Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 169 of 203
Found at i:53550937 original size:6 final size:6
Alignment explanation
Indices: 53550928--53551054 Score: 101
Period size: 6 Copynumber: 20.7 Consensus size: 6
53550918 AATGAAAAAG
** * *
53550928 AAGAAA AAGAAA AAGAAA GTGAAG AAGAAA AAGAAA ATGAAA AAGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
** * ** ** *
53550976 AAGAAA TTGCAA AAGAAA AAGAAA TCGAAA AAGTGA GAGAAA AAGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
* *
53551024 ACGAAGAA AAGAAA ATTGAAA AAGAAA AAGA
1 AAG-A-AA AAGAAA A-AGAAA AAGAAA AAGA
53551055 TGTTGAAAAA
Statistics
Matches: 90, Mismatches: 28, Indels: 6
0.73 0.23 0.05
Matches are distributed among these distances:
6 79 0.88
7 7 0.08
8 4 0.04
ACGTcount: A:0.71, C:0.02, G:0.20, T:0.06
Consensus pattern (6 bp):
AAGAAA
Found at i:53552840 original size:16 final size:15
Alignment explanation
Indices: 53552821--53552859 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
53552811 CTTAACTTAA
53552821 TTAATTGTGTCTAGTT
1 TTAATTGTGTCTA-TT
* *
53552837 TTAATTATGTGTATT
1 TTAATTGTGTCTATT
53552852 TTAATTGT
1 TTAATTGT
53552860 CCAGGTTATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.23, C:0.03, G:0.15, T:0.59
Consensus pattern (15 bp):
TTAATTGTGTCTATT
Found at i:53556432 original size:13 final size:13
Alignment explanation
Indices: 53556414--53556458 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
53556404 GAAAACTCAA
53556414 GAGAAAATTCTTG
1 GAGAAAATTCTTG
* *
53556427 GAGAAAACTC-TA
1 GAGAAAATTCTTG
*
53556439 GACAAAATTCTTG
1 GAGAAAATTCTTG
53556452 GAGAAAA
1 GAGAAAA
53556459 CTCAAAGAGA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
12 9 0.36
13 16 0.64
ACGTcount: A:0.47, C:0.11, G:0.20, T:0.22
Consensus pattern (13 bp):
GAGAAAATTCTTG
Found at i:53556435 original size:25 final size:25
Alignment explanation
Indices: 53556403--53556469 Score: 107
Period size: 25 Copynumber: 2.6 Consensus size: 25
53556393 CTACTTCCAA
53556403 AGAAAACTCAAGAGAAAATTCTTGG
1 AGAAAACTCAAGAGAAAATTCTTGG
* *
53556428 AGAAAACTCTAGACAAAATTCTTGG
1 AGAAAACTCAAGAGAAAATTCTTGG
53556453 AGAAAACTCAAAGAGAA
1 AGAAAACTC-AAGAGAA
53556470 TTTTCATTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
25 32 0.86
26 5 0.14
ACGTcount: A:0.51, C:0.13, G:0.18, T:0.18
Consensus pattern (25 bp):
AGAAAACTCAAGAGAAAATTCTTGG
Found at i:53558201 original size:33 final size:33
Alignment explanation
Indices: 53558130--53558216 Score: 97
Period size: 33 Copynumber: 2.5 Consensus size: 33
53558120 CCTTGCTTTT
*
53558130 TCTTGATTGCTTTCTTCACTCGTTTCTTTTGCAAAC
1 TCTTG-TT-CTTT-TTCATTCGTTTCTTTTGCAAAC
53558166 TCTTGTTCTTTTTCATTCGATTTCTTTT-CAAAC
1 TCTTGTTCTTTTTCATTCG-TTTCTTTTGCAAAC
*
53558199 TCTCT-TTCTTTTTTATTC
1 TCT-TGTTCTTTTTCATTC
53558217 TCAATCTCTT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
33 27 0.57
34 13 0.28
35 2 0.04
36 5 0.11
ACGTcount: A:0.13, C:0.23, G:0.07, T:0.57
Consensus pattern (33 bp):
TCTTGTTCTTTTTCATTCGTTTCTTTTGCAAAC
Found at i:53558227 original size:35 final size:34
Alignment explanation
Indices: 53558154--53558228 Score: 82
Period size: 33 Copynumber: 2.2 Consensus size: 34
53558144 TTCACTCGTT
* *
53558154 TCTTTTGCAAACTCTTGTTCTTTTTCATTCGATT
1 TCTTTTGCAAACTCTTGTTCTTTTTCATTCAATC
*
53558188 TCTTTT-CAAACTCTCT-TTCTTTTTTATTCTCAATC
1 TCTTTTGCAAACTCT-TGTTCTTTTTCA-T-TCAATC
53558223 TCTTTT
1 TCTTTT
53558229 TGCTTTTCAC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
33 17 0.49
34 8 0.23
35 10 0.29
ACGTcount: A:0.15, C:0.23, G:0.04, T:0.59
Consensus pattern (34 bp):
TCTTTTGCAAACTCTTGTTCTTTTTCATTCAATC
Found at i:53560253 original size:33 final size:33
Alignment explanation
Indices: 53560182--53560268 Score: 97
Period size: 33 Copynumber: 2.5 Consensus size: 33
53560172 CCTTGCTTTT
*
53560182 TCTTGATTGCTTTCTTCACTCGTTTCTTTTGCAAAC
1 TCTTG-TT-CTTT-TTCATTCGTTTCTTTTGCAAAC
53560218 TCTTGTTCTTTTTCATTCGATTTCTTTT-CAAAC
1 TCTTGTTCTTTTTCATTCG-TTTCTTTTGCAAAC
*
53560251 TCTCT-TTCTTTTTTATTC
1 TCT-TGTTCTTTTTCATTC
53560269 TCAATCTCTT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
33 27 0.57
34 13 0.28
35 2 0.04
36 5 0.11
ACGTcount: A:0.13, C:0.23, G:0.07, T:0.57
Consensus pattern (33 bp):
TCTTGTTCTTTTTCATTCGTTTCTTTTGCAAAC
Found at i:53560279 original size:35 final size:34
Alignment explanation
Indices: 53560206--53560280 Score: 82
Period size: 33 Copynumber: 2.2 Consensus size: 34
53560196 TTCACTCGTT
* *
53560206 TCTTTTGCAAACTCTTGTTCTTTTTCATTCGATT
1 TCTTTTGCAAACTCTTGTTCTTTTTCATTCAATC
*
53560240 TCTTTT-CAAACTCTCT-TTCTTTTTTATTCTCAATC
1 TCTTTTGCAAACTCT-TGTTCTTTTTCA-T-TCAATC
53560275 TCTTTT
1 TCTTTT
53560281 TGCTTTTCAC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
33 17 0.49
34 8 0.23
35 10 0.29
ACGTcount: A:0.15, C:0.23, G:0.04, T:0.59
Consensus pattern (34 bp):
TCTTTTGCAAACTCTTGTTCTTTTTCATTCAATC
Found at i:53563806 original size:24 final size:22
Alignment explanation
Indices: 53563754--53563808 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 22
53563744 TTCGGCTACT
*
53563754 GATGTGTTCACACAACAATTAAA
1 GATG-GTTCACACAAAAATTAAA
*
53563777 -AGGGTTCACACTAAAACATTAAA
1 GATGGTTCACAC-AAAA-ATTAAA
53563800 GATGGTTCA
1 GATGGTTCA
53563809 TGAATTTGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 8 0.31
22 5 0.19
23 6 0.23
24 7 0.27
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.25
Consensus pattern (22 bp):
GATGGTTCACACAAAAATTAAA
Found at i:53565856 original size:13 final size:13
Alignment explanation
Indices: 53565838--53565862 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53565828 TAGAAAAAAA
53565838 TAAAAAAATTTAT
1 TAAAAAAATTTAT
53565851 TAAAAAAATTTA
1 TAAAAAAATTTA
53565863 GTTGTAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAAAAAAATTTAT
Found at i:53565939 original size:11 final size:12
Alignment explanation
Indices: 53565913--53565943 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
53565903 TGTGATATAT
*
53565913 AAAAGAAGTTCA
1 AAAAAAAGTTCA
53565925 AAAAAAAGTTCA
1 AAAAAAAGTTCA
53565937 AAAAAAA
1 AAAAAAA
53565944 TGTTGTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.71, C:0.06, G:0.10, T:0.13
Consensus pattern (12 bp):
AAAAAAAGTTCA
Found at i:53566059 original size:14 final size:14
Alignment explanation
Indices: 53566027--53566073 Score: 69
Period size: 14 Copynumber: 3.3 Consensus size: 14
53566017 GAAAAAAATC
53566027 AAAA-AAATTCAAAA
1 AAAAGAAATTC-AAA
53566041 GAAAAGAAATTCAAA
1 -AAAAGAAATTCAAA
53566056 AAAAGAAATTCAAA
1 AAAAGAAATTCAAA
53566070 AAAA
1 AAAA
53566074 AGTGTGAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
14 18 0.58
15 7 0.23
16 6 0.19
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.13
Consensus pattern (14 bp):
AAAAGAAATTCAAA
Found at i:53566914 original size:6 final size:6
Alignment explanation
Indices: 53566884--53567021 Score: 80
Period size: 6 Copynumber: 22.5 Consensus size: 6
53566874 ACATTGTAAT
* * ** * *
53566884 AAAAATG AAAAAT AAAAAA AAAAAG AAAAAG AAAGTG AAGAAG AAAATG
1 AAAAA-G AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
* ** * **
53566933 AAAATG -AAAAG AAAAAG AAATTG TAAAAG AAAAAG AAATCG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
** * * *
53566980 TGAGAG AAAAAG AAAACG AAGAAAAG AAAATTG AAAAAG AAA
1 AAAAAG AAAAAG AAAAAG -A-AAAAG AAAA-AG AAAAAG AAA
53567022 TTGAGATTGA
Statistics
Matches: 96, Mismatches: 31, Indels: 9
0.71 0.23 0.07
Matches are distributed among these distances:
5 4 0.04
6 76 0.79
7 12 0.12
8 4 0.04
ACGTcount: A:0.72, C:0.01, G:0.18, T:0.09
Consensus pattern (6 bp):
AAAAAG
Found at i:53566927 original size:18 final size:17
Alignment explanation
Indices: 53566885--53566970 Score: 90
Period size: 18 Copynumber: 5.2 Consensus size: 17
53566875 CATTGTAATA
*
53566885 AAAATGAAAA-ATAAA-
1 AAAATGAAAAGAAAAAG
53566900 AAAA--AAAAGAAAAAG
1 AAAATGAAAAGAAAAAG
* *
53566915 AAAGTGAAGAAGAAAATG
1 AAAATGAA-AAGAAAAAG
53566933 AAAATGAAAAGAAAAAG
1 AAAATGAAAAGAAAAAG
*
53566950 AAATTGTAAAAGAAAAAG
1 AAAATG-AAAAGAAAAAG
53566968 AAA
1 AAA
53566971 TCGAAAAAGT
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
13 4 0.07
14 4 0.07
15 7 0.12
17 15 0.25
18 29 0.49
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.09
Consensus pattern (17 bp):
AAAATGAAAAGAAAAAG
Found at i:53566977 original size:35 final size:35
Alignment explanation
Indices: 53566904--53566970 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
53566894 AATAAAAAAA
*
53566904 AAAAGAAAAAGAAAGTGAAGAAGAAAATGAAAATG
1 AAAAGAAAAAGAAAGTGAAGAAGAAAAAGAAAATG
*
53566939 AAAAGAAAAAGAAATTGTAA-AAGAAAAAGAAA
1 AAAAGAAAAAGAAAGTG-AAGAAGAAAAAGAAA
53566971 TCGAAAAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 27 0.93
36 2 0.07
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.09
Consensus pattern (35 bp):
AAAAGAAAAAGAAAGTGAAGAAGAAAAAGAAAATG
Found at i:53567021 original size:18 final size:18
Alignment explanation
Indices: 53566903--53567076 Score: 110
Period size: 18 Copynumber: 9.8 Consensus size: 18
53566893 AAATAAAAAA
*
53566903 AAAAAGAAAAAGAAAGTG
1 AAAAAGAAAAAGAAATTG
* * *
53566921 AAGAAGAAAATGAAAATG
1 AAAAAGAAAAAGAAATTG
53566939 -AAAAGAAAAAGAAATTG
1 AAAAAGAAAAAGAAATTG
* *
53566956 TAAAAGAAAAAGAAATCG
1 AAAAAGAAAAAGAAATTG
** * **
53566974 AAAAAGTGAGAGAAAAAG
1 AAAAAGAAAAAGAAATTG
*
53566992 AAAACGAAGAAAAGAAAATTG
1 AAAAAG-A-AAAAG-AAATTG
** *
53567013 AAAAAGAAATTGAGATTG
1 AAAAAGAAAAAGAAATTG
53567031 ----AG-AAAA-AAATTG
1 AAAAAGAAAAAGAAATTG
**
53567043 AAAAAGAAAAAGATGTTG
1 AAAAAGAAAAAGAAATTG
53567061 AAAAAGAAAAGAGAAA
1 AAAAAGAAAA-AGAAA
53567077 AAATGAAGAT
Statistics
Matches: 115, Mismatches: 30, Indels: 21
0.69 0.18 0.13
Matches are distributed among these distances:
12 5 0.04
13 2 0.02
14 2 0.02
16 2 0.02
