Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000422.1 Hibiscus syriacus cultivar Beakdansim tig00000773_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2457469
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 12
Found at i:1138433 original size:73 final size:72
Alignment explanation
Indices: 1138260--1138683 Score: 501
Period size: 72 Copynumber: 5.8 Consensus size: 72
1138250 ATTCTATTTT
* ** * * *
1138260 AAGGAAAACAATCTCAAGCAAGATAAAATTTTGTTTCTAGTGAAACTGTCTTGAGTGAGAC--AA
1 AAGGAAAA-TATCTCAAGTGAGATAAAATTTTGTTTCAAGAGAAACTGTCTCGAGTGAGACGAAA
1138323 AATATTTCA
65 AAT-TTTCA
* * * * * *
1138332 AGGGAAAATATCACAAGTGAGATGAAATTTTTGTTTCGACAGAAATTGTCTCGAGTGAGACGAAA
1 AAGGAAAATATCTCAAGTGAGAT-AAAATTTTGTTTCAAGAGAAACTGTCTCGAGTGAGACGAAA
1138397 AATTTTCA
65 AATTTTCA
* * *
1138405 AAGGAAAATATCTCAAGGGAGATAAAATTTTGTTTCAAGAAAAACTGTCTCAAGTGAGACGAAAA
1 AAGGAAAATATCTCAAGTGAGATAAAATTTTGTTTCAAGAGAAACTGTCTCGAGTGAGACGAAAA
1138470 ATTTTCA
66 ATTTTCA
* * * *
1138477 AAGGGAAAATATCTCAAGTGAGATGAAATTTTTGTTTCAAGAGAAATTGTCTTGAGTGAGATGAA
1 AA-GGAAAATATCTCAAGTGAGAT-AAAATTTTGTTTCAAGAGAAACTGTCTCGAGTGAGACGAA
*
1138542 AAGTTTTCA
64 AAATTTTCA
* * * ** * *
1138551 AGGGAAAATATCTCATGGGAGATAAAATTTTGTTTTGAGAGAAACTGTCTCAAGTGAGACGGAAA
1 AAGGAAAATATCTCAAGTGAGATAAAATTTTGTTTCAAGAGAAACTGTCTCGAGTGAGACGAAAA
1138616 ATTTTCA
66 ATTTTCA
* * *
1138623 AAGGGAAAATATCTCAAGTGAGATGAAATTTTTGTTTCAAGAGAAGCTGCCTCGAGTGAGA
1 AA-GGAAAATATCTCAAGTGAGAT-AAAATTTTGTTTCAAGAGAAACTGTCTCGAGTGAGA
1138684 TGAAGTGAGA
Statistics
Matches: 296, Mismatches: 49, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
71 11 0.04
72 124 0.42
73 83 0.28
74 78 0.26
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.29
Consensus pattern (72 bp):
AAGGAAAATATCTCAAGTGAGATAAAATTTTGTTTCAAGAGAAACTGTCTCGAGTGAGACGAAAA
ATTTTCA
Found at i:1138534 original size:146 final size:145
Alignment explanation
Indices: 1138260--1138683 Score: 609
Period size: 146 Copynumber: 2.9 Consensus size: 145
1138250 ATTCTATTTT
* ** * * **
1138260 AAGGAAAACAATCTCAAGCAAGATAAAATTTTGTTTCTAGTGAAACTGTCTTGAGTGAGAC-AAA
1 AAGGAAAA-TATCTCAAGGGAGATAAAATTTTGTTTCAAGAGAAACTGTCTCAAGTGAGACGAAA
* * *
1138324 ATATTTC-AAGGGAAAATATCACAAGTGAGATGAAATTTTTGTTTCGACAGAAATTGTCTCGAGT
65 AT-TTTCAAAGGGAAAATATCTCAAGTGAGATGAAATTTTTGTTTCAAGAGAAATTGTCTCGAGT
1138388 GAGACGAAAAATTTTCA
129 GAGACGAAAAATTTTCA
*
1138405 AAGGAAAATATCTCAAGGGAGATAAAATTTTGTTTCAAGAAAAACTGTCTCAAGTGAGACGAAAA
1 AAGGAAAATATCTCAAGGGAGATAAAATTTTGTTTCAAGAGAAACTGTCTCAAGTGAGACG-AAA
*
1138470 ATTTTCAAAGGGAAAATATCTCAAGTGAGATGAAATTTTTGTTTCAAGAGAAATTGTCTTGAGTG
65 ATTTTCAAAGGGAAAATATCTCAAGTGAGATGAAATTTTTGTTTCAAGAGAAATTGTCTCGAGTG
* *
1138535 AGATGAAAAGTTTTCA
130 AGACGAAAAATTTTCA
* * **
1138551 AGGGAAAATATCTCATGGGAGATAAAATTTTGTTTTGAGAGAAACTGTCTCAAGTGAGACGGAAA
1 AAGGAAAATATCTCAAGGGAGATAAAATTTTGTTTCAAGAGAAACTGTCTCAAGTGAGAC-GAAA
** *
1138616 ATTTTCAAAGGGAAAATATCTCAAGTGAGATGAAATTTTTGTTTCAAGAGAAGCTGCCTCGAGTG
65 ATTTTCAAAGGGAAAATATCTCAAGTGAGATGAAATTTTTGTTTCAAGAGAAATTGTCTCGAGTG
1138681 AGA
130 AGA
1138684 TGAAGTGAGA
Statistics
Matches: 252, Mismatches: 23, Indels: 7
0.89 0.08 0.02
Matches are distributed among these distances:
144 44 0.17
145 12 0.05
146 195 0.77
147 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.29
Consensus pattern (145 bp):
AAGGAAAATATCTCAAGGGAGATAAAATTTTGTTTCAAGAGAAACTGTCTCAAGTGAGACGAAAA
TTTTCAAAGGGAAAATATCTCAAGTGAGATGAAATTTTTGTTTCAAGAGAAATTGTCTCGAGTGA
GACGAAAAATTTTCA
Found at i:1138714 original size:18 final size:19
Alignment explanation
Indices: 1138691--1138730 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
1138681 AGATGAAGTG
1138691 AGATAAAATTT-TGTTTCA
1 AGATAAAATTTATGTTTCA
1138709 AGATAAAATTTATGTTTCA
1 AGATAAAATTTATGTTTCA
1138728 AGA
1 AGA
1138731 GAAACAATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.40
Consensus pattern (19 bp):
AGATAAAATTTATGTTTCA
Found at i:1139968 original size:11 final size:11
Alignment explanation
Indices: 1139937--1139970 Score: 50
Period size: 11 Copynumber: 2.9 Consensus size: 11
1139927 TTTTTTCATT
1139937 TTTTCTTGTTTC
1 TTTTCTT-TTTC
1139949 TTATTCTTTTTC
1 TT-TTCTTTTTC
1139961 TTTTCTTTTT
1 TTTTCTTTTT
1139971 ATTAATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 8 0.38
12 8 0.38
13 5 0.24
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:1144352 original size:12 final size:12
Alignment explanation
Indices: 1144335--1144364 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1144325 TATTTTTTTC
1144335 TTTTTTGATTCT
1 TTTTTTGATTCT
*
1144347 TTTTTTGTTTCT
1 TTTTTTGATTCT
1144359 TTTTTT
1 TTTTTT
1144365 TTTCGTCCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.03, C:0.07, G:0.07, T:0.83
Consensus pattern (12 bp):
TTTTTTGATTCT
Found at i:1144368 original size:11 final size:11
Alignment explanation
Indices: 1144327--1144368 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
1144317 ATACTTTGTA
1144327 TTTTTTTCTTT
1 TTTTTTTCTTT
**
1144338 TTTGATTCTTT
1 TTTTTTTCTTT
1144349 TTTTGTTTCTTT
1 TTTT-TTTCTTT
1144361 TTTTTTTC
1 TTTTTTTC
1144369 GTCCCTATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.02, C:0.10, G:0.05, T:0.83
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:1145501 original size:24 final size:24
Alignment explanation
Indices: 1145444--1145501 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
1145434 ATCTTACTGG
*
1145444 TCATCATGAACATCACCACACACA
1 TCATCCTGAACATCACCACACACA
***
1145468 TCA-CCTTGAACATCACCGTGCACA
1 TCATCC-TGAACATCACCACACACA
1145492 TCATCCTGAA
1 TCATCCTGAA
1145502 TAGGTTCTGG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 1 0.04
24 25 0.89
25 2 0.07
ACGTcount: A:0.34, C:0.36, G:0.09, T:0.21
Consensus pattern (24 bp):
TCATCCTGAACATCACCACACACA
Found at i:1147907 original size:20 final size:20
Alignment explanation
Indices: 1147882--1147919 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1147872 CAATACTAAC
1147882 CAACCA-AACATCAAATAATG
1 CAACCACAACA-CAAATAATG
1147902 CAACCACAACACAAATAA
1 CAACCACAACACAAATAA
1147920 ATCGACACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.58, C:0.29, G:0.03, T:0.11
Consensus pattern (20 bp):
CAACCACAACACAAATAATG
Found at i:1148518 original size:18 final size:18
Alignment explanation
Indices: 1148468--1148519 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
1148458 CAACAAACAA
*
1148468 GCAACATATTTTATGGTT
1 GCAACCTATTTTATGGTT
1148486 G---CC-ATTTTA-GGTT
1 GCAACCTATTTTATGGTT
1148499 GCAACCTATTTTATGGTT
1 GCAACCTATTTTATGGTT
1148517 GCA
1 GCA
1148520 CCACTTTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 10
0.72 0.03 0.26
Matches are distributed among these distances:
13 5 0.18
14 6 0.21
15 1 0.04
16 2 0.07
17 6 0.21
18 8 0.29
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.42
Consensus pattern (18 bp):
GCAACCTATTTTATGGTT
Found at i:1148527 original size:17 final size:16
Alignment explanation
Indices: 1148475--1148527 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
1148465 CAAGCAACAT
1148475 ATTTTATGGTTG--CC
1 ATTTTATGGTTGCACC
1148489 ATTTTA-GGTTGCAACC
1 ATTTTATGGTTGC-ACC
1148505 TATTTTATGGTTGCACC
1 -ATTTTATGGTTGCACC
1148522 ACTTTT
1 A-TTTT
1148528 TCAAGTTGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
13 5 0.15
14 6 0.18
16 3 0.09
17 13 0.39
18 6 0.18
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (16 bp):
ATTTTATGGTTGCACC
Found at i:1148552 original size:17 final size:16
Alignment explanation
Indices: 1148525--1148586 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 16
1148515 TTGCACCACT
1148525 TTTTCAAGTTGCTCTATA
1 TTTT-AAGTTGCTC-ATA
1148543 TTTTAAGTTGCATCACT-
1 TTTTAAGTTGC-TCA-TA
* *
1148560 TTTCAAGCTGCTCCATA
1 TTTTAAGTTGCT-CATA
1148577 TTTTAAGTTG
1 TTTTAAGTTG
1148587 TATATGCTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
16 2 0.06
17 27 0.75
18 7 0.19
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.47
Consensus pattern (16 bp):
TTTTAAGTTGCTCATA
Found at i:1148572 original size:34 final size:35
Alignment explanation
Indices: 1148505--1148586 Score: 112
Period size: 34 Copynumber: 2.3 Consensus size: 35
1148495 GGTTGCAACC
* * *
1148505 TATTTTATGGTTGCACCACTTTTTCAAGTTGCTCTA
1 TATTTTA-AGTTGCACCACTTTTTCAAGCTGCTCCA
*
1148541 TATTTTAAGTTGCATCAC-TTTTCAAGCTGCTCCA
1 TATTTTAAGTTGCACCACTTTTTCAAGCTGCTCCA
1148575 TATTTTAAGTTG
1 TATTTTAAGTTG
1148587 TATATGCTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
34 26 0.62
35 9 0.21
36 7 0.17
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.46
Consensus pattern (35 bp):
TATTTTAAGTTGCACCACTTTTTCAAGCTGCTCCA
Found at i:1148965 original size:3 final size:3
Alignment explanation
Indices: 1148957--1149058 Score: 82
Period size: 3 Copynumber: 33.3 Consensus size: 3
1148947 TTTGTCTAGG
* * *
1148957 TTA TTA TTA TTA TTA TTA TTA TTA TTTA ATA ATA TTA TTA TTTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA -TTA TTA
* * * *
1149004 ATA ATA TTA TTA TTTA ATA TTA TTA TTA TT- TGT- TTA ATA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
*
1149049 TTT TTA TTA T
1 TTA TTA TTA T
1149059 AGTTTTTGGT
Statistics
Matches: 84, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.02
3 73 0.87
4 9 0.11
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1148994 original size:16 final size:16
Alignment explanation
Indices: 1148958--1149051 Score: 100
Period size: 16 Copynumber: 5.7 Consensus size: 16
1148948 TTGTCTAGGT
* *
1148958 TATTATTA-TTATTAT
1 TATTATTATTTAATAA
1148973 TATTATTATTTAATAA
1 TATTATTATTTAATAA
1148989 TATTATTATTTAATAATAA
1 TATTATTA-TT--TAATAA
*
1149008 TATTATTATTTAATAT
1 TATTATTATTTAATAA
**
1149024 TATTATTATTTGTTTAA
1 TATTATTATTT-AATAA
1149041 TATTATTATTT
