGCTCT
1 GAGCTGAGAACAGTAAGCTCTAATGAGATGAAAACAGTAAGCTCT
27977015 TACAAGCTGA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
46 20 0.50
47 13 0.32
48 7 0.17
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (48 bp):
GAGCTGAGAACAGTAAGCTCTAATGAGATGAAAACAGTAAGCTCTATC
Found at i:27977009 original size:24 final size:24
Alignment explanation
Indices: 27976908--27977014 Score: 112
Period size: 23 Copynumber: 4.5 Consensus size: 24
27976898 GAGGCATGAT
** *
27976908 CAGTAAGCTCCTCCTGAGCTGATGAA
1 CAGTAAGCT-CTAATGAGCTGA-AAA
27976934 CAGTAAGCTCTAATGAGCT-AAAA
1 CAGTAAGCTCTAATGAGCTGAAAA
**
27976957 TGGTAAGCTCT-ATCGAGCTG-AAA
1 CAGTAAGCTCTAAT-GAGCTGAAAA
*
27976980 CAGTAAGCTCTAATGAGATGAAAA
1 CAGTAAGCTCTAATGAGCTGAAAA
27977004 CAGTAAGCTCT
1 CAGTAAGCTCT
27977015 TACAAGCTGA
Statistics
Matches: 69, Mismatches: 8, Indels: 10
0.79 0.09 0.11
Matches are distributed among these distances:
22 2 0.03
23 33 0.48
24 17 0.25
25 8 0.12
26 9 0.13
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (24 bp):
CAGTAAGCTCTAATGAGCTGAAAA
Found at i:27981934 original size:43 final size:43
Alignment explanation
Indices: 27981887--27982003 Score: 182
Period size: 43 Copynumber: 2.7 Consensus size: 43
27981877 TGTCACATAT
27981887 CGATGCCAATGTCCCAGACATGGTCTTACACGAAATCAT-ATAA
1 CGATGCCAATGTCCCAGACATGGTCTTACACGAAATCATAAT-A
* * *
27981930 CGATGCCAATGTCCCAGACATGGTCTTACATGTAATCGTAATA
1 CGATGCCAATGTCCCAGACATGGTCTTACACGAAATCATAATA
*
27981973 TGATGCCAATGTCCCAGACATGGTCTTACAC
1 CGATGCCAATGTCCCAGACATGGTCTTACAC
27982004 ATAATCACAT
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
43 66 0.97
44 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (43 bp):
CGATGCCAATGTCCCAGACATGGTCTTACACGAAATCATAATA
Found at i:27982853 original size:14 final size:14
Alignment explanation
Indices: 27982830--27982862 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
27982820 CTAGGTGATG
27982830 AAAT-TTGAAAGAA
1 AAATGTTGAAAGAA
27982843 AAATGTTGAAAGAA
1 AAATGTTGAAAGAA
27982857 AAATGT
1 AAATGT
27982863 CTTTTGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.58, C:0.00, G:0.18, T:0.24
Consensus pattern (14 bp):
AAATGTTGAAAGAA
Found at i:27987192 original size:21 final size:20
Alignment explanation
Indices: 27987168--27987206 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
27987158 AAACTTGTAT
27987168 ATCTATCAACAAACATTCATA
1 ATCTATCAACAAAC-TTCATA
*
27987189 ATCTATCAAGAAACTTCA
1 ATCTATCAACAAACTTCA
27987207 AAATACACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.46, C:0.23, G:0.03, T:0.28
Consensus pattern (20 bp):
ATCTATCAACAAACTTCATA
Found at i:27992600 original size:46 final size:46
Alignment explanation
Indices: 27992439--27992654 Score: 142
Period size: 46 Copynumber: 4.7 Consensus size: 46
27992429 ATTGTGGGCT
* * * *
27992439 AGTGTAAGA-CATGTCTGGGACATGCATCAGCCAC-ATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCCTCGA-GACGA-AGCC
* * *
27992485 TGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGAGAC-AAGTGCT
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGGCCTCGAGACGAA--GCC
*
27992533 AGTGTAA-ATCATGTCCT-GGACATGCATCGGCCTCGAGACGTAAGCC
1 AGTGTAAGACCATGT-CTGGGACATGCATCGGCCTCGAGACG-AAGCC
* * * **
27992579 AGTGTAAGA-CATGTCTAGGACA-ACATCGG-CTACGAGATGATAGTT
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCCT-CGAGACGA-AGCC
* * *
27992624 AGTGTAAGACCATATCTAGGATATGACATCG
1 AGTGTAAGACCATGTCTGGGACATG-CATCG
27992655 ACACCCTACC
Statistics
Matches: 137, Mismatches: 18, Indels: 28
0.75 0.10 0.15
Matches are distributed among these distances:
44 3 0.02
45 25 0.18
46 54 0.39
47 28 0.20
48 26 0.19
49 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACCATGTCTGGGACATGCATCGGCCTCGAGACGAAGCC
Found at i:27993824 original size:21 final size:22
Alignment explanation
Indices: 27993785--27993825 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
27993775 TCAAATTGGT
27993785 CACACGGGCGTGTTGCCCCTCC
1 CACACGGGCGTGTTGCCCCTCC
27993807 CACACGGGCGTG-TGCCCCT
1 CACACGGGCGTGTTGCCCCT
27993826 GTGTCAAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.10, C:0.44, G:0.29, T:0.17
Consensus pattern (22 bp):
CACACGGGCGTGTTGCCCCTCC
Found at i:28000265 original size:27 final size:27
Alignment explanation
Indices: 28000215--28000302 Score: 126
Period size: 27 Copynumber: 3.3 Consensus size: 27
28000205 TGGAGGAAGC
28000215 GTTT-TGGTGGCTCTGCCACAAATATCT
