Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 162 of 343
Found at i:53609247 original size:27 final size:27
Alignment explanation
Indices: 53608900--53609255 Score: 333
Period size: 27 Copynumber: 13.3 Consensus size: 27
53608890 TCGATTGTGA
* ** *
53608900 AATTACTGAAATACCCCCGTAGGATAG
1 AATTACCGAAATACCCCTATAGGGTAG
* ** *
53608927 AATTACCAAAATACCCCTAGT-TTGTAA
1 AATTACCGAAATACCCCTA-TAGGGTAG
* ** *
53608954 AATTACCAAAATACCCCTAGT-TTGTAA
1 AATTACCGAAATACCCCTA-TAGGGTAG
53608981 AATTACCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTATAGGGTAG
*
53609008 AATTACCGGAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTATAGGGTAG
* * * *
53609035 AATTACAGGAATACCCCTGTAGGATAG
1 AATTACCGAAATACCCCTATAGGGTAG
* * * * *
53609062 AATTATCGCAAGACCTCTGTAGGGTAG
1 AATTACCGAAATACCCCTATAGGGTAG
* *
53609089 AATTACCGAAATACCCCTATAAGGTAA
1 AATTACCGAAATACCCCTATAGGGTAG
*
53609116 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTATAGGGTAG
* *
53609143 AATTATCGCAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTATAGGGTAG
*
53609170 AATTACCGAAATA-CCCTGTA-GGTAG
1 AATTACCGAAATACCCCTATAGGGTAG
** * * *
53609195 AATTACTAAAATACTCCTGTAAGGTAG
1 AATTACCGAAATACCCCTATAGGGTAG
* * * *
53609222 AATTACCGAGATACCCTTATGGGGTAA
1 AATTACCGAAATACCCCTATAGGGTAG
53609249 AATTACC
1 AATTACC
53609256 ATTTTACCCC
Statistics
Matches: 275, Mismatches: 50, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
25 16 0.06
26 13 0.05
27 245 0.89
28 1 0.00
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTATAGGGTAG
Found at i:53609735 original size:22 final size:22
Alignment explanation
Indices: 53609683--53609747 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
53609673 TTAAAGCCTT
* *
53609683 CTGATTATGGCTTTGTGTCAAC
1 CTGATTATGGCTCTGTGCCAAC
*
53609705 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
*
53609727 CTGATTATGGCTGTGTGCCAA
1 CTGATTATGGCTCTGTGCCAA
53609748 ACGTATTTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.03
22 34 0.94
23 1 0.03
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:53609936 original size:27 final size:26
Alignment explanation
Indices: 53609906--53610004 Score: 99
Period size: 27 Copynumber: 3.7 Consensus size: 26
53609896 ATTTTGTTAA
* *
53609906 GTGGCTTTGCCACATTATCTATTTCTG
1 GTGGCTATGCCACAATATCT-TTTCTG
*
53609933 GTGGCTATGCCACAAATATCTGTTCTG
1 GTGGCTATGCCAC-AATATCTTTTCTG
* *
53609960 GTGGCTCTGCCACAATATCTGTATCTG
1 GTGGCTATGCCACAATATCT-TTTCTG
* * *
53609987 GTGACTCTGTCACAATAT
1 GTGGCTATGCCACAATAT
53610005 TTGATATCTG
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
26 7 0.11
27 49 0.79
28 6 0.10
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (26 bp):
GTGGCTATGCCACAATATCTTTTCTG
Found at i:53610183 original size:6 final size:6
Alignment explanation
Indices: 53610144--53610282 Score: 65
Period size: 6 Copynumber: 22.3 Consensus size: 6
53610134 TTGCATTCAC
* *
53610144 ATTCTG ATTTTTG ATTCT- ATTACCTG ATAT-TG ATTCTG ATTTTG ATTCTG
1 ATTCTG A-TTCTG ATTCTG ATT--CTG AT-TCTG ATTCTG ATTCTG ATTCTG
* * * * *
53610194 -TTACCTG ATACTA ATTCTG ATTTTG ATTCTG -TTACCTG ATACTG ATTCTA
1 ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG
*
53610244 ATTCTG ATTCTG -TCACCTG ATTCTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG A-TTCTG AT
53610283 AATGTTTCTT
Statistics
Matches: 100, Mismatches: 16, Indels: 34
0.67 0.11 0.23
Matches are distributed among these distances:
5 10 0.10
6 67 0.67
7 17 0.17
8 5 0.05
9 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:53610190 original size:31 final size:31
Alignment explanation
Indices: 53610144--53610273 Score: 188
Period size: 31 Copynumber: 4.2 Consensus size: 31
53610134 TTGCATTCAC
* *
53610144 ATTCTGATTTTTGATTCTATTACCTGATATTG
1 ATTCTGA-TTTTGATTCTGTTACCTGATACTG
*
53610176 ATTCTGATTTTGATTCTGTTACCTGATACTA
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
53610207 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
* * * *
53610238 ATTCTAATTCTGATTCTGTCACCTGATTCTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
53610269 ATTCT
1 ATTCT
53610274 AGTTCTGATA
Statistics
Matches: 90, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
31 83 0.92
32 7 0.08
ACGTcount: A:0.21, C:0.17, G:0.13, T:0.49
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGTTACCTGATACTG
Found at i:53613942 original size:45 final size:43
Alignment explanation
Indices: 53613890--53614010 Score: 126
Period size: 41 Copynumber: 2.8 Consensus size: 43
53613880 ATGTGTTTTT
*
53613890 GTGTAAGACCACT-TCTGGGACGTTGGCATCGATATATGTGGTTAC
1 GTGTAAGACCACTGTCTGGGACGTTGGCATCGATAT-T-TGATT-C
* ** *
53613935 GTGTAAGACCA-TGTCTAGGATATTGGTATCG-TATTTGATTC
1 GTGTAAGACCACTGTCTGGGACGTTGGCATCGATATTTGATTC
53613976 GTGTAAGACC-CTGTCTGGGACAG-TGGCATCGATAT
1 GTGTAAGACCACTGTCTGGGAC-GTTGGCATCGATAT
53614011 GAGATGACAT
Statistics
Matches: 63, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
41 26 0.41
42 7 0.11
43 1 0.02
44 4 0.06
45 25 0.40
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (43 bp):
GTGTAAGACCACTGTCTGGGACGTTGGCATCGATATTTGATTC
Found at i:53618016 original size:27 final size:27
Alignment explanation
Indices: 53617978--53618032 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
53617968 ACTTAGCCTG
53617978 TCACATTGAAGTGTTTTTCGAAAACCA
1 TCACATTGAAGTGTTTTTCGAAAACCA
53618005 TCACATTGAAGTGTTTTTCGAAAACCA
1 TCACATTGAAGTGTTTTTCGAAAACCA
53618032 T
1 T
53618033 GTTTCCATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.35
Consensus pattern (27 bp):
TCACATTGAAGTGTTTTTCGAAAACCA
Found at i:53618634 original size:6 final size:6
Alignment explanation
Indices: 53618623--53618797 Score: 148
Period size: 6 Copynumber: 28.8 Consensus size: 6
53618613 AACCAAAATG
* *
53618623 AGAATC AGAATC AGAATC AGTAA-C AGAATC AGGATC A-ATATT AGTAA-C
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGA-ATC AG-AATC
* *
53618671 AGAATC AGAATC AGAATC AGAATT AG-GTGAC AGAATC AGTAA-C AGAATC
1 AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AG-AATC AGAATC
* * *
53618720 AGAATC AGAATC AGTATT AGTAA-C AGAATC AGAATC AGAATC AGAATT
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGAATC
*
53618768 ACGTGA-C AGAATC AGAATC AGAATC AGAAT
1 A-G-AATC AGAATC AGAATC AGAATC AGAAT
53618798 GTGAATGCAA
Statistics
Matches: 137, Mismatches: 16, Indels: 32
0.74 0.09 0.17
Matches are distributed among these distances:
5 10 0.07
6 114 0.83
7 10 0.07
8 3 0.02
ACGTcount: A:0.47, C:0.14, G:0.18, T:0.20
Consensus pattern (6 bp):
AGAATC
Found at i:53618682 original size:30 final size:31
Alignment explanation
Indices: 53618646--53618724 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 31
53618636 GAATCAGTAA
*
53618646 CAGAATCAGGATCA-ATATTA-GTAACAGAAT
1 CAGAATCAGAATCAGA-ATTAGGTAACAGAAT
*
53618676 CAGAATCAGAATCAGAATTAGGTGACAGAAT
1 CAGAATCAGAATCAGAATTAGGTAACAGAAT
53618707 CAGTAA-CAGAATCAGAAT
1 CAG-AATCAGAATCAGAAT
53618725 CAGAATCAGT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
30 17 0.39
31 25 0.57
32 2 0.05
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGAATCAGAATCAGAATTAGGTAACAGAAT
Found at i:53618741 original size:73 final size:73
Alignment explanation
Indices: 53618628--53618797 Score: 281
Period size: 73 Copynumber: 2.3 Consensus size: 73
53618618 AAATGAGAAT
*
53618628 CAGAATCAGAATCAGTAA-CAGAATCAGGATCAATATTAGTAACAGAATCAGAATCAGAATCAGA
1 CAGAATCAGAATCAG-AATCAGAATCAGAATCAATATTAGTAACAGAATCAGAATCAGAATCAGA
*
53618692 ATTAGGTGA
65 ATTACGTGA
*
53618701 CAGAATCAGTAA-CAGAATCAGAATCAGAATCAGTATTAGTAACAGAATCAGAATCAGAATCAGA
1 CAGAATCAG-AATCAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAGAATCAGAATCAGA
53618765 ATTACGTGA
65 ATTACGTGA
53618774 CAGAATCAGAATCAGAATCAGAAT
1 CAGAATCAGAATCAGAATCAGAAT
53618798 GTGAATGCAA
Statistics
Matches: 91, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
72 4 0.04
73 85 0.93
74 2 0.02
ACGTcount: A:0.47, C:0.15, G:0.18, T:0.20
Consensus pattern (73 bp):
CAGAATCAGAATCAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAGAATCAGAATCAGAA
TTACGTGA
Found at i:53618952 original size:27 final size:26
Alignment explanation
Indices: 53618915--53618980 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
53618905 AGCATGGCTG
*
53618915 CCAGAACAGATATCGTGAAAGAGTCA
1 CCAGAACAGATATCGTGAAAGAGCCA
* **
53618941 CCAGATACAGATATTGTGGCAGAGCCA
1 CCAGA-ACAGATATCGTGAAAGAGCCA
53618968 CCAGAATCAGATA
1 CCAGAA-CAGATA
53618981 ATGTGGCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 6 0.18
27 28 0.82
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATATCGTGAAAGAGCCA
Found at i:53618985 original size:27 final size:27
Alignment explanation
Indices: 53618934--53618988 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
53618924 ATATCGTGAA
* *
53618934 AGAGTCACCAGATACAGATATTGTGGC
1 AGAGCCACCAGATACAGATAATGTGGC
53618961 AGAGCCACCAGA-ATCAGATAATGTGGC
1 AGAGCCACCAGATA-CAGATAATGTGGC
53618988 A
1 A
53618989 AACCCACCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 24 0.96
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.18
Consensus pattern (27 bp):
AGAGCCACCAGATACAGATAATGTGGC
Found at i:53618995 original size:27 final size:27
Alignment explanation
Indices: 53618939--53618996 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
53618929 GTGAAAGAGT
* * *
53618939 CACCAGATACAGATATTGTGGCAGAGC
1 CACCAGATACAGATAATGTGGCAAACC
53618966 CACCAGA-ATCAGATAATGTGGCAAACC
1 CACCAGATA-CAGATAATGTGGCAAACC
53618993 CACC
1 CACC
53618997 TAACAGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.36, C:0.28, G:0.21, T:0.16
Consensus pattern (27 bp):
CACCAGATACAGATAATGTGGCAAACC
Found at i:53619378 original size:27 final size:26
Alignment explanation
Indices: 53619299--53619381 Score: 87
Period size: 27 Copynumber: 3.1 Consensus size: 26
53619289 TCGATCGGTC
** * * *
53619299 AACAGATATTGTGATAGAGTCACCAA
1 AACAGATATTGTGGCAAAGCCACCAG
53619325 ATACAGATATTGTGGCAAAGCCACCAG
1 A-ACAGATATTGTGGCAAAGCCACCAG
53619352 AACAGATATTTGTGGCATAA-CCACCAG
1 AACAGATA-TTGTGGCA-AAGCCACCAG
53619379 AAC
1 AAC
53619382 GCTTCCTCCG
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
26 8 0.16
27 39 0.80
28 2 0.04
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.20
Consensus pattern (26 bp):
AACAGATATTGTGGCAAAGCCACCAG
Found at i:53619619 original size:27 final size:27
Alignment explanation
Indices: 53619588--53619767 Score: 225
Period size: 27 Copynumber: 6.7 Consensus size: 27
53619578 ATGGTTATTT
* *
53619588 TACCCTACAAGGGTATCTCGGTAATTC
1 TACCCTACAGGGGTATTTCGGTAATTC
* *
53619615 TACCCTACAGGGGTATTTTGGTATTTC
1 TACCCTACAGGGGTATTTCGGTAATTC
* *
53619642 TACCCTACAAGGGTATTTCGATAATTC
1 TACCCTACAGGGGTATTTCGGTAATTC
*
53619669 TACCCTACAGGGGTATTTTGGTAATTC
1 TACCCTACAGGGGTATTTCGGTAATTC
* * * *
53619696 TATCCTATAAGGGTATTTCAGTAATTC
1 TACCCTACAGGGGTATTTCGGTAATTC
* * *
53619723 TACCCTATAGGGGTATTTCAGAAATTC
1 TACCCTACAGGGGTATTTCGGTAATTC
*
53619750 TACCCTATAGGGGTATTT
1 TACCCTACAGGGGTATTT
53619768 TAGTAATTTC
Statistics
Matches: 134, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 134 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (27 bp):
TACCCTACAGGGGTATTTCGGTAATTC
Found at i:53619749 original size:54 final size:54
Alignment explanation
Indices: 53619579--53619775 Score: 252
Period size: 54 Copynumber: 3.6 Consensus size: 54
53619569 AGGGGCAAAA
* * * *
53619579 TGGTTATTTTACCCTACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTT
*
53619633 TGGTATTTCTACCCTACAAGGGTATTTC-GATAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAAGGGTATTTCAG-TAATTCTACCCTACAGGGGTATTT
* * *
53619687 TGGTAATTCTATCCTATAAGGGTATTTCAGTAATTCTACCCTATAGGGGTATTT
1 TGGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTT
** * * * *
53619741 CAGAAATTCTACCCTATAGGGGTATTTTAGTAATT
1 TGGTAATTCTACCCTACAAGGGTATTTCAGTAATT
53619776 TCACAATCAA
Statistics
Matches: 127, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
53 1 0.01
54 125 0.98
55 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (54 bp):
TGGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTT
Found at i:53619817 original size:27 final size:27
Alignment explanation
Indices: 53619780--53620135 Score: 423
Period size: 27 Copynumber: 13.2 Consensus size: 27
53619770 GTAATTTCAC
* * *
53619780 AATCAAGGGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
53619807 AA-CTGAGGGT-AACCTAGTAATTCTGTA
1 AATC-GAGGGTAAAAC-GGTAATTCTGTA
* * **
53619834 AATCAAGGGTAAAACGGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
53619861 AATCGAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
53619888 AA-CTGAGGGTAAAACGGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
53619915 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
**
53619942 AA-CTGAGGGTAAAATAGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
* * **
53619969 AATCGAGGGTAAAATGGTAATTTTAAA
1 AATCGAGGGTAAAACGGTAATTCTGTA
53619996 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* * **
53620023 AATCAAGGGTAAAACGGTAATTTTAAA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* **
53620050 AATCGAGGGTAAAACGGTAATTTTAAA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
53620077 AATTGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
53620104 AATCGAGGGTAAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
53620131 AATCG
1 AATCG
53620136 GGAGTACTTT
Statistics
Matches: 283, Mismatches: 38, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
26 6 0.02
27 271 0.96
28 6 0.02
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.27
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTCTGTA
Found at i:53624849 original size:13 final size:14
Alignment explanation
Indices: 53624817--53624850 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
53624807 ATTGGTTAAA
53624817 AATAATAATAAAATG
1 AATAA-AATAAAATG
53624832 AATAAAATAAAA-G
1 AATAAAATAAAATG
53624845 AATAAA
1 AATAAA
53624851 GGTGTCATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
14 7 0.37
15 5 0.26
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (14 bp):
AATAAAATAAAATG
Found at i:53625824 original size:28 final size:28
Alignment explanation
Indices: 53625783--53625861 Score: 106
Period size: 28 Copynumber: 2.8 Consensus size: 28
53625773 GCAATCAAAT
** *
53625783 ATGGCACTCGGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
53625811 ATGGCACTTAGTGTGC-AAGATATTGAGA
1 ATGGCACTTAGTGTGCGAA-ATATTGAGA
*
53625839 ATGACACTTAGTGTGCGAAATAT
1 ATGGCACTTAGTGTGCGAAATAT
53625862 CAAATGATTC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
27 2 0.04
28 41 0.91
29 2 0.04
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.28
Consensus pattern (28 bp):
ATGGCACTTAGTGTGCGAAATATTGAGA
Found at i:53626302 original size:21 final size:22
Alignment explanation
Indices: 53626271--53626311 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
53626261 GAATGTATTG
*
53626271 TGATGTATGTGGAAATGAAATA
1 TGATGTATGTGCAAATGAAATA
*
53626293 TGAT-TATGTGCCAATGAAA
1 TGATGTATGTGCAAATGAAA
53626312 CATAAATGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.32
Consensus pattern (22 bp):
TGATGTATGTGCAAATGAAATA
Found at i:53627563 original size:14 final size:13
Alignment explanation
Indices: 53627543--53627574 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
53627533 AATATTTGAC
53627543 TTGTTCTTAATTA
1 TTGTTCTTAATTA
53627556 TGTGTTCTTAATTA
1 T-TGTTCTTAATTA
53627570 TTGTT
1 TTGTT
53627575 TTGATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.19, C:0.06, G:0.12, T:0.62
Consensus pattern (13 bp):
TTGTTCTTAATTA
Found at i:53633920 original size:64 final size:64
Alignment explanation
Indices: 53633839--53634023 Score: 180
Period size: 67 Copynumber: 2.9 Consensus size: 64
53633829 AGACATTATG
* *
53633839 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
53633903 ATGTAGCTAGGTCGCATGCGTGGTTGC-AGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGA
1 ATGTAGCTAGGTCGCATGGGT-GATACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGA
53633967 TAA
62 TAA
* * * * *
53633970 AT-TGGCTAGGTCACATGGGTGGTTCTGA-GTGTTCACCATGT-GTACAAGAGAGCT
1 ATGTAGCTAGGTCGCATGGGTGATACT-ATGTGTACACCATGTAG-ACAAGAGAGCT
53634024 GAACTATATG
Statistics
Matches: 99, Mismatches: 15, Indels: 15
0.77 0.12 0.12
Matches are distributed among these distances:
62 1 0.01
63 20 0.20
64 22 0.22
65 6 0.06
66 17 0.17
67 33 0.33
ACGTcount: A:0.28, C:0.16, G:0.31, T:0.24
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:53645385 original size:28 final size:28
Alignment explanation
Indices: 53645325--53645385 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
53645315 CAGTGTACGG
* *
53645325 AATATTGAGAATGACATTTAGCGTGCGA
1 AATATTGAGAATGACACTTAGCGTGCAA
* * *
53645353 GATATTGAGAATGACACTTAGTGTTCAA
1 AATATTGAGAATGACACTTAGCGTGCAA
53645381 AATAT
1 AATAT
53645386 CGAATGATTC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (28 bp):
AATATTGAGAATGACACTTAGCGTGCAA
Found at i:53650118 original size:8 final size:8
Alignment explanation
Indices: 53650105--53650135 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
53650095 CTAGATCGGT
53650105 AAAAGCCG
1 AAAAGCCG
53650113 AAAAGCCG
1 AAAAGCCG
*
53650121 AAATGCCG
1 AAAAGCCG
53650129 AAAAGCC
1 AAAAGCC
53650136 AGTATTTTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.48, C:0.26, G:0.23, T:0.03
Consensus pattern (8 bp):
AAAAGCCG
Found at i:53650425 original size:28 final size:27
Alignment explanation
Indices: 53650385--53650448 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 27
53650375 ATGTACTAGA
*
53650385 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACC-TT
53650413 ATACCCCTATGTATGCAAAATGACCTT
1 ATACCCCTATGTATGCAAAATGACCTT
53650440 ATACCCCTA
1 ATACCCCTA
53650449 GGGTTAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 11 0.31
28 24 0.69
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.30
Consensus pattern (27 bp):
ATACCCCTATGTATGCAAAATGACCTT
Found at i:53650595 original size:28 final size:27
Alignment explanation
Indices: 53650554--53650643 Score: 92
Period size: 27 Copynumber: 3.2 Consensus size: 27
53650544 AGGAAGCGTC
*
53650554 CTGGTGGCTA-TGCCATAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* * *
53650582 CTGGTGGCCCTGCCGCATATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
*
53650609 CTGGTGGCACTGCCACAAAATATCTATAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
53650638 CTGGTG
1 CTGGTG
53650644 ACTCTGTCAC
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
27 22 0.43
28 22 0.43
29 7 0.14
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.33
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:53650654 original size:29 final size:28
Alignment explanation
Indices: 53650564--53650654 Score: 67
Period size: 27 Copynumber: 3.2 Consensus size: 28
53650554 CTGGTGGCTA
* * * * *
53650564 TGCCATAAATTATCTGTTCTGGTGGCCC
1 TGCCACAAAATATCTATTCTGGTGACAC
* * * *
53650592 TGCCGC-ATATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTATTCTGGTGACAC
*
53650619 TGCCACAAAATATCTATATCTGGTGACTC
1 TGCCACAAAATATCTAT-TCTGGTGACAC
*
53650648 TGTCACA
1 TGCCACA
53650655 TTTTCTGTAT
Statistics
Matches: 50, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
27 23 0.46
28 12 0.24
29 15 0.30
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (28 bp):
TGCCACAAAATATCTATTCTGGTGACAC
Found at i:53651757 original size:11 final size:10
Alignment explanation
Indices: 53651729--53651762 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
53651719 AGCCTGTAAG
53651729 TATTCTGAAT
1 TATTCTGAAT
*
53651739 TTTTCTGAAT
1 TATTCTGAAT
53651749 ATATTCTGAAT
1 -TATTCTGAAT
53651760 TAT
1 TAT
53651763 CTATCTGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (10 bp):
TATTCTGAAT
Found at i:53658285 original size:28 final size:28
Alignment explanation
Indices: 53658245--53658306 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
53658235 ATGTACTAGA
*
53658245 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
*
53658273 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
53658301 ATACCC
1 ATACCC
53658307 TTAGGGTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.34, C:0.27, G:0.08, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:53658515 original size:29 final size:28
Alignment explanation
Indices: 53658461--53658515 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 28
53658451 CCTGCCGCAT
*
53658461 ATATCTATTCTGGTGGCACTGCCACAAA
1 ATATCTATTCTGGTGACACTGCCACAAA
* * *
53658489 ATATCTGTATCTGGTGACTCTGTCACA
1 ATATCTAT-TCTGGTGACACTGCCACA
53658516 TTTTCTGTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 7 0.32
29 15 0.68
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (28 bp):
ATATCTATTCTGGTGACACTGCCACAAA
Found at i:53663754 original size:179 final size:179
Alignment explanation
Indices: 53663454--53663805 Score: 512
Period size: 179 Copynumber: 2.0 Consensus size: 179
53663444 TAAAAAACTC
* *
53663454 CAAATTAAGATCTGTTAATTTTCCTAGAAACTACACCCACATATATTCTTACCATAAAATTTTCA
1 CAAATTAAGATCTGCTAATTTTCCTAGAAACTAAACCCACATATATTCTTACCATAAAATTTTCA
* * **
53663519 GAATTTTTGGTTTATCCAATTAGTACAATTTATTCATTAAATTTACCCTTGTTTCACTATCCAAC
66 AAATTTTTGGTTTAGCCAATTAGTACAATTTATTCATTAAAGATACCCTTGTTTCACTATCCAAC
53663584 AGTTCCGACCTCTCTTCACTAAAAAATATTTATCTCATGGTACGGACTT
131 AGTTCCGACCTCTCTTCACTAAAAAATATTTATCTCATGGTACGGACTT
* * * *
53663633 CAAATTAAGAATC-GCTAATTTTTCC-AGAAACTAAACTCATATATATTCTTACCATTAACTTTT
1 CAAATTAAG-ATCTGCTAA-TTTTCCTAGAAACTAAACCCACATATATTCTTACCATAAAATTTT
* * *
53663696 CAAAATTTTTGGTTTAGCCAATTAGTATAGTTTATTCATTAAAGATACGCC-TGTTTCACTGTCC
64 CAAAATTTTTGGTTTAGCCAATTAGTACAATTTATTCATTAAAGATAC-CCTTGTTTCACTATCC
* * *
53663760 AACAGTTCCGATCTTTCTTCACTAAAAATTATTTATCTCATGGTAC
128 AACAGTTCCGACCTCTCTTCACTAAAAAATATTTATCTCATGGTAC
53663806 AGTTATTGGA
Statistics
Matches: 154, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
179 143 0.93
180 11 0.07
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (179 bp):
CAAATTAAGATCTGCTAATTTTCCTAGAAACTAAACCCACATATATTCTTACCATAAAATTTTCA
AAATTTTTGGTTTAGCCAATTAGTACAATTTATTCATTAAAGATACCCTTGTTTCACTATCCAAC
AGTTCCGACCTCTCTTCACTAAAAAATATTTATCTCATGGTACGGACTT
Found at i:53664431 original size:50 final size:50
Alignment explanation
Indices: 53664363--53664807 Score: 376
Period size: 50 Copynumber: 8.8 Consensus size: 50
53664353 ACCAAAGCTC
**
53664363 TCTGGTATGCATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
* * ** *
53664413 TCTGCTACACATAGTAGCCTACCACTTAGTACTACACACATGACTTATTC-A
1 TCTGGTACACATAGTAGCCT-GCACTTAGTACTACACATGTGACCTA-TCAA
* * * ** *
53664464 TCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGA-CCTA-TCAA
* * * * *
53664516 T-GGGTACGCATAGTAGCCTACATTTAGTACTACACATGCGACCTATCAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
* * * * *
