Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008527.1 Hibiscus syriacus cultivar Beakdansim tig00111402_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: 9057482
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 37
Found at i:1281793 original size:31 final size:31
Alignment explanation
Indices: 1281721--1281833 Score: 120
Period size: 33 Copynumber: 3.5 Consensus size: 31
1281711 ATACTATTTC
*
1281721 TATAAACTATAGTTTATATTTAT-ATACTATATA
1 TATAAACTATAGTTTACA--TATGA-ACTATATA
* *
1281754 TATGAACTATAGTTTACATATGAATTATATA
1 TATAAACTATAGTTTACATATGAACTATATA
*
1281785 TATAAACTATATAGTTTACATATGACCTATATA
1 TATAAAC--TATAGTTTACATATGAACTATATA
* *
1281818 TATATACTATATTTTA
1 TATAAACTATAGTTTA
1281834 TATTTATATA
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
31 24 0.35
32 1 0.01
33 44 0.64
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (31 bp):
TATAAACTATAGTTTACATATGAACTATATA
Found at i:1281835 original size:20 final size:20
Alignment explanation
Indices: 1281812--1281849 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1281802 ACATATGACC
1281812 TATATATATATACTATATTT
1 TATATATATATACTATATTT
*
1281832 TATATTTATATACTATAT
1 TATATATATATACTATAT
1281850 GTAGACACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (20 bp):
TATATATATATACTATATTT
Found at i:1281901 original size:14 final size:14
Alignment explanation
Indices: 1281882--1281940 Score: 64
Period size: 14 Copynumber: 4.0 Consensus size: 14
1281872 AAAAATAAAA
*
1281882 AATTATAATATAAT
1 AATTATAATATTAT
*
1281896 AATTATTATATTAT
1 AATTATAATATTAT
*
1281910 AATTATTATTATTAT
1 AATTA-TAATATTAT
1281925 AAATTATAATTATTAT
1 -AATTATAA-TATTAT
1281941 TAGTATTAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
14 17 0.46
15 9 0.24
16 11 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AATTATAATATTAT
Found at i:1281903 original size:3 final size:3
Alignment explanation
Indices: 1281897--1281953 Score: 53
Period size: 3 Copynumber: 19.0 Consensus size: 3
1281887 TAATATAATA
* * *
1281897 ATT ATT A-T ATT ATA ATT ATT ATT ATT ATAA ATT ATA ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT
* *
1281942 AGT ATT AAT ATT
1 ATT ATT ATT ATT
1281954 GTGTATATTT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
2 2 0.05
3 38 0.90
4 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:1281935 original size:22 final size:22
Alignment explanation
Indices: 1281881--1281942 Score: 83
Period size: 22 Copynumber: 2.8 Consensus size: 22
1281871 AAAAAATAAA
*
1281881 AAATTATAATATAATAATTATTAT
1 AAATTATAAT-T-ATTATTATTAT
1281905 --ATTATAATTATTATTATTAT
1 AAATTATAATTATTATTATTAT
1281925 AAATTATAATTATTATTA
1 AAATTATAATTATTATTA
1281943 GTATTAATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
20 10 0.29
21 1 0.03
22 24 0.69
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AAATTATAATTATTATTATTAT
Found at i:1283262 original size:30 final size:31
Alignment explanation
Indices: 1283204--1283262 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1283194 ATATATATAT