17 18 0.16
18 67 0.58
19 6 0.05
20 4 0.03
21 9 0.08
ACGTcount: A:0.67, C:0.01, G:0.21, T:0.11
Consensus pattern (18 bp):
AAAAAGAAAAAGAAATTG
Found at i:53570406 original size:27 final size:27
Alignment explanation
Indices: 53570367--53570419 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
53570357 TTCATTGAAG
*
53570367 TATCTTCATTGCTGTCCATGCATGTAA
1 TATCTTCAATGCTGTCCATGCATGTAA
53570394 TATCTTCAATGCTGTCCATGCATGTA
1 TATCTTCAATGCTGTCCATGCATGTA
53570420 CCTACAAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.40
Consensus pattern (27 bp):
TATCTTCAATGCTGTCCATGCATGTAA
Found at i:53571155 original size:36 final size:36
Alignment explanation
Indices: 53571115--53571186 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
53571105 TCACAACAAG
53571115 TTATAAGACATATATAATATGCACATTCAACTATCA
1 TTATAAGACATATATAATATGCACATTCAACTATCA
*
53571151 TTATAAGACATTTATAATATGCACATTCAACTATCA
1 TTATAAGACATATATAATATGCACATTCAACTATCA
53571187 CTTTCATTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.35
Consensus pattern (36 bp):
TTATAAGACATATATAATATGCACATTCAACTATCA
Found at i:53572989 original size:50 final size:51
Alignment explanation
Indices: 53572880--53573010 Score: 158
Period size: 50 Copynumber: 2.5 Consensus size: 51
53572870 ATGACAAATG
* * *
53572880 AGTTACTTAATGCAAGACTTAATTTAATGATGCAGACTTAAACTAACATGGG
1 AGTTACATAATGCATGACTT-ATTTAATGATGCAGACTTAAACTAACATGGA
* *
53572932 AGTTACATAATGCATGACATTATTT-ATGATGCATACTT-AACTAGCATGGA
1 AGTTACATAATGCATGAC-TTATTTAATGATGCAGACTTAAACTAACATGGA
* *
53572982 AGTTACATAATGCATAACTTTATTAAATG
1 AGTTACATAATGCATGAC-TTATTTAATG
53573011 CAGAACAAAC
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
50 32 0.46
51 15 0.22
52 20 0.29
53 2 0.03
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (51 bp):
AGTTACATAATGCATGACTTATTTAATGATGCAGACTTAAACTAACATGGA
Found at i:53582548 original size:50 final size:52
Alignment explanation
Indices: 53582423--53582553 Score: 133
Period size: 50 Copynumber: 2.6 Consensus size: 52
53582413 ATGACAAATG
* * * *
53582423 AGTTACTTAATGCA-AGACTTAATTTAATGATGCAGATTTAAACTAACATGGG
1 AGTTACATAATGCATA-ACTTTATTTAATGATGCAGACTTAAACTAACATGGA
* ** * * *
53582475 AGTTTCATAATGCATGCCATTATTT-ATGATGCATACTT-AACTAGCATGGA
1 AGTTACATAATGCATAACTTTATTTAATGATGCAGACTTAAACTAACATGGA
*
53582525 AGTTACATAATGCATAACTTTATTAAATG
1 AGTTACATAATGCATAACTTTATTTAATG
53582554 CAGAACACAC
Statistics
Matches: 62, Mismatches: 15, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
50 30 0.48
51 14 0.23
52 18 0.29
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (52 bp):
AGTTACATAATGCATAACTTTATTTAATGATGCAGACTTAAACTAACATGGA
Found at i:53583489 original size:191 final size:191
Alignment explanation
Indices: 53583154--53583536 Score: 730
Period size: 191 Copynumber: 2.0 Consensus size: 191
53583144 GTGGCTGTTC
53583154 AAATTCATCCATTCACACCTTTTGACCATTTATATTCAAACATTCACACAAAGGGGGTTGTTTGT
1 AAATTCATCCATTCACACCTTTTGACCATTTATATTCAAACATTCACACAAAGGGGGTTGTTTGT
*
53583219 ATGCCAAATGACATTAATTTTTTGGCTGCTGTTCATTTGGCTGTCCAATGAGAAATTAAAAGGCT
66 ATCCCAAATGACATTAATTTTTTGGCTGCTGTTCATTTGGCTGTCCAATGAGAAATTAAAAGGCT
* *
53583284 GTTATGACTCTTTAGCTGATCAAGCATTGAATCAAGTTTATTCAGCTCATTAGAGTTAATT
131 CTTATGAATCTTTAGCTGATCAAGCATTGAATCAAGTTTATTCAGCTCATTAGAGTTAATT
*
53583345 AAATTCGTCCATTCACACCTTTTGACCATTTATATTCAAACATTCACACAAAGGGGGTTGTTTGT
1 AAATTCATCCATTCACACCTTTTGACCATTTATATTCAAACATTCACACAAAGGGGGTTGTTTGT
53583410 ATCCCAAATGACATTAATTTTTTGGCTGCTGTTCATTTGGCTGTCCAATGAGAAATTAAAAGGCT
66 ATCCCAAATGACATTAATTTTTTGGCTGCTGTTCATTTGGCTGTCCAATGAGAAATTAAAAGGCT
53583475 CTTATGAATCTTTAGCTGATCAAGCATTGAATCAAGTTTATTCAGCTCATTAGAGTTAATT
131 CTTATGAATCTTTAGCTGATCAAGCATTGAATCAAGTTTATTCAGCTCATTAGAGTTAATT
53583536 A
1 A
53583537 TTAGTTGAAT
Statistics
Matches: 188, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
191 188 1.00
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (191 bp):
AAATTCATCCATTCACACCTTTTGACCATTTATATTCAAACATTCACACAAAGGGGGTTGTTTGT
ATCCCAAATGACATTAATTTTTTGGCTGCTGTTCATTTGGCTGTCCAATGAGAAATTAAAAGGCT
CTTATGAATCTTTAGCTGATCAAGCATTGAATCAAGTTTATTCAGCTCATTAGAGTTAATT
Found at i:53585240 original size:44 final size:44
Alignment explanation
Indices: 53585191--53585331 Score: 115
Period size: 44 Copynumber: 3.2 Consensus size: 44
53585181 ATTTTCTTGA
53585191 TTCTTGAAATCGCTCAAAACAACAAAATTGGACCAAGATTCGGT
1 TTCTTGAAATCGCTCAAAACAACAAAATTGGACCAAGATTCGGT
** * * * * * * ** * *
53585235 TTCTTGATTTTC-TTAAAAACAA-GAAAGTGAATCTTGATTTTCTTGA
1 TTCTTGA-AATCGCTCAAAACAACAAAATTGGACCAAGA--TTC-GGT
*
53585281 TTCTTGAAATCGCTCAAAACAGCAAAATTGGACCAAGATTCGGT
1 TTCTTGAAATCGCTCAAAACAACAAAATTGGACCAAGATTCGGT
53585325 TTCTTGA
1 TTCTTGA
53585332 TTTTCTTAAA
Statistics
Matches: 66, Mismatches: 25, Indels: 12
0.64 0.24 0.12
Matches are distributed among these distances:
43 9 0.14
44 23 0.35
45 10 0.15
46 15 0.23
47 9 0.14
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Consensus pattern (44 bp):
TTCTTGAAATCGCTCAAAACAACAAAATTGGACCAAGATTCGGT
Found at i:53585243 original size:51 final size:51
Alignment explanation
Indices: 53585183--53585333 Score: 137
Period size: 51 Copynumber: 3.2 Consensus size: 51
53585173 AAATCTTGAT
53585183 TTTCTTGATTCTTGAAATCGCTCAAAACAACAAAATTGGACCAAGATTCGG
1 TTTCTTGATTCTTGAAATCGCTCAAAACAACAAAATTGGACCAAGATTCGG
* * * * * * **
53585234 TTTCTTGA-T-TT----TC-TTAAAAACAA-GAAAGTGAATCTTGA-T---
1 TTTCTTGATTCTTGAAATCGCTCAAAACAACAAAATTGGACCAAGATTCGG
*
53585273 TTTCTTGATTCTTGAAATCGCTCAAAACAGCAAAATTGGACCAAGATTCGG
1 TTTCTTGATTCTTGAAATCGCTCAAAACAACAAAATTGGACCAAGATTCGG
53585324 TTTCTTGATT
1 TTTCTTGATT
53585334 TTCTTAAAAA
Statistics
Matches: 71, Mismatches: 17, Indels: 24
0.63 0.15 0.21
Matches are distributed among these distances:
39 8 0.11
40 1 0.01
41 2 0.03
42 1 0.01
43 9 0.13
44 8 0.11
45 4 0.06
46 7 0.10
47 9 0.13
48 1 0.01
49 2 0.03
50 1 0.01
51 18 0.25
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (51 bp):
TTTCTTGATTCTTGAAATCGCTCAAAACAACAAAATTGGACCAAGATTCGG
Found at i:53585375 original size:90 final size:90
Alignment explanation
Indices: 53585174--53585368 Score: 381
Period size: 90 Copynumber: 2.2 Consensus size: 90
53585164 CAAGATTTGA
53585174 AATCTTGATTTTCTTGATTCTTGAAATCGCTCAAAACAACAAAATTGGACCAAGATTCGGTTTCT
1 AATCTTGATTTTCTTGATTCTTGAAATCGCTCAAAACAACAAAATTGGACCAAGATTCGGTTTCT
53585239 TGATTTTCTTAAAAACAAGAAAGTG
66 TGATTTTCTTAAAAACAAGAAAGTG
*
53585264 AATCTTGATTTTCTTGATTCTTGAAATCGCTCAAAACAGCAAAATTGGACCAAGATTCGGTTTCT
1 AATCTTGATTTTCTTGATTCTTGAAATCGCTCAAAACAACAAAATTGGACCAAGATTCGGTTTCT
53585329 TGATTTTCTTAAAAACAAGAAAGTG
66 TGATTTTCTTAAAAACAAGAAAGTG
53585354 AATCTTGATTTTCTT
1 AATCTTGATTTTCTT
53585369 TTTTCTTCGT
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 104 1.00
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.36
Consensus pattern (90 bp):
AATCTTGATTTTCTTGATTCTTGAAATCGCTCAAAACAACAAAATTGGACCAAGATTCGGTTTCT
TGATTTTCTTAAAAACAAGAAAGTG
Found at i:53586044 original size:25 final size:25
Alignment explanation
Indices: 53586001--53586048 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
53585991 TGAGCTATGA
*
53586001 ATCGGTATGCTTACTCGAGCTGTAG
1 ATCGGTATGCTTACACGAGCTGTAG
53586026 ATCGGTATGCTCT-CACGAGCTGT
1 ATCGGTATGCT-TACACGAGCTGT
53586049 GGAGTATCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.19, C:0.23, G:0.27, T:0.31
Consensus pattern (25 bp):
ATCGGTATGCTTACACGAGCTGTAG
Found at i:53586681 original size:9 final size:9
Alignment explanation
Indices: 53586667--53586696 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
53586657 TAATTCAATT
53586667 TTAGTTAAA
1 TTAGTTAAA
53586676 TTAGTTAAA
1 TTAGTTAAA
*
53586685 TTAGTTACA
1 TTAGTTAAA
53586694 TTA
1 TTA
53586697 TGTTTCGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (9 bp):
TTAGTTAAA
Found at i:53586844 original size:25 final size:25
Alignment explanation
Indices: 53586811--53586883 Score: 103
Period size: 25 Copynumber: 2.9 Consensus size: 25
53586801 AATATATGAT
*
53586811 TTAAATTGGTCTTAGTTTAGACGAA
1 TTAAATTGGTCTTAGTTTAGACAAA
*
53586836 TTAAATTGGACTTAGTTGT-GACAAA
1 TTAAATTGGTCTTAGTT-TAGACAAA
*
53586861 TTAAATTGGTCTTAGTTCAGACA
1 TTAAATTGGTCTTAGTTTAGACA
53586884 CCTTAATTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
25 41 0.98
26 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (25 bp):
TTAAATTGGTCTTAGTTTAGACAAA
Found at i:53589170 original size:10 final size:10
Alignment explanation
Indices: 53589155--53589193 Score: 60
Period size: 10 Copynumber: 3.7 Consensus size: 10
53589145 CAAGATTGTA
53589155 AAAAAAATTG
1 AAAAAAATTG
53589165 AAAAAAATTCG
1 AAAAAAATT-G
53589176 AAAAAAAATTG
1 -AAAAAAATTG
53589187 AAAAAAA
1 AAAAAAA
53589194 ATTATTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 16 0.59
11 2 0.07
12 9 0.33
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.15
Consensus pattern (10 bp):
AAAAAAATTG
Found at i:53589170 original size:11 final size:11
Alignment explanation
Indices: 53589149--53589196 Score: 71
Period size: 12 Copynumber: 4.3 Consensus size: 11
53589139 GTATTACAAG
53589149 ATTGTAAAAAAA
1 ATTG-AAAAAAA
53589161 ATTG-AAAAAA
1 ATTGAAAAAAA
53589171 ATTCGAAAAAAA
1 ATT-GAAAAAAA
53589183 ATTGAAAAAAA
1 ATTGAAAAAAA
53589194 ATT
1 ATT
53589197 ATTATTTGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
10 9 0.26
11 12 0.35
12 13 0.38
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.23
Consensus pattern (11 bp):
ATTGAAAAAAA
Found at i:53590212 original size:15 final size:16
Alignment explanation
Indices: 53590192--53590223 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
53590182 AGAAAATGAA
53590192 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
53590207 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
53590223 A
1 A