53664565 TCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
* ** * * * * * *
53664615 TCTGATACATGTAGTAGCTTGCACTTAGTACTACACAAGTGATCGAACTA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
* * * ** *
53664665 TCAGGTACGCATACTAGCCTGCACTTAGTACTACACATGCAACCTAACAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
* ** *
53664715 TATGGTACATGTAGTAGCCTGCACTTAGTATTACACATGTGACCTA--AA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
* * * *
53664763 ACTGTCTTAAACACATAGTAGCCTACACATAGTACTACACATGTG
1 TCTG--GT--ACACATAGTAGCCTGCACTTAGTACTACACATGTG
53664808 TTCTCACAAT
Statistics
Matches: 313, Mismatches: 73, Indels: 16
0.78 0.18 0.04
Matches are distributed among these distances:
48 4 0.01
49 4 0.01
50 195 0.62
51 76 0.24
52 34 0.11
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.27
Consensus pattern (50 bp):
TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
Found at i:53664549 original size:101 final size:101
Alignment explanation
Indices: 53664374--53664651 Score: 296
Period size: 101 Copynumber: 2.8 Consensus size: 101
53664364 CTGGTATGCA
* * *
53664374 TAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTGCTACACATAGTAGCCTACCACT
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATCAATCGGCTACACATAGTAGCCTACCACT
* * *
53664439 TAGTACTACACACATGACTTATTC-ATCTGATACACG
66 TAGTACTACACACACGACCTA-TCAATCCGATACACG
* * * *
53664475 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTAAT-GGGTACGCATAGTAGCCTA-CA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TCAATCGGCTACACATAGTAGCCTACCA
* ** *
53664538 TTTAGTACTACACATGCGACCTATCAATCCGGTACACG
64 CTTAGTACTACACACACGACCTATCAATCCGATACACG
* * * ** **
53664576 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAA-CCATCTGATACATGTAGTAG-CTTGCAC
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATCAATCGGCTACACATAGTAGCCTACCAC
53664639 TTAGTACTACACA
65 TTAGTACTACACA
53664652 AGTGATCGAA
Statistics
Matches: 147, Mismatches: 24, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
99 4 0.03
100 28 0.19
101 93 0.63
102 18 0.12
103 4 0.03
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (101 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATCAATCGGCTACACATAGTAGCCTACCACT
TAGTACTACACACACGACCTATCAATCCGATACACG
Found at i:53671797 original size:26 final size:23
Alignment explanation
Indices: 53671749--53671806 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 23
53671739 TTGCTCCCCA
*
53671749 TCTTTTTCTCAATTTTCTATTCT
1 TCTTTTTCTCAATTTTCGATTCT
53671772 TCTTTCTTCTCAATATTTCGATTTCT
1 TCTTT-TTCTCAAT-TTTCGA-TTCT
*
53671798 TCTTGTTCT
1 TCTTTTTCT
53671807 GAGTTGGCCG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 5 0.17
24 8 0.27
25 9 0.30
26 8 0.27
ACGTcount: A:0.12, C:0.22, G:0.03, T:0.62
Consensus pattern (23 bp):
TCTTTTTCTCAATTTTCGATTCT
Found at i:53677966 original size:27 final size:26
Alignment explanation
Indices: 53677918--53677977 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
53677908 GCAAGGCTGT
*
53677918 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
53677945 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
53677971 CAGATAT
1 CAGATAT
53677978 ATATATATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:53679076 original size:27 final size:27
Alignment explanation
Indices: 53679055--53679203 Score: 154
Period size: 27 Copynumber: 5.4 Consensus size: 27
53679045 ACCCTGATTT
*
53679055 GTAAAATGACCGTATTACCCCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
* * *
53679082 ATAAAATGACCGTAATACCCTTATAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
*
53679109 GTAAAATGACTGTAATACCCCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
* * * *
53679136 GTAAAACGACCGTATTACCCCTTCCTTCAAG
1 GTAAAATGACCGTAATACCCC-T--GT-AGG
* **
53679167 GTAAAATGATCGTAATACCCCTGTATT
1 GTAAAATGACCGTAATACCCCTGTAGG
53679194 GTAAAATGAC
1 GTAAAATGAC
53679204 AATTATGTCG
Statistics
Matches: 98, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
27 74 0.76
28 2 0.02
30 2 0.02
31 20 0.20
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (27 bp):
GTAAAATGACCGTAATACCCCTGTAGG
Found at i:53679662 original size:33 final size:33
Alignment explanation
Indices: 53679614--53679712 Score: 137
Period size: 33 Copynumber: 3.0 Consensus size: 33
53679604 TTAGGCCTAC
*
53679614 ACTGCTACTGTATAGGGCTAGGGCCCAGATTGT
1 ACTGATACTGTATAGGGCTAGGGCCCAGATTGT
* * *
53679647 ACTGATACTGAATAGGGCTTA-AGCCCAGACTGT
1 ACTGATACTGTATAGGGC-TAGGGCCCAGATTGT
*
53679680 ACTGATACTGTATAGGGCTTGGGCCCAGATTGT
1 ACTGATACTGTATAGGGCTAGGGCCCAGATTGT
53679713 GTTATTCACT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
32 1 0.02
33 53 0.95
34 2 0.04
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (33 bp):
ACTGATACTGTATAGGGCTAGGGCCCAGATTGT
Found at i:53682011 original size:12 final size:12
Alignment explanation
Indices: 53681994--53682018 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53681984 AGTAGTCTCT
53681994 TATTTTGGTTTC
1 TATTTTGGTTTC
53682006 TATTTTGGTTTC
1 TATTTTGGTTTC
53682018 T
1 T
53682019 GGCATTGTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.16, T:0.68
Consensus pattern (12 bp):
TATTTTGGTTTC
Found at i:53683575 original size:27 final size:27
Alignment explanation
Indices: 53683545--53683633 Score: 92
Period size: 27 Copynumber: 3.3 Consensus size: 27
53683535 ACCCCAGTTT
*
53683545 GTAAAATGACTGTAATAC-CCGTATAGG
1 GTAAAATGACCGTAATACTCC-TATAGG
*
53683572 GTAAAATGACCGTAGTACTCCTATAGG
1 GTAAAATGACCGTAATACTCCTATAGG
* * * **
53683599 GTAAAATGATCATAATAC-CCTGTATT
1 GTAAAATGACCGTAATACTCCTATAGG
53683625 GTAAAATGA
1 GTAAAATGA
53683634 AGATTATGCC
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
26 14 0.26
27 37 0.70
28 2 0.04
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (27 bp):
GTAAAATGACCGTAATACTCCTATAGG
Found at i:53683832 original size:27 final size:27
Alignment explanation
Indices: 53683775--53683853 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
53683765 GGAAGTACTG
* * * *
53683775 TACTGGTGACTATGTCACAATCACTAT
1 TACTGGTGGCTATGCCACAATTACTAA
53683802 TACTGGTGGCTATGCCACAATTAC-AGA
1 TACTGGTGGCTATGCCACAATTACTA-A
* * *
53683829 TACTAGTGGCTTTGCCACATTTACT
1 TACTGGTGGCTATGCCACAATTACT
53683854 GTTTCTGGCA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
26 1 0.02
27 42 0.98
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.33
Consensus pattern (27 bp):
TACTGGTGGCTATGCCACAATTACTAA
Found at i:53684093 original size:33 final size:33
Alignment explanation
Indices: 53684045--53684143 Score: 101
Period size: 33 Copynumber: 3.0 Consensus size: 33
53684035 TTAGGCCTAC
* *
53684045 ACTGCTACTGTATAGGGCTAGGGCCCAGACTAT
1 ACTGATACTGAATAGGGCTAGGGCCCAGACTAT
* * *
53684078 ACTGATACTGAATAGGGCTTA-CGCCTAGACTGT
1 ACTGATACTGAATAGGGC-TAGGGCCCAGACTAT
* * * *
53684111 ACTGATATTGAATAAGTCTTGGGCCCAGACTAT
1 ACTGATACTGAATAGGGCTAGGGCCCAGACTAT
53684144 GTTATTCACT
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
32 1 0.02
33 49 0.94
34 2 0.04
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (33 bp):
ACTGATACTGAATAGGGCTAGGGCCCAGACTAT
Found at i:53690501 original size:27 final size:26
Alignment explanation
Indices: 53690453--53690512 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
53690443 GCGAGGCTGC
*
53690453 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
53690480 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
53690506 CAGATAT
1 CAGATAT
53690513 ATATATATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:53691277 original size:27 final size:27
Alignment explanation
Indices: 53691247--53691499 Score: 353
Period size: 27 Copynumber: 9.4 Consensus size: 27
53691237 TATCCCATGA
*
53691247 GGGTATCTCGGTAATTCTACCCTACAG
1 GGGTATTTCGGTAATTCTACCCTACAG
* *
53691274 GGGTATTTCAGTATTTCTACCCTACAG
1 GGGTATTTCGGTAATTCTACCCTACAG
*
53691301 GGGTATTTCGGTAATTCTACCATACAG
1 GGGTATTTCGGTAATTCTACCCTACAG
*
53691328 GGGTATTTCAGTAATTCTACCCTACAG
1 GGGTATTTCGGTAATTCTACCCTACAG
* * *
53691355 GGGTATTTCGATAATTCTACCTTACAA
1 GGGTATTTCGGTAATTCTACCCTACAG
* *
53691382 GGGTATTTTGGTAATTCTACCCTATAG
1 GGGTATTTCGGTAATTCTACCCTACAG
* *
53691409 GGGTATTTCGGTAATTCTACCTTACAA
1 GGGTATTTCGGTAATTCTACCCTACAG
** *
53691436 GGGTATTTTAGTAATTCTACCCTATAG
1 GGGTATTTCGGTAATTCTACCCTACAG
* *
53691463 GGGTATTTCGGTAATTCTACCTTATAG
1 GGGTATTTCGGTAATTCTACCCTACAG
53691490 GGGTATTTCG
1 GGGTATTTCG
53691500 AAAATTTTAA
Statistics
Matches: 197, Mismatches: 29, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 197 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.37
Consensus pattern (27 bp):
GGGTATTTCGGTAATTCTACCCTACAG
Found at i:53691532 original size:81 final size:80
Alignment explanation
Indices: 53691247--53691532 Score: 274
Period size: 81 Copynumber: 3.5 Consensus size: 80
53691237 TATCCCATGA
* * * * * *
53691247 GGGTATCTCGGTAATTCTACCCTACAGGGGTA-TTTCAGTATTTCTACCCTACAGGGGTATTTCG
1 GGGTATTTCGATAATTCTAACCT-TAGGGGTATTTTGA-TAATTCTACCCTACAGGGGTATTTCG
*
53691311 GTAATTCTACCATACAG
64 GTAATTCTACCATATAG
* * * * * *
53691328 GGGTATTTC-AGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCTTACAAGGGTATTTTG
1 GGGTATTTCGA-TAATTCTAACCT-TAGGGGTATTTTGATAATTCTACCCTACAGGGGTATTTCG
*
53691392 GTAATTCTACCCTATAG
64 GTAATTCTACCATATAG
* * *
53691409 GGGTATTTCGGTAATTCT-ACCTTACAAGGGTATTTT-AGTAATTCTACCCTATAGGGGTATTTC
1 GGGTATTTCGATAATTCTAACCTT--AGGGGTATTTTGA-TAATTCTACCCTACAGGGGTATTTC
*
53691472 GGTAATTCTACCTTATAG
63 GGTAATTCTACCATATAG
* * **
53691490 GGGTATTTCGAAAATTTTAAAAATTAGGGGTATTTTGATAATT
1 GGGTATTTCGATAATTCT-AACCTTAGGGGTATTTTGATAATT
53691533 TTACAAACCA
Statistics
Matches: 170, Mismatches: 26, Indels: 18
0.79 0.12 0.08
Matches are distributed among these distances:
80 4 0.02
81 159 0.94
82 4 0.02
83 3 0.02
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.37
Consensus pattern (80 bp):
GGGTATTTCGATAATTCTAACCTTAGGGGTATTTTGATAATTCTACCCTACAGGGGTATTTCGGT
AATTCTACCATATAG
Found at i:53691548 original size:27 final size:27
Alignment explanation
Indices: 53691491--53691561 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
53691481 ACCTTATAGG
* * ** *
53691491 GGTATTTCGAAAATTTTAAAAATTAGG
1 GGTATTTTGATAATTTTAAAAACCAGA
*
53691518 GGTATTTTGATAATTTTACAAACCAGA
1 GGTATTTTGATAATTTTAAAAACCAGA
*
53691545 GGTATTTTGGTAATTTT
1 GGTATTTTGATAATTTT
53691562 GCTAATCGAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.42
Consensus pattern (27 bp):
GGTATTTTGATAATTTTAAAAACCAGA
Found at i:53691574 original size:27 final size:27
Alignment explanation
Indices: 53691518--53691614 Score: 106
Period size: 27 Copynumber: 3.6 Consensus size: 27
53691508 AAAAATTAGG
* * *
53691518 GGTATTTTGATAATTTTAC-AAACCAGA
1 GGTATTTTGGTAATTTTACTAATCGA-A
*
53691545 GGTATTTTGGTAATTTTGCTAATCGAA
1 GGTATTTTGGTAATTTTACTAATCGAA
* * * *
53691572 GGTATTTTGGTACTTTTTCTAATTGAG
1 GGTATTTTGGTAATTTTACTAATCGAA
53691599 GGTATTTTGGTAATTT
1 GGTATTTTGGTAATTT
53691615 GGTAAACTAA
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
27 56 0.93
28 4 0.07
ACGTcount: A:0.26, C:0.07, G:0.21, T:0.46
Consensus pattern (27 bp):
GGTATTTTGGTAATTTTACTAATCGAA
Found at i:53710452 original size:46 final size:46
Alignment explanation
Indices: 53710399--53710489 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
53710389 TATATATACA
* * *
53710399 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATCTCACATTAACCATTCGGCTTTACCACATATC
* * *