1 GTTTCTGGTGGCTCTGCCAC-AATATCT
28000242 GTTTCTGGTGGCTCTGCCACAATATCT
1 GTTTCTGGTGGCTCTGCCACAATATCT
* * *
28000269 GTATCTGGTGACTCTGTCACAATATCT
1 GTTTCTGGTGGCTCTGCCACAATATCT
28000296 G-TTCTGG
1 GTTTCTGG
28000303 CAGCCATGCT
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
26 5 0.09
27 36 0.64
28 15 0.27
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.38
Consensus pattern (27 bp):
GTTTCTGGTGGCTCTGCCACAATATCT
Found at i:28002840 original size:25 final size:25
Alignment explanation
Indices: 28002812--28002864 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
28002802 AGTGTTACAG
* *
28002812 TGAAACACTTCAGGAAGTATTTCAA
1 TGAAACACTCCAGGAACTATTTCAA
* *
28002837 TGAAACTCTCCAGGAACTATTTCGA
1 TGAAACACTCCAGGAACTATTTCAA
28002862 TGA
1 TGA
28002865 TCGTATCCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (25 bp):
TGAAACACTCCAGGAACTATTTCAA
Found at i:28004149 original size:13 final size:13
Alignment explanation
Indices: 28004131--28004157 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28004121 GGAGCAATCG
28004131 CACACGGGTGTGT
1 CACACGGGTGTGT
28004144 CACACGGGTGTGT
1 CACACGGGTGTGT
28004157 C
1 C
28004158 CTTGTCAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.26, G:0.37, T:0.22
Consensus pattern (13 bp):
CACACGGGTGTGT
Found at i:28014553 original size:50 final size:50
Alignment explanation
Indices: 28014478--28014584 Score: 135
Period size: 50 Copynumber: 2.1 Consensus size: 50
28014468 CCTTGTCACC
* *
28014478 AAGGCTTCCCAAATAATATGCCACATAGACTTTTCA-AGTAACAAGCCACA
1 AAGGCTTCCCAAATAATACGCCACATAGACCTTTCAGA-TAACAAGCCACA
** * * *
28014528 AAGGCTTCTGAAATAATACGCCACATAGGCCTTTCAGATAACTATCCACA
1 AAGGCTTCCCAAATAATACGCCACATAGACCTTTCAGATAACAAGCCACA
28014578 AAGGCTT
1 AAGGCTT
28014585 TTTTGGTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
50 48 0.98
51 1 0.02
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.23
Consensus pattern (50 bp):
AAGGCTTCCCAAATAATACGCCACATAGACCTTTCAGATAACAAGCCACA
Found at i:28014870 original size:20 final size:20
Alignment explanation
Indices: 28014845--28014885 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
28014835 AGATAGGGGC
28014845 ACATGCCCGTGTGGCCTGGG
1 ACATGCCCGTGTGGCCTGGG
*
28014865 ACATGCCCGTGTGGCTTGGG
1 ACATGCCCGTGTGGCCTGGG
28014885 A
1 A
28014886 TATGGCCATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.12, C:0.27, G:0.39, T:0.22
Consensus pattern (20 bp):
ACATGCCCGTGTGGCCTGGG
Found at i:28019446 original size:41 final size:41
Alignment explanation
Indices: 28019389--28019475 Score: 165
Period size: 41 Copynumber: 2.1 Consensus size: 41
28019379 TCTCTTTGCT
28019389 TCTTTTCAACTTTAGTTCGCAACTTTATTCAGAGGTAACTA
1 TCTTTTCAACTTTAGTTCGCAACTTTATTCAGAGGTAACTA
*
28019430 TCTTTTCAACTTTAGTTTGCAACTTTATTCAGAGGTAACTA
1 TCTTTTCAACTTTAGTTCGCAACTTTATTCAGAGGTAACTA
28019471 TCTTT
1 TCTTT
28019476 CTCTTTCTCT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.25, C:0.18, G:0.11, T:0.45
Consensus pattern (41 bp):
TCTTTTCAACTTTAGTTCGCAACTTTATTCAGAGGTAACTA
Found at i:28019482 original size:6 final size:6
Alignment explanation
Indices: 28019471--28019495 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
28019461 GAGGTAACTA
28019471 TCTTTC TCTTTC TCTTTC TCTTTC T
1 TCTTTC TCTTTC TCTTTC TCTTTC T
28019496 ATTATTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (6 bp):
TCTTTC
Found at i:28056678 original size:50 final size:49
Alignment explanation
Indices: 28056515--28056739 Score: 290
Period size: 49 Copynumber: 4.5 Consensus size: 49
28056505 CTGGTACGCT
* * *
28056515 TAGTAGCCTGCACATAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
28056564 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
* * ** * *
28056613 TAGTAGCCTGTACTTAGTACTACGCACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATCCGGTACACG
* * * *
28056663 TAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTT-TTCGAGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAATTATCCG-GTACACG
28056714 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
28056740 TGCAACCTCA
Statistics
Matches: 153, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
49 77 0.50
50 43 0.28
51 32 0.21
52 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
Found at i:28058924 original size:30 final size:31
Alignment explanation
Indices: 28058880--28058949 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