53590224 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:53591111 original size:12 final size:12
Alignment explanation
Indices: 53591094--53591120 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
53591084 GACGTCAAGC
53591094 CAAGGTGAGTAT
1 CAAGGTGAGTAT
53591106 CAAGGTGAGTAT
1 CAAGGTGAGTAT
53591118 CAA
1 CAA
53591121 ATTGAAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.11, G:0.30, T:0.22
Consensus pattern (12 bp):
CAAGGTGAGTAT
Found at i:53596724 original size:21 final size:21
Alignment explanation
Indices: 53596681--53596724 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
53596671 ACACACTCAG
*
53596681 CTTAATTGAGCTATTAATGAA
1 CTTAATTGAGCTATTAATAAA
53596702 CTTAATTGAGCTAATTAA-AAA
1 CTTAATTGAGCT-ATTAATAAA
53596723 CT
1 CT
53596725 ACAAGACCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.36
Consensus pattern (21 bp):
CTTAATTGAGCTATTAATAAA
Found at i:53599219 original size:25 final size:25
Alignment explanation
Indices: 53599191--53599263 Score: 103
Period size: 25 Copynumber: 2.9 Consensus size: 25
53599181 AATATATGAT
*
53599191 TTAAATTGGTCTTAGTTTAGACGAA
1 TTAAATTGGTCTTAGTTTAGACAAA
*
53599216 TTAAATTGGACTTAGTTGT-GACAAA
1 TTAAATTGGTCTTAGTT-TAGACAAA
*
53599241 TTAAATTGGTCTTAGTTCAGACA
1 TTAAATTGGTCTTAGTTTAGACA
53599264 CCTTAATTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
25 41 0.98
26 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (25 bp):
TTAAATTGGTCTTAGTTTAGACAAA
Found at i:53604194 original size:39 final size:40
Alignment explanation
Indices: 53604099--53604360 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
53604089 TTGAATGATG
*
53604099 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
53604137 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
53604178 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
53604217 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
53604256 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
53604295 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
53604334 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
53604361 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:53615727 original size:35 final size:35
Alignment explanation
Indices: 53615686--53615758 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
53615676 GTGTAATCCT
53615686 TAAAAATTAGTGTTATGTATTTGGATACTTGTCAA
1 TAAAAATTAGTGTTATGTATTTGGATACTTGTCAA
53615721 TAAAAATTAGTGTTATGTATTTGGATACTTGTCAA
1 TAAAAATTAGTGTTATGTATTTGGATACTTGTCAA
53615756 TAA
1 TAA
53615759 GAAAAGCCCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.42
Consensus pattern (35 bp):
TAAAAATTAGTGTTATGTATTTGGATACTTGTCAA
Found at i:53625392 original size:20 final size:20
Alignment explanation
Indices: 53625345--53625393 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
53625335 GATGAGCTGA
* * *
53625345 AAGTAAGCTAAATTGAGCTC
1 AAGTGAGCTAAAATAAGCTC
**
53625365 AAACGAGCTAAAATAAGCTC
1 AAGTGAGCTAAAATAAGCTC
53625385 AAGTGAGCT
1 AAGTGAGCT
53625394 GATTTGAGCT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.20
Consensus pattern (20 bp):
AAGTGAGCTAAAATAAGCTC
Found at i:53635696 original size:14 final size:14
Alignment explanation
Indices: 53635677--53635719 Score: 86
Period size: 14 Copynumber: 3.1 Consensus size: 14
53635667 TAGTACATTA
53635677 GCCTTGCATGACTT
1 GCCTTGCATGACTT
53635691 GCCTTGCATGACTT
1 GCCTTGCATGACTT
53635705 GCCTTGCATGACTT
1 GCCTTGCATGACTT
53635719 G
1 G
53635720 TAAGATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.14, C:0.28, G:0.23, T:0.35
Consensus pattern (14 bp):
GCCTTGCATGACTT
Found at i:53636911 original size:14 final size:13
Alignment explanation
Indices: 53636885--53636915 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
53636875 TTGTTGCTAG
53636885 TTAAATTAGTTAA
1 TTAAATTAGTTAA
53636898 TTAAATTAAGTTAA
1 TTAAATT-AGTTAA
53636912 TTAA
1 TTAA
53636916 TTTGTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (13 bp):
TTAAATTAGTTAA
Found at i:53637046 original size:28 final size:27
Alignment explanation
Indices: 53636962--53637046 Score: 75
Period size: 28 Copynumber: 3.1 Consensus size: 27
53636952 AATGTGTTTC
* *
53636962 ATTGCATG-CTTTAATATGTCATAGCT
1 ATTGCATGTTTTTAATATGTCCTAGCT
* * *
53636988 ATTGCATGTTATTAAT-TTTTCTAAGCCT
1 ATTGCATGTTTTTAATATGTCCT-AG-CT
*
53637016 ATTGCATGTTTTTTAATATGTCCTAGTT
1 ATTGCATG-TTTTTAATATGTCCTAGCT
53637044 ATT
1 ATT
53637047 ACATAGCATA
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
26 11 0.24
27 7 0.16
28 14 0.31
29 9 0.20
30 4 0.09
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.49
Consensus pattern (27 bp):
ATTGCATGTTTTTAATATGTCCTAGCT
Found at i:53642777 original size:76 final size:76
Alignment explanation
Indices: 53642657--53642808 Score: 304
Period size: 76 Copynumber: 2.0 Consensus size: 76
53642647 TCAAAGTGGC
53642657 CCAATTTGTTAAGTTTTAATTCTTTAAATACTTAGTTTAATTTTTTAGACTTCATGATTAAATTC
1 CCAATTTGTTAAGTTTTAATTCTTTAAATACTTAGTTTAATTTTTTAGACTTCATGATTAAATTC
53642722 CTATGTAAAAA
66 CTATGTAAAAA
53642733 CCAATTTGTTAAGTTTTAATTCTTTAAATACTTAGTTTAATTTTTTAGACTTCATGATTAAATTC
1 CCAATTTGTTAAGTTTTAATTCTTTAAATACTTAGTTTAATTTTTTAGACTTCATGATTAAATTC
53642798 CTATGTAAAAA
66 CTATGTAAAAA
53642809 AAATTCAGCC
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (76 bp):
CCAATTTGTTAAGTTTTAATTCTTTAAATACTTAGTTTAATTTTTTAGACTTCATGATTAAATTC
CTATGTAAAAA
Found at i:53646139 original size:132 final size:132
Alignment explanation
Indices: 53645976--53646221 Score: 404
Period size: 132 Copynumber: 1.9 Consensus size: 132
53645966 GTCTTGAATG
* **
53645976 ATTCCATTTAGTTTCATACGGATTTGCCTGGCCTTTGACCTTGTTATTGGGT-CTTGTGGTAATT
1 ATTCCATTTAGTTTCATACGCATTTGCCTGGCCTTTGACCTCATTATT-GGTCCTTGTGGTAATT
*
53646040 TGAGCCCATCACGTCCTTGAGCTTGAATTGGGCCTTTGTGACTCGTATCACTAATGAAGTTTTTA
65 TGAGCCCATCACGTCCTTGAGCTTGAATTAGGCCTTTGTGACTCGTATCACTAATGAAGTTTTTA
53646105 ACA
130 ACA
*
53646108 ATTCCATTTAGTTTGATACGCATTTGCCTGGCCTTTGACCTCATTATTGGTCCTTGTGGTAATTT
1 ATTCCATTTAGTTTCATACGCATTTGCCTGGCCTTTGACCTCATTATTGGTCCTTGTGGTAATTT
* * *
53646173 GAGCCCATCACGTTCTTGAGCTTGAGTTAGGCCTTTGTGTCTCGTATCA
66 GAGCCCATCACGTCCTTGAGCTTGAATTAGGCCTTTGTGACTCGTATCA
53646222 TTTCCCCATA
Statistics
Matches: 105, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
131 3 0.03
132 102 0.97
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.40
Consensus pattern (132 bp):
ATTCCATTTAGTTTCATACGCATTTGCCTGGCCTTTGACCTCATTATTGGTCCTTGTGGTAATTT
GAGCCCATCACGTCCTTGAGCTTGAATTAGGCCTTTGTGACTCGTATCACTAATGAAGTTTTTAA
CA
Found at i:53655835 original size:20 final size:21
Alignment explanation
Indices: 53655812--53655850 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
53655802 TGATTTCATA
*
53655812 TTTTTCTA-TTTTTTTTTGAC
1 TTTTTCTACTATTTTTTTGAC
53655832 TTTTTCTACTATTTTTTTG
1 TTTTTCTACTATTTTTTTG
53655851 CGAGAGATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.10, C:0.10, G:0.05, T:0.74
Consensus pattern (21 bp):
TTTTTCTACTATTTTTTTGAC
Found at i:53665833 original size:33 final size:33
Alignment explanation
Indices: 53665791--53665857 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
53665781 TACCAAAAAG
53665791 TACATGTGCTTTGTGCGAGGACAGATTCAAGTC
1 TACATGTGCTTTGTGCGAGGACAGATTCAAGTC
53665824 TACATGTGCTTTGTGCGAGGACAGATTCAAGTC
1 TACATGTGCTTTGTGCGAGGACAGATTCAAGTC
53665857 T
1 T
53665858 TCCCCACTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (33 bp):
TACATGTGCTTTGTGCGAGGACAGATTCAAGTC
Found at i:53668155 original size:41 final size:41
Alignment explanation
Indices: 53668097--53668287 Score: 172
Period size: 41 Copynumber: 4.7 Consensus size: 41
53668087 ATTGGAGTGT
** * ***
53668097 AAACA-GGGCACGCATGTGCATTTCAAGGGTATTGAAGTAC
1 AAACAGGGGCACATATGTGCAATTCAAGGGTACCAAAGTAC
* *
53668137 AAATAGGGGCACATATGTGCAATTC-AGTGGTACTAAAGTAC
1 AAACAGGGGCACATATGTGCAATTCAAG-GGTACCAAAGTAC
* ** * * * * *
53668178 AAACA-GGGCACGTATGTATAATCCAGGGGCATCGAAGTAC
1 AAACAGGGGCACATATGTGCAATTCAAGGGTACCAAAGTAC
* * *
53668218 AAACAGGGGCACGTATGTGCAATTTAGGGGTACCAAAGTAC
1 AAACAGGGGCACATATGTGCAATTCAAGGGTACCAAAGTAC
*
53668259 AAATAGGGGCACATATGTGCAATTCAAGG
1 AAACAGGGGCACATATGTGCAATTCAAGG
53668288 AATAATTAGG
Statistics
Matches: 120, Mismatches: 27, Indels: 7
0.78 0.18 0.05
Matches are distributed among these distances:
40 35 0.29
41 85 0.71
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (41 bp):
AAACAGGGGCACATATGTGCAATTCAAGGGTACCAAAGTAC
Found at i:53668189 original size:81 final size:81
Alignment explanation
Indices: 53668097--53668287 Score: 238
Period size: 81 Copynumber: 2.3 Consensus size: 81
53668087 ATTGGAGTGT
* * * * *
53668097 AAACAGGGCACGCATGTGCATTTCAAGGGTATTGAAGTACAAATAGGGGCACATATGTGCAATTC
1 AAACAGGGCACGTATGTGCAATTCAAGGGCATCGAAGTACAAACAGGGGCACATATGTGCAATTC
* *
53668162 AGTGGTACTAAAGTAC
66 AGGGGTACCAAAGTAC
** * * * *
53668178 AAACAGGGCACGTATGTATAATCCAGGGGCATCGAAGTACAAACAGGGGCACGTATGTGCAATTT
1 AAACAGGGCACGTATGTGCAATTCAAGGGCATCGAAGTACAAACAGGGGCACATATGTGCAATTC
53668243 AGGGGTACCAAAGTAC
66 AGGGGTACCAAAGTAC
* *
53668259 AAATAGGGGCACATATGTGCAATTCAAGG
1 AAACA-GGGCACGTATGTGCAATTCAAGG
53668288 AATAATTAGG
Statistics
Matches: 90, Mismatches: 19, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
81 72 0.80
82 18 0.20
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (81 bp):
AAACAGGGCACGTATGTGCAATTCAAGGGCATCGAAGTACAAACAGGGGCACATATGTGCAATTC
AGGGGTACCAAAGTAC
Found at i:53668208 original size:21 final size:20
Alignment explanation
Indices: 53668174--53668235 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
53668164 TGGTACTAAA
53668174 GTACAAACA-GGGCACGTAT
1 GTACAAACAGGGGCACGTAT
* * *
53668193 GTATAATCCAGGGGCATCG-AA
1 GTACAA-ACAGGGGCA-CGTAT
53668214 GTACAAACAGGGGCACGTAT
1 GTACAAACAGGGGCACGTAT
53668234 GT
1 GT