1 TATTATTATTT
1149052 TTATTATAGT
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
15 8 0.12
16 29 0.43
17 15 0.22
18 2 0.03
19 14 0.21
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (16 bp):
TATTATTATTTAATAA
Found at i:1148994 original size:19 final size:19
Alignment explanation
Indices: 1148957--1149056 Score: 118
Period size: 19 Copynumber: 5.4 Consensus size: 19
1148947 TTTGTCTAGG
*
1148957 TTATTA-TTATTATTATTA
1 TTATTATTTAATATTATTA
1148975 TTATTATTTAATA--A-TA
1 TTATTATTTAATATTATTA
* *
1148991 TTATTATTTAATAATAATA
1 TTATTATTTAATATTATTA
1149010 TTATTATTTAATATTATTA
1 TTATTATTTAATATTATTA
*
1149029 TTATTTGTTTAATATTATTA
1 TTA-TTATTTAATATTATTA
*
1149049 TTTTTATT
1 TTATTATT
1149057 ATAGTTTTTG
Statistics
Matches: 71, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
16 15 0.21
17 1 0.01
18 7 0.10
19 31 0.44
20 17 0.24
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (19 bp):
TTATTATTTAATATTATTA
Found at i:1151882 original size:12 final size:12
Alignment explanation
Indices: 1151861--1151894 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1151851 ACAAACAATT
1151861 TCTTTTGTTTTA
1 TCTTTTGTTTTA
* *
1151873 TCTTTAGTTTTT
1 TCTTTTGTTTTA
1151885 TCTTTTGTTT
1 TCTTTTGTTT
1151895 GCATTTGCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.09, G:0.09, T:0.76
Consensus pattern (12 bp):
TCTTTTGTTTTA
Found at i:1155412 original size:29 final size:29
Alignment explanation
Indices: 1155360--1155513 Score: 242
Period size: 29 Copynumber: 5.4 Consensus size: 29
1155350 AACTATTACG
*
1155360 AAAATAACACCTTTTTCGAAATAATTCCC
1 AAAATATCACCTTTTTCGAAATAATTCCC
* *
1155389 AAACTATCACCTTTTTCGACATAATTCCC
1 AAAATATCACCTTTTTCGAAATAATTCCC
1155418 AAAATATCACC-TTTTCGAAATAATTCCC
1 AAAATATCACCTTTTTCGAAATAATTCCC
*
1155446 AGAATATCA--TTTTTCGAAATAATTCCC
1 AAAATATCACCTTTTTCGAAATAATTCCC
*
1155473 AAAATATCACCTTTTTCAAAATAATTCCC
1 AAAATATCACCTTTTTCGAAATAATTCCC
1155502 AAAATATCACCT
1 AAAATATCACCT
1155514 AACAACAATT
Statistics
Matches: 114, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
27 25 0.22
28 24 0.21
29 65 0.57
ACGTcount: A:0.39, C:0.25, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAATATCACCTTTTTCGAAATAATTCCC
Found at i:1161556 original size:32 final size:31
Alignment explanation
Indices: 1161518--1161594 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
1161508 TGGGGTCGTG
*
1161518 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
1161550 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
1161581 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
1161595 GTCATATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:1162541 original size:29 final size:29
Alignment explanation
Indices: 1162489--1162640 Score: 215
Period size: 28 Copynumber: 5.4 Consensus size: 29
1162479 AACTATTACG
*
1162489 AAAATAACACCTTTTT-GAAATAATTCCC
1 AAAATATCACCTTTTTCGAAATAATTCCC
* *
1162517 AAACTATCACCTTTTTCGACATAATTCCC
1 AAAATATCACCTTTTTCGAAATAATTCCC
1162546 AAAATATCACC-TTTTCGAAATAATTCCC
1 AAAATATCACCTTTTTCGAAATAATTCCC
1162574 AAAATATCA--TTTTT-GAAATAATTCCC
1 AAAATATCACCTTTTTCGAAATAATTCCC
* **
1162600 AAAATATCACCTTTTTCAAAATAATTATC
1 AAAATATCACCTTTTTCGAAATAATTCCC
1162629 AAAATATCACCT
1 AAAATATCACCT
1162641 AACAACAATT
Statistics
Matches: 111, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
26 21 0.19
27 4 0.04
28 44 0.40
29 42 0.38
ACGTcount: A:0.41, C:0.22, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAATATCACCTTTTTCGAAATAATTCCC
Found at i:1162569 original size:28 final size:28
Alignment explanation
Indices: 1162489--1162640 Score: 200
Period size: 29 Copynumber: 5.4 Consensus size: 28
1162479 AACTATTACG
* *
1162489 AAAATAACACCTTTTTGAAATAATTCCC
1 AAAATATCACCTTTTCGAAATAATTCCC
* *
1162517 AAACTATCACCTTTTTCGACATAATTCCC
1 AAAATATCACC-TTTTCGAAATAATTCCC
1162546 AAAATATCACCTTTTCGAAATAATTCCC
1 AAAATATCACCTTTTCGAAATAATTCCC
*
1162574 AAAATATCA--TTTTTGAAATAATTCCC
1 AAAATATCACCTTTTCGAAATAATTCCC
* **
1162600 AAAATATCACCTTTTTCAAAATAATTATC
1 AAAATATCACC-TTTTCGAAATAATTCCC
1162629 AAAATATCACCT
1 AAAATATCACCT
1162641 AACAACAATT
Statistics
Matches: 109, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
26 25 0.23
28 35 0.32
29 49 0.45
ACGTcount: A:0.41, C:0.22, G:0.03, T:0.34
Consensus pattern (28 bp):
AAAATATCACCTTTTCGAAATAATTCCC
Found at i:1167974 original size:42 final size:41
Alignment explanation
Indices: 1167899--1167999 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 41
1167889 CCAAAATTGG
* *
1167899 TAAATCCTTCAGGCCATCAATAAGTCTTCCGAGC-ATGATGA
1 TAAATCCTTCGGGCCATCAATAAGCCTTCCGAGCAAT-ATGA
* * * *
1167940 TTAAATCCTTCGGGTCATCTATCAGCCTTTCGAGCAATATGA
1 -TAAATCCTTCGGGCCATCAATAAGCCTTCCGAGCAATATGA
*
1167982 TAAGTCCTTCGGGCCATC
1 TAAATCCTTCGGGCCATC
1168000 CATATGACCT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
41 16 0.32
42 32 0.64
43 2 0.04
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.30
Consensus pattern (41 bp):
TAAATCCTTCGGGCCATCAATAAGCCTTCCGAGCAATATGA
Found at i:1168355 original size:246 final size:247
Alignment explanation
Indices: 1167797--1168580 Score: 1031
Period size: 246 Copynumber: 3.1 Consensus size: 247
1167787 AATTTCCAAA
* *
1167797 ATTTTCAAAGTTTCTCATTTAATGTTTTCAG-AAATGAAATTTTTGAAAAGTAAGAAAGCGATCT
1 ATTTTCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGCAATTT
*
1167861 CCAAAGTTTCTTACATAGTAAACTATTTCCAAAATTGGTAAATCCTTCAGGCCATCAATAAGTCT
66 CCAAAGTTTCTTACATAGTAAACTATTTCCAAAATTGGTAAGTCCTT-----CATCAATAAGTCT
* *
1167926 TCCGAGCATGATGATTAAATCCTTCGGGTCATCTATCAGCCTTTCGAGCAATATGATAAGTCCTT
126 TTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGCC-TT-------TATGATAAGTCCTT
*
1167991 CGGGCCATCCATATGACCTTTGGGCATGATGTTTTCATATGA---TTGTGAAAAATGAGAAAAAC
183 CGGGCCATCCATAAGACCTTTGGGCATGATGTTTTCATATGATGTTTGTGAAAAATGAG-AAAAC
*
1168053 A
247 C
*
1168054 ATTTTCAAAGTTTCTCATTTAATGTATTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGCAATTT
1 ATTTTCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGCAATTT
* *
1168119 CCAAAGTGTCTTACTTAGTAAACTATTTCCAAAATTGGTAAGTCCTTC-TCAATAAGTCTTTCGA
66 CCAAAGTTTCTTACATAGTAAACTATTTCCAAAATTGGTAAGTCCTTCATCAATAAGTCTTTCGA
* *
1168183 GCATGATGATTAAATCCTCCGGGTCATCTGTCAGCCTTT-TGAGAAGTCCTTCGGGCCATCCATA
131 GCATGATGATTAAATCCTTCGGGTCATCTGTCAGCCTTTATGATAAGTCCTTCGGGCCATCCATA
* *
1168247 AGACCTTTGGGTAGGATGTTTTCATATGATGTTTGTGAAAAATGAGAAAAGCC
196 AGACCTTTGGGCATGATGTTTTCATATGATGTTTGTGAAAAATGAGAAAA-CC
* *
1168300 ATTTTCAAAGTTTCTTATTTAATGTTTTTAGAAAATGAAATTTTTGAAAAGTAAGAAAGCAATTT
1 ATTTTCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGCAATTT
* ** * ** *
1168365 CTAAAGTTTCTTACCCAGTAAACTATTTTCAAGTTTGGTAAGTTCTTCATGCCATCAGTAAGTCT
66 CCAAAGTTTCTTACATAGTAAACTATTTCCAAAATTGGTAAGTCCTTCAT--CA--A-TAAGTCT
* *
1168430 TTCGAGCATGATGATTAAATGCTTCGGGTCATATGTCAGCCTTTCGAGCAAGATGATAAGTCCTT
126 TTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGCCTTT--------ATGATAAGTCCTT
*
1168495 CGGGCCATCCATAAGACCTTTGGACATGATGTTTTCATATGATGTTTGTGAAAAATGAGAAAACC
183 CGGGCCATCCATAAGACCTTTGGGCATGATGTTTTCATATGATGTTTGTGAAAAATGAGAAAACC
1168560 AATTTTCAAAGTTTCTCATTT
1 -ATTTTCAAAGTTTCTCATTT
1168581 TAGTCATTTA
Statistics
Matches: 473, Mismatches: 33, Indels: 38
0.87 0.06 0.07
Matches are distributed among these distances:
243 50 0.11
244 1 0.00
245 4 0.01
246 117 0.25
247 1 0.00
249 2 0.00
251 3 0.01
252 97 0.21
253 1 0.00
257 30 0.06
258 75 0.16
260 2 0.00
261 90 0.19
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (247 bp):
ATTTTCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGCAATTT
CCAAAGTTTCTTACATAGTAAACTATTTCCAAAATTGGTAAGTCCTTCATCAATAAGTCTTTCGA
GCATGATGATTAAATCCTTCGGGTCATCTGTCAGCCTTTATGATAAGTCCTTCGGGCCATCCATA
AGACCTTTGGGCATGATGTTTTCATATGATGTTTGTGAAAAATGAGAAAACC
Found at i:1169038 original size:14 final size:15
Alignment explanation
Indices: 1169015--1169046 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
1169005 TACTTGAGTA
1169015 ATTATCTTTTATTTT
1 ATTATCTTTTATTTT
1169030 ATTAT-TTTTATTTT
1 ATTATCTTTTATTTT
1169044 ATT
1 ATT
1169047 TTATATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (15 bp):
ATTATCTTTTATTTT
Found at i:1169459 original size:4 final size:4
Alignment explanation
Indices: 1169450--1169480 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1169440 GCGACTCAAA
*
1169450 ATTT ATTT ATTT ATTT ATCT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATT
1169481 AAAAAAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:1176535 original size:31 final size:31
Alignment explanation
Indices: 1176492--1176562 Score: 99
Period size: 30 Copynumber: 2.3 Consensus size: 31
1176482 TTGGGTCGGA
*
1176492 TTTTTTTTAAAAAATTTCGGGATC-GGTCAG
1 TTTTTTTAAAAAAATTTCGGGATCGGGTCAG
* *
1176522 TTTTTTTAAAAAAATTTCGGGTTCGGGTCGG
1 TTTTTTTAAAAAAATTTCGGGATCGGGTCAG
*
1176553 GTTTTTTAAA
1 TTTTTTTAAA
1176563 GTTTGATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 22 0.61
31 14 0.39
ACGTcount: A:0.25, C:0.08, G:0.21, T:0.45
Consensus pattern (31 bp):
TTTTTTTAAAAAAATTTCGGGATCGGGTCAG
Found at i:1176582 original size:33 final size:33
Alignment explanation
Indices: 1176545--1176615 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
1176535 ATTTCGGGTT
*
1176545 CGGGTCGGGTTTTT-TAAAGTTTGATATTCGGGC
1 CGGGTCGGGTTTTTGT-AAGTGTGATATTCGGGC
* *
1176578 CGGGTCGGGTTTTTGTAAGTGTGATATTTGGGT
1 CGGGTCGGGTTTTTGTAAGTGTGATATTCGGGC
1176611 CGGGT
1 CGGGT
1176616 GTTTTTTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 33 0.97
34 1 0.03
ACGTcount: A:0.13, C:0.10, G:0.38, T:0.39
Consensus pattern (33 bp):
CGGGTCGGGTTTTTGTAAGTGTGATATTCGGGC
Found at i:1176683 original size:30 final size:30
Alignment explanation