28058870 TAAAGATAAC
* * *
28058880 AAGAAAACC-GAATAAAGAAATCCAAGA-TA
1 AAGAAACCCAGAATAAAAAAAACCAAGAGTA
* *
28058909 GAGAAACCCAGAATAAAAAAAACCTAGAGTA
1 AAGAAACCCAGAATAAAAAAAACCAAGAGTA
28058940 AAGAAACCCA
1 AAGAAACCCA
28058950 AGATACGATA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 7 0.21
30 15 0.45
31 11 0.33
ACGTcount: A:0.60, C:0.17, G:0.14, T:0.09
Consensus pattern (31 bp):
AAGAAACCCAGAATAAAAAAAACCAAGAGTA
Found at i:28061788 original size:27 final size:27
Alignment explanation
Indices: 28061757--28061967 Score: 237
Period size: 27 Copynumber: 7.9 Consensus size: 27
28061747 GAATACTTTA
* *
28061757 GTTTACCAAATTACTAAAATACCCTTG
1 GTTTACAAAATTACCAAAATACCCTTG
* * * *
28061784 GTTTATAAAATCACAAAAATACCCCTG
1 GTTTACAAAATTACCAAAATACCCTTG
*
28061811 GTTT-CAAAATTACCAAAATACCCTTA
1 GTTTACAAAATTACCAAAATACCCTTG
*
28061837 GTTTACAAAATTACCAAAATACCCCTG
1 GTTTACAAAATTACCAAAATACCCTTG
** *
28061864 GTTTGTAAAATTACTAAAATACCCTTG
1 GTTTACAAAATTACCAAAATACCCTTG
*
28061891 GTTTATAAAATTACCAAAATACCCTTG
1 GTTTACAAAATTACCAAAATACCCTTG
** * * *
28061918 GTTTGTAAAATTATCAAAATACCCCTA
1 GTTTACAAAATTACCAAAATACCCTTG
**
28061945 GTTTGTAAAATTACC-AAATACCC
1 GTTTACAAAATTACCAAAATACCC
28061968 CTGATTTGTG
Statistics
Matches: 160, Mismatches: 23, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
26 29 0.18
27 131 0.82
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (27 bp):
GTTTACAAAATTACCAAAATACCCTTG
Found at i:28061991 original size:53 final size:54
Alignment explanation
Indices: 28061764--28061993 Score: 313
Period size: 54 Copynumber: 4.3 Consensus size: 54
28061754 TTAGTTTACC
* * * *
28061764 AAATTACTAAAATACCCTTGGTTTATAAAATCACAAAAATACCCCTGGTTT-CA
1 AAATTACTAAAATACCCTTAGTTTATAAAATTACCAAAATACCCCTGGTTTGTA
* *
28061817 AAATTACCAAAATACCCTTAGTTTACAAAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACTAAAATACCCTTAGTTTATAAAATTACCAAAATACCCCTGGTTTGTA
* *
28061871 AAATTACTAAAATACCCTTGGTTTATAAAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACTAAAATACCCTTAGTTTATAAAATTACCAAAATACCCCTGGTTTGTA
* * * *
28061925 AAATTA-TCAAAATACCCCTAGTTTGTAAAATTACC-AAATACCCCTGATTTGTG
1 AAATTACT-AAAATACCCTTAGTTTATAAAATTACCAAAATACCCCTGGTTTGTA
*
28061978 AAATTACTGAAATACC
1 AAATTACTAAAATACC
28061994 TTCGACCTGT
Statistics
Matches: 157, Mismatches: 17, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
53 75 0.48
54 82 0.52
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.31
Consensus pattern (54 bp):
AAATTACTAAAATACCCTTAGTTTATAAAATTACCAAAATACCCCTGGTTTGTA
Found at i:28062005 original size:53 final size:54
Alignment explanation
Indices: 28061764--28062010 Score: 229
Period size: 53 Copynumber: 4.6 Consensus size: 54
28061754 TTAGTTTACC
* * * * *
28061764 AAATTACTAAAATACCCTT-GGTTTATAAAATCACAAAAATACCCCTGGTTT-CA
1 AAATTACTAAAATA-CCTTCGATTTGTAAAATTACCAAAATACCCCTGGTTTGTA
* * **
28061817 AAATTACCAAAATACCCTTAG-TTTACAAAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACTAAAATA-CCTTCGATTTGTAAAATTACCAAAATACCCCTGGTTTGTA
* * *
28061871 AAATTACTAAAATACCCTT-GGTTTATAAAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACTAAAATA-CCTTCGATTTGTAAAATTACCAAAATACCCCTGGTTTGTA
* * * *
28061925 AAATTA-TCAAAATACC-CCTAGTTTGTAAAATTACC-AAATACCCCTGATTTGTG
1 AAATTACT-AAAATACCTTCGA-TTTGTAAAATTACCAAAATACCCCTGGTTTGTA
* **
28061978 AAATTACTGAAATACCTTCGACCTGTAAAATTA
1 AAATTACTAAAATACCTTCGATTTGTAAAATTA
28062011 TTGAAATACC
Statistics
Matches: 166, Mismatches: 20, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
53 87 0.52
54 79 0.48
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.32
Consensus pattern (54 bp):
AAATTACTAAAATACCTTCGATTTGTAAAATTACCAAAATACCCCTGGTTTGTA
Found at i:28062011 original size:80 final size:80
Alignment explanation
Indices: 28061764--28062056 Score: 238
Period size: 80 Copynumber: 3.6 Consensus size: 80
28061754 TTAGTTTACC
* * * * * * * *
28061764 AAATTA-CTAAAATACCCTTGGTTTATAAAATCACAAAAATACCCCTGGTTT-CAAAATTACCAA
1 AAATTATC-AAAATACCCCTAGTTTGTAAAATTAC-CAAATACCCTTGATTTATAAAATTACCAA
* *
28061827 AATACCCTT-A-GTTTACA
64 AATACCCTTGACCTGT--A
* * * *
28061844 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTGGTTTATAAAATTACCAAA
1 AAATTATCAAAATACCCCTAGTTTGTAAAATTAC-CAAATACCCTTGATTTATAAAATTACCAAA
***
28061909 ATACCCTTGGTTTGTA
65 ATACCCTTGACCTGTA
* * * **
28061925 AAATTATCAAAATACCCCTAGTTTGTAAAATTACCAAATACCCCTGATTTGTGAAATTACTGAAA