53668236 GCAATTTAGG
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
19 7 0.21
20 13 0.39
21 11 0.33
22 2 0.06
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.18
Consensus pattern (20 bp):
GTACAAACAGGGGCACGTAT
Found at i:53675237 original size:43 final size:42
Alignment explanation
Indices: 53675071--53675269 Score: 161
Period size: 39 Copynumber: 4.9 Consensus size: 42
53675061 TTCTACAAGC
*
53675071 TGTGTATCAACAAAGCTCCACC--GTGAGC-TAA-AGATAAGT
1 TGTGTATCAACAAAGCTCC-CCATGTGAGCTTAAGTGATAAGT
* * * *
53675110 TGTGTATCAACGAAGCT-CCC-TCGTAAGC-TAA-AGATAAGC
1 TGTGTATCAACAAAGCTCCCCAT-GTGAGCTTAAGTGATAAGT
*
53675149 TGTGTATTAGA-AAAGCTCCCC-TGTGAGC-TAAG-GATAAGT
1 TGTGTATCA-ACAAAGCTCCCCATGTGAGCTTAAGTGATAAGT
* * * * * *
53675188 TTTGTATCAGCGAGGTTCCTCATGTGAGCTTAAGTGATGAAGT
1 TGTGTATCAACAAAGCTCCCCATGTGAGCTTAAGTGAT-AAGT
*
53675231 TGTGTATCAACAAAGCTCCCCATGCGAGCTTAAGTGATA
1 TGTGTATCAACAAAGCTCCCCATGTGAGCTTAAGTGATA
53675270 GTGCTCCTCA
Statistics
Matches: 129, Mismatches: 21, Indels: 17
0.77 0.13 0.10
Matches are distributed among these distances:
37 2 0.02
38 1 0.01
39 71 0.55
40 12 0.09
41 4 0.03
42 4 0.03
43 35 0.27
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (42 bp):
TGTGTATCAACAAAGCTCCCCATGTGAGCTTAAGTGATAAGT
Found at i:53677157 original size:18 final size:17
Alignment explanation
Indices: 53677109--53677149 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
53677099 AATCTTAATC
*
53677109 TCTTTTTTCTTTCTTTT
1 TCTTTTTTATTTCTTTT
*
53677126 TCCTTTTTAATTTCTTTT
1 T-CTTTTTTATTTCTTTT
53677144 TCTTTT
1 TCTTTT
53677150 ATTTTTTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (17 bp):
TCTTTTTTATTTCTTTT
Found at i:53680980 original size:15 final size:15
Alignment explanation
Indices: 53680957--53680992 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
53680947 GTAAGCATTT
53680957 AAAAAAAATTT-AAA
1 AAAAAAAATTTGAAA
53680971 AAAAAGAAATTTGAAA
1 AAAAA-AAATTTGAAA
53680987 AAAAAA
1 AAAAAA
53680993 TCCAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.25
15 7 0.35
16 8 0.40
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.17
Consensus pattern (15 bp):
AAAAAAAATTTGAAA
Found at i:53682108 original size:13 final size:12
Alignment explanation
Indices: 53682090--53682129 Score: 50
Period size: 10 Copynumber: 3.5 Consensus size: 12
53682080 TGTGAGCGAG
53682090 AAAAGAACATTGA
1 AAAAGAA-ATTGA
53682103 AAAAGAAATTG-
1 AAAAGAAATTGA
53682114 -AAAGAAA-TGA
1 AAAAGAAATTGA
53682124 AAAAGA
1 AAAAGA
53682130 GAAAGAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 2 0.08
10 7 0.28
11 5 0.20
12 4 0.16
13 7 0.28
ACGTcount: A:0.68, C:0.03, G:0.17, T:0.12
Consensus pattern (12 bp):
AAAAGAAATTGA
Found at i:53696642 original size:25 final size:25
Alignment explanation
Indices: 53696607--53696660 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
53696597 TGAACCTCTA
53696607 ACCTCCATACCACACCTCTGACGCC
1 ACCTCCATACCACACCTCTGACGCC
* * *
53696632 ACCTCCTTACCACACCTGTGTCGCC
1 ACCTCCATACCACACCTCTGACGCC
53696657 ACCT
1 ACCT
53696661 TGCCACTACG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.20, C:0.50, G:0.09, T:0.20
Consensus pattern (25 bp):
ACCTCCATACCACACCTCTGACGCC
Found at i:53697367 original size:48 final size:48
Alignment explanation
Indices: 53697296--53697393 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
53697286 GAAAAATAAG
53697296 TATGTAATTACAATTATCTCATGATTGGTCTTTGGGCATACTATAGCA
1 TATGTAATTACAATTATCTCATGATTGGTCTTTGGGCATACTATAGCA
53697344 TATGTAATTACAATTATCTCATGATTGGTCTTTGGGCATACTATAGCA
1 TATGTAATTACAATTATCTCATGATTGGTCTTTGGGCATACTATAGCA
53697392 TA
1 TA
53697394 CTTTATATGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (48 bp):
TATGTAATTACAATTATCTCATGATTGGTCTTTGGGCATACTATAGCA
Found at i:53699110 original size:14 final size:14
Alignment explanation
Indices: 53699091--53699120 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
53699081 AGATTGTTGC
*
53699091 TATTATTTTATTGT
1 TATTATTATATTGT
53699105 TATTATTATATTGT
1 TATTATTATATTGT
53699119 TA
1 TA
53699121 CAACCAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (14 bp):
TATTATTATATTGT
Found at i:53702396 original size:20 final size:20
Alignment explanation
Indices: 53702363--53702407 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
53702353 TAAATTCACA
53702363 TAATTAAAACAAGACAC-AAT
1 TAATTAAAACAAGAC-CTAAT
**
53702383 TAATTAAATTAAGACCTAAT
1 TAATTAAAACAAGACCTAAT
53702403 TAATT
1 TAATT
53702408 CGGTTAGGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.31
Consensus pattern (20 bp):
TAATTAAAACAAGACCTAAT
Found at i:53715962 original size:18 final size:18
Alignment explanation
Indices: 53715941--53715975 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53715931 TTTCTCTTTT
*
53715941 TCAATTTCTTTCTCAATC
1 TCAACTTCTTTCTCAATC
*
53715959 TCAACTTCTTTTTCAAT
1 TCAACTTCTTTCTCAAT
53715976 TTTCTTTTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.26, G:0.00, T:0.51
Consensus pattern (18 bp):
TCAACTTCTTTCTCAATC
Found at i:53715996 original size:25 final size:24
Alignment explanation
Indices: 53715966--53716014 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
53715956 ATCTCAACTT
53715966 CTTTTTCAATTTTCTTTTTCTTTCA
1 CTTTTTCAA-TTTCTTTTTCTTTCA
**
53715991 CTTTTTTGATTTCTTTTTCTTTCA
1 CTTTTTCAATTTCTTTTTCTTTCA
53716015 TTTCTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.10, C:0.18, G:0.02, T:0.69
Consensus pattern (24 bp):
CTTTTTCAATTTCTTTTTCTTTCA
Found at i:53733837 original size:617 final size:617
Alignment explanation
Indices: 53732664--53733898 Score: 2452
Period size: 617 Copynumber: 2.0 Consensus size: 617
53732654 GGCTCTTTTC
53732664 TACACTCGGTCCAATCACATTCAACACTCCAAAAAAAAATTAACAAACCTCACCGTTAATCACTC
1 TACACTCGGTCCAATCACATTCAACACTCCAAAAAAAAATTAACAAACCTCACCGTTAATCACTC
53732729 AAAAAGGAAAATCAAATTCTCAAAGAGGTAGAATTCAGTCTTGTGAGTTCTTTAGTAGAGTCTAT
66 AAAAAGGAAAATCAAATTCTCAAAGAGGTAGAATTCAGTCTTGTGAGTTCTTTAGTAGAGTCTAT
*
53732794 ATCAATCAATTAGAAAGTGTATGAACCGTAACTACCAAAGAATCCTAATTGCACTAGGAATCCAA
131 ATCAATCAATTAGAAAGTGTAAGAACCGTAACTACCAAAGAATCCTAATTGCACTAGGAATCCAA
53732859 AAAAGTGACGAGACACCAATTGATTTGTGTTGCACCGAGGAAGAATTGTGCACACTTTTAAATCC
196 AAAAGTGACGAGACACCAATTGATTTGTGTTGCACCGAGGAAGAATTGTGCACACTTTTAAATCC
53732924 TACTAACACAAGAAACAAGAAGGTGTTAGATAGTTTAAAGGAAGAATAAACGCAAAACAAATGAA
261 TACTAACACAAGAAACAAGAAGGTGTTAGATAGTTTAAAGGAAGAATAAACGCAAAACAAATGAA
53732989 ATCCTACAGCTAAGAATCAATAAAAATTGCTGATACCCGAAAACCTGAAAAACTGCGGAGTAACT
326 ATCCTACAGCTAAGAATCAATAAAAATTGCTGATACCCGAAAACCTGAAAAACTGCGGAGTAACT
53733054 TGAAAACTTCGTTCGAGGTGTTCCCGATCTCCAAAAATCACGAAATTTAAACTGGAATGTCCTTA
391 TGAAAACTTCGTTCGAGGTGTTCCCGATCTCCAAAAATCACGAAATTTAAACTGGAATGTCCTTA
53733119 GATATTTTATTTTTGATCAGAAAAGTTTCGGCACTAAACTCAACCCGCTGAATATTTTTTTAATT
456 GATATTTTATTTTTGATCAGAAAAGTTTCGGCACTAAACTCAACCCGCTGAATATTTTTTTAATT
53733184 TTTATTTGATTTGGTATTTTTATTTTTTTATTTTACTTTTTCCACTGATTTTTTTGCGGTAAATA
521 TTTATTTGATTTGGTATTTTTATTTTTTTATTTTACTTTTTCCACTGATTTTTTTGCGGTAAATA
53733249 TTTTTTAATATTCTATCACAGTGCCACAAATA
586 TTTTTTAATATTCTATCACAGTGCCACAAATA
53733281 TACACTCGGTCCAATCACATTCAACACTCCAAAAAAAAATTAACAAACCTCACCGTTAATCACTC
1 TACACTCGGTCCAATCACATTCAACACTCCAAAAAAAAATTAACAAACCTCACCGTTAATCACTC
53733346 AAAAAGGAAAATCAAATTCTCAAAGAGGTAGAATTCAGTCTTGTGAGTTCTTTAGTAGAGTCTAT
66 AAAAAGGAAAATCAAATTCTCAAAGAGGTAGAATTCAGTCTTGTGAGTTCTTTAGTAGAGTCTAT
*
53733411 ATCAATCAATTAGAAAGTGTAAGAACCGTAACTACCAAATAATCCTAATTGCACTAGGAATCCAA
131 ATCAATCAATTAGAAAGTGTAAGAACCGTAACTACCAAAGAATCCTAATTGCACTAGGAATCCAA
53733476 AAAAGTGACGAGACACCAATTGATTTGTGTTGCACCGAGGAAGAATTGTGCACACTTTTAAATCC
196 AAAAGTGACGAGACACCAATTGATTTGTGTTGCACCGAGGAAGAATTGTGCACACTTTTAAATCC
53733541 TACTAACACAAGAAACAAGAAGGTGTTAGATAGTTTAAAGGAAGAATAAACGCAAAACAAATGAA
261 TACTAACACAAGAAACAAGAAGGTGTTAGATAGTTTAAAGGAAGAATAAACGCAAAACAAATGAA
53733606 ATCCTACAGCTAAGAATCAATAAAAATTGCTGATACCCGAAAACCTGAAAAACTGCGGAGTAACT
326 ATCCTACAGCTAAGAATCAATAAAAATTGCTGATACCCGAAAACCTGAAAAACTGCGGAGTAACT
53733671 TGAAAACTTCGTTCGAGGTGTTCCCGATCTCCAAAAATCACGAAATTTAAACTGGAATGTCCTTA
391 TGAAAACTTCGTTCGAGGTGTTCCCGATCTCCAAAAATCACGAAATTTAAACTGGAATGTCCTTA
53733736 GATATTTTATTTTTGATCAGAAAAGTTTCGGCACTAAACTCAACCCGCTGAATATTTTTTTAATT
456 GATATTTTATTTTTGATCAGAAAAGTTTCGGCACTAAACTCAACCCGCTGAATATTTTTTTAATT
53733801 TTTATTTGATTTGGTATTTTTATTTTTTTATTTTACTTTTTCCACTGATTTTTTTGCGGTAAATA
521 TTTATTTGATTTGGTATTTTTATTTTTTTATTTTACTTTTTCCACTGATTTTTTTGCGGTAAATA
53733866 TTTTTTAATATTCTATCACAGTGCCACAAATA
586 TTTTTTAATATTCTATCACAGTGCCACAAATA
53733898 T
1 T
53733899 GCATATAAAA
Statistics
Matches: 616, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
617 616 1.00
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (617 bp):
TACACTCGGTCCAATCACATTCAACACTCCAAAAAAAAATTAACAAACCTCACCGTTAATCACTC
AAAAAGGAAAATCAAATTCTCAAAGAGGTAGAATTCAGTCTTGTGAGTTCTTTAGTAGAGTCTAT
ATCAATCAATTAGAAAGTGTAAGAACCGTAACTACCAAAGAATCCTAATTGCACTAGGAATCCAA
AAAAGTGACGAGACACCAATTGATTTGTGTTGCACCGAGGAAGAATTGTGCACACTTTTAAATCC
TACTAACACAAGAAACAAGAAGGTGTTAGATAGTTTAAAGGAAGAATAAACGCAAAACAAATGAA
ATCCTACAGCTAAGAATCAATAAAAATTGCTGATACCCGAAAACCTGAAAAACTGCGGAGTAACT
TGAAAACTTCGTTCGAGGTGTTCCCGATCTCCAAAAATCACGAAATTTAAACTGGAATGTCCTTA
GATATTTTATTTTTGATCAGAAAAGTTTCGGCACTAAACTCAACCCGCTGAATATTTTTTTAATT
TTTATTTGATTTGGTATTTTTATTTTTTTATTTTACTTTTTCCACTGATTTTTTTGCGGTAAATA
TTTTTTAATATTCTATCACAGTGCCACAAATA
Found at i:53755349 original size:40 final size:40
Alignment explanation
Indices: 53755101--53755351 Score: 312
Period size: 40 Copynumber: 6.3 Consensus size: 40
53755091 TCTTCGGAAT
* * * *
53755101 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
* * * *
53755140 TTAACCCAGG-T-ATAGCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCC-GGATAAAATC-ACTAGCACAAATGCCTTCGGGTC
* *