Indices: 1176616--1176687 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 30
1176606 TGGGTCGGGT
1176616 GTTTTTTTCAAAAAATTTCGGGATCAGGTCTG
1 GTTTTTTT--AAAAATTTCGGGATCAGGTCTG
* * *
1176648 ATTTTTTTAAAAATTTCGGGTTCGGGT-TGG
1 GTTTTTTTAAAAATTTCGGGATCAGGTCT-G
1176678 GTTTTTTTAA
1 GTTTTTTTAA
1176688 GTGTGATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 1 0.03
30 27 0.77
32 7 0.20
ACGTcount: A:0.22, C:0.08, G:0.22, T:0.47
Consensus pattern (30 bp):
GTTTTTTTAAAAATTTCGGGATCAGGTCTG
Found at i:1176699 original size:125 final size:116
Alignment explanation
Indices: 1176479--1176736 Score: 347
Period size: 125 Copynumber: 2.1 Consensus size: 116
1176469 AATCTTTTGG
*
1176479 TATTTGGGTCGGATTTTTTTTAAAAAATTTCGGGATCGGTCAGTTTTTTTAAAAAAATTTCGGGT
1 TATTTGGGTCGGGTTTTTTTTAAAAAATTTCGGGATCGGTCAGTTTTTTT-AAAAAATTTCGGGT
*
1176544 TCGGGTCGGGTTTTTTAAAGTTTGATATTCGGGCCGGGTCGGGTTTTTGTAAGTGTGA
65 TCGGGTCGGGTTTTTTAAAGTGTGATATT-----CGGGTCGGGTTTTT-TAAGTGTGA
*
1176602 TATTTGGGTCGGGTGTTTTTTTCAAAAAATTTCGGGATCAGGTCTGATTTTTTT-AAAAATTTCG
1 TATTTGGGTCGGGT-TTTTTTT-AAAAAATTTCGGGATC-GGTCAG-TTTTTTTAAAAAATTTCG
* *
1176666 GGTTCGGGTTGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTTTTTAAGTGTGA
62 GGTTCGGGTCGGGTTTTTTAAAGTGTGATATTCGGGTCGGGTTTTTTAAGTGTGA
* *
1176721 TATTAGGGCCGGGTTT
1 TATTTGGGTCGGGTTT
1176737 GGATTTAGGG
Statistics
Matches: 124, Mismatches: 7, Indels: 13
0.86 0.05 0.09
Matches are distributed among these distances:
118 2 0.02
119 21 0.17
120 14 0.11
123 13 0.10
124 7 0.06
125 55 0.44
126 5 0.04
127 7 0.06
ACGTcount: A:0.19, C:0.09, G:0.29, T:0.43
Consensus pattern (116 bp):
TATTTGGGTCGGGTTTTTTTTAAAAAATTTCGGGATCGGTCAGTTTTTTTAAAAAATTTCGGGTT
CGGGTCGGGTTTTTTAAAGTGTGATATTCGGGTCGGGTTTTTTAAGTGTGA
Found at i:1176718 original size:27 final size:27
Alignment explanation
Indices: 1176668--1176736 Score: 102
Period size: 27 Copynumber: 2.5 Consensus size: 27
1176658 AAATTTCGGG
*
1176668 TTCGGGTTGGGTTTTTTTAAGTGTGATA
1 TTCGGGTCGGG-TTTTTTAAGTGTGATA
1176696 TTCGGGTCGGGTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTTTTTTAAGTGTGATA
* *
1176723 TTAGGGCCGGGTTT
1 TTCGGGTCGGGTTT
1176737 GGATTTAGGG
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
27 28 0.74
28 10 0.26
ACGTcount: A:0.13, C:0.07, G:0.35, T:0.45
Consensus pattern (27 bp):
TTCGGGTCGGGTTTTTTAAGTGTGATA
Found at i:1177387 original size:20 final size:20
Alignment explanation
Indices: 1177362--1177400 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1177352 TCACAGATTC
*
1177362 CAATTTCCTCAGAAATATTT
1 CAATTTCCTCAAAAATATTT
1177382 CAATTTCCTCAAAAATATT
1 CAATTTCCTCAAAAATATT
1177401 ACAGCGAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (20 bp):
CAATTTCCTCAAAAATATTT
Found at i:1180920 original size:34 final size:34
Alignment explanation
Indices: 1180839--1180923 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 34
1180829 ATGATAGTTG
* * *
1180839 ATGTGGCGATGACGTGGAAATGATGTGATAGCTG
1 ATGTGGCGATGACATGGAAATGATGTGACAGCTA
** *
1180873 ACATGGC-ACTGACATGGAAATGATGTGGCAGCTA
1 ATGTGGCGA-TGACATGGAAATGATGTGACAGCTA
1180907 ATGTGGCGATGACATGG
1 ATGTGGCGATGACATGG
1180924 TAGCTGACGT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
33 1 0.02
34 39 0.95
35 1 0.02
ACGTcount: A:0.28, C:0.13, G:0.35, T:0.24
Consensus pattern (34 bp):
ATGTGGCGATGACATGGAAATGATGTGACAGCTA
Found at i:1187418 original size:23 final size:22
Alignment explanation
Indices: 1187368--1187420 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 22
1187358 GTCATGGCGC
1187368 CCAATCAACAGCTTTTAGAAGG
1 CCAATCAACAGCTTTTAGAAGG
* *
1187390 CTCAATCAACATCTTTTAGAAGAT
1 C-CAATCAACAGCTTTTAGAAG-G
1187414 CCAATCA
1 CCAATCA
1187421 GTAGTAGCGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 1 0.04
23 25 0.93
24 1 0.04
ACGTcount: A:0.38, C:0.25, G:0.11, T:0.26
Consensus pattern (22 bp):
CCAATCAACAGCTTTTAGAAGG
Found at i:1195516 original size:13 final size:13
Alignment explanation
Indices: 1195498--1195523 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1195488 TTATTTATTT
1195498 TAAATAATTAAAA
1 TAAATAATTAAAA
1195511 TAAATAATTAAAA
1 TAAATAATTAAAA
1195524 GTAATGAACT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAATAATTAAAA
Found at i:1200915 original size:2 final size:2
Alignment explanation
Indices: 1200908--1200984 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
1200898 AAAATTTATC
1200908 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1200950 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1200985 GAATTGTTTT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1204047 original size:59 final size:60
Alignment explanation
Indices: 1203949--1204065 Score: 141
Period size: 59 Copynumber: 2.0 Consensus size: 60
1203939 TAAAATAAAC
** * *
1203949 AAATGGTCTTCTGATTATAGGGTATTGTTTTATTAAGTCCAC-CAATTATTAAAAGTTATA
1 AAATGGTCTTCTGATTATAGGACATTGCTTTATTAAGTCC-CTCAACTATTAAAAGTTATA
* *
1204009 AAATGGT-TTCTGACTT-TAGGACATTGCTTTGTTGAGTCCCTCAACTATTAAAAGTTA
1 AAATGGTCTTCTGA-TTATAGGACATTGCTTTATTAAGTCCCTCAACTATTAAAAGTTA
1204066 CAATATTGCC
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
58 1 0.02
59 39 0.80
60 9 0.18
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (60 bp):
AAATGGTCTTCTGATTATAGGACATTGCTTTATTAAGTCCCTCAACTATTAAAAGTTATA
Found at i:1207195 original size:2 final size:2
Alignment explanation
Indices: 1207190--1207224 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1207180 AGGTTCTAAT
1207190 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1207225 TAAGAGTAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1207348 original size:147 final size:147
Alignment explanation
Indices: 1207076--1207358 Score: 485
Period size: 147 Copynumber: 1.9 Consensus size: 147
1207066 AATTGTTGAG
* *
1207076 ATTAGGAGTAGAAATGAGAAGATATTCGCGGAAAATTCAATGAGTTAATCTCAACCTTCTATTTT
1 ATTAAGAGTAGAAATGAGAAGATATTCGCGGAAAAATCAATGAGTTAATCTCAACCTTCTATTTT
* * *
1207141 CATTCATCCAACGGTTCCAAATTTGTGTTGAGTTAAAAAAGGTTCTAATTATATATATATATATA
66 CATTCATCCAACAGTTCCAAATTTGTGTTAAGTTAAAAAAAGTTCTAATTATATATATATATATA
1207206 TATATATATATATATAT
131 TATATATATATATATAT
* * *
1207223 ATTAAGAGTAGAAATGAGAAGTTATTCTCGGAAAAATCAATGAGTTAATCTCAACCTTTTATTTT
1 ATTAAGAGTAGAAATGAGAAGATATTCGCGGAAAAATCAATGAGTTAATCTCAACCTTCTATTTT
*
1207288 CATTCGTCCAACAGTTCCAAATTTGTGTTAAGTTAAAAAAAGTTCTAATTATATATATATATATA
66 CATTCATCCAACAGTTCCAAATTTGTGTTAAGTTAAAAAAAGTTCTAATTATATATATATATATA
1207353 TATATA
131 TATATA
1207359 AAGCTTACCT
Statistics
Matches: 127, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
147 127 1.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (147 bp):
ATTAAGAGTAGAAATGAGAAGATATTCGCGGAAAAATCAATGAGTTAATCTCAACCTTCTATTTT
CATTCATCCAACAGTTCCAAATTTGTGTTAAGTTAAAAAAAGTTCTAATTATATATATATATATA
TATATATATATATATAT
Found at i:1219336 original size:26 final size:26
Alignment explanation
Indices: 1219307--1219356 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
1219297 TATGTATTTT
1219307 ATCTATTTACTATAAAACTTTATCTA
1 ATCTATTTACTATAAAACTTTATCTA
*
1219333 ATCTATTTACTATAAAATTTTATC
1 ATCTATTTACTATAAAACTTTATC
1219357 ATCCAACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48
Consensus pattern (26 bp):
ATCTATTTACTATAAAACTTTATCTA
Found at i:1219746 original size:19 final size:20
Alignment explanation
Indices: 1219702--1219746 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1219692 ATTTGTTTTT
*
1219702 AATAAATTTTTATCTGTGAA
1 AATAAATTTTTATCTGTCAA
* *
1219722 ATTAAATTTTTAT-TTTCAA
1 AATAAATTTTTATCTGTCAA
1219741 AATAAA
1 AATAAA
1219747 ATATTAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (20 bp):
AATAAATTTTTATCTGTCAA
Found at i:1219775 original size:14 final size:13
Alignment explanation
Indices: 1219747--1219782 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
1219737 TCAAAATAAA
1219747 ATATTAAAATAGT
1 ATATTAAAATAGT
*
1219760 ATATTAATATTAGT
1 ATATTAA-AATAGT
1219774 ATATTAAAA
1 ATATTAAAA
1219783 GATAATTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.42
Consensus pattern (13 bp):
ATATTAAAATAGT
Found at i:1229552 original size:41 final size:42
Alignment explanation
Indices: 1229462--1229553 Score: 98
Period size: 43 Copynumber: 2.2 Consensus size: 42
1229452 CTAAACAAAT
*
1229462 GACACTAATGTAATGTCAAATTGGGACGCTTTCTTCAAAACA
1 GACACTAATGTAATGTCAAATTGGGACGCTTTCTTAAAAACA
* * ** *
1229504 TACCACTAATGTAATGTGAAATTGCGG-CTTTTTTTTAAAAAC-
1 GA-CACTAATGTAATGTCAAATTG-GGACGCTTTCTTAAAAACA
1229546 GACACTAA
1 GACACTAA
1229554 AATACGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
41 6 0.15
42 2 0.05
43 31 0.76
44 2 0.05
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (42 bp):
GACACTAATGTAATGTCAAATTGGGACGCTTTCTTAAAAACA
Found at i:1233024 original size:2 final size:2
Alignment explanation
Indices: 1233017--1233046 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1233007 TAGACAAATC
1233017 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1233047 CCATGCATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1233245 original size:20 final size:20
Alignment explanation
Indices: 1233216--1233264 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1233206 AAATTTCATT
* *
1233216 AAAAATGGAGCTTAATTATG
1 AAAAACGGAGCTTAATTATA
*
1233236 AAAAACGGAGCTTAATTGTA
1 AAAAACGGAGCTTAATTATA
1233256 AAAAACGGA
1 AAAAACGGA
1233265 TCGAATCAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.49, C:0.08, G:0.20, T:0.22
Consensus pattern (20 bp):
AAAAACGGAGCTTAATTATA
Found at i:1233592 original size:24 final size:24
Alignment explanation
Indices: 1233562--1233629 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
1233552 GTCGGGTCGG
* * *
1233562 GTCGGGTCAAACCGGGTTAAACGA
1 GTCGGGTCAAACCGAGTCAAACAA