53710445 CATCTCATACACATTTCGCATTAACCATTCGGCTTTCCCACATAT
1 CATCTCATACACATCTCACATTAACCATTCGGCTTTACCACATAT
53710490 ATACACTTCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.27, C:0.32, G:0.07, T:0.34
Consensus pattern (46 bp):
CATCTCATACACATCTCACATTAACCATTCGGCTTTACCACATATC
Found at i:53710532 original size:22 final size:22
Alignment explanation
Indices: 53710506--53710675 Score: 70
Period size: 23 Copynumber: 7.3 Consensus size: 22
53710496 TTCCACGTTC
53710506 ATCACATTGGCCATTCTGCCTT
1 ATCACATTGGCCATTCTGCCTT
*
53710528 ATCACATATATG-CATGT-T-CACATTT
1 ATCACAT-T-GGCCAT-TCTGC-C--TT
*
53710553 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCTGCCTT
53710575 ATCACATATGTG-CATGT-T-CACATT
1 ATCACAT-TG-GCCAT-TCTGC-C-TT
*
53710599 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCTGCCTT
*
53710622 ATCACACATTTG-CATGT-T-CACATT
1 AT--CACATTGGCCAT-TCTGC-C-TT
*
53710646 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCTGCCTT
53710669 ATCACAT
1 ATCACAT
53710676 ATATGCATGT
Statistics
Matches: 112, Mismatches: 9, Indels: 54
0.64 0.05 0.31
Matches are distributed among these distances:
22 28 0.25
23 32 0.29
24 31 0.28
25 21 0.19
ACGTcount: A:0.24, C:0.28, G:0.13, T:0.35
Consensus pattern (22 bp):
ATCACATTGGCCATTCTGCCTT
Found at i:53710534 original size:47 final size:47
Alignment explanation
Indices: 53710503--53710748 Score: 420
Period size: 47 Copynumber: 5.2 Consensus size: 47
53710493 CACTTCCACG
*
53710503 TTCATCACATTGGCCATTCTGCCTTATCACATATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
* *
53710550 TTTATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
* *
53710597 TTCATCACATTGGCCATTCGGCCTTATCACACATTTGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
53710644 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
* * *
53710691 TTCATCACATCGGCCATTCGGCCTTATCACATATGTACATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
53710738 TTCATCACATT
1 TTCATCACATT
53710749 AAATCCTAAA
Statistics
Matches: 187, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 187 1.00
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.35
Consensus pattern (47 bp):
TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
Found at i:53713065 original size:13 final size:13
Alignment explanation
Indices: 53713047--53713072 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53713037 ATTTTTATTT
53713047 TTAACATAAAATA
1 TTAACATAAAATA
53713060 TTAACATAAAATA
1 TTAACATAAAATA
53713073 ATTATATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAACATAAAATA
Found at i:53730171 original size:28 final size:28
Alignment explanation
Indices: 53730126--53730187 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
53730116 CAATATTAGT
* * * * *
53730126 ACAGTTTGGGCCTTAGCCCTATACAGTA
1 ACAGTATGGACCTAAGCCCAATAAAGTA
53730154 ACAGTATGGACCTAAGCCCAATAAAGTA
1 ACAGTATGGACCTAAGCCCAATAAAGTA
*
53730182 TCAGTA
1 ACAGTA
53730188 CAGTGTAATG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (28 bp):
ACAGTATGGACCTAAGCCCAATAAAGTA
Found at i:53730375 original size:27 final size:27
Alignment explanation
Indices: 53730342--53730423 Score: 92
Period size: 27 Copynumber: 3.0 Consensus size: 27
53730332 AGTTGCCAAA
*
53730342 AACAGTAAATGTGGCAAAGTCACCAGT
1 AACAGTAAATGTGGCATAGTCACCAGT
** * *
53730369 ATTAGTAATTGTGGCATAGCCACCAGT
1 AACAGTAAATGTGGCATAGTCACCAGT
* * *
53730396 AACACTGAATGTGACATAGTCACCAGT
1 AACAGTAAATGTGGCATAGTCACCAGT
53730423 A
1 A
53730424 CAATACTTCC
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.23
Consensus pattern (27 bp):
AACAGTAAATGTGGCATAGTCACCAGT
Found at i:53730594 original size:27 final size:27
Alignment explanation
Indices: 53730564--53730626 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
53730554 GGGCATAATC
53730564 GTCATTTTACCATATAAAGGTATTACG
1 GTCATTTTACCATATAAAGGTATTACG
* **
53730591 GTCATTTTACCCTATAGGGGTATTACG
1 GTCATTTTACCATATAAAGGTATTACG
53730618 GTCATTTTA
1 GTCATTTTA
53730627 TGTATTTTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (27 bp):
GTCATTTTACCATATAAAGGTATTACG
Found at i:53733236 original size:29 final size:29
Alignment explanation
Indices: 53733175--53733251 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 29
53733165 CACATACCTG
* *
53733175 TATATGGTCTACTAGGCCC-AATCACATT
1 TATATGGACCACTAGGCCCAAATCACATT
*
53733203 TATATGGCCCACTAGGCCCAAATCACATT
1 TATATGGACCACTAGGCCCAAATCACATT
53733232 TATATGGACCATCT-GGCCCA
1 TATATGGACCA-CTAGGCCCA
53733252 TTAAGTCTGT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 17 0.39
29 25 0.57
30 2 0.05
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (29 bp):
TATATGGACCACTAGGCCCAAATCACATT
Found at i:53739994 original size:20 final size:18
Alignment explanation
Indices: 53739960--53739996 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
53739950 GCAACTCATA
53739960 ATTTCAACTATTTTACAC
1 ATTTCAACTATTTTACAC
53739978 ATTTACAACTCATTTTACA
1 ATTT-CAACT-ATTTTACA
53739997 ACTTAGCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTTCAACTATTTTACAC
Found at i:53745535 original size:13 final size:13
Alignment explanation
Indices: 53745517--53745545 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
53745507 GGTTGTTTAT
53745517 TAAACTAATTAAC
1 TAAACTAATTAAC
53745530 TAAACTAATTAAC
1 TAAACTAATTAAC
53745543 TAA
1 TAA
53745546 TTAAACTAAA
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:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:53748911 original size:13 final size:12
Alignment explanation
Indices: 53748890--53748926 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
53748880 GCCAATTAAA
53748890 ACCAAAAAAATT
1 ACCAAAAAAATT
*
53748902 AGCAAAAAAATT
1 ACCAAAAAAATT
53748914 ACCAAAATAAATT
1 ACCAAAA-AAATT
53748927 CTAATGTCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 17 0.77
13 5 0.23
ACGTcount: A:0.65, C:0.14, G:0.03, T:0.19
Consensus pattern (12 bp):
ACCAAAAAAATT
Found at i:53751325 original size:17 final size:18
Alignment explanation
Indices: 53751292--53751326 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
53751282 TTTTAAGAAG
53751292 GGTTTTCAATGAAAACAC
1 GGTTTTCAATGAAAACAC
*
53751310 GGTTTTCACT-AAAACAC
1 GGTTTTCAATGAAAACAC
53751327 TTCAATATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (18 bp):
GGTTTTCAATGAAAACAC
Found at i:53757422 original size:15 final size:15
Alignment explanation
Indices: 53757383--53757462 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
53757373 GTATCTTGGG
*
53757383 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
53757398 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
* *
53757413 TTTCTTTATTCCGGG
1 TTTCTTTATTCTGGA
*
53757428 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
53757443 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
53757457 TTTCTT
1 TTTCTT
53757463 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
14 10 0.19
15 41 0.77
16 2 0.04
ACGTcount: A:0.10, C:0.19, G:0.14, T:0.57
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:53757452 original size:30 final size:30
Alignment explanation
Indices: 53757374--53757461 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
53757364 CATAGTATCG
* * *
53757374 TATCTTGGGTTTCTTTA-TCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCC-GGATTTCTC
*
53757404 TAT-TCTGGATTTCTTTATTCCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCCGGATTTCTC
*
53757434 TATCTTGGATTTCTTTATT-CGGTTTTCT
1 TATCTTGGATTTCTTTATTCCGGATTTCT
53757462 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
29 9 0.18
30 37 0.74
31 4 0.08
ACGTcount: A:0.10, C:0.18, G:0.16, T:0.56
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCCGGATTTCTC
Found at i:53759887 original size:46 final size:45
Alignment explanation
Indices: 53759834--53760008 Score: 192
Period size: 46 Copynumber: 3.8 Consensus size: 45
53759824 TATTTGGGCA
*
53759834 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGC
*** * * *
53759879 GTCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGGC
1 -TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGA-GC
* *
53759926 ATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC
1 -TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGC
* *
53759972 TCCAGAGCTCGTTGAGTTGAGTCTGAGTTCAC-TATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
53760009 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 17, Indels: 9
0.81 0.13 0.07
Matches are distributed among these distances:
45 8 0.07
46 63 0.58
47 37 0.34
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGC
Found at i:53759989 original size:93 final size:93
Alignment explanation
Indices: 53759830--53760001 Score: 283
Period size: 93 Copynumber: 1.8 Consensus size: 93
53759820 GGGATATTTG
*
53759830 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
53759895 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * *
53759923 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC-TCCAGAGCTCGTTGA
1 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGA
*
53759987 GTTGAGTCTGAGTTC
65 GTTGAGTCCGAGTTC
53760002 ACTATGGGCG
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 3 0.04
93 70 0.96
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:53761395 original size:48 final size:47
Alignment explanation
Indices: 53761309--53761497 Score: 193
Period size: 48 Copynumber: 4.0 Consensus size: 47
53761299 TGGGGCGTTA
*
53761309 CATGATATGAGAGCCA-TGTAAGACCATGTTTGGAACATGGCATCAG
1 CATGACATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCAG
*** *
53761355 CGATGTTTTGAGAGCCAGTGTAAGACCATGTCTTGG-ACATGGCATTAG
1 C-ATGACATGAGAGCCAGTGTAAGACCATGT-TTGGAACATGGCATCAG
* * * * * * * *
53761403 CATTGAGATGAGAGCTAGTTTAAGACCATGTCTGGGATATGGCAACGG
1 CA-TGACATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCAG
* *
53761451 CCTCGACATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCA
1 CAT-GACATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCA
53761498 ACAATTTACC
Statistics
Matches: 114, Mismatches: 23, Indels: 10
0.78 0.16 0.07
Matches are distributed among these distances:
46 1 0.01
47 18 0.16
48 91 0.80
49 4 0.04
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (47 bp):
CATGACATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCAG
Found at i:53767275 original size:42 final size:43
Alignment explanation
Indices: 53767170--53767326 Score: 131
Period size: 43 Copynumber: 3.7 Consensus size: 43
53767160 TGTGTTATCG
** * * * *
53767170 TGTAAGAGTACGTTTGGGACGTTGGCATCGATTTGA-GATTTACA
1 TGTAAGACCACGTCTGGGACATTGGCATCGATAT-ATGA-TTACC
* * * * *
53767214 TGTAAAACAATGTCTGGGACATTGGCATC-ATATATGATTTCG
1 TGTAAGACCACGTCTGGGACATTGGCATCGATATATGATTACC
* * * *
53767256 TGTAAGACC-CTGTTTGGGACAGTGGCATCGATGTTTGATTACC
1 TGTAAGACCAC-GTCTGGGACATTGGCATCGATATATGATTACC
53767299 TGTAAGACCACGTCTGGGACATTGGCAT
1 TGTAAGACCACGTCTGGGACATTGGCAT
53767327 TGTACGAGCT
Statistics
Matches: 89, Mismatches: 20, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
42 27 0.30
43 38 0.43
44 24 0.27
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACATTGGCATCGATATATGATTACC
Found at i:53772451 original size:48 final size:48
Alignment explanation
Indices: 53772390--53772707 Score: 293
Period size: 48 Copynumber: 6.6 Consensus size: 48
53772380 ATATGTGTGA
* * **
53772390 CAGTGTAAGACCATGTCTAGGACATGGCGTCAACCACAATATGAGAGC