53755180 TTAGCCCGGAT-ATATCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTC
53755220 TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
* * *
53755260 TTAACCCGGATAAAATCACTAGCATAAATGCCCTCGGGTC
1 TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
* *
53755300 TTAACCCGGATAAAATCACTAGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
53755340 TTAGCCCGGATA
1 TTAGCCCGGATA
53755352 TCATTCAAAT
Statistics
Matches: 189, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
39 7 0.04
40 176 0.93
41 6 0.03
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (40 bp):
TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
Found at i:53759313 original size:19 final size:17
Alignment explanation
Indices: 53759282--53759326 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
53759272 CAAATGAAGG
*
53759282 TTCATGTAATTAAAAGAA
1 TTCATGTACTTAAAAG-A
*
53759300 TTCATTGTACTTAAGAGA
1 TTCA-TGTACTTAAAAGA
53759318 TTCATGTAC
1 TTCATGTAC
53759327 GACATAGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 5 0.21
18 9 0.38
19 10 0.42
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (17 bp):
TTCATGTACTTAAAAGA
Found at i:53761671 original size:24 final size:25
Alignment explanation
Indices: 53761625--53761671 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
53761615 AGGAATTTGG
*
53761625 CTAAATGAATTGATGATGGAAATGA
1 CTAAATGAATTGATGATGAAAATGA
* *
53761650 CTAAGTGAA-TGATGGTGAAAAT
1 CTAAATGAATTGATGATGAAAAT
53761672 TCGGCTAAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.43, C:0.04, G:0.26, T:0.28
Consensus pattern (25 bp):
CTAAATGAATTGATGATGAAAATGA
Found at i:53767370 original size:19 final size:19
Alignment explanation
Indices: 53767326--53767390 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
53767316 TTTTCTTTTG
** *
53767326 TTTCTTTTTCTAAC-TCAT
1 TTTCTTTTTCTTTCTTCAA
53767344 TTTC-TTTTCTTTCTTCAA
1 TTTCTTTTTCTTTCTTCAA
53767362 TTTCTTTTTCTTTCTTCAA
1 TTTCTTTTTCTTTCTTCAA
53767381 TTTCTTTTTC
1 TTTCTTTTTC
53767391 GATTTCCTCT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.17
18 11 0.26
19 24 0.57
ACGTcount: A:0.11, C:0.22, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTCTTTTTCTTTCTTCAA
Found at i:53767433 original size:45 final size:45
Alignment explanation
Indices: 53767351--53767459 Score: 134
Period size: 45 Copynumber: 2.4 Consensus size: 45
53767341 CATTTTCTTT
*
53767351 TCTTTCTTCAATTTCTTTTTCTTTCTTCAATTTCTTTTTCGATTTCC
1 TCTTTCTTCAATTTC--TTTCTTTCTTCAATTTCTTTTTCAATTTCC
*
53767398 TCTTT-TTCAATTTCTTTCTTAATC-TCAATTTCTTTTTCAATTTTC
1 TCTTTCTTCAATTTCTTTCTT--TCTTCAATTTCTTTTTCAATTTCC
*
53767443 T-TTTCTTCATTTTCTTT
1 TCTTTCTTCAATTTCTTT
53767460 TTCTCTTACT
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
44 9 0.16
45 31 0.55
46 11 0.20
47 5 0.09
ACGTcount: A:0.13, C:0.21, G:0.01, T:0.65
Consensus pattern (45 bp):
TCTTTCTTCAATTTCTTTCTTTCTTCAATTTCTTTTTCAATTTCC
Found at i:53794310 original size:17 final size:16
Alignment explanation
Indices: 53794287--53794328 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
53794277 CTCTTTTTTC
53794287 TTTCTTTTGC-TTTCTT
1 TTTCTTTT-CATTTCTT
53794303 TTTCCTTTTCAATTTCTT
1 TTT-CTTTTC-ATTTCTT
53794321 TTTCTTTT
1 TTTCTTTT
53794329 TTTTCATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 4 0.17
17 10 0.43
18 9 0.39
ACGTcount: A:0.05, C:0.19, G:0.02, T:0.74
Consensus pattern (16 bp):
TTTCTTTTCATTTCTT
Found at i:53799178 original size:11 final size:12
Alignment explanation
Indices: 53799158--53799196 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
53799148 TTTTTTTTTG
53799158 AATTTCTTTTCAA
1 AATTT-TTTTCAA
53799171 AATTTTTTTCGAA
1 AATTTTTTTC-AA
*
53799184 ATTTTTTTTCAA
1 AATTTTTTTCAA
53799196 A
1 A
53799197 TACTTACTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.31, C:0.10, G:0.03, T:0.56
Consensus pattern (12 bp):
AATTTTTTTCAA
Found at i:53799186 original size:25 final size:24
Alignment explanation
Indices: 53799149--53799196 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
53799139 TGTTCACAAT
*
53799149 TTTTTTTTGAATTTCTTTTCAAAA
1 TTTTTTTCGAATTTCTTTTCAAAA
*
53799173 TTTTTTTCGAAATTTTTTTTCAAA
1 TTTTTTTCG-AATTTCTTTTCAAA
53799197 TACTTACTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.25, C:0.08, G:0.04, T:0.62
Consensus pattern (24 bp):
TTTTTTTCGAATTTCTTTTCAAAA
Found at i:53799197 original size:12 final size:12
Alignment explanation
Indices: 53799141--53799197 Score: 60
Period size: 12 Copynumber: 4.6 Consensus size: 12
53799131 TACAACCATG
53799141 TTCACAATTTTTT
1 TTCA-AATTTTTT
** *
53799154 TTTGAATTTCTT
1 TTCAAATTTTTT
*
53799166 TTCAAAATTTTT
1 TTCAAATTTTTT
53799178 TTCGAAATTTTTT
1 TTC-AAATTTTTT
53799191 TTCAAAT
1 TTCAAAT
53799198 ACTTACTCCG
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
12 22 0.63
13 13 0.37
ACGTcount: A:0.26, C:0.11, G:0.04, T:0.60
Consensus pattern (12 bp):
TTCAAATTTTTT
Found at i:53799403 original size:24 final size:25
Alignment explanation
Indices: 53799357--53799403 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
53799347 AGGAATTTGG
*
53799357 CTAAATGAATTGATGATGGAAATGA
1 CTAAATGAATTGATGATGAAAATGA
* *
53799382 CTAAGTGAA-TGATGGTGAAAAT
1 CTAAATGAATTGATGATGAAAAT
53799404 TCAGCCAAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.43, C:0.04, G:0.26, T:0.28
Consensus pattern (25 bp):
CTAAATGAATTGATGATGAAAATGA
Found at i:53800323 original size:11 final size:12
Alignment explanation
Indices: 53800303--53800341 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
53800293 TTTTTTTTTG
53800303 AATTTCTTTTCAA
1 AATTT-TTTTCAA
53800316 AATTTTTTTCGAA
1 AATTTTTTTC-AA
*
53800329 ATTTTTTTTCAA
1 AATTTTTTTCAA
53800341 A
1 A
53800342 TACTTACTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.31, C:0.10, G:0.03, T:0.56
Consensus pattern (12 bp):
AATTTTTTTCAA
Found at i:53800331 original size:25 final size:24
Alignment explanation
Indices: 53800294--53800341 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
53800284 TGTTCACAAT
*
53800294 TTTTTTTTGAATTTCTTTTCAAAA
1 TTTTTTTCGAATTTCTTTTCAAAA
*
53800318 TTTTTTTCGAAATTTTTTTTCAAA
1 TTTTTTTCG-AATTTCTTTTCAAA
53800342 TACTTACTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.25, C:0.08, G:0.04, T:0.62
Consensus pattern (24 bp):
TTTTTTTCGAATTTCTTTTCAAAA
Found at i:53800342 original size:12 final size:12
Alignment explanation
Indices: 53800286--53800342 Score: 60
Period size: 12 Copynumber: 4.6 Consensus size: 12
53800276 TACAACCATG
53800286 TTCACAATTTTTT
1 TTCA-AATTTTTT
** *
53800299 TTTGAATTTCTT
1 TTCAAATTTTTT
*
53800311 TTCAAAATTTTT
1 TTCAAATTTTTT
53800323 TTCGAAATTTTTT
1 TTC-AAATTTTTT
53800336 TTCAAAT
1 TTCAAAT
53800343 ACTTACTCCG
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
12 22 0.63
13 13 0.37
ACGTcount: A:0.26, C:0.11, G:0.04, T:0.60
Consensus pattern (12 bp):
TTCAAATTTTTT
Found at i:53800548 original size:24 final size:25
Alignment explanation
Indices: 53800502--53800548 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
53800492 AGGAATTTGG
*
53800502 CTAAATGAATTGATGATGGAAATGA
1 CTAAATGAATTGATGATGAAAATGA
* *
53800527 CTAAGTGAA-TGATGGTGAAAAT
1 CTAAATGAATTGATGATGAAAAT
53800549 TCAGCCAAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.43, C:0.04, G:0.26, T:0.28
Consensus pattern (25 bp):
CTAAATGAATTGATGATGAAAATGA
Found at i:53808268 original size:90 final size:90
Alignment explanation
Indices: 53808115--53808294 Score: 324
Period size: 90 Copynumber: 2.0 Consensus size: 90
53808105 TGTGGTAAGA
* *
53808115 CTTCATGGCATCCCTAAAACAATTGTTTCCGACAGAGATGTCAAATTCCTTAGCCACTTTTGGAA
1 CTTCATGGCATCCCTAAAACAATTATTTCCGACAAAGATGTCAAATTCCTTAGCCACTTTTGGAA
*
53808180 GGTATTGTGGGGTAAGCTTGGTACG
66 GGTATTGTAGGGTAAGCTTGGTACG
*
53808205 CTTCATGGCATCCCTAAAATAATTATTTCCGACAAAGATGTCAAATTCCTTAGCCACTTTTGGAA
1 CTTCATGGCATCCCTAAAACAATTATTTCCGACAAAGATGTCAAATTCCTTAGCCACTTTTGGAA
53808270 GGTATTGTAGGGTAAGCTTGGTACG
66 GGTATTGTAGGGTAAGCTTGGTACG
53808295 AAATTACTGT
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 86 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (90 bp):
CTTCATGGCATCCCTAAAACAATTATTTCCGACAAAGATGTCAAATTCCTTAGCCACTTTTGGAA
GGTATTGTAGGGTAAGCTTGGTACG
Found at i:53808847 original size:18 final size:19
Alignment explanation
Indices: 53808824--53808861 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
53808814 CTGGTGAGTA
53808824 CAATGTA-AG-TTCTACTTT
1 CAATGTAGAGATTC-ACTTT
53808842 CAATGTAGAGATTCACTTT
1 CAATGTAGAGATTCACTTT
53808861 C
1 C
53808862 TTGTTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 8 0.44
20 3 0.17
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.39
Consensus pattern (19 bp):
CAATGTAGAGATTCACTTT
Found at i:53816036 original size:66 final size:67
Alignment explanation
Indices: 53815959--53816087 Score: 197
Period size: 67 Copynumber: 1.9 Consensus size: 67
53815949 TCCATTTCAA
* *
53815959 AGAGCACACTCCCGCGAACCTCA-TCCTTGCAGCGGGATTACCAGTCCAGACTACATCCCCTGCA
1 AGAGCACACTCCCGCGAACCTCATTCCTTACAGCGGGATTACCAGTCCAGACTAAATCCCCTGCA
53816023 AG
66 AG
* * * *
53816025 AGAGCACACTCCCGTGAACCTTATTCCTTACAGTGGGATTACCAGTCCAGGCTAAATCCCCTG
1 AGAGCACACTCCCGCGAACCTCATTCCTTACAGCGGGATTACCAGTCCAGACTAAATCCCCTG
53816088 TAATATAAAC
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
66 21 0.38
67 35 0.62
ACGTcount: A:0.26, C:0.35, G:0.19, T:0.20
Consensus pattern (67 bp):
AGAGCACACTCCCGCGAACCTCATTCCTTACAGCGGGATTACCAGTCCAGACTAAATCCCCTGCA
AG
Found at i:53816302 original size:57 final size:57
Alignment explanation
Indices: 53816209--53816322 Score: 160
Period size: 57 Copynumber: 2.0 Consensus size: 57
53816199 ACCCTAATTC
* * *
53816209 AGATTACCCGTCCGGGCTAAATCCATTTTTCACATATTCTTCGGGAGGGCTATATCA
1 AGATCACCCGTCCAGGCTAAATCCATTTTTCACATATTCTTCAGGAGGGCTATATCA
*