1 AAATTATCAAAATACCCCTAGTTTGTAAAATTACCAAATACCCTTGATTTATAAAATTACCAAAA
28061990 TA-CCTTCGACCTGTA
66 TACCCTT-GACCTGTA
** * *
28062005 AAATTATTGAAATA-CCCTCGACTTGTAAAATTACCAAAGTACCCTTGATTTA
1 AAATTATCAAAATACCCCTAG-TTTGTAAAATTACCAAA-TACCCTTGATTTA
28062057 CAGAATTATC
Statistics
Matches: 179, Mismatches: 27, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
79 9 0.05
80 103 0.58
81 65 0.36
83 2 0.01
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (80 bp):
AAATTATCAAAATACCCCTAGTTTGTAAAATTACCAAATACCCTTGATTTATAAAATTACCAAAA
TACCCTTGACCTGTA
Found at i:28062047 original size:27 final size:27
Alignment explanation
Indices: 28061764--28062055 Score: 202
Period size: 27 Copynumber: 10.9 Consensus size: 27
28061754 TTAGTTTACC
* * * *
28061764 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCTCGATTTGTA
* * * *
28061791 AAATCACAAAAATACCC-CTGGTTT-CA
1 AAATTACCAAAATACCCTC-GATTTGTA
* **
28061817 AAATTACCAAAATACCCT-TAGTTTACA
1 AAATTACCAAAATACCCTCGA-TTTGTA
*
28061844 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GATTTGTA
* * * *
28061871 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCTCGATTTGTA
* *
28061898 AAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
* *
28061925 AAATTATCAAAATACCC-CTAGTTTGTA
1 AAATTACCAAAATACCCTCGA-TTTGTA
*
28061952 AAATTACC-AAATACCC-CTGATTTGTG
1 AAATTACCAAAATACCCTC-GATTTGTA
** * **
28061978 AAATTACTGAAATACCTTCGACCTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
*** *
28062005 AAATTATTGAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
* *
28062032 AAATTACCAAAGTACCCTTGATTT
1 AAATTACCAAAATACCCTCGATTT
28062056 ACAGAATTAT
Statistics
Matches: 216, Mismatches: 38, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
26 40 0.19
27 175 0.81
28 1 0.00
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGATTTGTA
Found at i:28062101 original size:27 final size:27
Alignment explanation
Indices: 28061758--28062102 Score: 112
Period size: 27 Copynumber: 12.9 Consensus size: 27
28061748 AATACTTTAG
* ** * *
28061758 TTTACCAAATTACTAAAATACCCTTGG
1 TTTACAAAATTACCGAAATACCCTCGA
* * ** *
28061785 TTTATAAAATCACAAAAATACCC-CTGG
1 TTTACAAAATTACCGAAATACCCTC-GA
* *
28061812 TTT-CAAAATTACCAAAATACCCT-TA
1 TTTACAAAATTACCGAAATACCCTCGA
* *
28061837 GTTTACAAAATTACCAAAATACCC-CTGG
1 -TTTACAAAATTACCGAAATACCCTC-GA
** ** * *
28061865 TTTGTAAAATTACTAAAATACCCTTGG
1 TTTACAAAATTACCGAAATACCCTCGA
* * * *
28061892 TTTATAAAATTACCAAAATACCCTTGG
1 TTTACAAAATTACCGAAATACCCTCGA
** * * *
28061919 TTTGTAAAATTATCAAAATACCC-CTA
1 TTTACAAAATTACCGAAATACCCTCGA
**
28061945 GTTTGTAAAATTACC-AAATACCC-CTGA
1 -TTTACAAAATTACCGAAATACCCTC-GA
*** * *
28061972 TTTGTGAAATTACTGAAATACCTTCGA
1 TTTACAAAATTACCGAAATACCCTCGA
** ** **
28061999 CCTGTAAAATTATTGAAATACCCTCGA
1 TTTACAAAATTACCGAAATACCCTCGA
* ** *
28062026 CTTGTAAAATTACC-AAAGTACCCTTGA
1 TTTACAAAATTACCGAAA-TACCCTCGA
* * *** *
28062053 TTTACAGAATTATCGTTTTACCCTCAA
1 TTTACAAAATTACCGAAATACCCTCGA
28062080 TTTACAAAATTACCGAAATACCC
1 TTTACAAAATTACCGAAATACCC
28062103 CTGTAGGGTA
Statistics
Matches: 253, Mismatches: 52, Indels: 26
0.76 0.16 0.08
Matches are distributed among these distances:
26 43 0.17
27 209 0.83
28 1 0.00
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.32
Consensus pattern (27 bp):
TTTACAAAATTACCGAAATACCCTCGA
Found at i:28062117 original size:27 final size:27
Alignment explanation
Indices: 28062087--28062415 Score: 437
Period size: 27 Copynumber: 12.3 Consensus size: 27
28062077 CAATTTACAA
28062087 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
28062114 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
28062141 AATTATCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
28062168 AATTACTGGAATACCCCTGTAGGATAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
28062195 AATTATCGAAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
28062222 AATTATCGCAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
28062249 AATTACCGAAATATCCCTGTAGGGTA-
1 AATTACCGAAATACCCCTGTAGGGTAG
*
28062275 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
28062302 AATTACCGAAAGACCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
28062329 AATTATCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** * *
28062356 AATTACTAAAATACCCCTATAGGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
28062383 AATTATCGAGATA-CCTTGTAGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