*
1233586 GTCGGGTTAAACCGAGTCAAACAA
1 GTCGGGTCAAACCGAGTCAAACAA
**
1233610 GTTAGGTCAAACCGAGTCAA
1 GTCGGGTCAAACCGAGTCAA
1233630 CTGCCCCAAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.34, C:0.21, G:0.28, T:0.18
Consensus pattern (24 bp):
GTCGGGTCAAACCGAGTCAAACAA
Found at i:1233593 original size:14 final size:15
Alignment explanation
Indices: 1233574--1233603 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1233564 CGGGTCAAAC
1233574 CGGGTTAAA-CGAGT
1 CGGGTTAAACCGAGT
1233588 CGGGTTAAACCGAGT
1 CGGGTTAAACCGAGT
1233603 C
1 C
1233604 AAACAAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.27, C:0.20, G:0.33, T:0.20
Consensus pattern (15 bp):
CGGGTTAAACCGAGT
Found at i:1239240 original size:73 final size:73
Alignment explanation
Indices: 1239121--1239276 Score: 312
Period size: 73 Copynumber: 2.1 Consensus size: 73
1239111 CTAGTCTGTT
1239121 AACGAAAGTGAACCCTTGGTGACCACATTTTAATTTAATAAAAATGAATGTGACAATATCTTAAT
1 AACGAAAGTGAACCCTTGGTGACCACATTTTAATTTAATAAAAATGAATGTGACAATATCTTAAT
1239186 TAAATAAA
66 TAAATAAA
1239194 AACGAAAGTGAACCCTTGGTGACCACATTTTAATTTAATAAAAATGAATGTGACAATATCTTAAT
1 AACGAAAGTGAACCCTTGGTGACCACATTTTAATTTAATAAAAATGAATGTGACAATATCTTAAT
1239259 TAAATAAA
66 TAAATAAA
1239267 AACGAAAGTG
1 AACGAAAGTG
1239277 GCCATATATT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 83 1.00
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.29
Consensus pattern (73 bp):
AACGAAAGTGAACCCTTGGTGACCACATTTTAATTTAATAAAAATGAATGTGACAATATCTTAAT
TAAATAAA
Found at i:1240133 original size:60 final size:60
Alignment explanation
Indices: 1240058--1240180 Score: 183
Period size: 60 Copynumber: 2.0 Consensus size: 60
1240048 AAACACCAGA
* * *
1240058 ACATACATCCATAAGGACTTACCCTAGACCTCTAGGATCTAGAAGTCCAATATGGAAGAT
1 ACATACATCCATAAGGACTTACCCTAGACCACTAGGATATAGAAGTCCAAGATGGAAGAT
* * * *
1240118 ACATGCATTCATAAGGACTTGCCCTAGACCACTAGGATATAGGAGTCCAAGATGGAAGAT
1 ACATACATCCATAAGGACTTACCCTAGACCACTAGGATATAGAAGTCCAAGATGGAAGAT
1240178 ACA
1 ACA
1240181 AACTAGGATC
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (60 bp):
ACATACATCCATAAGGACTTACCCTAGACCACTAGGATATAGAAGTCCAAGATGGAAGAT
Found at i:1240211 original size:34 final size:34
Alignment explanation
Indices: 1240148--1240214 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
1240138 GCCCTAGACC
*
1240148 ACTAGGATATAGGAGTCCAAGATGGAAGATACAA
1 ACTAGGATATAGGAGTCCAAGATGAAAGATACAA
* * *
1240182 ACTAGGATCTAGGAGTCCAATATTAAAGATACA
1 ACTAGGATATAGGAGTCCAAGATGAAAGATACA
1240215 TGAATCCATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.21
Consensus pattern (34 bp):
ACTAGGATATAGGAGTCCAAGATGAAAGATACAA
Found at i:1240269 original size:94 final size:94
Alignment explanation
Indices: 1240089--1240271 Score: 249
Period size: 94 Copynumber: 1.9 Consensus size: 94
1240079 CCCTAGACCT
* * * *
1240089 CTAGGATCTAGAAGTCCAATATGGAAGATACATGCATTCATAAGGACTTGCCCTAGACCACTAGG
1 CTAGGATCTAGAAGTCCAATATGAAAGATACATGAATCCATAAGGACTTACCCTAGACCACTAGG
* *
1240154 ATATAGGAGTCCAAGATGGAAGATACAAA
66 ACATAGGAGTCCAAGACGGAAGATACAAA
* * *
1240183 CTAGGATCTAGGAGTCCAATATTAAAGATACATGAATCCATAAGGTCTTACCCTAGACCACTAGG
1 CTAGGATCTAGAAGTCCAATATGAAAGATACATGAATCCATAAGGACTTACCCTAGACCACTAGG
* * * *
1240248 ACCTATGAGTTCAATACGGAAGAT
66 ACATAGGAGTCCAAGACGGAAGAT
1240272 CAGAAAAGGA
Statistics
Matches: 76, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
94 76 1.00
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (94 bp):
CTAGGATCTAGAAGTCCAATATGAAAGATACATGAATCCATAAGGACTTACCCTAGACCACTAGG
ACATAGGAGTCCAAGACGGAAGATACAAA
Found at i:1241942 original size:28 final size:27
Alignment explanation
Indices: 1241893--1241947 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
1241883 TTGACTTTTT
*
1241893 AGTCAAAGTTAACCCTGATCAAAGTCAA
1 AGTCAAAGTCAACCCTGATC-AAGTCAA
** *
1241921 AGTCAAAGTCAACTTTGGTCAAGTCAA
1 AGTCAAAGTCAACCCTGATCAAGTCAA
1241948 CGCAACACGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (27 bp):
AGTCAAAGTCAACCCTGATCAAGTCAA
Found at i:1242039 original size:34 final size:34
Alignment explanation
Indices: 1241974--1242040 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
1241964 AATCAACCCG
* **
1241974 ACTTGATAGCTAACTCGGCTCTCTACATGGCTCA
1 ACTTGATAGATAACTCGGCTCGATACATGGCTCA
*
1242008 ACTTGATAGATAGCTCGGCTCGAT-CAGTGGCTC
1 ACTTGATAGATAACTCGGCTCGATACA-TGGCTC
1242041 GGTTTAGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 2 0.07
34 26 0.93
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.28
Consensus pattern (34 bp):
ACTTGATAGATAACTCGGCTCGATACATGGCTCA
Found at i:1244775 original size:59 final size:60
Alignment explanation
Indices: 1244652--1244886 Score: 273
Period size: 59 Copynumber: 4.0 Consensus size: 60
1244642 CCCAGAACAA
* * * *
1244652 GCATCTATAAGGACTTACCCTAGA-CACCTAGGATCTAAGAGTCCAATATGGAAGATGCAG
1 GCATCCATAAGGACTTACCCTAGATCA-CTAGGATCTAGGATTCCAATATGGAAGATACAG
* * *
1244712 GCATCCATAAGGACTTA-CCTAGATCACTAGAATTTAGGATTCCGAAT-TGGAAGATACAT
1 GCATCCATAAGGACTTACCCTAGATCACTAGGATCTAGGATTCC-AATATGGAAGATACAG
** * * * *
1244771 GCATCCATAAGGACTTGTCATAG-TAACTAGGATCTAGAACTCCAATATGGAAGATACAG
1 GCATCCATAAGGACTTACCCTAGATCACTAGGATCTAGGATTCCAATATGGAAGATACAG
* *
1244830 GCATCCATAAGAACTTACCCTAGAACACTAGGATCTAGGAGTT-CAATATGGAAGATA
1 GCATCCATAAGGACTTACCCTAGATCACTAGGATCTAGGA-TTCCAATATGGAAGATA
1244887 AGAACAGGCA
Statistics
Matches: 146, Mismatches: 23, Indels: 12
0.81 0.13 0.07
Matches are distributed among these distances:
58 3 0.02
59 90 0.62
60 52 0.36
61 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (60 bp):
GCATCCATAAGGACTTACCCTAGATCACTAGGATCTAGGATTCCAATATGGAAGATACAG
Found at i:1249442 original size:60 final size:59
Alignment explanation
Indices: 1249285--1249457 Score: 242
Period size: 58 Copynumber: 2.9 Consensus size: 59
1249275 CCATAACAGA
* *
1249285 CATCTATAAGGACTTACCCTAGACACCTAGGATATAGGAGTCTAATATGGAAGATACATG
1 CATCCATAAGGACTTACCCTAGACA-CTAGGATATAGGAGTCTAATATAGAAGATACATG
* * *
1249345 CAT-C-GAAGGACTTACCCTAGATCACTAAGATATAGGAGTCCAATATAGAAGATACATG
1 CATCCATAAGGACTTACCCTAGA-CACTAGGATATAGGAGTCTAATATAGAAGATACATG
* *
1249403 CATCCATAAGGACTTACCCTAGACCACTAGGATCTAGGAGTCTAATATAAAAGAT
1 CATCCATAAGGACTTACCCTAGA-CACTAGGATATAGGAGTCTAATATAGAAGAT
1249458 CAGAACAAGC
Statistics
Matches: 99, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
58 50 0.51
59 3 0.03
60 46 0.46
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (59 bp):
CATCCATAAGGACTTACCCTAGACACTAGGATATAGGAGTCTAATATAGAAGATACATG
Found at i:1256480 original size:20 final size:20
Alignment explanation
Indices: 1256454--1256506 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1256444 ATTTTGGTGC
1256454 AGAGGGAATCGATCCCCCCA
1 AGAGGGAATCGATCCCCCCA
* *
1256474 TGAGGGAACCGATTCCCCCCA
1 AGAGGGAATCGA-TCCCCCCA
1256495 AG-GGGAATCGAT
1 AGAGGGAATCGAT
1256507 ACCCTCCCTG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.04
20 18 0.64
21 9 0.32
ACGTcount: A:0.28, C:0.30, G:0.28, T:0.13
Consensus pattern (20 bp):
AGAGGGAATCGATCCCCCCA
Found at i:1256519 original size:20 final size:19
Alignment explanation
Indices: 1256457--1256519 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 19
1256447 TTGGTGCAGA
1256457 GGGAATCGATCCCCCCATG
1 GGGAATCGATCCCCCCATG
* *
1256476 AGGGAACCGATTCCCCCCAAG
1 -GGGAATCGA-TCCCCCCATG
1256497 GGGAATCGATACCCTCCC-TG
1 GGGAATCGAT-CCC-CCCATG
1256517 GGG
1 GGG
1256520 TTCTGGATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 1 0.03
20 23 0.64
21 12 0.33
ACGTcount: A:0.22, C:0.35, G:0.29, T:0.14
Consensus pattern (19 bp):
GGGAATCGATCCCCCCATG
Found at i:1263546 original size:16 final size:16
Alignment explanation
Indices: 1263527--1263562 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1263517 GACCTGATCA
1263527 GATATTTACCTAACTT
1 GATATTTACCTAACTT
*
1263543 GATATTTACCTTACTT
1 GATATTTACCTAACTT
1263559 -ATAT
1 GATAT
1263563 AATACCATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.47
Consensus pattern (16 bp):
GATATTTACCTAACTT
Found at i:1263807 original size:52 final size:53
Alignment explanation
Indices: 1263749--1263869 Score: 149
Period size: 61 Copynumber: 2.2 Consensus size: 53
1263739 TTAAATGTAA
1263749 ATTATATAAAACATGATTAATAATGCAAAGAAAAAAAAATAATATAGTTTAATTTATAT
1 ATTATATAAAACATGATTAATAATGCAAAG--AAAAAAATAATATAG--T--TTTATAT
1263808 AAATTATATAAAACATGATTAATAATGCAAAGAAAAAAATAATATAG-TTTA-AT
1 --ATTATATAAAACATGATTAATAATGCAAAGAAAAAAATAATATAGTTTTATAT
1263861 -TTATATAAA
1 ATTATATAAA
1263870 TTATATAGTT
Statistics
Matches: 60, Mismatches: 0, Indels: 11
0.85 0.00 0.15
Matches are distributed among these distances:
50 9 0.15
53 2 0.03
54 4 0.07
59 15 0.25
61 30 0.50
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (53 bp):
ATTATATAAAACATGATTAATAATGCAAAGAAAAAAATAATATAGTTTTATAT
Found at i:1263873 original size:59 final size:60
Alignment explanation
Indices: 1263746--1263876 Score: 246
Period size: 59 Copynumber: 2.2 Consensus size: 60
1263736 TATTTAAATG
1263746 TAAATTATATAAAACATGATTAATAATGCAAAGAAAAAAAAATAATATAGTTTAATTTATA
1 TAAATTATATAAAACATGATTAATAATGCAAAG-AAAAAAAATAATATAGTTTAATTTATA
1263807 TAAATTATATAAAACATGATTAATAATGCAAAG-AAAAAAATAATATAGTTTAATTTATA
1 TAAATTATATAAAACATGATTAATAATGCAAAGAAAAAAAATAATATAGTTTAATTTATA
1263866 TAAATTATATA
1 TAAATTATATA
1263877 GTTTAATTTA
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
59 37 0.53
61 33 0.47
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.34
Consensus pattern (60 bp):
TAAATTATATAAAACATGATTAATAATGCAAAGAAAAAAAATAATATAGTTTAATTTATA
Found at i:1263875 original size:23 final size:23
Alignment explanation
Indices: 1263844--1263892 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
1263834 GCAAAGAAAA
1263844 AAATAATATAGTTTAATTTATAT