53816266 AGATCACCCGTCCAGGCTAGAT-C-TTTTTCACACATATTCTTCAGGAGGGCTATATCA
1 AGATCACCCGTCCAGGCTAAATCCATTTTT--CACATATTCTTCAGGAGGGCTATATCA
53816323 GGATAGGATC
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
55 5 0.10
56 1 0.02
57 45 0.88
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (57 bp):
AGATCACCCGTCCAGGCTAAATCCATTTTTCACATATTCTTCAGGAGGGCTATATCA
Found at i:53819447 original size:16 final size:16
Alignment explanation
Indices: 53819417--53819473 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
53819407 AAACTTTTTT
* *
53819417 CCCAAATTATAAAATC
1 CCCAAATCATGAAATC
* *
53819433 CCCAACTCATTAAATTC
1 CCCAAATCATGAAA-TC
* *
53819450 CCTAAATCGTGAAATC
1 CCCAAATCATGAAATC
53819466 CCCAAATC
1 CCCAAATC
53819474 CATAACATCT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
16 20 0.62
17 12 0.38
ACGTcount: A:0.40, C:0.32, G:0.04, T:0.25
Consensus pattern (16 bp):
CCCAAATCATGAAATC
Found at i:53819595 original size:23 final size:23
Alignment explanation
Indices: 53819569--53819636 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
53819559 TTAATCGCTT
53819569 AGAACCAAATCGTGAAATCCCTC
1 AGAACCAAATCGTGAAATCCCTC
* *
53819592 AGAACCAAATCATGAAATCCCTT
1 AGAACCAAATCGTGAAATCCCTC
* *
53819615 AAAACCAAATTGTGAAATCCCT
1 AGAACCAAATCGTGAAATCCCT
53819637 AATCTTTTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.21
Consensus pattern (23 bp):
AGAACCAAATCGTGAAATCCCTC
Found at i:53820490 original size:52 final size:51
Alignment explanation
Indices: 53820400--53820505 Score: 133
Period size: 52 Copynumber: 2.1 Consensus size: 51
53820390 GCTGTTTATT
* * *
53820400 TCTCTTTAATTTTTTTGCTTGTGCCGATTCATTGATTAAATTGTTTTAATC
1 TCTCTTTAATTTTTTTGCTTGAGCCGATTCATTAATTAAATTATTTTAATC
* * *
53820451 TCTCTTTAAATTTTTTTGCTTGAGTCGA-TCTATTAATTAACTTATTTTGATC
1 TCTCTTT-AATTTTTTTGCTTGAGCCGATTC-ATTAATTAAATTATTTTAATC
53820503 TCT
1 TCT
53820506 TTGTTGTGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
51 9 0.19
52 38 0.81
ACGTcount: A:0.21, C:0.14, G:0.10, T:0.55
Consensus pattern (51 bp):
TCTCTTTAATTTTTTTGCTTGAGCCGATTCATTAATTAAATTATTTTAATC
Found at i:53821108 original size:22 final size:22
Alignment explanation
Indices: 53821083--53821129 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
53821073 CTAAGAGTCG
* * *
53821083 TAAACAGGATAGCTATAAGCTA
1 TAAACAGAATAGCTAGAAGCCA
*
53821105 TAAACAGAATGGCTAGAAGCCA
1 TAAACAGAATAGCTAGAAGCCA
53821127 TAA
1 TAA
53821130 GTGTAGTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.19
Consensus pattern (22 bp):
TAAACAGAATAGCTAGAAGCCA
Found at i:53821189 original size:32 final size:32
Alignment explanation
Indices: 53821147--53821387 Score: 229
Period size: 32 Copynumber: 7.5 Consensus size: 32
53821137 AATGTGATTG
*
53821147 GCACAAAGCCATCAGTAGCAGTGATATGATCA
1 GCACAAAGCCATCAGTAACAGTGATATGATCA
* ** * * *
53821179 GCACACAGCCATCAGTAATGGTAACATGATCG
1 GCACAAAGCCATCAGTAACAGTGATATGATCA
* **
53821211 GCACAAAGCCATCAATGGCAGTGATATGATCA
1 GCACAAAGCCATCAGTAACAGTGATATGATCA
* * * *
53821243 GCACACAGCCATCAGTAACATTGAAATGATCG
1 GCACAAAGCCATCAGTAACAGTGATATGATCA
* ** *
53821275 GCACACAGCCATC-GATAATGGTAATATGATCA
1 GCACAAAGCCATCAG-TAACAGTGATATGATCA
* * *
53821307 GTACAAAGCCATTAGTAACGGT-ACTATGATCA
1 GCACAAAGCCATCAGTAACAGTGA-TATGATCA
53821339 GCACAAAGCCATCAGTAACAGT-ACTATGATC-
1 GCACAAAGCCATCAGTAACAGTGA-TATGATCA
53821370 GACACAAAGCCATCAGTA
1 G-CACAAAGCCATCAGTA
53821388 GCATCGTAGC
Statistics
Matches: 169, Mismatches: 36, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
31 3 0.02
32 165 0.98
33 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (32 bp):
GCACAAAGCCATCAGTAACAGTGATATGATCA
Found at i:53821224 original size:64 final size:64
Alignment explanation
Indices: 53821141--53821387 Score: 254
Period size: 64 Copynumber: 3.9 Consensus size: 64
53821131 TGTAGTAATG
* * *
53821141 TGATTGGCACAAAGCCATCAGTAGCAGTGATATGATCAGCACACAGCCATCAGTAATGGTAACA
1 TGATCGGCACAAAGCCATCAGTAACAGTGATATGATCAGCACAAAGCCATCAGTAATGGTAACA
* ** * *
53821205 TGATCGGCACAAAGCCATCAATGGCAGTGATATGATCAGCACACAGCCATCAGTAACATTG-AA-
1 TGATCGGCACAAAGCCATCAGTAACAGTGATATGATCAGCACAAAGCCATCAGT-A-ATGGTAAC
53821268 A
64 A
* ** * * * *
53821269 TGATCGGCACACAGCCATC-GATAATGGTAATATGATCAGTACAAAGCCATTAGTAACGGT-ACT
1 TGATCGGCACAAAGCCATCAG-TAACAGTGATATGATCAGCACAAAGCCATCAGTAATGGTAAC-
53821332 A
64 A
*
53821333 TGATCAGCACAAAGCCATCAGTAACAGT-ACTATGATC-GACACAAAGCCATCAGTA
1 TGATCGGCACAAAGCCATCAGTAACAGTGA-TATGATCAG-CACAAAGCCATCAGTA
53821388 GCATCGTAGC
Statistics
Matches: 152, Mismatches: 22, Indels: 18
0.79 0.11 0.09
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 139 0.91
65 4 0.03
66 3 0.02
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (64 bp):
TGATCGGCACAAAGCCATCAGTAACAGTGATATGATCAGCACAAAGCCATCAGTAATGGTAACA
Found at i:53821313 original size:96 final size:96
Alignment explanation
Indices: 53821147--53821387 Score: 283
Period size: 96 Copynumber: 2.5 Consensus size: 96
53821137 AATGTGATTG
* * *
53821147 GCACAAAGCCATCAGTAGCAGTGATATGATCAGCACACAGCCATCAGTAATGGTAACATGATCGG
1 GCACAAAGCCATCAGTAACAGTGAAATGATCAGCACACAGCCATCAGTAATGGTAACATGATCAG
**
53821212 CACAAAGCCATCAATGGCAGTGA-TATGATCA
66 CACAAAGCCATCAATAACAGT-ACTATGATCA
* * * *
53821243 GCACACAGCCATCAGTAACATTGAAATGATCGGCACACAGCCATC-GATAATGGTAATATGATCA
1 GCACAAAGCCATCAGTAACAGTGAAATGATCAGCACACAGCCATCAG-TAATGGTAACATGATCA
* * * *
53821307 GTACAAAGCCATTAGTAACGGTACTATGATCA
65 GCACAAAGCCATCAATAACAGTACTATGATCA
* *
53821339 GCACAAAGCCATCAGTAACAGT-ACTATGATC-GACACAAAGCCATCAGTA
1 GCACAAAGCCATCAGTAACAGTGA-AATGATCAG-CACACAGCCATCAGTA
53821388 GCATCGTAGC
Statistics
Matches: 123, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
95 4 0.03
96 118 0.96
97 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (96 bp):
GCACAAAGCCATCAGTAACAGTGAAATGATCAGCACACAGCCATCAGTAATGGTAACATGATCAG
CACAAAGCCATCAATAACAGTACTATGATCA
Found at i:53821442 original size:26 final size:26
Alignment explanation
Indices: 53821390--53821443 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
53821380 CATCAGTAGC
* * *
53821390 ATCGTAGCAAAGCTGCCAGCAACAGT
1 ATCGCAGCAAACCTGCCAACAACAGT
* *
53821416 ATCGCAGCAAACCTGCCAATAATAGT
1 ATCGCAGCAAACCTGCCAACAACAGT
53821442 AT
1 AT
53821444 ATGTGGCCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.19
Consensus pattern (26 bp):
ATCGCAGCAAACCTGCCAACAACAGT
Found at i:53821591 original size:24 final size:23
Alignment explanation
Indices: 53821559--53821631 Score: 92
Period size: 24 Copynumber: 3.1 Consensus size: 23
53821549 CCATGCTCAG
*
53821559 AATCAGTCATTCAAATCATAGACA
1 AATCAGTCATTCAAA-CACAGACA
*
53821583 AATCAGTCATACCAAACACAGACA
1 AATCAGTCAT-TCAAACACAGACA
* *
53821607 AATCAGTCATTTAACCACAGACA
1 AATCAGTCATTCAAACACAGACA
53821630 AA
1 AA
53821632 ATAATCATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
23 12 0.28
24 27 0.63
25 4 0.09
ACGTcount: A:0.48, C:0.25, G:0.08, T:0.19
Consensus pattern (23 bp):
AATCAGTCATTCAAACACAGACA
Found at i:53821733 original size:27 final size:26
Alignment explanation
Indices: 53821710--53821909 Score: 251
Period size: 27 Copynumber: 7.5 Consensus size: 26
53821700 GGTATTACAG
53821710 TCATTTTACCCTACAGGAGCATTACGA
1 TCATTTTACCCTACAGG-GCATTACGA
*
53821737 TCATTTTACCCTACAAGGGCATTACGG
1 TCATTTTACCCTAC-AGGGCATTACGA
*
53821764 TCATTTTACCCTATAGGGGCATTAC-A
1 TCATTTTACCCTACA-GGGCATTACGA
53821790 GTCATTTTACCCTACAGGGGCATTACGA
1 -TCATTTTACCCTACA-GGGCATTACGA
*
53821818 CCATTTTACCCTACAGGGCATTACGA
1 TCATTTTACCCTACAGGGCATTACGA
*
53821844 CCATTTTACCCTACAGTGGCATTACGA
1 TCATTTTACCCTACAG-GGCATTACGA
* * *
53821871 TCATTTTACCC-ATCAAGGGTATTTCGG
1 TCATTTTACCCTA-C-AGGGCATTACGA
53821898 TCATTTTACCCT
1 TCATTTTACCCT
53821910 TCGGGAGTAT
Statistics
Matches: 156, Mismatches: 9, Indels: 15
0.87 0.05 0.08
Matches are distributed among these distances:
26 29 0.19
27 121 0.78
28 6 0.04
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.32
Consensus pattern (26 bp):
TCATTTTACCCTACAGGGCATTACGA
Found at i:53821806 original size:81 final size:80
Alignment explanation
Indices: 53821694--53821881 Score: 288
Period size: 81 Copynumber: 2.3 Consensus size: 80
53821684 ACAATCATTT
* *
53821694 TACAGGGGTATTACAGTCATTTTACCCTACAGGAGCATTACGATCATTTTACCCTACAAGGGCAT
1 TACAGGGGCATTACAGTCATTTTACCCTACAGGAGCATTACGACCATTTTACCCTAC-AGGGCAT
**
53821759 TACGGTCATTTTACCC
65 TACGACCATTTTACCC
* *
53821775 TATAGGGGCATTACAGTCATTTTACCCTACAGGGGCATTACGACCATTTTACCCTACAGGGCATT
1 TACAGGGGCATTACAGTCATTTTACCCTACAGGAGCATTACGACCATTTTACCCTACAGGGCATT
53821840 ACGACCATTTTACCC
66 ACGACCATTTTACCC
*
53821855 TACAGTGGCATTAC-GATCATTTTACCC
1 TACAGGGGCATTACAG-TCATTTTACCC
53821882 ATCAAGGGTA
Statistics
Matches: 98, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
79 1 0.01
80 44 0.45
81 53 0.54
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (80 bp):
TACAGGGGCATTACAGTCATTTTACCCTACAGGAGCATTACGACCATTTTACCCTACAGGGCATT
ACGACCATTTTACCC
Found at i:53821903 original size:80 final size:81
Alignment explanation
Indices: 53821694--53821909 Score: 287
Period size: 80 Copynumber: 2.7 Consensus size: 81
53821684 ACAATCATTT
*
53821694 TACAGGGGTATTACAGTCATTTTACCCTAC-AGGAGCATTACGATCATTTTACCCTACAAGGGCA
1 TACAGGGGCATTACAGTCATTTTACCCTACAAGG-GCATTACGATCATTTTACCCTACAAGGGCA
**
53821758 TTACGGTCATTTTACCC
65 TTACGACCATTTTACCC
* * *
53821775 TATAGGGGCATTACAGTCATTTTACCCTACAGGGGCATTACGACCATTTTACCCTAC-AGGGCAT
1 TACAGGGGCATTACAGTCATTTTACCCTACAAGGGCATTACGATCATTTTACCCTACAAGGGCAT
53821839 TACGACCATTTTACCC
66 TACGACCATTTTACCC
* * * *
53821855 TACAGTGGCATTAC-GATCATTTTACCC-ATCAAGGGTATTTCGGTCATTTTACCCT
1 TACAGGGGCATTACAG-TCATTTTACCCTA-CAAGGGCATTACGATCATTTTACCCT
53821910 TCGGGAGTAT
Statistics
Matches: 119, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
79 2 0.02
80 65 0.55
81 50 0.42
82 2 0.02