28062409 AATTACC
1 AATTACC
28062416 ATTTTGCCCC
Statistics
Matches: 264, Mismatches: 37, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
26 39 0.15
27 225 0.85
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:28063095 original size:27 final size:27
Alignment explanation
Indices: 28063065--28063166 Score: 134
Period size: 27 Copynumber: 3.8 Consensus size: 27
28063055 ATTCTGTTAA
* *
28063065 GTGGCTTTGCCACATTATCTGTTTCTG
1 GTGGCTCTGCCACAATATCTGTTTCTG
*
28063092 GTGGCTATGCCACAAATATCTG-TTCTG
1 GTGGCTCTGCCAC-AATATCTGTTTCTG
*
28063119 GTGGCTCTGCCACAATATCTGTATCTG
1 GTGGCTCTGCCACAATATCTGTTTCTG
* *
28063146 GTGACTCTGTCACAATATCTG
1 GTGGCTCTGCCACAATATCTG
28063167 ATAACTGAGC
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
26 8 0.12
27 52 0.78
28 7 0.10
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.36
Consensus pattern (27 bp):
GTGGCTCTGCCACAATATCTGTTTCTG
Found at i:28063352 original size:25 final size:25
Alignment explanation
Indices: 28063314--28063370 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
28063304 TTCTAATTTT
* *
28063314 TGATTCTGTTACCTGATACTGATTC
1 TGATTCTGTCACCTGATACTAATTC
*
28063339 TGATTCTGTCACCTGATTCTAATTC
1 TGATTCTGTCACCTGATACTAATTC
28063364 TGATTCT
1 TGATTCT
28063371 AGTTCTGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.19, C:0.21, G:0.14, T:0.46
Consensus pattern (25 bp):
TGATTCTGTCACCTGATACTAATTC
Found at i:28065151 original size:49 final size:49
Alignment explanation
Indices: 28065069--28065293 Score: 263
Period size: 49 Copynumber: 4.5 Consensus size: 49
28065059 CTGGTACGCA
* * * *
28065069 TAGTAGCCTGCACATAGTACTACACATGCGACCAATTATCCAGTACAAG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACAAG
* * *
28065118 TATTAGCCTGCACTTAGTACTACATACGTGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACAAG
** * * *
28065167 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACATG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATCCGGTACAAG
* * * *
28065217 TAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTCGGGTACGCA-
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAATTATCCGGTAC-AAG
28065268 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
28065294 TGCAACCTCA
Statistics
Matches: 150, Mismatches: 22, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
49 73 0.49
50 42 0.28
51 34 0.23
52 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACAAG
Found at i:28065289 original size:101 final size:98
Alignment explanation
Indices: 28065056--28065293 Score: 298
Period size: 98 Copynumber: 2.4 Consensus size: 98
28065046 TAGCCAAAGC
* * * ** *
28065056 TATCTGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCAATTATCCAGTACAAGTAT
1 TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGACCAACCATCCAGTACAAGTAG
*
28065121 TAGCCTGCACTTAGTACTACATACGTGACCAAT
66 TAGCCTGCACTTAGTACTACACACGTGACCAAT
* * * * *
28065154 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCAT-CTGATACATGT
1 TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGACC-AACCATCCAG-TACAAGT
*
28065218 AGTAGCCTGCACTTAGTACTACACACGTGATCACAGT
64 AGTAGCCTGCACTTAGTACTACACACGTGA-C-CAAT
* *
28065255 TTTCGGGTACGCATAGTAGCCTGCACTTAGTACTACACA
1 TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACA
28065294 TGCAACCTCA
Statistics
Matches: 119, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
98 42 0.35
99 38 0.32
100 1 0.01
101 38 0.32
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.26
Consensus pattern (98 bp):
TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGACCAACCATCCAGTACAAGTAG
TAGCCTGCACTTAGTACTACACACGTGACCAAT
Found at i:28068108 original size:55 final size:55
Alignment explanation
Indices: 28068041--28068147 Score: 160
Period size: 55 Copynumber: 1.9 Consensus size: 55
28068031 GCCATGGGTG
** * *
28068041 TTCCACACGGGCGTGTTGCACGCCCGTGTTGTTTTGGCAGGCTCGCCCACGGTTA
1 TTCCACACGGGCGTGTCACACGCCCGTGTTGTTTTGACAGGCTCGACCACGGTTA
* *
28068096 TTCCACATGGGCGTGTCACATGCCCGTGTTGTTTTGACAGGCTCGACCACGG
1 TTCCACACGGGCGTGTCACACGCCCGTGTTGTTTTGACAGGCTCGACCACGG
28068148 CCTTGTCACA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 46 1.00
ACGTcount: A:0.13, C:0.30, G:0.30, T:0.27
Consensus pattern (55 bp):
TTCCACACGGGCGTGTCACACGCCCGTGTTGTTTTGACAGGCTCGACCACGGTTA
Found at i:28074417 original size:24 final size:24
Alignment explanation
Indices: 28074342--28074421 Score: 81