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACAATATGAGAGC
* * * *** *
53772438 CAGTGTAAGACCATGTTTGGAACATGGCATCGGCGATGTTGTGAGAGC
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACAATATGAGAGC
* ** * *
53772486 CAGTATAAGACCATGT-TCGGGACATGGCATCGG-CATTGATA-CATGCGC
1 CAGTGTAAGACCATGTCT-GGGACATGGCATCGGCCA-CAATATGA-GAGC
* * *
53772534 TAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGATC
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACAATATGAGAGC
* ** *
53772582 CAGTGTAAGACCATGTCTAGGACATGGCATCGG-CATTGAGATGAGAGC
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCCA-CAATATGAGAGC
* * * * *
53772630 TAGTGTAAGACCATGTCTGGGACATGGCATTGGCCTCAACATGTGAGC
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACAATATGAGAGC
* * *
53772678 CAGTGTAATACCATGTTTGGAACATGGCAT
1 CAGTGTAAGACCATGTCTGGGACATGGCAT
53772708 TAGCAATTCA
Statistics
Matches: 217, Mismatches: 45, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
47 5 0.02
48 207 0.95
49 5 0.02
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (48 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACAATATGAGAGC
Found at i:53772639 original size:144 final size:144
Alignment explanation
Indices: 53772391--53772659 Score: 384
Period size: 144 Copynumber: 1.9 Consensus size: 144
53772381 TATGTGTGAC
* *
53772391 AGTGTAAGACCATGTCTAGGACATGGCGTCAACCACAATATGAGAGCCAGTGTAAGACCATGTTT
1 AGTGTAAGACCATGTCTAGGACATGGCATCAACCACAATATGAGAGCCAGTGTAAGACCATGTTA
*
53772456 GGAACATGGCATCGGCGATGTTGTGAGAGCCAGTATAAGACCATGT-TCGGGACATGGCATCGGC
66 GGAACATGGCATCGGCGATGTAGTGAGAGCCAGTATAAGACCATGTCT-GGGACATGGCATCGGC
53772520 ATTGATACATGCGCT
130 ATTGATACATGCGCT
* ** * *
53772535 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGATCCAGTGTAAGACCATGTCT
1 AGTGTAAGACCATGTCTAGGACATGGCATCAACCACAATATGAGAGCCAGTGTAAGACCATGT-T
* *
53772600 AGG-ACATGGCATCGGC-AT-TGAGATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCAT
65 AGGAACATGGCATCGGCGATGT-AG-TGAGAGCCAGTATAAGACCATGTCTGGGACATGGCAT
53772660 TGGCCTCAAC
Statistics
Matches: 111, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
142 1 0.01
143 3 0.03
144 103 0.93
145 4 0.04
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (144 bp):
AGTGTAAGACCATGTCTAGGACATGGCATCAACCACAATATGAGAGCCAGTGTAAGACCATGTTA
GGAACATGGCATCGGCGATGTAGTGAGAGCCAGTATAAGACCATGTCTGGGACATGGCATCGGCA
TTGATACATGCGCT
Found at i:53772683 original size:144 final size:144
Alignment explanation
Indices: 53772390--53772707 Score: 378
Period size: 144 Copynumber: 2.2 Consensus size: 144
53772380 ATATGTGTGA
* *
53772390 CAGTGTAAGACCATGTCTAGGACATGGCGTCAACCACAATATGAGAGCCAGTGTAAGACCATGTT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCAACCACAATATGAGAGCCAGTGTAAGACCATGTT
* *
53772455 TGGAACATGGCATCGGCGATGTTGTGAGAGCCAGTATAAGACCATGTTCGGGACATGGCATCGGC
66 AGGAACATGGCATCGGCGATGTAGTGAGAGCCAGTATAAGACCATGTTCGGGACATGGCATCGGC
* * *
53772520 ATTGATACATGCGC
131 ACTCATACATGAGC
* ** * *
53772534 TAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGATCCAGTGTAAGACCATGTC
1 CAGTGTAAGACCATGTCTGGGACATGGCATCAACCACAATATGAGAGCCAGTGTAAGACCATGT-
* *
53772599 TAGG-ACATGGCATCGGC-AT-TGAGATGAGAGCTAGTGTAAGACCATG-TCTGGGACATGGCAT
65 TAGGAACATGGCATCGGCGATGT-AG-TGAGAGCCAGTATAAGACCATGTTC-GGGACATGGCAT
*
53772660 TGGC-CTCA-ACATGTGAGC
127 CGGCACTCATACA--TGAGC
* * *
53772678 CAGTGTAATACCATGTTTGGAACATGGCAT
1 CAGTGTAAGACCATGTCTGGGACATGGCAT
53772708 TAGCAATTCA
Statistics
Matches: 149, Mismatches: 19, Indels: 12
0.83 0.11 0.07
Matches are distributed among these distances:
142 4 0.03
143 7 0.05
144 135 0.91
145 3 0.02
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (144 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCAACCACAATATGAGAGCCAGTGTAAGACCATGTT
AGGAACATGGCATCGGCGATGTAGTGAGAGCCAGTATAAGACCATGTTCGGGACATGGCATCGGC
ACTCATACATGAGC
Found at i:53776272 original size:47 final size:49
Alignment explanation
Indices: 53776068--53776432 Score: 226
Period size: 47 Copynumber: 7.7 Consensus size: 49
53776058 GTTAAGTTGT
* * * *
53776068 CGATGCCATGTCCCAGACATTATCTTACACTGGCTATCTTCATCGAGGT
1 CGATGCCATGTCCCAGACATTGTCTTACACTGGCTATCATCGTCGAGGC
* * * * **
53776117 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGT-GTATACGTGC
1 CGATGCCATGTCCCAGACATTGTCTTACACTGGCTATCATCGTCGA-G-GC
* * * *
53776167 TGATG-CATGTCCCAGACA-TGTCTTACACTAGC-A-CGA-AG-CTTA-GC
1 CGATGCCATGTCCCAGACATTGTCTTACACTGGCTATC-ATCGTC-GAGGC
* *
53776211 CAATG-CATGTCCCAGACA-CGTCTTACACTGGCTATCATCGTCGAGGC
1 CGATGCCATGTCCCAGACATTGTCTTACACTGGCTATCATCGTCGAGGC
* * *
53776258 CGATG-CATGTCCCAGACA-TGTCTTACACTGGC-ACTCCTC-TCTACGC
1 CGATGCCATGTCCCAGACATTGTCTTACACTGGCTA-TCATCGTCGAGGC
* * * * ** * *
53776304 TGATGCCATGTCCTAGATATGGTCTTACACTGGCTATCATAAT-GTGGT
1 CGATGCCATGTCCCAGACATTGTCTTACACTGGCTATCATCGTCGAGGC
* * * ** * *
53776352 TGAT-ACATGTCCCAGACA-TGTCTTACACTAGCCCTCATC-TCAATGC
1 CGATGCCATGTCCCAGACATTGTCTTACACTGGCTATCATCGTCGAGGC
* * *
53776398 CGAGGCCATGTCCCAGACATGGTCTTACATTGGCT
1 CGATGCCATGTCCCAGACATTGTCTTACACTGGCT
53776433 CTCACATAAC
Statistics
Matches: 244, Mismatches: 54, Indels: 37
0.73 0.16 0.11
Matches are distributed among these distances:
44 30 0.12
45 3 0.01
46 33 0.14
47 75 0.31
48 47 0.19
49 51 0.21
50 5 0.02
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (49 bp):
CGATGCCATGTCCCAGACATTGTCTTACACTGGCTATCATCGTCGAGGC
Found at i:53776361 original size:141 final size:138
Alignment explanation
Indices: 53776074--53776431 Score: 364
Period size: 141 Copynumber: 2.5 Consensus size: 138
53776064 TTGTCGATGC
* * *
53776074 CATGTCCCAGACATTATCTTACACTGGCTATCTTCATCGAGGTCGATGCCATGTCCCAGACATGG
1 CATGTCCCAGACA-TGTCTTACACTGGCTATCATC-TCGAGGCCGATGCCATGTCCCAGACATGG
* * * *
53776139 TCTTACACTAGCTCTCGTGTATACGTGCTGATGCATGTCCCAGACATGTCTTACACTAGCACGAA
64 TCTTACACTGGCACTCCTCTATACG-GCTGATGCATGTCCCAGACATGTCTTACACTAGCACGAA
*
53776204 GCTTAGCCAATG
128 GC-TAGCCAATA
*
53776216 CATGTCCCAGACACGTCTTACACTGGCTATCATCGTCGAGGCCGATG-CATGTCCCAGACAT-GT
1 CATGTCCCAGACATGTCTTACACTGGCTATCATC-TCGAGGCCGATGCCATGTCCCAGACATGGT
* * * *
53776279 CTTACACTGGCACTCCTCTCTAC-GCTGATGCCATGTCCTAGATATGGTCTTACACTGGCTATCA
65 CTTACACTGGCACTCCTCTATACGGCTGATG-CATGTCCCAGACAT-GTCTTACACTAGC-A-C-
* * ***
53776343 TAATG-TGGTTGATA
125 GAA-GCTAGCCAATA
* ** * * *
53776357 CATGTCCCAGACATGTCTTACACTAGCCCTCATCTCAATGCCGAGGCCATGTCCCAGACATGGTC
1 CATGTCCCAGACATGTCTTACACTGGCTATCATCTCGAGGCCGATGCCATGTCCCAGACATGGTC
*
53776422 TTACATTGGC
66 TTACACTGGC
53776432 TCTCACATAA
Statistics
Matches: 181, Mismatches: 27, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
137 7 0.04
138 12 0.07
139 32 0.18
140 24 0.13
141 78 0.43
142 27 0.15
143 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (138 bp):
CATGTCCCAGACATGTCTTACACTGGCTATCATCTCGAGGCCGATGCCATGTCCCAGACATGGTC
TTACACTGGCACTCCTCTATACGGCTGATGCATGTCCCAGACATGTCTTACACTAGCACGAAGCT
AGCCAATA
Found at i:53776377 original size:94 final size:93
Alignment explanation
Indices: 53776117--53776432 Score: 334
Period size: 94 Copynumber: 3.4 Consensus size: 93
53776107 TCATCGAGGT
* * * *
53776117 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTGTATACGT-GCTGATGCATGTCCCA
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTATC--ATA-ATGTGGCTGATGCATGTCCCA
** *
53776181 GACATGTCTTACACTAGCACGAAGCT-TAGC
63 GACATGTCTTACACTAGCACTCATCTCTAGC
* * ** * *
53776211 CAATG-CATGTCCCAGACA-CGTCTTACACTGGCTATCATCGTCGAGGCCGATGCATGTCCCAGA
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATAAT-GTGGCTGATGCATGTCCCAGA
* *
53776274 CATGTCTTACACTGGCACTCCTCTCTACGC
65 CATGTCTTACACTAGCACTCATCTCTA-GC
* * * * *
53776304 TGATGCCATGTCCTAGATATGGTCTTACACTGGCTATCATAATGTGGTTGATACATGTCCCAGAC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATAATGTGGCTGATGCATGTCCCAGAC
* *
53776369 ATGTCTTACACTAGCCCTCATCTCAATGC
66 ATGTCTTACACTAGCACTCATCTCTA-GC
* *
53776398 CGAGGCCATGTCCCAGACATGGTCTTACATTGGCT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCT
53776433 CTCACATAAC
Statistics
Matches: 180, Mismatches: 36, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
90 2 0.01
91 36 0.20
92 17 0.09
93 18 0.10
94 87 0.48
95 20 0.11
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (93 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATAATGTGGCTGATGCATGTCCCAGAC
ATGTCTTACACTAGCACTCATCTCTAGC
Found at i:53783746 original size:47 final size:49
Alignment explanation
Indices: 53783542--53783906 Score: 226
Period size: 47 Copynumber: 7.7 Consensus size: 49
53783532 GTTAAGTTGT
* * * *
53783542 CGATGCCATGTCCCAGACATTATCTTACACTGGCTATCTTCATCGAGGT
1 CGATGCCATGTCCCAGACATTGTCTTACACTGGCTATCATCGTCGAGGC
* * * * **
53783591 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGT-GTATACGTGC
1 CGATGCCATGTCCCAGACATTGTCTTACACTGGCTATCATCGTCGA-G-GC
* * * *
53783641 TGATG-CATGTCCCAGACA-TGTCTTACACTAGC-A-CGA-AG-CTTA-GC
1 CGATGCCATGTCCCAGACATTGTCTTACACTGGCTATC-ATCGTC-GAGGC
* *
53783685 CAATG-CATGTCCCAGACA-CGTCTTACACTGGCTATCATCGTCGAGGC
1 CGATGCCATGTCCCAGACATTGTCTTACACTGGCTATCATCGTCGAGGC
* * *
53783732 CGATG-CATGTCCCAGACA-TGTCTTACACTGGC-ACTCCTC-TCTACGC
1 CGATGCCATGTCCCAGACATTGTCTTACACTGGCTA-TCATCGTCGAGGC
* * * * ** * *
53783778 TGATGCCATGTCCTAGATATGGTCTTACACTGGCTATCATAAT-GTGGT
1 CGATGCCATGTCCCAGACATTGTCTTACACTGGCTATCATCGTCGAGGC
* * * ** * *
53783826 TGAT-ACATGTCCCAGACA-TGTCTTACACTAGCCCTCATC-TCAATGC
1 CGATGCCATGTCCCAGACATTGTCTTACACTGGCTATCATCGTCGAGGC
* * *
53783872 CGAGGCCATGTCCCAGACATGGTCTTACATTGGCT
1 CGATGCCATGTCCCAGACATTGTCTTACACTGGCT
53783907 CTCACATAAC
Statistics
Matches: 244, Mismatches: 54, Indels: 37
0.73 0.16 0.11
Matches are distributed among these distances:
44 30 0.12
45 3 0.01
46 33 0.14
47 75 0.31
48 47 0.19
49 51 0.21
50 5 0.02
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (49 bp):
CGATGCCATGTCCCAGACATTGTCTTACACTGGCTATCATCGTCGAGGC
Found at i:53783835 original size:141 final size:138
Alignment explanation
Indices: 53783548--53783905 Score: 364
Period size: 141 Copynumber: 2.5 Consensus size: 138
53783538 TTGTCGATGC
* * *
53783548 CATGTCCCAGACATTATCTTACACTGGCTATCTTCATCGAGGTCGATGCCATGTCCCAGACATGG
1 CATGTCCCAGACA-TGTCTTACACTGGCTATCATC-TCGAGGCCGATGCCATGTCCCAGACATGG
* * * *
53783613 TCTTACACTAGCTCTCGTGTATACGTGCTGATGCATGTCCCAGACATGTCTTACACTAGCACGAA
64 TCTTACACTGGCACTCCTCTATACG-GCTGATGCATGTCCCAGACATGTCTTACACTAGCACGAA
*
53783678 GCTTAGCCAATG
128 GC-TAGCCAATA
*
53783690 CATGTCCCAGACACGTCTTACACTGGCTATCATCGTCGAGGCCGATG-CATGTCCCAGACAT-GT
1 CATGTCCCAGACATGTCTTACACTGGCTATCATC-TCGAGGCCGATGCCATGTCCCAGACATGGT
* * * *
53783753 CTTACACTGGCACTCCTCTCTAC-GCTGATGCCATGTCCTAGATATGGTCTTACACTGGCTATCA
65 CTTACACTGGCACTCCTCTATACGGCTGATG-CATGTCCCAGACAT-GTCTTACACTAGC-A-C-
* * ***
53783817 TAATG-TGGTTGATA
125 GAA-GCTAGCCAATA
* ** * * *
53783831 CATGTCCCAGACATGTCTTACACTAGCCCTCATCTCAATGCCGAGGCCATGTCCCAGACATGGTC
1 CATGTCCCAGACATGTCTTACACTGGCTATCATCTCGAGGCCGATGCCATGTCCCAGACATGGTC
*
53783896 TTACATTGGC
66 TTACACTGGC
53783906 TCTCACATAA
Statistics
Matches: 181, Mismatches: 27, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
137 7 0.04
138 12 0.07
139 32 0.18
140 24 0.13
141 78 0.43
142 27 0.15
143 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (138 bp):
CATGTCCCAGACATGTCTTACACTGGCTATCATCTCGAGGCCGATGCCATGTCCCAGACATGGTC
TTACACTGGCACTCCTCTATACGGCTGATGCATGTCCCAGACATGTCTTACACTAGCACGAAGCT
AGCCAATA
Found at i:53783851 original size:94 final size:93
Alignment explanation
Indices: 53783591--53783906 Score: 334