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.31
Consensus pattern (81 bp):
TACAGGGGCATTACAGTCATTTTACCCTACAAGGGCATTACGATCATTTTACCCTACAAGGGCAT
TACGACCATTTTACCC
Found at i:53823458 original size:40 final size:40
Alignment explanation
Indices: 53823360--53823622 Score: 309
Period size: 40 Copynumber: 6.6 Consensus size: 40
53823350 TCCTCGTTCA
* * * ** *
53823360 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
53823399 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
53823439 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
53823479 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
53823519 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
53823559 AAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCACG
* *
53823599 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
53823623 CAGCATTCAA
Statistics
Matches: 199, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
39 37 0.19
40 154 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:53831453 original size:80 final size:80
Alignment explanation
Indices: 53831310--53831612 Score: 387
Period size: 80 Copynumber: 3.8 Consensus size: 80
53831300 TCCTCGTTCA
* * * * * *
53831310 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGACATAACCCGGAT
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
53831374 TTAACAACTCGCACG
66 TTAACAACTCGCACG
*
53831389 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
53831454 TTAACAACTCGCACG
66 TTAACAACTCGCACG
53831469 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
** * *
53831534 TTAGTATCTCGCACA
66 TTAACAACTCGCACG
* ** * * * * * *
53831549 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-AAAGCCTTCGGGACTTAGCCCGG
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACGAATGCCTTCGGGACTTAACCCGG
53831612 A
64 A
53831613 CAGCATTCAA
Statistics
Matches: 200, Mismatches: 21, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
79 36 0.18
80 159 0.80
81 5 0.03
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
TTAACAACTCGCACG
Found at i:53831572 original size:120 final size:120
Alignment explanation
Indices: 53831340--53831612 Score: 363
Period size: 120 Copynumber: 2.3 Consensus size: 120
53831330 CGGTTTTAGT
* *
53831340 AACTCACACAATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTT
1 AACTCGCACAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTT
* * *
53831405 AACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA-AC
66 AACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATATAC
*
53831459 AACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACT
1 AACTCGCAC-AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACT
** * ** *
53831524 TAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATATATTC
65 TAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATATATAC
* * *
53831580 -ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AAC-TCGCACAATGCCTTCGGGACTTAACCCGGA
53831613 CAGCATTCAA
Statistics
Matches: 135, Mismatches: 15, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
119 11 0.08
120 118 0.87
121 6 0.04
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.23
Consensus pattern (120 bp):
AACTCGCACAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTT
AACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATATAC
Found at i:53831573 original size:40 final size:40
Alignment explanation
Indices: 53831310--53831559 Score: 376
Period size: 40 Copynumber: 6.3 Consensus size: 40
53831300 TCCTCGTTCA
* * * ** *
53831310 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
53831349 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
53831389 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
53831429 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
53831469 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
53831509 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
53831549 AAGGCCTTCGG
1 AATGCCTTCGG
53831560 ATCTTAGTCC
Statistics
Matches: 199, Mismatches: 11, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
39 34 0.17
40 165 0.83
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:53831621 original size:41 final size:41
Alignment explanation
Indices: 53831544--53831621 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
53831534 TTAGTATCTC
* * *
53831544 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
53831585 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
53831622 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:53836976 original size:12 final size:11
Alignment explanation
Indices: 53836958--53836988 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
53836948 ACTCCCGGAA
53836958 TAAAAAAAATT
1 TAAAAAAAATT
53836969 TGAAAAAAAATT
1 T-AAAAAAAATT
53836981 TAAAAAAA
1 TAAAAAAA
53836989 GTTCAAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (11 bp):
TAAAAAAAATT
Found at i:53839348 original size:29 final size:28
Alignment explanation
Indices: 53839312--53839389 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
53839302 TCATGAGATT
53839312 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
53839342 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
53839369 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
53839390 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:53839607 original size:174 final size:174
Alignment explanation
Indices: 53839342--53839669 Score: 620
Period size: 174 Copynumber: 1.9 Consensus size: 174
53839332 AAATTGTACA
53839342 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
* *
53839407 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
53839472 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* *
53839516 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
53839581 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
53839646 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
53839670 ACCTTGAGTT
Statistics
Matches: 150, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 150 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:53847624 original size:27 final size:26
Alignment explanation
Indices: 53847568--53847718 Score: 115
Period size: 27 Copynumber: 5.6 Consensus size: 26
53847558 AAATTGTACA
* * *
53847568 GCACTAAGTGTGCG-ATTCTACTTTGTT
1 GCACTAAGTGTGCGAAAT-GACTATG-T
*
53847595 GCACTAAGTGTGCGAAATGAATATGAT
1 GCACTAAGTGTGCGAAATGACTATG-T
* * *
53847622 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAAATGACTATG-T
*
53847649 GCACTAAGTGTGCGAGATGGACTATGT
1 GCACTAAGTGTGCGAAAT-GACTATGT
** * *
53847676 GGCACTAAGTGTGCGATTTGATTACGT
1 -GCACTAAGTGTGCGAAATGACTATGT
*
53847703 GGCACTAAATGTGCGA
1 -GCACTAAGTGTGCGA
53847719 GTTGATTATA
Statistics
Matches: 102, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
27 78 0.76
28 24 0.24
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (26 bp):
GCACTAAGTGTGCGAAATGACTATGT
Found at i:53847628 original size:54 final size:54
Alignment explanation
Indices: 53847568--53847693 Score: 148
Period size: 54 Copynumber: 2.3 Consensus size: 54
53847558 AAATTGTACA
* ** **
53847568 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAAT-GAATATGAT-
1 GCACTAAGTGTGCGATT-GACCATGCGGCACTAAGTGTGCGAAATGGAATATG-TG
* *
53847622 GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGATGGACTATGTG
1 GCACTAAGTGTGCG-ATTGACCATGCGGCACTAAGTGTGCGAAATGGAATATGTG
53847677 GCACTAAGTGTGCGATT
1 GCACTAAGTGTGCGATT
53847694 TGATTACGTG
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
54 39 0.63
55 23 0.37
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAGTGTGCGATTGACCATGCGGCACTAAGTGTGCGAAATGGAATATGTG
Found at i:53847691 original size:55 final size:54
Alignment explanation
Indices: 53847595--53847744 Score: 160
Period size: 55 Copynumber: 2.8 Consensus size: 54
53847585 CTACTTTGTT
* *
53847595 GCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAGATGAATATGATGCACTAAGTGTGCGAATTGACCACGCG
* * ** *
53847649 GCACTAAGTGTGCGAGATGGACTATG-TGGCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAGAT-GAATATGAT-GCACTAAGTGTGCGAATTGACCACGCG
* * * *
53847704 GCACTAAATGTGCGAGTTGATTAT-ATAGCACTGAGTGTGCG
1 GCACTAAGTGTGCGAGATGAATATGAT-GCACTAAGTGTGCG
53847745 GGCTCAATAT
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
54 37 0.46
55 44 0.54
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.27
Consensus pattern (54 bp):
GCACTAAGTGTGCGAGATGAATATGATGCACTAAGTGTGCGAATTGACCACGCG
Found at i:53847708 original size:82 final size:81
Alignment explanation
Indices: 53847568--53847723 Score: 188
Period size: 82 Copynumber: 1.9 Consensus size: 81
53847558 AAATTGTACA
* * * * * *
53847568 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGAATCGACTATGTGGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
53847633 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** *
53847649 GCACTAAGTGTGCGAGATGGACTATGTGGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAAT
1 GCACTAAGTGTGCGA-ATCGACTATGTGGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAAT
*
53847713 GTGCGAGTTGA
64 GTGCGAATTGA
53847724 TTATATAGCA
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
81 16 0.26
82 46 0.74
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGAATCGACTATGTGGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
GCGAATTGACCATGCG
Found at i:53847723 original size:27 final size:27
Alignment explanation
Indices: 53847595--53847744 Score: 113
Period size: 27 Copynumber: 5.5 Consensus size: 27
53847585 CTACTTTGTT
** * *
53847595 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGAGTTGATTACG-TG
* ** * *
53847622 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAGTTGATTACGTG
* * *
53847649 GCACTAAGTGTGCGAGATGGACTATGTG
1 GCACTAAGTGTGCGAG-TTGATTACGTG
*