Period size: 25 Copynumber: 3.2 Consensus size: 24
28074332 ATGTTCTCAC
*
28074342 GAGCTGGAAATCAGTAAGCTAATAT
1 GAGCT-GAAATCAGTAAGCTCATAT
* **
28074367 GAACTGAGAATTGGTAAGCTC-TAAT
1 GAGCTGA-AATCAGTAAGCTCAT-AT
*
28074392 GAGCTGAAATCAATAAGCTCATAT
1 GAGCTGAAATCAGTAAGCTCATAT
28074416 GAGCTG
1 GAGCTG
28074422 CGGTGTGTCC
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
24 21 0.48
25 23 0.52
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.25
Consensus pattern (24 bp):
GAGCTGAAATCAGTAAGCTCATAT
Found at i:28077118 original size:27 final size:27
Alignment explanation
Indices: 28077087--28077141 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
28077077 TACAGAGCAT
28077087 AAGGGCATAATCG-TCATTTTACCATAC
1 AAGGGCATAA-CGATCATTTTACCATAC
* * *
28077114 AAGGGTATTACGATCATTTTACCCTAC
1 AAGGGCATAACGATCATTTTACCATAC
28077141 A
1 A
28077142 GGGGTATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 2 0.08
27 22 0.92
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.31
Consensus pattern (27 bp):
AAGGGCATAACGATCATTTTACCATAC
Found at i:28085485 original size:20 final size:20
Alignment explanation
Indices: 28085460--28085497 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28085450 GACTAAACTG
28085460 AAAACTTTAG-AAATTTTTAC
1 AAAAC-TTAGAAAATTTTTAC
28085480 AAAACTTAGAAAATTTTT
1 AAAACTTAGAAAATTTTT
28085498 CCATTAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.39
Consensus pattern (20 bp):
AAAACTTAGAAAATTTTTAC
Found at i:28093562 original size:48 final size:48
Alignment explanation
Indices: 28093406--28093686 Score: 237
Period size: 48 Copynumber: 5.9 Consensus size: 48
28093396 CATTTGGGTG
* * *
28093406 ATATGTGTGCCAGTGTAAGACCATGTCTGGGACATGGCGTCAGCCA-CA
1 ATATGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAG-CATTA
* * * * * * *
28093454 ATATGAGAGCCAGTGTAAAATCATGTTTGGAACATGGCATCGGGGA-T-
1 ATATGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATC-AGCATTA
* * *
28093501 GT-TGTGAAAGCTAGTGTAAGACCATGTTTGGGACATGGCATCAGCATTA
1 ATATGTG--AGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCATTA
* * * *
28093550 ATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCACCAGCATTG
1 ATATGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCATTA
* * * * * * * *
28093598 AGACGAGAGCTAGTGTAAGACCATGTCTAGGACATGGTATCAGCCTTG
1 ATATGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCATTA
* * * *
28093646 ACATGTGAGCCAGTGTAAGATCATGTTTGGAACATGGCATC
1 ATATGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATC
28093687 GGCAATTCAC
Statistics
Matches: 187, Mismatches: 40, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
46 3 0.02
47 3 0.02
48 175 0.94
49 2 0.01
50 4 0.02
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (48 bp):
ATATGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCATTA
Found at i:28093585 original size:96 final size:96
Alignment explanation
Indices: 28093417--28093688 Score: 309
Period size: 96 Copynumber: 2.8 Consensus size: 96
28093407 TATGTGTGCC
* * * *
28093417 AGTGTAAGACCATGTCTGGGACATGGCGTCAGCCA-CAATATGAGAGCCAGTGTAAAATCATGTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAG-CATTAATATGTGAGCCAGTGTAAGATCATGTT
* *
28093481 TGGAACATGGCATCGGGGATGTTGTGA-A-AGCT
65 TGGAACATGGCATCGGGCA--TTGAGACAGAGCT
* * * * *
28093513 AGTGTAAGACCATGTTTGGGACATGGCATCAGCATTAATATGTGTGCTAGTGTAAGACCATGTCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCATTAATATGTGAGCCAGTGTAAGATCATGTTT
* **
28093578 GGGACATGGCA-CCAGCATTGAGACGAGAGCT
66 GGAACATGGCATCGGGCATTGAGAC-AGAGCT
* * * * *
28093609 AGTGTAAGACCATGTCTAGGACATGGTATCAGCCTTGACATGTGAGCCAGTGTAAGATCATGTTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCATTAATATGTGAGCCAGTGTAAGATCATGTTT
28093674 GGAACATGGCATCGG
66 GGAACATGGCATCGG
28093689 CAATTCACCC
Statistics
Matches: 144, Mismatches: 27, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
93 5 0.03
95 6 0.04
96 132 0.92
97 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.25
Consensus pattern (96 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCAGCATTAATATGTGAGCCAGTGTAAGATCATGTTT
GGAACATGGCATCGGGCATTGAGACAGAGCT
Found at i:28095331 original size:26 final size:24
Alignment explanation
Indices: 28095287--28095336 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
28095277 ATTTGTTTTA
* *
28095287 ATATTTGTTTTTATGTTTTTAAAT
1 ATATTTGTTTTTATATTTTAAAAT
28095311 ATATTTGATTTATTATATTTTAAAAT