* *
1283204 ATATACTGGTTTATTGTTGTTGATGTAAATG
1 ATATACTGGTTTATTGCTGTTAATGTAAATG
1283235 ATATACTGGTTTATTGCTG-TAATGTAAA
1 ATATACTGGTTTATTGCTGTTAATGTAAA
1283263 CTAACTATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.29, C:0.05, G:0.20, T:0.46
Consensus pattern (31 bp):
ATATACTGGTTTATTGCTGTTAATGTAAATG
Found at i:1286177 original size:51 final size:51
Alignment explanation
Indices: 1286130--1286237 Score: 128
Period size: 51 Copynumber: 2.1 Consensus size: 51
1286120 AAATTATAAT
* *
1286130 TAATATAAAACT-AAATTTCAAAAAAAGTAATTATATTAATTTGATTATCATAG
1 TAATATAAAA-TAAAATTTC-AAAAAA-TAATCATATTAATTTAATTATCATAG
* ** *
1286183 TAATTTATGATAAAATTTCAAAAAATAATCATATTAATTTAATTATCATAA
1 TAATATAAAATAAAATTTCAAAAAATAATCATATTAATTTAATTATCATAG
1286234 TAAT
1 TAAT
1286238 TTAATTATCA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
51 27 0.56
52 7 0.15
53 14 0.29
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.40
Consensus pattern (51 bp):
TAATATAAAATAAAATTTCAAAAAATAATCATATTAATTTAATTATCATAG
Found at i:1286232 original size:17 final size:17
Alignment explanation
Indices: 1286210--1286250 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
1286200 TCAAAAAATA
*
1286210 ATCATATTAATTTAATT
1 ATCATAATAATTTAATT
1286227 ATCATAATAATTTAATT
1 ATCATAATAATTTAATT
1286244 ATCATAA
1 ATCATAA
1286251 GTTTATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (17 bp):
ATCATAATAATTTAATT
Found at i:1286238 original size:51 final size:53
Alignment explanation
Indices: 1286142--1286240 Score: 157
Period size: 51 Copynumber: 1.9 Consensus size: 53
1286132 ATATAAAACT
* * *
1286142 AAATTTCAAAAAAAGTAATTATATTAATTTGATTATCATAGTAATTTATGATA
1 AAATTTCAAAAAAAGTAATCATATTAATTTAATTATCATAATAATTTATGATA
1286195 AAATTTC-AAAAAA-TAATCATATTAATTTAATTATCATAATAATTTA
1 AAATTTCAAAAAAAGTAATCATATTAATTTAATTATCATAATAATTTA
1286241 ATTATCATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 30 0.70
52 6 0.14
53 7 0.16
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.41
Consensus pattern (53 bp):
AAATTTCAAAAAAAGTAATCATATTAATTTAATTATCATAATAATTTATGATA
Found at i:1286351 original size:16 final size:17
Alignment explanation
Indices: 1286330--1286370 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1286320 TATCACTTTA
*
1286330 ACATGTCAGA-TCATTT
1 ACATGTCAGAGTCAATT
*
1286346 ACATGT-TGAGTCAATT
1 ACATGTCAGAGTCAATT
1286362 ACATGTCAG
1 ACATGTCAG
1286371 GTTCATAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 2 0.10
16 17 0.85
17 1 0.05
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (17 bp):
ACATGTCAGAGTCAATT
Found at i:1286385 original size:16 final size:16
Alignment explanation
Indices: 1286366--1286400 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1286356 TCAATTACAT
*
1286366 GTCAGGTTCATAACAG
1 GTCAGGTTCAAAACAG
*
1286382 GTCAGGTTGAAAACAG
1 GTCAGGTTCAAAACAG
1286398 GTC
1 GTC
1286401 GGGTAATACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (16 bp):
GTCAGGTTCAAAACAG
Found at i:1290851 original size:18 final size:18
Alignment explanation