Period size: 94 Copynumber: 3.4 Consensus size: 93
53783581 TCATCGAGGT
* * * *
53783591 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTGTATACGT-GCTGATGCATGTCCCA
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTATC--ATA-ATGTGGCTGATGCATGTCCCA
** *
53783655 GACATGTCTTACACTAGCACGAAGCT-TAGC
63 GACATGTCTTACACTAGCACTCATCTCTAGC
* * ** * *
53783685 CAATG-CATGTCCCAGACA-CGTCTTACACTGGCTATCATCGTCGAGGCCGATGCATGTCCCAGA
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATAAT-GTGGCTGATGCATGTCCCAGA
* *
53783748 CATGTCTTACACTGGCACTCCTCTCTACGC
65 CATGTCTTACACTAGCACTCATCTCTA-GC
* * * * *
53783778 TGATGCCATGTCCTAGATATGGTCTTACACTGGCTATCATAATGTGGTTGATACATGTCCCAGAC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATAATGTGGCTGATGCATGTCCCAGAC
* *
53783843 ATGTCTTACACTAGCCCTCATCTCAATGC
66 ATGTCTTACACTAGCACTCATCTCTA-GC
* *
53783872 CGAGGCCATGTCCCAGACATGGTCTTACATTGGCT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCT
53783907 CTCACATAAC
Statistics
Matches: 180, Mismatches: 36, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
90 2 0.01
91 36 0.20
92 17 0.09
93 18 0.10
94 87 0.48
95 20 0.11
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (93 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATAATGTGGCTGATGCATGTCCCAGAC
ATGTCTTACACTAGCACTCATCTCTAGC
Found at i:53789394 original size:27 final size:27
Alignment explanation
Indices: 53789341--53789550 Score: 143
Period size: 27 Copynumber: 7.7 Consensus size: 27
53789331 TTTCATCCTA
* * * * *
53789341 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTCGGTAATTTTATAAAC
* *
53789368 CAAGGGTATTTCAGTAATTTTGTAAAC
1 CAAGGGTATTTCGGTAATTTTATAAAC
* ** * *
53789395 CAATGGTATTTCTATAATTTTTAGAAAGT
1 CAAGGGTATTTCGGTAA-TTTTATAAA-C
* * *
53789424 CAAGGGTATTTCTGTAATTTTGTAAAT
1 CAAGGGTATTTCGGTAATTTTATAAAC
* * * *
53789451 CAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTCGGTAATTTTATAAAC
** * *
53789478 TGAGGGTATTTCGGTAATTTCACAAAC
1 CAAGGGTATTTCGGTAATTTTATAAAC
*
53789505 C-AGTGGTATTTTGGTAATTTTATAAAC
1 CAAG-GGTATTTCGGTAATTTTATAAAC
* * *
53789532 TAGGGGTATTTTGGTAATT
1 CAAGGGTATTTCGGTAATT
53789551 CTACCCTATC
Statistics
Matches: 145, Mismatches: 34, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
26 2 0.01
27 113 0.78
28 15 0.10
29 15 0.10
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.40
Consensus pattern (27 bp):
CAAGGGTATTTCGGTAATTTTATAAAC
Found at i:53789469 original size:56 final size:55
Alignment explanation
Indices: 53789361--53789525 Score: 181
Period size: 54 Copynumber: 3.0 Consensus size: 55
53789351 TTGGTAAATC
* * *
53789361 TACAAACCAAGGGTATTTCAGTAATTTTGTAAACCAATGGTATTTCT-ATAATTTT
1 TACAAATCAAGGGTATTTCAGTAATTTTGTAAACCAGTGGTATTT-TGGTAATTTT
* * * *
53789416 TAGAAAGTCAAGGGTATTTCTGTAATTTTGTAAATCAGGGGTATTTTGGTAA-TTT
1 TACAAA-TCAAGGGTATTTCAGTAATTTTGTAAACCAGTGGTATTTTGGTAATTTT
** * ***
53789471 TACAAATTGAGGGTATTTCGGTAATTTCACAAACCAGTGGTATTTTGGTAATTTT
1 TACAAATCAAGGGTATTTCAGTAATTTTGTAAACCAGTGGTATTTTGGTAATTTT
53789526 ATAAACTAGG
Statistics
Matches: 91, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
54 37 0.41
55 17 0.19
56 37 0.41
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.41
Consensus pattern (55 bp):
TACAAATCAAGGGTATTTCAGTAATTTTGTAAACCAGTGGTATTTTGGTAATTTT
Found at i:53789544 original size:81 final size:81
Alignment explanation
Indices: 53789428--53789583 Score: 210
Period size: 81 Copynumber: 1.9 Consensus size: 81
53789418 GAAAGTCAAG
* * * *
53789428 GGTATTTCTGTAATTTTGTAAATCAGGGGTATTTTGGTAATTTTA-CAAATTGAGGGTATTTCGG
1 GGTATTTCTGTAATTTTATAAATCAGGGGTATTTTGGTAATTCTACCAAATCG-GGGTATTTCAG
53789492 TAATTTCACAAACCAGT
65 TAATTTCACAAACCAGT
**
53789509 GGTATTT-TGGTAATTTTATAAA-CTAGGGGTATTTTGGTAATTCTACCCTATCGGGGTATTTCA
1 GGTATTTCT-GTAATTTTATAAATC-AGGGGTATTTTGGTAATTCTACCAAATCGGGGTATTTCA
53789572 GTAATTTCACAA
64 GTAATTTCACAA
53789584 TCGAGGGTAA
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
80 2 0.03
81 60 0.91
82 4 0.06
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.41
Consensus pattern (81 bp):
GGTATTTCTGTAATTTTATAAATCAGGGGTATTTTGGTAATTCTACCAAATCGGGGTATTTCAGT
AATTTCACAAACCAGT
Found at i:53789672 original size:26 final size:27
Alignment explanation
Indices: 53789582--53789672 Score: 112
Period size: 27 Copynumber: 3.4 Consensus size: 27
53789572 GTAATTTCAC
* ** *
53789582 AATCGAGGGTAAAATGGTAATTTTGTA
1 AATCAAGGGTAAAACAGTAATTCTGTA
53789609 AATCAAGGGTAAAACAGTAATTCTGTA
1 AATCAAGGGTAAAACAGTAATTCTGTA
* *
53789636 AATCAATGGTAAAA-AGTAATTCTATA
1 AATCAAGGGTAAAACAGTAATTCTGTA
*
53789662 AATCGAGGGTA
1 AATCAAGGGTA
53789673 CTTTGGTAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
26 20 0.36
27 36 0.64
ACGTcount: A:0.43, C:0.08, G:0.21, T:0.29
Consensus pattern (27 bp):
AATCAAGGGTAAAACAGTAATTCTGTA
Found at i:53791063 original size:86 final size:85
Alignment explanation
Indices: 53790967--53791126 Score: 218
Period size: 86 Copynumber: 1.9 Consensus size: 85
53790957 ATATGTGTTA
* * *
53790967 TCGTGTAAGACCAC-GTCTGGGA-CGTTGGCATCGAT-TTGTGATTTACGTGTAAGACCATGTCT
1 TCGTGTAAGACC-CTGTCTGGGATAG-TGGCATCGATATT-TGA-TTACATGTAAGACCACGTCT
53791029 GGGACATTGGCATCGTATATGATT
62 GGGACATTGGCATCGTATATGATT
*
53791053 TCGTGTAAGACCCTGTCTGGGATAGTGGTATCGATATTTGATTACATGTAAGACCACGTCTGGGA
1 TCGTGTAAGACCCTGTCTGGGATAGTGGCATCGATATTTGATTACATGTAAGACCACGTCTGGGA
*
53791118 CGTTGGCAT
66 CATTGGCAT
53791127 TGTACGAGCT
Statistics
Matches: 66, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
85 31 0.47
86 32 0.48
87 3 0.05
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (85 bp):
TCGTGTAAGACCCTGTCTGGGATAGTGGCATCGATATTTGATTACATGTAAGACCACGTCTGGGA
CATTGGCATCGTATATGATT
Found at i:53791095 original size:43 final size:42
Alignment explanation
Indices: 53790967--53791126 Score: 164
Period size: 43 Copynumber: 3.7 Consensus size: 42
53790957 ATATGTGTTA
*
53790967 TCGTGTAAGACCACGTCTGGGACGTTGGCATCGAT-TTGTGATT
1 TCGTGTAAGACCACGTCTGGGAAG-TGGCATCGATATT-TGATT
* * *
53791010 TACGTGTAAGACCATGTCTGGGACATTGGCATCG-TATATGATT
1 T-CGTGTAAGACCACGTCTGGGA-AGTGGCATCGATATTTGATT
*
53791053 TCGTGTAAGACC-CTGTCTGGGATAGTGGTATCGATATTTGATT
1 TCGTGTAAGACCAC-GTCTGGGA-AGTGGCATCGATATTTGATT
* * *
53791096 ACATGTAAGACCACGTCTGGGACGTTGGCAT
1 TCGTGTAAGACCACGTCTGGGAAG-TGGCAT
53791127 TGTACGAGCT
Statistics
Matches: 97, Mismatches: 13, Indels: 14
0.78 0.10 0.11
Matches are distributed among these distances:
42 28 0.29
43 39 0.40
44 30 0.31
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (42 bp):
TCGTGTAAGACCACGTCTGGGAAGTGGCATCGATATTTGATT
Found at i:53797715 original size:38 final size:38
Alignment explanation
Indices: 53797673--53797782 Score: 105
Period size: 41 Copynumber: 2.8 Consensus size: 38
53797663 TCGGATAGTT
*
53797673 CGAAGCAAAGTTGACACCCAGTGTCTCATCG-GCCTAGC
1 CGAAGCAAAG-TGACACCCAGTGTCTCATCGAACCTAGC
* ** * * *
53797711 CGAAGTAAAGTGGTACCCAGTATCTCATCGAATCTATC
1 CGAAGCAAAGTGACACCCAGTGTCTCATCGAACCTAGC
*
53797749 CGAAGTACAATAGTGACACCTAGTGTCTCATCGA
1 CGAAG--CAA-AGTGACACCCAGTGTCTCATCGA
53797783 CTCGAGGTCG
Statistics
Matches: 56, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
37 17 0.30
38 18 0.32
40 2 0.04
41 19 0.34
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (38 bp):
CGAAGCAAAGTGACACCCAGTGTCTCATCGAACCTAGC
Found at i:53797781 original size:41 final size:40
Alignment explanation
Indices: 53797684--53797782 Score: 98
Period size: 38 Copynumber: 2.5 Consensus size: 40
53797674 GAAGCAAAGT
* *
53797684 TGACACCCAGTGTCTCATCG-GCCTAGCCGAAGTAAAGTGG
1 TGACA-CCAGTGTCTCATCGAACCTAGCCGAAGTAAAGTAG
* * *
53797724 T-AC-CCAGTATCTCATCGAATCTATCCGAAGTACAA-TAG
1 TGACACCAGTGTCTCATCGAACCTAGCCGAAGTA-AAGTAG
53797762 TGACACCTAGTGTCTCATCGA
1 TGACACC-AGTGTCTCATCGA
53797783 CTCGAGGTCG
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
37 13 0.27
38 14 0.29
39 6 0.12
40 3 0.06
41 12 0.25
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.24
Consensus pattern (40 bp):
TGACACCAGTGTCTCATCGAACCTAGCCGAAGTAAAGTAG
Found at i:53802253 original size:16 final size:16
Alignment explanation
Indices: 53802232--53802270 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
53802222 AACTTGAAAC
53802232 CCGAGCCAATTTGTCA
1 CCGAGCCAATTTGTCA
53802248 CCGAGCCAATTTGTCA
1 CCGAGCCAATTTGTCA
53802264 CCGAGCC
1 CCGAGCC
53802271 GATGTTGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.23, C:0.36, G:0.21, T:0.21
Consensus pattern (16 bp):
CCGAGCCAATTTGTCA
Found at i:53802896 original size:28 final size:28
Alignment explanation
Indices: 53802852--53802909 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
53802842 CCTCTCACCG
53802852 GACCAATACTCTAGCCGGTTTCTAATCT
1 GACCAATACTCTAGCCGGTTTCTAATCT
*
53802880 GACCAATACTCTGGCCGGTTTCTAATCT
1 GACCAATACTCTAGCCGGTTTCTAATCT
53802908 GA
1 GA
53802910 TTGGTATAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.31
Consensus pattern (28 bp):
GACCAATACTCTAGCCGGTTTCTAATCT
Found at i:53804604 original size:31 final size:32
Alignment explanation
Indices: 53804569--53804640 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 32
53804559 AAGAAAAGAT
*
53804569 AATAGTTCAACT-ACTTAAATAAAAACTTTTG
1 AATAGTTCAACTGACTTAAATAAAAACTTTTA
* * *
53804600 AATAGTTC-AGTGACTTAAATGAAAATTTTTA
1 AATAGTTCAACTGACTTAAATAAAAACTTTTA
*
53804631 AATAATTCAA
1 AATAGTTCAA
53804641 TAACTAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 2 0.06
31 31 0.91
32 1 0.03
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (32 bp):
AATAGTTCAACTGACTTAAATAAAAACTTTTA
Found at i:53806045 original size:13 final size:13
Alignment explanation
Indices: 53806023--53806052 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
53806013 TGATATTGGC
*
53806023 ATTTGGGTTTAAA
1 ATTTGAGTTTAAA
53806036 ATTTGAGTTTAAA
1 ATTTGAGTTTAAA
53806049 ATTT
1 ATTT
53806053 TATCTAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (13 bp):
ATTTGAGTTTAAA
Found at i:53807091 original size:20 final size:20
Alignment explanation
Indices: 53807066--53807103 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
53807056 CAAAGGCAGC
*
53807066 CATATACCCAAGTTGTTAAG
1 CATATACCCAAGTAGTTAAG
*
53807086 CATATACTCAAGTAGTTA
1 CATATACCCAAGTAGTTA
53807104 CGAAGAATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (20 bp):
CATATACCCAAGTAGTTAAG
Found at i:53809859 original size:56 final size:56
Alignment explanation
Indices: 53809773--53809889 Score: 189
Period size: 56 Copynumber: 2.1 Consensus size: 56
53809763 ACAAGGGATG
53809773 ATGGGAAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGAAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
* * * * *
53809829 ATGGGCAAAACTTGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGGAGT
1 ATGGGAAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
53809885 ATGGG
1 ATGGG
53809890 TAATAAAATA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.44, C:0.07, G:0.25, T:0.25
Consensus pattern (56 bp):
ATGGGAAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:53811374 original size:40 final size:40
Alignment explanation
Indices: 53811143--53811367 Score: 269
Period size: 40 Copynumber: 5.7 Consensus size: 40
53811133 TCGAATGATG
* * * *
53811143 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
53811183 TCCGGACTAAGAT-TCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
53811223 TCCGGGCTAAG-CTCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