1 ATATTTG-TTT-TTATATTTTAAAAT
28095337 TTTTATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 12 0.55
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (24 bp):
ATATTTGTTTTTATATTTTAAAAT
Found at i:28097525 original size:26 final size:26
Alignment explanation
Indices: 28097496--28097546 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
28097486 ATATTCGGCT
28097496 ATAACA-AATATAAATTCTAACATTTC
1 ATAACAGAATATAAATT-TAACATTTC
* *
28097522 ATAACAGCATATATATTTAACATTT
1 ATAACAGAATATAAATTTAACATTT
28097547 AACTACAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (26 bp):
ATAACAGAATATAAATTTAACATTTC
Found at i:28098327 original size:16 final size:16
Alignment explanation
Indices: 28098306--28098336 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28098296 CCTTTATTTA
28098306 ATAATACAAAATCATT
1 ATAATACAAAATCATT
*
28098322 ATAATACAAAGTCAT
1 ATAATACAAAATCAT
28098337 AGCCGTCCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.13, G:0.03, T:0.29
Consensus pattern (16 bp):
ATAATACAAAATCATT
Found at i:28103032 original size:47 final size:47
Alignment explanation
Indices: 28102980--28103325 Score: 491
Period size: 47 Copynumber: 7.3 Consensus size: 47
28102970 TGTACAAGTA
* * *
28102980 TATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGAA-AGTA
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TG
28103027 TATATATGCGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
1 TATATAT--GTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
* * *
28103076 TGTATGTGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAACATG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
* *
28103123 TGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
* *
28103170 TGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
* *
28103217 CATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-AGTG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TG
* *
28103264 TATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGGAA-GTG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGT-GAACATG
*
28103311 TATAAATGTGATAAG
1 TATATATGTGATAAG
28103326 TCCCGAAGGG
Statistics
Matches: 278, Mismatches: 16, Indels: 10
0.91 0.05 0.03
Matches are distributed among these distances:
46 1 0.00
47 233 0.84
48 3 0.01
49 40 0.14
50 1 0.00
ACGTcount: A:0.32, C:0.10, G:0.31, T:0.27
Consensus pattern (47 bp):
TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
Found at i:28103203 original size:22 final size:22
Alignment explanation
Indices: 28103176--28103297 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
28103166 CATGTGTATG
28103176 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * *
28103198 TGTGATGAATG-TGAACAT-GCATATA
1 TGTGAT-AAGGCCG-A-ATGGC-CA-A
*
28103223 TGAGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * ***
28103245 TGTGATGAATG-TGAAAGTGTATATA
1 TGTGAT-AAGGCCG-AA-TGGCCA-A
28103270 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
28103292 TGTGAT
1 TGTGAT
28103298 GGATGTGGAA
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 21 0.30
23 17 0.24
24 17 0.24
25 15 0.21
ACGTcount: A:0.34, C:0.11, G:0.30, T:0.25
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:28105820 original size:38 final size:38
Alignment explanation
Indices: 28105756--28105830 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
28105746 AATCCGAGTT
*
28105756 TAAAGACCCGCTGACTATATGAAGAGATTATGTCCGGG
1 TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
* *
28105794 TAAAGACCCGATGGCTATGT-ACAGAGATTATGTCCGG
1 TAAAGACCCGATGACTATATGA-AGAGATTATGTCCGG
28105831 ATTAAAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (38 bp):
TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
Found at i:28106163 original size:40 final size:40
Alignment explanation
Indices: 28105884--28106151 Score: 403
Period size: 40 Copynumber: 6.7 Consensus size: 40
28105874 AGGTCTCGAC
28105884 GATG-ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* *
28105923 GATGTATCCGGGCTAAGTCCTGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
28105963 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
*
28106003 GATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* *
28106043 GATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* * ** *
28106083 GATATATCCGTGCTAAACCCCGAAGAGCATTCGTGCTGGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* * * *