Indices: 1290830--1290870 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
1290820 GGGGTATTAT
1290830 TATAATTATTCTTAAATA
1 TATAATTATTCTTAAATA
1290848 TATAATTATTCTTAAATA
1 TATAATTATTCTTAAATA
1290866 TATAA
1 TATAA
1290871 GGTAAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (18 bp):
TATAATTATTCTTAAATA
Found at i:1293423 original size:12 final size:12
Alignment explanation
Indices: 1293406--1293453 Score: 62
Period size: 12 Copynumber: 3.9 Consensus size: 12
1293396 TGATATTATT
1293406 TTTAAAAAGTGA
1 TTTAAAAAGTGA
1293418 TTTAAAAAGTGA
1 TTTAAAAAGTGA
*
1293430 TGTAAAAAG-GTA
1 TTTAAAAAGTG-A
1293442 TTTTAAAAAGTG
1 -TTTAAAAAGTG
1293454 TTTTTGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 1 0.03
12 21 0.68
13 8 0.26
14 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.33
Consensus pattern (12 bp):
TTTAAAAAGTGA
Found at i:1293448 original size:13 final size:13
Alignment explanation
Indices: 1293404--1293465 Score: 58
Period size: 12 Copynumber: 4.9 Consensus size: 13
1293394 TTTGATATTA
1293404 TTTTTAAAAAGTG
1 TTTTTAAAAAGTG
*
1293417 -ATTTAAAAAGTG
1 TTTTTAAAAAGTG
* *
1293429 -ATGTAAAAAG-G
1 TTTTTAAAAAGTG
1293440 TATTTTAAAAAGTG
1 T-TTTTAAAAAGTG
*
1293454 TTTTTGAAAAGT
1 TTTTTAAAAAGT
1293466 ACACTTTAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
11 1 0.02
12 20 0.49
13 18 0.44
14 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.18, T:0.39
Consensus pattern (13 bp):
TTTTTAAAAAGTG
Found at i:1293490 original size:31 final size:32
Alignment explanation
Indices: 1293452--1293519 Score: 129
Period size: 32 Copynumber: 2.2 Consensus size: 32
1293442 TTTTAAAAAG
1293452 TGTTTTTG-AAAAGTACACTTTAGAATTTAAT
1 TGTTTTTGAAAAAGTACACTTTAGAATTTAAT
1293483 TGTTTTTGAAAAAGTACACTTTAGAATTTAAT
1 TGTTTTTGAAAAAGTACACTTTAGAATTTAAT
1293515 TGTTT
1 TGTTT
1293520 AAAATTACCG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 8 0.22
32 28 0.78
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.47
Consensus pattern (32 bp):
TGTTTTTGAAAAAGTACACTTTAGAATTTAAT
Found at i:1293553 original size:2 final size:2
Alignment explanation
Indices: 1293546--1293593 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1293536 GATAATTTAA
1293546 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
1293588 AT AT AT
1 AT AT AT
1293594 TTTAAACATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1294144 original size:26 final size:26
Alignment explanation
Indices: 1294105--1294168 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
1294095 TAGTTGGTAG
**
1294105 TTGATTTTGA-TAGTTGATTTGATCAA
1 TTGA-TTTGATTAGTTGATTTGAGAAA
1294131 TTGATTTGATTAGTTGATTTGAGAAA
1 TTGATTTGATTAGTTGATTTGAGAAA
*
1294157 TTAATTTGATTA
1 TTGATTTGATTA
1294169 ATTGTTTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
25 5 0.15
26 29 0.85
ACGTcount: A:0.30, C:0.02, G:0.19, T:0.50
Consensus pattern (26 bp):
TTGATTTGATTAGTTGATTTGAGAAA
Found at i:1294171 original size:13 final size:13
Alignment explanation
Indices: 1294105--1294172 Score: 66