1 AAATAATATAGTTTAATTTATAT
* *
1263867 AAATTATATAGTTTAATTTATGT
1 AAATAATATAGTTTAATTTATAT
1263890 AAA
1 AAA
1263893 GAAAAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (23 bp):
AAATAATATAGTTTAATTTATAT
Found at i:1265078 original size:32 final size:31
Alignment explanation
Indices: 1265040--1265116 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
1265030 CGGGGCTGTG
*
1265040 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
1265072 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
1265103 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
1265117 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:1265998 original size:7 final size:7
Alignment explanation
Indices: 1265986--1266030 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
1265976 GTCAAAGAAA
1265986 GTCAACG
1 GTCAACG
1265993 GTCAACG
1 GTCAACG
1266000 GTCAACG
1 GTCAACG
1266007 GTCAACG
1 GTCAACG
*
1266014 GTCAATG
1 GTCAACG
*
1266021 ATCAACG
1 GTCAACG
1266028 GTC
1 GTC
1266031 GGGTCGGGTC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:1266071 original size:14 final size:14
Alignment explanation
Indices: 1266033--1266092 Score: 75
Period size: 14 Copynumber: 4.1 Consensus size: 14
1266023 CAACGGTCGG
1266033 GTCGGGTCGGGTCAACA
1 GTCGGGTCGGGT---CA
1266050 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
*
1266064 GTCAGGTCGGGTCA
1 GTCGGGTCGGGTCA
*
1266078 GACGGGTCGGGTCA
1 GTCGGGTCGGGTCA
1266092 G
1 G
1266093 ACCGATCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
14 28 0.70
17 12 0.30
ACGTcount: A:0.13, C:0.22, G:0.47, T:0.18
Consensus pattern (14 bp):
GTCGGGTCGGGTCA
Found at i:1266116 original size:10 final size:10
Alignment explanation
Indices: 1266098--1266147 Score: 59
Period size: 9 Copynumber: 5.1 Consensus size: 10
1266088 GTCAGACCGA
1266098 TCAAACCGGT
1 TCAAACCGGT
*
1266108 TCGAACCGG-
1 TCAAACCGGT
1266117 TCAAACCGGT
1 TCAAACCGGT
*
1266127 TCAAAACTGG-
1 TC-AAACCGGT
1266137 TCAAACCGGT
1 TCAAACCGGT
1266147 T
1 T
1266148 TTCCAGCAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 14 0.42
10 13 0.39
11 6 0.18
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:1266120 original size:19 final size:20
Alignment explanation
Indices: 1266093--1266147 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
1266083 GTCGGGTCAG
* *
1266093 ACCGATCAAACCGGTTC-GA
1 ACCGGTCAAACCGGTTCAAA
1266112 ACCGGTCAAACCGGTTCAAA
1 ACCGGTCAAACCGGTTCAAA
*
1266132 ACTGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
1266148 TTCCAGCAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18
Consensus pattern (20 bp):
ACCGGTCAAACCGGTTCAAA
Found at i:1266123 original size:9 final size:9
Alignment explanation
Indices: 1266087--1266146 Score: 57
Period size: 9 Copynumber: 6.3 Consensus size: 9
1266077 AGACGGGTCG
*
1266087 GGTCAGACC
1 GGTCAAACC
*
1266096 GATCAAACC
1 GGTCAAACC
*
1266105 GGTTCGAACC
1 GG-TCAAACC
1266115 GGTCAAACC
1 GGTCAAACC
*
1266124 GGTTCAAAACT
1 GG-TC-AAACC
1266135 GGTCAAACC
1 GGTCAAACC
1266144 GGT
1 GGT
1266147 TTTCCAGCAG
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
9 23 0.56
10 12 0.29
11 6 0.15
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.17
Consensus pattern (9 bp):
GGTCAAACC
Found at i:1272420 original size:32 final size:31
Alignment explanation
Indices: 1272384--1272460 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
1272374 TGGGGCCGTG
*
1272384 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
1272416 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
1272447 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
1272461 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:1273343 original size:7 final size:7
Alignment explanation
Indices: 1273327--1273364 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
1273317 GTCAAAGAAA
*
1273327 GTCAATG
1 GTCAACG
1273334 GTCAACG
1 GTCAACG
*
1273341 GTCAATG
1 GTCAACG
1273348 GTCAACG
1 GTCAACG
1273355 GTCAACG
1 GTCAACG
1273362 GTC
1 GTC
1273365 GGGTCGGGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (7 bp):
GTCAACG
Found at i:1273346 original size:14 final size:14
Alignment explanation
Indices: 1273327--1273364 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
1273317 GTCAAAGAAA
1273327 GTCAATGGTCAACG
1 GTCAATGGTCAACG
1273341 GTCAATGGTCAACG
1 GTCAATGGTCAACG
*
1273355 GTCAACGGTC
1 GTCAATGGTC
1273365 GGGTCGGGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (14 bp):
GTCAATGGTCAACG
Found at i:1273376 original size:17 final size:17
Alignment explanation
Indices: 1273354--1273391 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
1273344 AATGGTCAAC
*
1273354 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
1273371 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
1273388 GGTC
1 GGTC
1273392 GGGTCAGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.13, C:0.24, G:0.45, T:0.18
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:1273407 original size:14 final size:14
Alignment explanation
Indices: 1273366--1273433 Score: 67
Period size: 14 Copynumber: 5.3 Consensus size: 14
1273356 TCAACGGTCG
1273366 GGTCGGGTCA-ACA
1 GGTCGGGTCAGACA
1273379 -GTCGGGTC-G---
1 GGTCGGGTCAGACA
*
1273388 GGTCGGGTCAGTCA
1 GGTCGGGTCAGACA
*
1273402 GGTCGGGTCAGACG
1 GGTCGGGTCAGACA
*
1273416 GGTCGGGTCAGACC
1 GGTCGGGTCAGACA
1273430 GGTC
1 GGTC
1273434 CAGACCCATC
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
10 8 0.17
11 1 0.02
12 8 0.17
14 29 0.63
ACGTcount: A:0.13, C:0.24, G:0.46, T:0.18
Consensus pattern (14 bp):
GGTCGGGTCAGACA
Found at i:1273424 original size:19 final size:18
Alignment explanation
Indices: 1273362--1273424 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 18
1273352 ACGGTCAACG
1273362 GTCGGGTCGGGTCA-ACA
1 GTCGGGTCGGGTCAGACA
* *
1273379 GTCGGGTCGGGTCGGGTCA
1 GTCGGGTCGGGTC-AGACA
* *
1273398 GTCAGGTCGGGTCAGACGG
1 GTCGGGTCGGGTCAGAC-A
1273417 GTCGGGTC
1 GTCGGGTC
1273425 AGACCGGTCC
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
17 13 0.36
18 2 0.06
19 21 0.58
ACGTcount: A:0.11, C:0.22, G:0.48, T:0.19
Consensus pattern (18 bp):
GTCGGGTCGGGTCAGACA
Found at i:1273458 original size:10 final size:10
Alignment explanation
Indices: 1273442--1273475 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
1273432 TCCAGACCCA
1273442 TCAAACCGGT
1 TCAAACCGGT
*
1273452 TCGAACCGG-
1 TCAAACCGGT
1273461 TCAAACCGGT
1 TCAAACCGGT
1273471 TCAAA
1 TCAAA
1273476 ACTAGTCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.32, C:0.29, G:0.21, T:0.18
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:1273485 original size:20 final size:19
Alignment explanation
Indices: 1273442--1273491 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
1273432 TCCAGACCCA
* *
1273442 TCAAACCGGTTCGAACCGG
1 TCAAACCGGTTCAAACCAG
*
1273461 TCAAACCGGTTCAAAACTAG
1 TCAAACCGGTTC-AAACCAG
*
1273481 TCAAATCGGTT
1 TCAAACCGGTT
1273492 TTCCAGCAGC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (19 bp):
TCAAACCGGTTCAAACCAG
Found at i:1277065 original size:18 final size:18
Alignment explanation
Indices: 1277044--1277157 Score: 104
Period size: 18 Copynumber: 6.2 Consensus size: 18
1277034 TTCAAATTTG
* *
1277044 GGTTTAGATATGGGTTTA
1 GGTTTAGGTTTGGGTTTA
* * *
1277062 GGTTTTAGGTTCGAGTTTT
1 GG-TTTAGGTTTGGGTTTA
* * *
1277081 GGATTTAGATTCGGGTTTG
1 GG-TTTAGGTTTGGGTTTA
* *
1277100 GGTTTGGGTTTGGGTTAA
1 GGTTTAGGTTTGGGTTTA
1277118 GGTTTAGGTTTGGGTTCTA
1 GGTTTAGGTTTGGGTT-TA
1277137 -GTTTAGGTTTGGGTTTA
1 GGTTTAGGTTTGGGTTTA
1277154 GGTT
1 GGTT
1277158 CAAGTTAGGG
Statistics
Matches: 77, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
17 2 0.03
18 46 0.60
19 29 0.38
ACGTcount: A:0.13, C:0.03, G:0.37, T:0.47
Consensus pattern (18 bp):
GGTTTAGGTTTGGGTTTA
Found at i:1277079 original size:19 final size:19
Alignment explanation
Indices: 1277057--1277104 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
1277047 TTAGATATGG
*
1277057 GTTTAGGTTTTAGGTTCGA
1 GTTTAGGTTTTAGATTCGA
* * *
1277076 GTTTTGGATTTAGATTCGG
1 GTTTAGGTTTTAGATTCGA
*
1277095 GTTTGGGTTT
1 GTTTAGGTTT
1277105 GGGTTTGGGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.12, C:0.04, G:0.33, T:0.50
Consensus pattern (19 bp):
GTTTAGGTTTTAGATTCGA
Found at i:1277102 original size:6 final size:6
Alignment explanation
Indices: 1277093--1277157 Score: 60
Period size: 6 Copynumber: 10.8 Consensus size: 6
1277083 ATTTAGATTC
* * * *
1277093 GGGTTT GGGTTT GGGTTT GGGTTA AGGTTT AGGTTT GGGTTCT -AGTTT
1 GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTT-T GGGTTT
* *
1277141 AGGTTT GGGTTT AGGTT
1 GGGTTT GGGTTT GGGTT
1277158 CAAGTTAGGG
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
5 1 0.02
6 47 0.96
7 1 0.02
ACGTcount: A:0.09, C:0.02, G:0.42, T:0.48
Consensus pattern (6 bp):
GGGTTT
Found at i:1277110 original size:12 final size:12
Alignment explanation
Indices: 1277094--1277157 Score: 67
Period size: 12 Copynumber: 5.3 Consensus size: 12
1277084 TTTAGATTCG
*
1277094 GGTTTGGGTTTG
1 GGTTTGGGTTTA
*
1277106 GGTTTGGGTTAA
1 GGTTTGGGTTTA
* *
1277118 GGTTTAGGTTTG
1 GGTTTGGGTTTA
*
1277130 GGTTCT-AGTTTA
1 GGTT-TGGGTTTA
1277142 GGTTTGGGTTTA
1 GGTTTGGGTTTA
1277154 GGTT
1 GGTT
1277158 CAAGTTAGGG
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 1 0.02
12 40 0.95
13 1 0.02
ACGTcount: A:0.09, C:0.02, G:0.41, T:0.48
Consensus pattern (12 bp):
GGTTTGGGTTTA
Found at i:1277844 original size:16 final size:16
Alignment explanation
Indices: 1277823--1277860 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1277813 GTTTTAGGTA
1277823 TTTTAGTTTAAATAGG
1 TTTTAGTTTAAATAGG
*
1277839 TTTTAGTTTAATTAGG
1 TTTTAGTTTAAATAGG
*
1277855 ATTTAG