28106123 GTTATATCTGGGCTAGGTCCCGAAGAGCA
1 GATGTATCCGGGCTAAGTCCCGAAGAGCA
28106152 ATCATGCTGG
Statistics
Matches: 207, Mismatches: 21, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
39 4 0.02
40 203 0.98
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.26
Consensus pattern (40 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
Found at i:28108058 original size:29 final size:27
Alignment explanation
Indices: 28108040--28108109 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
28108030 ATATTAAGTC
28108040 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
28108067 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
28108095 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
28108110 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:28108103 original size:28 final size:28
Alignment explanation
Indices: 28108040--28108137 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
28108030 ATATTAAGTC
*
28108040 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
28108067 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
28108095 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
28108124 CGCACACTTAGTGC
1 CGCACACTTAGTGC
28108138 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:28112761 original size:47 final size:48
Alignment explanation
Indices: 28112709--28113102 Score: 525
Period size: 47 Copynumber: 8.3 Consensus size: 48
28112699 TGTACAAGTA
* * * *
28112709 TATATATGTGATAGGGCCGAGTGGTCAATGTGATGAATGTGAA-AGTA
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACAGTG
28112756 TATATATGCGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTG
1 TATATAT--GTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-GTG
* * *
28112807 TATGTGTGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAACA-TG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACAGTG
* **
28112854 TGTACGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACAGTG
* *
28112901 TGTATGTGTGAT-AGGCCGAATGGCCAATGTGATGAATGTGAACA-TG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACAGTG
* *
28112947 CATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACAGTG
* *
28112994 CATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-AGTG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACAGTG
* * *
28113041 TATATATGTGATAAGGCCGAATTGCCAATGTGATGGATGTGGA-AGTG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACAGTG
*
28113088 TATAAATGTGATAAG
1 TATATATGTGATAAG
28113103 TCCTGAAGGG
Statistics
Matches: 319, Mismatches: 22, Indels: 12
0.90 0.06 0.03
Matches are distributed among these distances:
46 43 0.13
47 198 0.62
49 70 0.22
50 1 0.00
51 7 0.02
ACGTcount: A:0.32, C:0.10, G:0.30, T:0.27
Consensus pattern (48 bp):
TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACAGTG
Found at i:28112990 original size:140 final size:141
Alignment explanation
Indices: 28112714--28113081 Score: 497
Period size: 140 Copynumber: 2.6 Consensus size: 141
28112704 AAGTATATAT
* * * * *
28112714 ATGTGATAGGGCCGAGTGGTCAATGTGATGAATGTGAAAGTATATATATGCGTGATAAGGCCGAA
1 ATGTGATAAGGCCGAATGGCCAATGTGATGAATGTG-AA--ATGTATATGTGTGATAAGGCCGAA
* * * *
28112779 TGGCCAATGTGATGAATGTGAACATGTGTATGTGTGTGATAAGGCCGAATGGCCAATGTGACGAA
63 TGGCCAATGTGATGAATGTGAACA-GTGCATATATGAGATAAGGCCGAATGGCCAATGTGACGAA
**
28112844 TGTGAACATGTGTAC
127 TGTGAACATGCATAC
* *
28112859 GTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGAT-AGGCCGAATG
1 ATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-ATGTATATGTGTGATAAGGCCGAATG
*
28112923 GCCAATGTGATGAATGTGAACA-TGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGT
65 GCCAATGTGATGAATGTGAACAGTGCATATATGAGATAAGGCCGAATGGCCAATGTGACGAATGT
*
28112987 GAACATGCATAT
130 GAACATGCATAC
* * *
28112999 ATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATT
1 ATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA-TGTATATGTGTGATAAGGCCGAATG
*
28113064 GCCAATGTGATGGATGTG
65 GCCAATGTGATGAATGTG
28113082 GAAGTGTATA
Statistics
Matches: 199, Mismatches: 22, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
139 1 0.01
140 94 0.47
141 26 0.13
142 32 0.16
143 12 0.06
144 2 0.01
145 32 0.16
ACGTcount: A:0.32, C:0.11, G:0.31, T:0.26
Consensus pattern (141 bp):
ATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAATGTATATGTGTGATAAGGCCGAATGG
CCAATGTGATGAATGTGAACAGTGCATATATGAGATAAGGCCGAATGGCCAATGTGACGAATGTG
AACATGCATAC
Done.