Period size: 13 Copynumber: 5.2 Consensus size: 13
1294095 TAGTTGGTAG
*
1294105 TTGATTTTGA-TAG
1 TTGA-TTTGATTAA
*
1294118 TTGATTTGATCAA
1 TTGATTTGATTAA
*
1294131 TTGATTTGATTAG
1 TTGATTTGATTAA
**
1294144 TTGATTTGAGAAA
1 TTGATTTGATTAA
*
1294157 TTAATTTGATTAA
1 TTGATTTGATTAA
1294170 TTG
1 TTG
1294173 TTTATAAAGA
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
12 5 0.12
13 38 0.88
ACGTcount: A:0.29, C:0.01, G:0.19, T:0.50
Consensus pattern (13 bp):
TTGATTTGATTAA
Found at i:1305753 original size:29 final size:31
Alignment explanation
Indices: 1305718--1305777 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
1305708 GATAGTTTGG
* *
1305718 TTATTAAAT-TTTTAAA-TATTATAAAATAA
1 TTATTAAATCTGTCAAACTATTATAAAATAA
1305747 TTATTAAATCTGTCAAACTATTATAAAATAA
1 TTATTAAATCTGTCAAACTATTATAAAATAA
1305778 CTTTTAGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 9 0.33
30 5 0.19
31 13 0.48
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (31 bp):
TTATTAAATCTGTCAAACTATTATAAAATAA
Found at i:1316122 original size:2 final size:2
Alignment explanation
Indices: 1316112--1316222 Score: 68
Period size: 2 Copynumber: 60.0 Consensus size: 2
1316102 AATTAAAAAA
*
1316112 AT AT A- AT AT AT AT AGT AT AT AT -T A- AT AT A- AT AT AT AT AA
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1316151 ACT AT AT A- AT -T CAT -T AGT AT AT AT AA AT -T AT AT AT -T A-
1 A-T AT AT AT AT AT -AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
*
1316188 AT TT AT -T A- AT A- 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
1316223 TAATTTATTA
Statistics
Matches: 86, Mismatches: 6, Indels: 34
0.68 0.05 0.27
Matches are distributed among these distances:
1 13 0.15
2 67 0.78
3 6 0.07
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1316156 original size:26 final size:26
Alignment explanation
Indices: 1316111--1316189 Score: 92
Period size: 26 Copynumber: 3.1 Consensus size: 26
1316101 AAATTAAAAA
*
1316111 AATATAATATATAT--AGTATATATT
1 AATATAATATATATAAACTATATATT
1316135 AATATAATATATATAAACTATATAATT
1 AATATAATATATATAAACTATAT-ATT
* * *
1316162 CAT-TAGTATATATAAATTATATATT
1 AATATAATATATATAAACTATATATT
1316187 AAT
1 AAT
1316190 TTATTAATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
24 14 0.30
25 5 0.11
26 23 0.49
27 5 0.11
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (26 bp):
AATATAATATATATAAACTATATATT
Found at i:1316196 original size:8 final size:8
Alignment explanation
Indices: 1316128--1316237 Score: 61
Period size: 8 Copynumber: 13.6 Consensus size: 8
1316118 TATATATAGT
1316128 ATATATTA
1 ATATATTA
*
1316136 ATATAAT-
1 ATATATTA
*
1316143 ATATATAA
1 ATATATTA
1316151 ACTATA-TA
1 A-TATATTA
1316159 AT-TCATTA
1 ATAT-ATTA
*
1316167 GTATA-T-
1 ATATATTA
*
1316173 ATAAATT-
1 ATATATTA
1316180 ATATATTA
1 ATATATTA
*
1316188 ATTTATTA
1 ATATATTA
1316196 ATAATATATA
1 AT-ATAT-TA
1316206 TATATATATA
1 -ATATAT-TA
1316216 TATATATTA
1 -ATATATTA
*
1316225 ATTTATTA
1 ATATATTA
1316233 ATATA
1 ATATA
1316238 AACATTTATA
Statistics