53811262 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
53811302 TCCGGGTTAAGTCCTGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
53811343 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
53811368 AACGAGTAGC
Statistics
Matches: 161, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
39 34 0.21
40 117 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:53811374 original size:80 final size:78
Alignment explanation
Indices: 53811197--53811390 Score: 241
Period size: 80 Copynumber: 2.4 Consensus size: 78
53811187 GACTAAGATT
* *
53811197 CGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCTCGAAGGCATTGGTGCGAGTTACTAAA
1 CGAAGGCATTTGTGCGAG-TACTAAATCCGGGTTAAGCTCGAAGGCATTGGTGCGAGTTACTAAA
*
53811262 TCCGGGTTAAGTCC
65 TCCGGGCTAAGTCC
*
53811276 CGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAG-TCCTGAAGGCATTTGTGCGAGTTACTA
1 CGAAGGCATTTGTGCGAG-TACTAAATCCGGGTTAAGCT-C-GAAGGCATTGGTGCGAGTTACTA
*
53811340 TAA-CCGGGCTATGTCC
63 -AATCCGGGCTAAGTCC
** *
53811356 CGAAGGCATTTGAACGAGTAGCTATATCC-GGTTAA
1 CGAAGGCATTTGTGCGAGTA-CTAAATCCGGGTTAA
53811391 ATTCCGAAGG
Statistics
Matches: 102, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 43 0.42
80 56 0.55
81 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.27
Consensus pattern (78 bp):
CGAAGGCATTTGTGCGAGTACTAAATCCGGGTTAAGCTCGAAGGCATTGGTGCGAGTTACTAAAT
CCGGGCTAAGTCC
Found at i:53811389 original size:119 final size:119
Alignment explanation
Indices: 53811143--53811400 Score: 274
Period size: 119 Copynumber: 2.2 Consensus size: 119
53811133 TCGAATGATG
* * *
53811143 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATTCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* * **
53811208 GTGCGAGATACTAATTCCGGGCTAAGCTCGAAGGCATTGGTGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
* * * **
53811262 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCTGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGATCC-GAAGGCAT
* * * *
53811325 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-CTAAA
* *
53811382 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
53811401 TACGTGATTT
Statistics
Matches: 116, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
118 4 0.03
119 82 0.71
120 30 0.26
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
Found at i:53816579 original size:26 final size:26
Alignment explanation
Indices: 53816542--53816625 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
53816532 TGATACAAAT
* *
53816542 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
53816568 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
53816594 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
53816620 TGATAA
1 TGATAA
53816626 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:53818137 original size:25 final size:26
Alignment explanation
Indices: 53818109--53818160 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
53818099 TTTACAGTTT
53818109 TACCCCTAGAGATAAATT-ACCGAAA
1 TACCCCTAGAGATAAATTGACCGAAA
* * *
53818134 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGAGATAAATTGACCGAAA
53818160 T
1 T
53818161 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.25
Consensus pattern (26 bp):
TACCCCTAGAGATAAATTGACCGAAA
Found at i:53820296 original size:26 final size:26
Alignment explanation
Indices: 53820267--53820342 Score: 143
Period size: 26 Copynumber: 2.9 Consensus size: 26
53820257 ATTGATAACA
*
53820267 GGTTAGGTAAATGTTCCATGATAATG
1 GGTTAGGTAAATGTTTCATGATAATG
53820293 GGTTAGGTAAATGTTTCATGATAATG
1 GGTTAGGTAAATGTTTCATGATAATG
53820319 GGTTAGGTAAATGTTTCATGATAA
1 GGTTAGGTAAATGTTTCATGATAA
53820343 GAATTTCATG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.37
Consensus pattern (26 bp):
GGTTAGGTAAATGTTTCATGATAATG
Found at i:53821844 original size:25 final size:26
Alignment explanation
Indices: 53821816--53821867 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
53821806 TTTACAGTTT
53821816 TACCCCTAGAGATAAATT-ACCGAAA
1 TACCCCTAGAGATAAATTGACCGAAA
* * *
53821841 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGAGATAAATTGACCGAAA
53821867 T
1 T
53821868 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.25
Consensus pattern (26 bp):
TACCCCTAGAGATAAATTGACCGAAA
Found at i:53832565 original size:27 final size:26
Alignment explanation
Indices: 53832513--53832569 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 26
53832503 TTTTGCTCTC
*
53832513 TTTTTCCTTTTGTTTTCTTTCATTATT
1 TTTTTCCTTTTCTTTTCTTT-ATTATT
53832540 TTTTTCCTTTTTCTATTTCTTT-TTATT
1 TTTTTCC-TTTTCT-TTTCTTTATTATT
53832567 TTT
1 TTT
53832570 CACATGCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 15 0.56
28 5 0.19
29 7 0.26
ACGTcount: A:0.07, C:0.14, G:0.02, T:0.77
Consensus pattern (26 bp):
TTTTTCCTTTTCTTTTCTTTATTATT
Found at i:53832749 original size:57 final size:57
Alignment explanation
Indices: 53832676--53832790 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
53832666 AAAAGATAAT
53832676 TATTTCTTCAAAATTGATTCTTCATGGATGAATATCTTAGAGTATACGTAGAATTGC
1 TATTTCTTCAAAATTGATTCTTCATGGATGAATATCTTAGAGTATACGTAGAATTGC
53832733 TATTTCTTCAAAATTGATTCTTCATGGATGAATATCTTAGAGTATACGTAGAATTGC
1 TATTTCTTCAAAATTGATTCTTCATGGATGAATATCTTAGAGTATACGTAGAATTGC
53832790 T
1 T
53832791 TGAACCTTCT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (57 bp):
TATTTCTTCAAAATTGATTCTTCATGGATGAATATCTTAGAGTATACGTAGAATTGC
Found at i:53841067 original size:27 final size:28
Alignment explanation
Indices: 53841015--53841069 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
53841005 GGAGTAAGGT
53841015 GCCGATGCCATGTCCAGACATGGTCTTA
1 GCCGATGCCATGTCCAGACATGGTCTTA
53841043 GCCGATG-CATGTCCCAGACAT-GTCTTA
1 GCCGATGCCATGT-CCAGACATGGTCTTA
53841070 CACTGGCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 11 0.42
28 15 0.58
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (28 bp):
GCCGATGCCATGTCCAGACATGGTCTTA
Found at i:53841110 original size:46 final size:45
Alignment explanation
Indices: 53841043--53841213 Score: 191
Period size: 46 Copynumber: 3.7 Consensus size: 45
53841033 CATGGTCTTA
*
53841043 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACGTCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTT-CATCTCGAG
* * * *
53841089 GCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCTTCTCGAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGC-TTCATCTCGAG
* * * *
53841135 ACCGATGCTATGTCCTAGACATGGTCTTACACTGGCTCTCATAAT-GTG
1 GCCGATGC-ATGTCCCAGACAT-GTCTTACACTGGCT-TCAT-CTCGAG
*
53841183 GCCGATGCATGTCCCAAACATGTCTTACACT
1 GCCGATGCATGTCCCAGACATGTCTTACACT
53841214 AGCTCACAAT
Statistics
Matches: 105, Mismatches: 15, Indels: 10
0.81 0.12 0.08
Matches are distributed among these distances:
46 57 0.54
47 24 0.23
48 23 0.22
49 1 0.01
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (45 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTCATCTCGAG
Found at i:53841211 original size:94 final size:92
Alignment explanation
Indices: 53841044--53841216 Score: 251
Period size: 94 Copynumber: 1.9 Consensus size: 92
53841034 ATGGTCTTAG
* * *
53841044 CCGATGCATGTCCCAGACATGTCTTACACTGGCTTACGTCTCGAGGCCGATGCATGTCCCAGACA
1 CCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATATCGAGGCCGATGCATGTCCCAAACA
53841109 TGTCTTACACTAGCACTCTTCTCGATA
66 TGTCTTACACTAGCACTCTTCTCGATA
* *
53841136 CCGATGCTATGTCCTAGACATGGTCTTACACTGGCTCT-CATAAT-GTGGCCGATGCATGTCCCA
1 CCGATGC-ATGTCCCAGACAT-GTCTTACACTGGCT-TACAT-ATCGAGGCCGATGCATGTCCCA
53841199 AACATGTCTTACACTAGC
62 AACATGTCTTACACTAGC
53841217 TCACAATAAT
Statistics
Matches: 72, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
92 7 0.10
93 12 0.17
94 51 0.71
95 2 0.03
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.28
Consensus pattern (92 bp):
CCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATATCGAGGCCGATGCATGTCCCAAACA
TGTCTTACACTAGCACTCTTCTCGATA
Found at i:53844386 original size:49 final size:47
Alignment explanation
Indices: 53844295--53844615 Score: 491
Period size: 47 Copynumber: 6.7 Consensus size: 47
53844285 TTAGGATTCT
* * *
53844295 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
53844342 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
53844391 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
53844440 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
53844487 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
53844534 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
53844581 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
53844616 TCCCGAAGGG
Statistics
Matches: 258, Mismatches: 13, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
46 1 0.00
47 163 0.63
49 94 0.36
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:53844789 original size:37 final size:37
Alignment explanation
Indices: 53844733--53844811 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
53844723 CCGAGCTCTA
* * *
53844733 AAGACCCGATGACTACGTGTGGGGATTTTGTCCAGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCAGGT
* *
53844770 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCAGGT
53844807 AAGAC
1 AAGAC
53844812 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCAGGT
Found at i:53846370 original size:198 final size:198
Alignment explanation
Indices: 53846025--53846400 Score: 662
Period size: 198 Copynumber: 1.9 Consensus size: 198
53846015 GAGAATTGAG
53846025 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCG
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCG
* *
53846090 AGGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATAT
66 AGGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATAT
**
53846155 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAGGCATTCGT
131 CCGGGCTAAACCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAGGCATTCGT
53846220 GCT
196 GCT
* *
53846223 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCG
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCG
*
53846288 AGGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCTAGTGATATAT
66 AGGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATAT
* * *
53846353 CCGTGCTAAACCCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTA
131 CCGGGCTAAACCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTA
53846401 GGTCTCGAAG
Statistics
Matches: 168, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
198 168 1.00
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (198 bp):
AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCG
AGGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATAT
CCGGGCTAAACCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAGGCATTCGT
GCT
Found at i:53846426 original size:40 final size:40
Alignment explanation
Indices: 53846025--53846414 Score: 640
Period size: 40 Copynumber: 9.8 Consensus size: 40
53846015 GAGAATTGAG
53846025 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
53846065 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
53846105 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
53846145 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
53846185 AGTGATATATCCGGGCTAAGTCCCG-AG-GCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
53846223 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
53846263 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
53846303 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* **