1 TTTTAG
1277861 AATATTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (16 bp):
TTTTAGTTTAAATAGG
Found at i:1277872 original size:12 final size:12
Alignment explanation
Indices: 1277855--1277882 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1277845 TTTAATTAGG
1277855 ATTTAGAATATT
1 ATTTAGAATATT
1277867 ATTTAGAATATT
1 ATTTAGAATATT
1277879 ATTT
1 ATTT
1277883 TTTAGGTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (12 bp):
ATTTAGAATATT
Found at i:1277904 original size:68 final size:71
Alignment explanation
Indices: 1277714--1277930 Score: 209
Period size: 72 Copynumber: 3.1 Consensus size: 71
1277704 TAAACTCAAG
* * * *
1277714 TTTAGGATAATATTTTAAACATTATTT-TTACTT-TGTATTTAG-TTAAATAGGTTTTAGGTTTT
1 TTTAGAATATTATTTTAAATATTATTTGTT--TTAGGTATTTAGTTTAAATAGGTTTTAGGTTTT
* *
1277776 AATTAAGT
64 AATTAGGA
* * *
1277784 TTTAGGATATTATTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTA-G-TT
1 TTTAGAATATTATTTTAAATATTA--TTTGTTTTAGGTA-TTTAGTTTAAATAGGTTTTAGGTTT
1277847 TAATTAGGA
63 TAATTAGGA
1277856 TTTAGAATATTA-TTTAGAATATTA-TT-TTTTAGGTATCTTAGTTTAAATA-GTTTTAAGTGTT
1 TTTAGAATATTATTTTA-AATATTATTTGTTTTAGGTAT-TTAGTTTAAATAGGTTTT-AG-GTT
1277917 TTAATTAGGA
62 TTAATTAGGA
1277927 TTTA
1 TTTA
1277931 AGATGTTTAG
Statistics
Matches: 125, Mismatches: 10, Indels: 23
0.79 0.06 0.15
Matches are distributed among these distances:
67 6 0.05
68 22 0.18
69 2 0.02
70 21 0.17
71 21 0.17
72 31 0.25
73 8 0.06
74 14 0.11
ACGTcount: A:0.30, C:0.02, G:0.14, T:0.54
Consensus pattern (71 bp):
TTTAGAATATTATTTTAAATATTATTTGTTTTAGGTATTTAGTTTAAATAGGTTTTAGGTTTTAA
TTAGGA
Found at i:1278638 original size:16 final size:16
Alignment explanation
Indices: 1278612--1278653 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
1278602 TAAAAATCCC
1278612 CTTTT-ATATTTATTA
1 CTTTTAATATTTATTA
1278627 CTTTTAATATTTATTA
1 CTTTTAATATTTATTA
*
1278643 -TTTTATTATTT
1 CTTTTAATATTT
1278654 TTCTTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 15 0.60
16 10 0.40
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (16 bp):
CTTTTAATATTTATTA
Found at i:1278676 original size:15 final size:16
Alignment explanation
Indices: 1278618--1278674 Score: 55
Period size: 16 Copynumber: 3.5 Consensus size: 16
1278608 TCCCCTTTTA
1278618 TATTTATTACTTTTAA-
1 TATTTATTA-TTTTAAT
1278634 TATTTATTATTTT-AT
1 TATTTATTATTTTAAT
* *
1278649 TATTTTTCTTTTTTTAAT
1 TA--TTTATTATTTTAAT
1278667 TATTTATT
1 TATTTATT
1278675 TTATTATACA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
14 1 0.03
15 6 0.18
16 14 0.41
17 9 0.26
18 4 0.12
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.72
Consensus pattern (16 bp):
TATTTATTATTTTAAT
Found at i:1279056 original size:60 final size:60
Alignment explanation
Indices: 1278957--1279087 Score: 192
Period size: 60 Copynumber: 2.2 Consensus size: 60
1278947 GAGAATGCTG
* ** * *
1278957 ATATGTAAGATACATGCATCCATAAGGACTTACCTTAGACCACTAGGATCTAAGAGTCCA
1 ATATGGAAGATACAAACATCCATAAGGACTTAACTTAGACCACTAGAATCTAAGAGTCCA
*
1279017 ATATGGAAGATACAAACATCCATAAGGACTTATAC-TAGACCACTAGAATCTAGGAGTCCA
1 ATATGGAAGATACAAACATCCATAAGGACTTA-ACTTAGACCACTAGAATCTAAGAGTCCA
1279077 ATATGGAAGAT
1 ATATGGAAGAT
1279088 CAGAACAGGC
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
60 63 0.98
61 1 0.02
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.24
Consensus pattern (60 bp):
ATATGGAAGATACAAACATCCATAAGGACTTAACTTAGACCACTAGAATCTAAGAGTCCA
Found at i:1282920 original size:2 final size:2
Alignment explanation
Indices: 1282913--1282951 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1282903 GATCAAATTT
1282913 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1282952 CGATTAATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1284349 original size:222 final size:222
Alignment explanation
Indices: 1283963--1284408 Score: 892
Period size: 222 Copynumber: 2.0 Consensus size: 222
1283953 AAATGGTCCT
1283963 TCGATTATAAAGTGTTATTTTATTAAGTCTTATGACTATACAAAATTATAAAATGATTCCCTTAC
1 TCGATTATAAAGTGTTATTTTATTAAGTCTTATGACTATACAAAATTATAAAATGATTCCCTTAC
1284028 TATAAGATGTTACTTTGTTGAGTCCCTAGACTATTAAAAGTTACAAAATGACCACTCAACTATTC
66 TATAAGATGTTACTTTGTTGAGTCCCTAGACTATTAAAAGTTACAAAATGACCACTCAACTATTC
1284093 ATTATGTTTTAAATTCATCATTTTCCGTAAAAACAATTTGATGATTGTATGACTAGATGTTAATA
131 ATTATGTTTTAAATTCATCATTTTCCGTAAAAACAATTTGATGATTGTATGACTAGATGTTAATA
1284158 TGTTGTATGAAATATGATGAAATTTGA
196 TGTTGTATGAAATATGATGAAATTTGA
1284185 TCGATTATAAAGTGTTATTTTATTAAGTCTTATGACTATACAAAATTATAAAATGATTCCCTTAC
1 TCGATTATAAAGTGTTATTTTATTAAGTCTTATGACTATACAAAATTATAAAATGATTCCCTTAC
1284250 TATAAGATGTTACTTTGTTGAGTCCCTAGACTATTAAAAGTTACAAAATGACCACTCAACTATTC
66 TATAAGATGTTACTTTGTTGAGTCCCTAGACTATTAAAAGTTACAAAATGACCACTCAACTATTC
1284315 ATTATGTTTTAAATTCATCATTTTCCGTAAAAACAATTTGATGATTGTATGACTAGATGTTAATA
131 ATTATGTTTTAAATTCATCATTTTCCGTAAAAACAATTTGATGATTGTATGACTAGATGTTAATA
1284380 TGTTGTATGAAATATGATGAAATTTGA
196 TGTTGTATGAAATATGATGAAATTTGA
1284407 TC
1 TC
1284409 CTAGAACCTC
Statistics
Matches: 224, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
222 224 1.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.40
Consensus pattern (222 bp):
TCGATTATAAAGTGTTATTTTATTAAGTCTTATGACTATACAAAATTATAAAATGATTCCCTTAC
TATAAGATGTTACTTTGTTGAGTCCCTAGACTATTAAAAGTTACAAAATGACCACTCAACTATTC
ATTATGTTTTAAATTCATCATTTTCCGTAAAAACAATTTGATGATTGTATGACTAGATGTTAATA
TGTTGTATGAAATATGATGAAATTTGA
Found at i:1288283 original size:30 final size:30
Alignment explanation
Indices: 1288227--1288306 Score: 126
Period size: 30 Copynumber: 2.7 Consensus size: 30
1288217 AAATGATACG
*
1288227 CTCTCAACCCGTAAA-ATCAAACAACAATC
1 CTCTCAACCCGTAAACATCACACAACAATC
*
1288256 CTCTCAACCCGAAAACATCACACAACAATC
1 CTCTCAACCCGTAAACATCACACAACAATC
*
1288286 CTCTCAACCCGTGAACATCAC
1 CTCTCAACCCGTAAACATCAC
1288307 CCGTCAATCT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 14 0.30
30 32 0.70
ACGTcount: A:0.40, C:0.39, G:0.05, T:0.16
Consensus pattern (30 bp):
CTCTCAACCCGTAAACATCACACAACAATC
Found at i:1292207 original size:3 final size:3
Alignment explanation
Indices: 1292199--1292250 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
1292189 CTCCTCTCTG
* * * * *
1292199 TCA TCA TCA TCA CCA TCA TCA TCA TCG TCA TCG TCA TCA TCG TCG TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1292247 TCA T
1 TCA T
1292251 AAACATATAC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.25, C:0.35, G:0.08, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:1294265 original size:8 final size:8
Alignment explanation
Indices: 1294252--1294301 Score: 55
Period size: 8 Copynumber: 5.8 Consensus size: 8
1294242 TAACTGCAAA
1294252 AAATAATT
1 AAATAATT
1294260 AAATAAAATACT
1 AAAT--AAT--T
*
1294272 AAAAAATT
1 AAATAATT
1294280 AAATAATT
1 AAATAATT
1294288 AAATAATT
1 AAATAATT
1294296 AAATAA
1 AAATAA
1294302 AATACTAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
8 26 0.72
10 6 0.17
12 4 0.11
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (8 bp):
AAATAATT
Found at i:1294328 original size:36 final size:35
Alignment explanation
Indices: 1294252--1294330 Score: 106
Period size: 36 Copynumber: 2.2 Consensus size: 35
1294242 TAACTGCAAA
**
1294252 AAATAATTAAATAAAATACTAAAAAATTAAATAATT
1 AAATAATTAAATAAAATACTAAAAAATTAAAT-AGG
1294288 AAATAATTAAATAAAATACTAAAAAAATTTAAAT-GG
1 AAATAATTAAATAAAATACT-AAAAAA-TTAAATAGG
1294324 AAATAAT
1 AAATAAT
1294331 ATAATATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
36 27 0.69
37 6 0.15
38 6 0.15
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (35 bp):
AAATAATTAAATAAAATACTAAAAAATTAAATAGG
Found at i:1295196 original size:21 final size:21
Alignment explanation
Indices: 1295172--1295211 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1295162 AAACATGTTA
1295172 AAAAACATTAATGTTTTAGCT
1 AAAAACATTAATGTTTTAGCT
1295193 AAAAACATTAATGTTTTAG
1 AAAAACATTAATGTTTTAG
1295212 GTAATTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (21 bp):
AAAAACATTAATGTTTTAGCT
Found at i:1298071 original size:3 final size:3
Alignment explanation
Indices: 1298063--1298115 Score: 63
Period size: 3 Copynumber: 18.0 Consensus size: 3
1298053 ATTTTTTGAT
* * * *
1298063 TTA TTA TTA TAA TTG TTA -TA TTA TTA TTA TTA TTA TTA ATA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1298110 TTA TTA
1 TTA TTA
1298116 AATAATAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:1299527 original size:28 final size:28
Alignment explanation
Indices: 1299469--1299527 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
1299459 ATTTTATATG
* * * * * *
1299469 ATTATTTTCAATATATTTAATTATTATT
1 ATTATTATAAATATATATAATAAATAAT
1299497 ATTATTATAAATATATATAATAAATAAT
1 ATTATTATAAATATATATAATAAATAAT
1299525 ATT
1 ATT
1299528 TTTTATTATA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (28 bp):
ATTATTATAAATATATATAATAAATAAT
Found at i:1299885 original size:143 final size:142
Alignment explanation
Indices: 1299606--1299869 Score: 311
Period size: 143 Copynumber: 1.9 Consensus size: 142
1299596 TTTTAAATAT
* * *
1299606 ATATTTATTTTTCAATATTAAGAAAGGACAGTCTGAAAGCAACTAGATGTCCATTTTCTGATATT
1 ATATTTATTTTTCAATATTAAGAAAAGACAGTCTGAAAGCAACTAGAAGTCCATTTTCTGATAAT
* * * * * ** *
1299671 TTTAGATAAATAAATATCTTATTTTTTTAATAAATTATATATATTAATCTATTTTTTAGTTATTA
66 TCTAAATAAATAAATATCTTA-TTTTATAATAAATTATATAAATCAATAAATTTTTTAATTATTA
1299736 GATAAATGTTTTA
130 GATAAATGTTTTA
* * * * *
1299749 ATATTTATTTTTTAATATTAAGAAAATAGCTGTCTTAAAGCACCTAGAAG-CCATTTTCTGATAA
1 ATATTTATTTTTCAATATTAAGAAAAGA-CAGTCTGAAAGCAACTAGAAGTCCATTTTCTGATAA
**
1299813 TTCTAAATAAATAAATATCTTA-TTTAT-ATGTA-TATATAAATCAATAAATTTTCTTAA
65 TTCTAAATAAATAAATATCTTATTTTATAATAAATTATATAAATCAATAAATTTT-TTAA
1299870 AATTATAGTA