Matches: 80, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
6 4 0.05
7 15 0.19
8 33 0.41
9 10 0.12
10 16 0.20
11 2 0.03
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (8 bp):
ATATATTA
Found at i:1316767 original size:103 final size:102
Alignment explanation
Indices: 1316570--1316794 Score: 272
Period size: 103 Copynumber: 2.2 Consensus size: 102
1316560 TGTTCATCCT
* * * * *
1316570 TTGTTCATTTGTGTTCATCCCTAAAACCCTCATTTGATCTTCCCAAACACCAAAACCCAAACCAT
1 TTGTTCATATGTGTTCATCCCAAAAAACCTCATTTGATCTTCACAAACACCAAAACCCAAACCAA
* * * *
1316635 TTCCTTTTTTTTATATCAAACACCCAAAATTTAAACAA
66 TTCATGTTTTTTAGATCAAACA-CCAAAAATTAAACAA
* * * * *
1316673 TTTTTCATATGTGTTTATCCCAAAAAATCTCATTTGATCTTCACAAACACCAAAACCGAAAGCAA
1 TTGTTCATATGTGTTCATCCCAAAAAACCTCATTTGATCTTCACAAACACCAAAACCCAAACCAA
* *
1316738 TTCATGTTTTTT-GATCAAACACCAAAAAATTCAACCA
66 TTCATGTTTTTTAGATCAAACACC-AAAAATTAAACAA
*
1316775 TTGTTCATCTGTGTTCATCC
1 TTGTTCATATGTGTTCATCC
1316795 ATGTTATTCC
Statistics
Matches: 102, Mismatches: 19, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
101 2 0.02
102 35 0.34
103 65 0.64
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.34
Consensus pattern (102 bp):
TTGTTCATATGTGTTCATCCCAAAAAACCTCATTTGATCTTCACAAACACCAAAACCCAAACCAA
TTCATGTTTTTTAGATCAAACACCAAAAATTAAACAA
Found at i:1317184 original size:159 final size:158
Alignment explanation
Indices: 1316945--1317242 Score: 395
Period size: 159 Copynumber: 1.9 Consensus size: 158
1316935 ATCTCTTTTC
* * * * *
1316945 TCTAACCCTAACCCTTAGTGTTCATTATCATCTTCTTCTTTTATATATATTTTTTAACCCTAATC
1 TCTAACCCTAACCCTTAGTGTTCATCATCATCTTCTTCTTTTATACATATTCTCTAACCCTAACC
* * *
1317010 GATATTGTTTATCATCTTCTTCCTCTATCTATGTTCATCTTCTTTAACCCCAAACCTAAAAC-GA
66 AATATTG-TTATCATCTTCTTACTCTATCTATGTTCATCTTCTCTAACCCCAAACC-AAAACTGA
*
1317074 GTCTCTTCATTTTTATCTATGTTCATCTTT
129 GCCTCTTCATTTTTATCTATGTTCATCTTT
*
1317104 TCTAACCCTAACCCTTATTGTTCATCATCATCTTTTTCTTCTTTTATACATATTCTCTAACCCTA
1 TCTAACCCTAACCCTTAGTGTTCATCATCATC---TTCTTCTTTTATACATATTCTCTAACCCTA
* * * * *
1317169 ACCAATATTG-T-TCATCTTCTTATTTTATCTCTGTTTATCTTCTCTAACCCCAAACCCAAACTG
63 ACCAATATTGTTATCATCTTCTTACTCTATCTATGTTCATCTTCTCTAACCCCAAACCAAAACTG
1317232 AGCCTCTTCAT
128 AGCCTCTTCAT
1317243 ATTCTCTAAC
Statistics
Matches: 120, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
158 4 0.03
159 80 0.67
160 1 0.01
162 35 0.29
ACGTcount: A:0.23, C:0.27, G:0.04, T:0.45
Consensus pattern (158 bp):
TCTAACCCTAACCCTTAGTGTTCATCATCATCTTCTTCTTTTATACATATTCTCTAACCCTAACC
AATATTGTTATCATCTTCTTACTCTATCTATGTTCATCTTCTCTAACCCCAAACCAAAACTGAGC
CTCTTCATTTTTATCTATGTTCATCTTT
Found at i:1317218 original size:52 final size:52
Alignment explanation
Indices: 1317080--1317218 Score: 140
Period size: 55 Copynumber: 2.6 Consensus size: 52
1317070 ACGAGTCTCT
* * * **
1317080 TCAT-TTTTATCTATGTTCATCTTTTCTAACCCTAACCCTTATTGTTCATCA
1 TCATATTTTATCTCTGTTTATCTTCTCTAACCCTAACCAATATTGTTCATCA
* *
1317131 TCATCTTTT-TCTTCT-TTTATACATATTCTCTAACCCTAACCAATATTGTTCATCT
1 TCATATTTTATC-TCTGTTTAT-C---TTCTCTAACCCTAACCAATATTGTTCATCA