53847677 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAGTTGATTACGTG
* ** *
53847704 GCACTAAATGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGTTGATTACGTG
*
53847731 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
53847745 GGCTCAATAT
Statistics
Matches: 102, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
27 79 0.77
28 23 0.23
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.27
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGTTGATTACGTG
Found at i:53848423 original size:19 final size:18
Alignment explanation
Indices: 53848399--53848435 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
53848389 GATTGCCGAA
*
53848399 AAAGAAAGAGTGGAAAAAG
1 AAAGAAAGA-TAGAAAAAG
53848418 AAAGAAAGATAGAAAAAG
1 AAAGAAAGATAGAAAAAG
53848436 CAACGAGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.68, C:0.00, G:0.27, T:0.05
Consensus pattern (18 bp):
AAAGAAAGATAGAAAAAG
Found at i:53850305 original size:20 final size:21
Alignment explanation
Indices: 53850270--53850308 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
53850260 CAGCTCGATG
53850270 AGCTCAATTCAGCTCATTTCC
1 AGCTCAATTCAGCTCATTTCC
*
53850291 AGCTCAA-TGAGCTCATTT
1 AGCTCAATTCAGCTCATTT
53850309 GCTCATTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.33
Consensus pattern (21 bp):
AGCTCAATTCAGCTCATTTCC
Found at i:53855508 original size:27 final size:27
Alignment explanation
Indices: 53855478--53855655 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
53855468 ATATTGAGTC
* * * *
53855478 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
53855505 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
53855532 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
53855560 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
53855587 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
53855614 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
53855641 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
53855656 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:53855617 original size:82 final size:81
Alignment explanation
Indices: 53855499--53855654 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
53855489 TGCTATATAA
* *
53855499 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
53855564 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
53855581 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
53855645 CACTTAGTGC
65 CACTTAGTGC
53855655 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:53863006 original size:17 final size:17
Alignment explanation
Indices: 53862984--53863025 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
53862974 TCCAACACCT
53862984 TTTTTTTTGAAGTTTCA
1 TTTTTTTTGAAGTTTCA
* *
53863001 TTTTTTTTGAATTTTCG
1 TTTTTTTTGAAGTTTCA
53863018 TTTTTTTT
1 TTTTTTTT
53863026 CAATACTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.12, C:0.05, G:0.10, T:0.74
Consensus pattern (17 bp):
TTTTTTTTGAAGTTTCA
Found at i:53865077 original size:22 final size:23
Alignment explanation
Indices: 53865052--53865111 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
53865042 TGGACTGAAT
53865052 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
53865074 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
53865096 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
53865112 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:53865079 original size:4 final size:4
Alignment explanation
Indices: 53865061--53865094 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
53865051 TATAAAAATT
53865061 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
53865095 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:53866500 original size:23 final size:22
Alignment explanation
Indices: 53866448--53866500 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
53866438 TCCACGTCTT
*
53866448 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
53866470 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
53866493 TTTCTTTT
1 TTTCTTTT
53866501 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:53868874 original size:22 final size:23
Alignment explanation
Indices: 53868849--53868908 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
53868839 TGGACTGAAT
53868849 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
53868871 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
53868893 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
53868909 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:53868876 original size:4 final size:4
Alignment explanation
Indices: 53868858--53868891 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
53868848 TATAAAAATT
53868858 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
53868892 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:53874048 original size:24 final size:24
Alignment explanation
Indices: 53874007--53874065 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
53873997 AAAATAAAGA
*
53874007 AAAAGAAGGAAAAGGAAAAGGAAG
1 AAAAGAAGGAAAAAGAAAAGGAAG
*
53874031 AAAAGAA-GAAAACAGAAAAGGAGG
1 AAAAGAAGGAAAA-AGAAAAGGAAG
53874055 AAATA-AAGGAA
1 AAA-AGAAGGAA
53874066 GAAACAACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 5 0.17
24 21 0.70
25 4 0.13
ACGTcount: A:0.68, C:0.02, G:0.29, T:0.02
Consensus pattern (24 bp):
AAAAGAAGGAAAAAGAAAAGGAAG
Found at i:53887030 original size:40 final size:39
Alignment explanation
Indices: 53886840--53887023 Score: 194
Period size: 40 Copynumber: 4.6 Consensus size: 39
53886830 CGAATGATGT
* * * *
53886840 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA-AA
* * *
53886880 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA-A
*
53886920 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
53886958 TCCGAGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
53886999 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
53887024 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
39 33 0.27
40 79 0.65
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:53887046 original size:79 final size:79
Alignment explanation
Indices: 53886892--53887056 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
53886882 GGACTAAGAT
* **
53886892 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
53886957 ATCCGAGTTAAGTC
66 ATCCGAGTTAAATC
* * *
53886971 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
53887034 TATATCCG-GTTAAATT
63 TAAATCCGAGTTAAATC
53887050 CCGAAGG
1 CCGAAGG
53887057 TACGTGATTC
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGAGTTAAATC
Found at i:53890823 original size:24 final size:24
Alignment explanation
Indices: 53890791--53890841 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
53890781 AAAACAACAA
* *
53890791 CTTCTTTAATGCTGTCCATGCTTG
1 CTTCTTTAATGCCGTCCAGGCTTG
53890815 CTTCTTTAATGCCGTCCAGGCTTG
1 CTTCTTTAATGCCGTCCAGGCTTG
53890839 CTT
1 CTT
53890842 TAGCAAAGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.12, C:0.27, G:0.18, T:0.43
Consensus pattern (24 bp):
CTTCTTTAATGCCGTCCAGGCTTG
Found at i:53891148 original size:17 final size:17
Alignment explanation
Indices: 53891126--53891159 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
53891116 TATGACAAAT
53891126 TAATT-ATTTAAACTAAA
1 TAATTAATTT-AACTAAA
53891143 TAATTAATTTAACTAAA
1 TAATTAATTTAACTAAA
53891160 AACAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATTAATTTAACTAAA
Found at i:53898387 original size:16 final size:15
Alignment explanation
Indices: 53898366--53898413 Score: 64
Period size: 16 Copynumber: 3.2 Consensus size: 15
53898356 TAATGTGTTT
53898366 TGCTGCTATTGTTTAA
1 TGCTGCT-TTGTTTAA
53898382 TGCTGCTGTTGTTTAA
1 TGCTGCT-TTGTTTAA
53898398 TGCTG--TTGTTTAA
1 TGCTGCTTTGTTTAA
53898411 TGC
1 TGC
53898414 AGAATATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
13 11 0.35
16 20 0.65
ACGTcount: A:0.15, C:0.12, G:0.23, T:0.50
Consensus pattern (15 bp):
TGCTGCTTTGTTTAA
Found at i:53898492 original size:14 final size:14
Alignment explanation
Indices: 53898473--53898500 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53898463 TGAGCAGGTT
53898473 ACCGAATTTAATTG
1 ACCGAATTTAATTG
53898487 ACCGAATTTAATTG
1 ACCGAATTTAATTG
53898501 TTCTCTGTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
ACCGAATTTAATTG
Found at i:53899921 original size:13 final size:14
Alignment explanation
Indices: 53899905--53899937 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
53899895 AAAAAAATCG
53899905 AAAAAA-ATTCTAAA
1 AAAAAAGATTC-AAA
53899919 AAAAAAGATTCAAA
1 AAAAAAGATTCAAA
53899933 AAAAA
1 AAAAA
53899938 TTCGAAGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (14 bp):
AAAAAAGATTCAAA
Found at i:53900820 original size:6 final size:6
Alignment explanation
Indices: 53900811--53900844 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
53900801 AACAAAAAAG
**
53900811 AAGAAA AAGAAA AAGAAA GTGAAA AAGAAA AAGA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGA
53900845 GTGCGAGCGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (6 bp):
AAGAAA
Found at i:53900836 original size:18 final size:18
Alignment explanation
Indices: 53900813--53900903 Score: 65
Period size: 18 Copynumber: 4.6 Consensus size: 18
53900803 CAAAAAAGAA
53900813 GAAAAAGAAAAAGAAAGT
1 GAAAAAGAAAAAGAAAGT
* *
53900831 GAAAAAGAAAAAGAGTGCGAGC
1 GAAAAAGAAAAAGA----AAGT
*
53900853 GAGAAAATGAAAAAGAAATT
1 GA-AAAA-GAAAAAGAAAGT
* *
53900873 GCAAAAGAAAAAGAAAAT
1 GAAAAAGAAAAAGAAAGT
53900891 GAAGAAAAGAAAA
1 G-A-AAAAGAAAA
53900904 TTGAAAAAGA
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
18 26 0.46
19 4 0.07
20 11 0.19
22 4 0.07
23 4 0.07
24 8 0.14
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.07
Consensus pattern (18 bp):
GAAAAAGAAAAAGAAAGT
Done.