Statistics
Matches: 101, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
139 16 0.16
140 6 0.06
141 4 0.04
143 58 0.57
144 17 0.17
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (142 bp):
ATATTTATTTTTCAATATTAAGAAAAGACAGTCTGAAAGCAACTAGAAGTCCATTTTCTGATAAT
TCTAAATAAATAAATATCTTATTTTATAATAAATTATATAAATCAATAAATTTTTTAATTATTAG
ATAAATGTTTTA
Found at i:1301730 original size:18 final size:18
Alignment explanation
Indices: 1301707--1301745 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
1301697 CAGAAGGCTA
1301707 GGAGGTGGACGATTTTCG
1 GGAGGTGGACGATTTTCG
1301725 GGAGGTGGACGATTTTCG
1 GGAGGTGGACGATTTTCG
1301743 GGA
1 GGA
1301746 TGTGCACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.18, C:0.10, G:0.46, T:0.26
Consensus pattern (18 bp):
GGAGGTGGACGATTTTCG
Found at i:1307410 original size:8 final size:9
Alignment explanation
Indices: 1307383--1307413 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
1307373 GAATGGCAAT
1307383 CATTCTTTA
1 CATTCTTTA
1307392 CATTCTTTA
1 CATTCTTTA
1307401 CATT-TTTA
1 CATTCTTTA
1307409 CATTC
1 CATTC
1307414 ATTATTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.55
Consensus pattern (9 bp):
CATTCTTTA
Found at i:1309191 original size:30 final size:30
Alignment explanation
Indices: 1309150--1309214 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
1309140 TTTTCCAGAT
*
1309150 GAAGATTTGTTGTACATATCCATGAAAGAA
1 GAAGTTTTGTTGTACATATCCATGAAAGAA
*
1309180 GAAGTTTTGTTGTGCATATCCATGAAAGAA
1 GAAGTTTTGTTGTACATATCCATGAAAGAA
1309210 GAAGT
1 GAAGT
1309215 CAGAACAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.37, C:0.09, G:0.23, T:0.31
Consensus pattern (30 bp):
GAAGTTTTGTTGTACATATCCATGAAAGAA
Found at i:1310993 original size:12 final size:11
Alignment explanation
Indices: 1310962--1310987 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1310952 CTTAAAGAAG
1310962 AAAAAATGAAA
1 AAAAAATGAAA
1310973 AAAAAATGAAA
1 AAAAAATGAAA
1310984 AAAA
1 AAAA
1310988 TTATGATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAAAATGAAA
Found at i:1312766 original size:114 final size:109
Alignment explanation
Indices: 1312545--1312983 Score: 477
Period size: 114 Copynumber: 3.9 Consensus size: 109
1312535 GCAAAGATTC
* * * * * *
1312545 GAATTCATCACTCAATGGATCAACTTTTCTAGAGAA-AGTTCGTAATGAGAAGAACTTATCTGAA
1 GAATTCATCACTCGATGGATCAACATTAC-CG-GAAGAGTTCATAATGAGAAGAACTCATCTGAA
* *
1312609 TAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTTCT
64 GAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT-AACCTTTTTCT
* * *
1312656 CGAATTCATCACTCGATCGATCAGCATTGCCGGAAGAGTTCATAATGAGAAGAACTCATCTGAAG
1 -GAATTCATCACTCGATGGATCAACATTACCGGAAGAGTTCATAATGAGAAGAACTCATCTGAAG
*
1312721 AAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTCTAACCTTTTGCGT
65 -AG--GAAGAAGAAGTTCATAATGAGAAGAACTTGT-TAACCTTTTTC-T
* * * * * **
1312771 GAATCCATTACTCAATGGATCAACATTACCAGAGGAAGTTCATAATGAGAACTACTCATCTGAAG
1 GAATTCATCACTCGATGGATCAACATTACCGGAAG-AGTTCATAATGAGAAGAACTCATCTGAAG
*
1312836 AATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTTGCTT
65 -AGGAAGAAGAAGTTCATAATGAGAAGAACTTG-TTAACCTTTTT-C-T
** * * *
1312885 GAATTCATCGTTCGATGGATCAACTTTTCCAGAGAA-AGTTCATAATGAGAAGAACTTATCTGAA
1 GAATTCATCACTCGATGGATCAACATTACC-G-GAAGAGTTCATAATGAGAAGAACTCATCTGAA
* *
1312949 GAGGAAGAATAAGTTCATAATGAGAAGAGCTTGTT
64 GAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1312984 CAAACCCTTT
Statistics
Matches: 277, Mismatches: 39, Indels: 22
0.82 0.12 0.07
Matches are distributed among these distances:
110 3 0.01
111 27 0.10
112 28 0.10
113 68 0.25
114 118 0.43
115 31 0.11
116 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (109 bp):
GAATTCATCACTCGATGGATCAACATTACCGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGA
GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTAACCTTTTTCT
Found at i:1312965 original size:226 final size:225
Alignment explanation
Indices: 1312545--1312982 Score: 594
Period size: 226 Copynumber: 1.9 Consensus size: 225
1312535 GCAAAGATTC
* * * * * * * *
1312545 GAATTCATCACTCAATGGATCAACTTTTCTAGAGAAAGTTCGTAATGAGAAGAACTTATCTGAAT
1 GAATCCATCACTCAATGGATCAACATTACCAGAGAAAGTTCATAATGAGAACAACTCATCTGAAA
*
1312610 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTTCTCGAATTCATCACTCGATCG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTTCTCGAATTCATCACTCGATCG
*
1312675 ATCAGCATTGCCGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGAAGTTCA
131 ATCAACATTGCCGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAG-AGAAGAAGAAGTTCA
1312740 TAATGAGAAGAACTTGTCTAACCTTTTGCGT
195 TAATGAGAAGAACTTGTCTAACCTTTTGCGT
* * *
1312771 GAATCCATTACTCAATGGATCAACATTACCAGAGGAAGTTCATAATGAGAACTACTCATCTGAAG
1 GAATCCATCACTCAATGGATCAACATTACCAGAGAAAGTTCATAATGAGAACAACTCATCTGAA-
* * * **
1312836 AATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTTGCTTGAATTCATCGTTCGAT
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTT-CTCGAATTCATCACTCGAT
* * * * *
1312901 GGATCAACTTTTCCAGAGAA-AGTTCATAATGAGAAGAACTTATCTGAAG-AG-GAAGAATAAGT
129 CGATCAACATTGCC-G-GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAGAAGAAGAAGT
*
1312963 TCATAATGAGAAGAGCTTGT
192 TCATAATGAGAAGAACTTGT
1312983 TCAAACCCTT
Statistics
Matches: 184, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
226 83 0.45
227 41 0.22
228 28 0.15
229 29 0.16
230 3 0.02
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (225 bp):
GAATCCATCACTCAATGGATCAACATTACCAGAGAAAGTTCATAATGAGAACAACTCATCTGAAA
AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTTCTCGAATTCATCACTCGATCG
ATCAACATTGCCGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAGAAGAAGAAGTTCAT
AATGAGAAGAACTTGTCTAACCTTTTGCGT
Found at i:1313240 original size:3 final size:3
Alignment explanation
Indices: 1313234--1313271 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
1313224 ATTTTTTGAT
* *
1313234 TTA TTA TTA TAA TTT TTA -TA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1313272 AATAATAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1313269 original size:17 final size:17
Alignment explanation
Indices: 1313235--1313269 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1313225 TTTTTTGATT
*
1313235 TATTATTATAATTTTTA
1 TATTATTATAATTATTA
*
1313252 TATTATTATTATTATTA
1 TATTATTATAATTATTA
1313269 T
1 T
1313270 TAAATAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTATTATAATTATTA
Found at i:1329276 original size:24 final size:24
Alignment explanation
Indices: 1329249--1329294 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1329239 CACCATAGCT
1329249 CGTAAAAATTGCACTGAAGTGCTG
1 CGTAAAAATTGCACTGAAGTGCTG
*
1329273 CGTAGAAATTGCACTGAAGTGC
1 CGTAAAAATTGCACTGAAGTGC
1329295 CAGATAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (24 bp):
CGTAAAAATTGCACTGAAGTGCTG
Found at i:1329376 original size:46 final size:46
Alignment explanation
Indices: 1329299--1329395 Score: 142
Period size: 46 Copynumber: 2.1 Consensus size: 46
1329289 AAGTGCCAGA
*
1329299 TAGAAATGTACCGAAGGACCACATAGTATTGTCCCAAAGGACCGCG
1 TAGAAATGTACCGAAGGACCACATAGAATTGTCCCAAAGGACCGCG
* * *
1329345 TAGAAATGT-CCTGAAGGTCCACGTAGAATTGTCCCGAAGGACCGCG
1 TAGAAATGTACC-GAAGGACCACATAGAATTGTCCCAAAGGACCGCG
1329391 TAGAA
1 TAGAA
1329396 CCTCGACTCT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
45 2 0.04
46 44 0.96
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.19
Consensus pattern (46 bp):
TAGAAATGTACCGAAGGACCACATAGAATTGTCCCAAAGGACCGCG
Found at i:1329392 original size:23 final size:23
Alignment explanation
Indices: 1329299--1329395 Score: 104
Period size: 23 Copynumber: 4.2 Consensus size: 23
1329289 AAGTGCCAGA
* *
1329299 TAGAAATGTACCGAAGGACCACA
1 TAGAAATGTCCCGAAGGACCACG
* * * *
1329322 TAGTATTGTCCCAAAGGACCGCG
1 TAGAAATGTCCCGAAGGACCACG
* *
1329345 TAGAAATGTCCTGAAGGTCCACG
1 TAGAAATGTCCCGAAGGACCACG
* *
1329368 TAGAATTGTCCCGAAGGACCGCG
1 TAGAAATGTCCCGAAGGACCACG
1329391 TAGAA
1 TAGAA
1329396 CCTCGACTCT
Statistics
Matches: 58, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.19
Consensus pattern (23 bp):
TAGAAATGTCCCGAAGGACCACG
Found at i:1336061 original size:17 final size:17
Alignment explanation
Indices: 1336041--1336073 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1336031 TTTAGGGAAG
1336041 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
*
1336058 TAGTTCATTTATTAAA
1 TAGTTCATTAATTAAA
1336074 TTAACTCTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:1337079 original size:18 final size:18
Alignment explanation
Indices: 1337056--1337092 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1337046 CTTACAACAC
*
1337056 TTACCACGACAACCCCAT
1 TTACCACGACAACACCAT
1337074 TTACCACGACAACACCAT
1 TTACCACGACAACACCAT
1337092 T
1 T
1337093 CATATTTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.41, G:0.05, T:0.19
Consensus pattern (18 bp):
TTACCACGACAACACCAT
Found at i:1337416 original size:12 final size:11
Alignment explanation
Indices: 1337394--1337452 Score: 50
Period size: 10 Copynumber: 5.4 Consensus size: 11
1337384 CCGGGTTAGT
1337394 AAAAAAATAAA
1 AAAAAAATAAA
*
1337405 AATAAAAGT-AA
1 AA-AAAAATAAA
1337416 AAAAAAATCAAA
1 AAAAAAAT-AAA
*
1337428 AGAAAAA-AAA
1 AAAAAAATAAA
* *
1337438 AACAAAAGAAA
1 AAAAAAATAAA
1337449 AAAA
1 AAAA
1337453 GTTTAAAAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
10 13 0.34
11 12 0.32
12 13 0.34
ACGTcount: A:0.85, C:0.03, G:0.05, T:0.07
Consensus pattern (11 bp):
AAAAAAATAAA
Found at i:1337422 original size:17 final size:16
Alignment explanation
Indices: 1337396--1337452 Score: 78
Period size: 16 Copynumber: 3.4 Consensus size: 16
1337386 GGGTTAGTAA
1337396 AAAAATAAAAATAAAAG
1 AAAAA-AAAAATAAAAG
*
1337413 TAAAAAAAAATCAAAAG