53846343 AGTGATATATCCGTGCTAAACCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * * *
53846383 GGTGTTATATCCGGGCTAGGTCTCGAAGAGCA
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCA
53846415 ATCATGCTGG
Statistics
Matches: 326, Mismatches: 22, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
38 34 0.10
39 4 0.01
40 288 0.88
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (40 bp):
AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
Found at i:53847733 original size:47 final size:47
Alignment explanation
Indices: 53847679--53848044 Score: 599
Period size: 47 Copynumber: 7.7 Consensus size: 47
53847669 TTAGGATTCT
* * *
53847679 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
53847726 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
53847773 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
53847820 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
53847869 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
53847916 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
53847963 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
53848010 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
53848045 TCCCGAAGGG
Statistics
Matches: 303, Mismatches: 13, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
46 1 0.00
47 255 0.84
49 47 0.16
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:53847754 original size:25 final size:25
Alignment explanation
Indices: 53847726--53847804 Score: 65
Period size: 25 Copynumber: 3.3 Consensus size: 25
53847716 CTAATGGCCG
53847726 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
* *** ****
53847751 ATGTGAT-AAGGCCTAA-TG-GCCG
1 ATGTGATGAATGTGAAAGTGTATAT
53847773 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
53847798 ATGTGAT
1 ATGTGAT
53847805 AAGGCCTAAT
Statistics
Matches: 35, Mismatches: 16, Indels: 6
0.61 0.28 0.11
Matches are distributed among these distances:
22 7 0.20
23 7 0.20
24 7 0.20
25 14 0.40
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (25 bp):
ATGTGATGAATGTGAAAGTGTATAT
Found at i:53847864 original size:143 final size:141
Alignment explanation
Indices: 53847679--53848044 Score: 599
Period size: 143 Copynumber: 2.6 Consensus size: 141
53847669 TTAGGATTCT
* * *
53847679 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
53847743 GTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
65 GTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
53847808 GCCTAATGGCCG
130 GCCTAATGGCCG
53847820 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
53847885 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
64 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
53847950 GGCCTAATGGCCG
129 GGCCTAATGGCCG
* * * * * * *
53847963 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
*
53848028 TGTATAAATGTGATAAG
66 TGTATATATGTGATAAG
53848045 TCCCGAAGGG
Statistics
Matches: 211, Mismatches: 11, Indels: 6
0.93 0.05 0.03
Matches are distributed among these distances:
140 1 0.00
141 71 0.34
143 139 0.66
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (141 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
CCTAATGGCCG
Found at i:53848219 original size:37 final size:37
Alignment explanation
Indices: 53848163--53848241 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
53848153 CCGAGCTCTA
* * *
53848163 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
53848200 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
53848237 AAGAC
1 AAGAC
53848242 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:53856608 original size:27 final size:27
Alignment explanation
Indices: 53856577--53856629 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
53856567 GGTACAACCT
* *
53856577 ATGTAATAGTAATTTAACATTCAATTC
1 ATGTAACAATAATTTAACATTCAATTC
**
53856604 ATGTAACAATAATTTGTCATTCAATT
1 ATGTAACAATAATTTAACATTCAATT
53856630 TCACATGACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.42
Consensus pattern (27 bp):
ATGTAACAATAATTTAACATTCAATTC
Found at i:53865149 original size:18 final size:18
Alignment explanation
Indices: 53865128--53865162 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
53865118 AGAAAAGAAA
53865128 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
53865146 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
53865163 AAAAGAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:53865174 original size:27 final size:27
Alignment explanation
Indices: 53865104--53865174 Score: 74
Period size: 30 Copynumber: 2.5 Consensus size: 27
53865094 AATAGCGAGA
53865104 GAAAAAGAAAATGA-AGAAAAGAAAATT
1 GAAAAAGAAAA-GATAGAAAAGAAAATT
*
53865131 GAAAAAGAAATTGAGATTGAGAAA-AAAATT
1 GAAAAAGAAA---AGATAGA-AAAGAAAATT
53865161 GAAAAAGAAAAGAT
1 GAAAAAGAAAAGAT
53865175 GTTGAAGAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
27 14 0.37
29 2 0.05
30 19 0.50
31 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.20, T:0.14
Consensus pattern (27 bp):
GAAAAAGAAAAGATAGAAAAGAAAATT
Found at i:53870405 original size:19 final size:19
Alignment explanation
Indices: 53870368--53870405 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
53870358 ACCTGTCAGA
*
53870368 AGAAAATAAATGAAGAATT
1 AGAAAATAAATGAAAAATT
53870387 AGAAAATAAAAT-AAAAATT
1 AGAAAAT-AAATGAAAAATT
53870406 TAAATTGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (19 bp):
AGAAAATAAATGAAAAATT
Found at i:53874520 original size:29 final size:30
Alignment explanation
Indices: 53874477--53874535 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
53874467 ATTTAATACG
53874477 AACTTTGGCAAAATTACA-TTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
* * *
53874506 AACTTTTGCATAATTACACTTTTGCTCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
53874536 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.39
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:53875684 original size:13 final size:14
Alignment explanation
Indices: 53875660--53875693 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
53875650 TTTATGTTTC
53875660 TTCTTCTATTTTA-T
1 TTCTT-TATTTTATT
53875674 TTCTTTATTTTATT
1 TTCTTTATTTTATT
53875688 TTCTTT
1 TTCTTT
53875694 TATGTTATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (14 bp):
TTCTTTATTTTATT
Found at i:53882763 original size:46 final size:48
Alignment explanation
Indices: 53882665--53882774 Score: 134
Period size: 46 Copynumber: 2.3 Consensus size: 48
53882655 GTCATGTCCT
* * * * *
53882665 AGACAGGTCTTACACTAGCTTATATATCTCGAGGCCGATGCATGTCCT
1 AGACATGTCTTACACTAGCTTATACATCTCAAGGCCGATGCATATCCC
* * *
53882713 AGACATGTCTTACACTAGC-TCT-CATCTCAATGCTGATGCATATCCC
1 AGACATGTCTTACACTAGCTTATACATCTCAAGGCCGATGCATATCCC
53882759 AGACATGTCTTACACT
1 AGACATGTCTTACACT
53882775 TACTTTCGTA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
46 34 0.63
47 2 0.04
48 18 0.33
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.30
Consensus pattern (48 bp):
AGACATGTCTTACACTAGCTTATACATCTCAAGGCCGATGCATATCCC
Found at i:53888791 original size:49 final size:49
Alignment explanation
Indices: 53888712--53888906 Score: 228
Period size: 49 Copynumber: 3.9 Consensus size: 49
53888702 ACTATTGTGA
* * *
53888712 GGTCACATGTGTAGTACTAAATGCAAGCTACTACGTGTACCGGATAATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * * * *
53888761 GGTCGCATGTGTAGTACTAATTGCAGGCTACTATGCGTACCAAAAAATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * *
53888810 GTGATCACGTGTGTAGTAATAAGTGCAGGCTACTACGTGTACCAGATTATT
1 G-G-TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * *
53888861 GGTCGCATGTGTAGTACTAAGTGTAGGCTACTATGCGTACCAGATA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
53888907 GCTTCAGCTA
Statistics
Matches: 120, Mismatches: 24, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
49 79 0.66
50 2 0.02
51 39 0.32
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:53888892 original size:100 final size:101
Alignment explanation
Indices: 53888705--53888902 Score: 308
Period size: 100 Copynumber: 2.0 Consensus size: 101
53888695 CAAATGAACT
* *
53888705 ATTGTGAGGTCACATGTGTAGTACTAAATGCAAGCTACTACGTGTACCGGATAATTGGTCGCATG
1 ATTGTGA-GTCACATGTGTAGTAATAAATGCAAGCTACTACGTGTACCAGATAATTGGTCGCATG
*
53888770 TGTAGTACTAATTGCAGGCTACTATGCGTACCAAAAA
65 TGTAGTACTAAGTGCAGGCTACTATGCGTACCAAAAA
* * * *
53888807 ATTGTGA-TCACGTGTGTAGTAATAAGTGCAGGCTACTACGTGTACCAGATTATTGGTCGCATGT
1 ATTGTGAGTCACATGTGTAGTAATAAATGCAAGCTACTACGTGTACCAGATAATTGGTCGCATGT
*
53888871 GTAGTACTAAGTGTAGGCTACTATGCGTACCA
66 GTAGTACTAAGTGCAGGCTACTATGCGTACCA
53888903 GATAGCTTCA
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
100 81 0.92
102 7 0.08
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (101 bp):
ATTGTGAGTCACATGTGTAGTAATAAATGCAAGCTACTACGTGTACCAGATAATTGGTCGCATGT
GTAGTACTAAGTGCAGGCTACTATGCGTACCAAAAA
Found at i:53891916 original size:15 final size:15
Alignment explanation
Indices: 53891896--53891947 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
53891886 CTTGGGTTTT
53891896 TTTATTCTGGATTTC
1 TTTATTCTGGATTTC
*
53891911 TTTATTCTGGGTTT-
1 TTTATTCTGGATTTC
53891925 TTCTA-TCTTGGATTTC
1 TT-TATTC-TGGATTTC
53891941 TTTATTC
1 TTTATTC
53891948 AGTTTTCTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 4 0.13
15 23 0.74
16 4 0.13
ACGTcount: A:0.12, C:0.13, G:0.13, T:0.62
Consensus pattern (15 bp):
TTTATTCTGGATTTC
Found at i:53891924 original size:30 final size:30
Alignment explanation
Indices: 53891888--53891947 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
53891878 TATCATATCT
*
53891888 TGGGTTTTTTTAT-TCTGGATTTCTTTATTC
1 TGGGTTTTTCTATCT-TGGATTTCTTTATTC
53891918 TGGGTTTTTCTATCTTGGATTTCTTTATTC
1 TGGGTTTTTCTATCTTGGATTTCTTTATTC
53891948 AGTTTTCTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.10, C:0.12, G:0.17, T:0.62
Consensus pattern (30 bp):
TGGGTTTTTCTATCTTGGATTTCTTTATTC
Found at i:53894090 original size:49 final size:51
Alignment explanation
Indices: 53893960--53894101 Score: 157
Period size: 51 Copynumber: 2.8 Consensus size: 51
53893950 TAGGATAATA
*
53893960 GGTCGCATGTGTAGTACTAAGTGCAGGCTACT-TTGCGTACCCGAAAACTGT
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATT-CGTACCAGAAAACTGT
* * * * **
53894011 GATCACGTGTGTAATACTAAGTGCAGGCTACTACTT-GTACCAGATTA-T-T
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTA-TTCGTACCAGAAAACTGT
* *
53894060 GGTCGCATGTGTAGTACTAAGTGTAGGCTACTATACGTACCA
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATTCGTACCA
53894102 AATAGCTTCG
Statistics
Matches: 75, Mismatches: 13, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
48 1 0.01
49 35 0.47
50 1 0.01
51 36 0.48
53 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.30
Consensus pattern (51 bp):
GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATTCGTACCAGAAAACTGT
Found at i:53896298 original size:26 final size:26
Alignment explanation
Indices: 53896241--53896298 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
53896231 ACAAATTTTC
*
53896241 TCAAAATTTTACTAGCAGTAAAATCG
1 TCAAAATTTTAATAGCAGTAAAATCG
* * *
53896267 TTAAAATTTTAATGAG-GGTAAAATTG
1 TCAAAATTTTAAT-AGCAGTAAAATCG
53896293 TCAAAA
1 TCAAAA
53896299 ACATTACTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 24 0.92
27 2 0.08
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.33
Consensus pattern (26 bp):
TCAAAATTTTAATAGCAGTAAAATCG
Done.