1 AAAAAAAAAAT-AAAAG
*
1337430 AAAAAAAAAACAAAAG
1 AAAAAAAAAATAAAAG
1337446 AAAAAAA
1 AAAAAAA
1337453 GTTTAAAAGG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
16 18 0.50
17 18 0.50
ACGTcount: A:0.84, C:0.04, G:0.05, T:0.07
Consensus pattern (16 bp):
AAAAAAAAAATAAAAG
Found at i:1341487 original size:21 final size:22
Alignment explanation
Indices: 1341462--1341505 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
1341452 TTAAGGCCAA
* *
1341462 ATTCAGCTTCAAATTG-TCTAG
1 ATTCAGCCTCAAAATGATCTAG
*
1341483 ATTCATCCTCAAAATGATCTAG
1 ATTCAGCCTCAAAATGATCTAG
1341505 A
1 A
1341506 ATATTCAGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (22 bp):
ATTCAGCCTCAAAATGATCTAG
Found at i:1343912 original size:123 final size:123
Alignment explanation
Indices: 1343756--1344454 Score: 1091
Period size: 123 Copynumber: 5.7 Consensus size: 123
1343746 GAATCAAGGT
* * *
1343756 AAGGTTGAACAAGTTTTTCCCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTTTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* *
1343821 GAACTCTTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGCGATAGACTCGAGCAA
66 GAACTCCTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGCGATAGAGTCGAGCAA
* *
1343879 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCCTCAGATGAGTTCTTCTAATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * * * *
1343944 GAACTCCTTTTAGAAATATTGATGCTGATCTATCTCATTCTGCGATAGAGTCGAGCAA
66 GAACTCCTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGCGATAGAGTCGAGCAA
* * *
1344002 AAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTTCTTCTTCAGATTAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * * * *
1344067 GAACTCCTTCTGGAAATGTTGATGCTGGTCTATTTCCTTTTGCGATAGAGTCGAGCCA
66 GAACTCCTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGCGATAGAGTCGAGCAA
* * *
1344125 AAGTTTGAACAAGTTTTTCTCATTATGAACTTCTTCTTCCTCTTCATATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
*
1344190 GAACTCCTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTTCGATAGAGTCGAGCAA
66 GAACTCCTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGCGATAGAGTCGAGCAA
* *
1344248 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-T--TCTTCAAATGTGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* *
1344310 GAACTCCTTCTGGAAATGTTGATGTTGATCTATCTCCTTTTGCGATAGAGTCAAGCAA
66 GAACTCCTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGCGATAGAGTCGAGCAA
* *
1344368 AAGGTTGAACAAGTTCTTCTCATTATG-ATTTCTTCTTCCTCTTCAGATGAGTTCTTCACATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
*
1344432 GAACTCCTTTTGGAAATGTTGAT
66 GAACTCCTTCTGGAAATGTTGAT
1344455 CCATCGAGTG
Statistics
Matches: 524, Mismatches: 49, Indels: 7
0.90 0.08 0.01
Matches are distributed among these distances:
119 7 0.01
120 106 0.20
122 45 0.09
123 366 0.70
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (123 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
GAACTCCTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGCGATAGAGTCGAGCAA
Found at i:1344327 original size:33 final size:35
Alignment explanation
Indices: 1344260--1344328 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 35
1344250 GGTTGAACAA
*
1344260 GTTCTTCTCATTATGAACTTCTTCTTCTTCAAATGT
1 GTTCTTCTCATTATGAACTTC-TCTTCTGCAAATGT
*
1344296 GTTCTTCTCATTATGAAC-TC-CTTCTGGAAATGT
1 GTTCTTCTCATTATGAACTTCTCTTCTGCAAATGT
1344329 TGATGTTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
33 11 0.35
35 2 0.06
36 18 0.58
ACGTcount: A:0.20, C:0.22, G:0.12, T:0.46
Consensus pattern (35 bp):
GTTCTTCTCATTATGAACTTCTCTTCTGCAAATGT
Found at i:1344686 original size:36 final size:36
Alignment explanation
Indices: 1344646--1344764 Score: 105
Period size: 36 Copynumber: 3.3 Consensus size: 36
1344636 TGAAATTGTA
*
1344646 TCAAGCGAGACGAA-TCTTGTTTTAAGAAAAACAATC
1 TCAAGCGAGACAAAGT-TTGTTTTAAGAAAAACAATC
* * * ** ** ***
1344682 TCAAGTGAGATAAATTGTTGTTTCGAGTGAAATTGTC
1 TCAAGCGAGACAAAGT-TTGTTTTAAGAAAAACAATC
1344719 TCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATC
1 TCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATC
*
1344755 TCAAGTGAGA
1 TCAAGCGAGA
1344765 TAAATTGTTG
Statistics
Matches: 60, Mismatches: 22, Indels: 2
0.71 0.26 0.02
Matches are distributed among these distances:
36 33 0.55
37 27 0.45
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.29
Consensus pattern (36 bp):
TCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATC
Found at i:1344689 original size:73 final size:73
Alignment explanation
Indices: 1344476--1344800 Score: 309
Period size: 73 Copynumber: 4.4 Consensus size: 73
1344466 TGGAAATTTC
* * ** * * * **
1344476 TGTTTCTAGTGAAACTGTCTCAAGTAAGA-AAAATATTATTTTAAGAAAAACTATCTTGAGTGAG
1 TGTTTCGAGTGAAATTGTCTCAAGCGAGACAAAGT-TTGTTTTAAGAAAAACAATCTCAAGTGAG
*
1344540 ATAAAATTTCT
65 AT-AAA-TTGT
* * * ** * * * * *
1344551 TGTTTCAAGTGAAATAATTGTCT-TAGCGAGATAATTCTTTGCTTTGAGAAAAACTATATCGAGT
1 TGTTTCGAGTG--A-AATTGTCTCAAGCGAGACAA-AGTTTGTTTTAAGAAAAACAATCTCAAGT
*
1344615 GAGATAAGTT-T
62 GAGATAAATTGT
* *
1344626 ATGTTTC-ATGTGAAATTGTATCAAGCGAGACGAA-TCTTGTTTTAAGAAAAACAATCTCAAGTG
1 -TGTTTCGA-GTGAAATTGTCTCAAGCGAGACAAAGT-TTGTTTTAAGAAAAACAATCTCAAGTG
1344689 AGATAAATTGT
63 AGATAAATTGT
1344700 TGTTTCGAGTGAAATTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
1 TGTTTCGAGTGAAATTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
1344765 TAAATTGT
66 TAAATTGT
*
1344773 TGTTTCGAGTGAAACTGTCTCAAGCGAG
1 TGTTTCGAGTGAAATTGTCTCAAGCGAG
1344801 GCGTCGCTGG
Statistics
Matches: 211, Mismatches: 27, Indels: 26
0.80 0.10 0.10
Matches are distributed among these distances:
72 1 0.00
73 131 0.62
74 12 0.06
75 12 0.06
76 11 0.05
77 8 0.04
78 35 0.17
79 1 0.00
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (73 bp):
TGTTTCGAGTGAAATTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
TAAATTGT
Found at i:1344703 original size:37 final size:37
Alignment explanation
Indices: 1344662--1344777 Score: 135
Period size: 37 Copynumber: 3.2 Consensus size: 37
1344652 GAGACGAATC
1344662 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
** ** *** * * *
1344699 TTGTTTCGAGTGAAATTGTCTCAAGCGAGACAAAGT-
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
1344735 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
1344772 TTGTTT
1 TTGTTT
1344778 CGAGTGAAAC
Statistics
Matches: 58, Mismatches: 20, Indels: 2
0.73 0.25 0.03
Matches are distributed among these distances:
36 26 0.45
37 32 0.55
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.34
Consensus pattern (37 bp):
TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
Found at i:1344794 original size:37 final size:37
Alignment explanation
Indices: 1344680--1344796 Score: 137
Period size: 37 Copynumber: 3.2 Consensus size: 37
1344670 AGAAAAACAA
*
1344680 TCTCAAGTGAGATAAATTGTTGTTTCGAGTGAAATTG
1 TCTCAAGTGAGATAAATTGTTGTTTCGAGTGAAACTG
* * * ** ** **
1344717 TCTCAAGCGAGACAAAGT-TTGTTTTAAGAAAAACAA
1 TCTCAAGTGAGATAAATTGTTGTTTCGAGTGAAACTG
1344753 TCTCAAGTGAGATAAATTGTTGTTTCGAGTGAAACTG
1 TCTCAAGTGAGATAAATTGTTGTTTCGAGTGAAACTG
1344790 TCTCAAG
1 TCTCAAG
1344797 CGAGGCGTCG
Statistics
Matches: 60, Mismatches: 19, Indels: 2
0.74 0.23 0.02
Matches are distributed among these distances:
36 26 0.43
37 34 0.57
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.32
Consensus pattern (37 bp):
TCTCAAGTGAGATAAATTGTTGTTTCGAGTGAAACTG
Found at i:1346515 original size:38 final size:38
Alignment explanation
Indices: 1346455--1346530 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
1346445 TTCAAAATTG
* *
1346455 TTTCTTACTGATACGAGTCTTCAAAAT-TCCCTAACATT
1 TTTCATACTGATACGAGCCTTCAAAATGTCCC-AACATT
*
1346493 TTTCATACTGATATGAGCCTTCAAAATGTCCCAACATT
1 TTTCATACTGATACGAGCCTTCAAAATGTCCCAACATT
1346531 CTAAGTTGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 30 0.88
39 4 0.12
ACGTcount: A:0.30, C:0.24, G:0.09, T:0.37
Consensus pattern (38 bp):
TTTCATACTGATACGAGCCTTCAAAATGTCCCAACATT
Found at i:1348037 original size:9 final size:9
Alignment explanation
Indices: 1348025--1348085 Score: 72
Period size: 9 Copynumber: 6.9 Consensus size: 9
1348015 TTTTTATATT
1348025 TTTTTCATC
1 TTTTTCATC
1348034 TTTTTCATC
1 TTTTTCATC
1348043 TTTTT--TC
1 TTTTTCATC
1348050 TTTTTCATC
1 TTTTTCATC
**
1348059 TTTTTTTTC
1 TTTTTCATC
*
1348068 TTTTTTCTTC
1 -TTTTTCATC
1348078 TTTTTCAT
1 TTTTTCAT
1348086 GATGGATGAG
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
7 7 0.16
9 30 0.67
10 8 0.18
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTTCATC
Found at i:1348053 original size:16 final size:16
Alignment explanation
Indices: 1348032--1348064 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1348022 ATTTTTTTCA
1348032 TCTTTTTCATCTTTTT
1 TCTTTTTCATCTTTTT
1348048 TCTTTTTCATCTTTTT
1 TCTTTTTCATCTTTTT
1348064 T
1 T
1348065 TTCTTTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (16 bp):
TCTTTTTCATCTTTTT
Found at i:1348058 original size:25 final size:25
Alignment explanation
Indices: 1348025--1348076 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
1348015 TTTTTATATT
1348025 TTTTTCATCTTTTTCATCTTTTTTC
1 TTTTTCATCTTTTTCATCTTTTTTC
**
1348050 TTTTTCATCTTTTTTTTCTTTTTTC
1 TTTTTCATCTTTTTCATCTTTTTTC
1348075 TT
1 TT
1348077 CTTTTTCATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTTTCATCTTTTTCATCTTTTTTC
Found at i:1352757 original size:14 final size:14
Alignment explanation
Indices: 1352740--1352770 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1352730 AAAAGTAATG
*
1352740 AAATTAAATAACTA
1 AAATTAAATAAATA
1352754 AAATTAAATAAATA
1 AAATTAAATAAATA
1352768 AAA
1 AAA
1352771 AATAAATGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATTAAATAAATA
Done.