*
1317186 TCTTATTTTATCTCTGTTTATCTTCTCTAACCC
1 TCATATTTTATCTCTGTTTATCTTCTCTAACCC
1317219 CAAACCCAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
51 10 0.14
52 18 0.25
55 37 0.51
56 7 0.10
ACGTcount: A:0.21, C:0.26, G:0.03, T:0.50
Consensus pattern (52 bp):
TCATATTTTATCTCTGTTTATCTTCTCTAACCCTAACCAATATTGTTCATCA
Found at i:1323142 original size:20 final size:20
Alignment explanation
Indices: 1323117--1323338 Score: 119
Period size: 20 Copynumber: 10.9 Consensus size: 20
1323107 CTATCGCAAA
* *
1323117 TTCGCGTTGCGATTTTTCAT
1 TTCGCGTTGCGATTTTCCAG
1323137 TTCGCGTTGCGATTTTCCAG
1 TTCGCGTTGCGATTTTCCAG
* ** *
1323157 TTCGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGAT-TTTCCAG
* **
1323178 ATCGC-ACGCGATTTTCCAG
1 TTCGCGTTGCGATTTTCCAG
* * ** *
1323197 CTCGCGTTGCGATAGTTAAAA
1 TTCGCGTTGCGAT-TTTCCAG
* *
1323218 ATCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATTTTCCAG
* * ** *
1323238 TTCGCGTTGCGGTAGTTAAAA
1 TTCGCGTTGCGAT-TTTCCAG
* *
1323259 ATCGCGTTGCGATTTTCCAC
1 TTCGCGTTGCGATTTTCCAG
* *
1323279 TTCGCGTTGCGATAGTCTACAG
1 TTCGCGTTGCGAT--TTTCCAG
*
1323301 TT-GTCGTTGCGATTTTCCAAA
1 TTCG-CGTTGCGATTTTCC-AG
1323322 TT--CGTTGCGATTTTCCA
1 TTCGCGTTGCGATTTTCCA
1323339 AATTCGTTGC
Statistics
Matches: 150, Mismatches: 44, Indels: 18
0.71 0.21 0.08
Matches are distributed among these distances:
18 1 0.01
19 21 0.14
20 73 0.49
21 40 0.27
22 15 0.10
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.37
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCCAG
Found at i:1323223 original size:21 final size:21
Alignment explanation
Indices: 1323198--1323271 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
1323188 ATTTTCCAGC
1323198 TCGCGTTGCGATAGTTAAAAA
1 TCGCGTTGCGATAGTTAAAAA
* ** **
1323219 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTAAAAA
*
1323239 TCGCGTTGCGGTAGTTAAAAA
1 TCGCGTTGCGATAGTTAAAAA
1323260 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1323272 TTTCCACTTC
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 14 0.35
21 26 0.65
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTAAAAA
Found at i:1323243 original size:41 final size:41
Alignment explanation
Indices: 1323138--1323294 Score: 244
Period size: 41 Copynumber: 3.9 Consensus size: 41
1323128 ATTTTTCATT
*
1323138 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTAAAAA
** *
1323179 TCGC-ACGCGATTTTCCAGCTCGCGTTGCGATAGTTAAAAA
1 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTAAAAA
* *
1323219 TCGCGTTGCGATTTTCCATTTCGCGTTGCGGTAGTTAAAAA
1 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTAAAAA
*
1323260 TCGCGTTGCGATTTTCCACTTCGCGTTGCGATAGT
1 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGT
1323295 CTACAGTTGT
Statistics
Matches: 104, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
40 36 0.35
41 68 0.65
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.34
Consensus pattern (41 bp):
TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTAAAAA
Found at i:1323254 original size:81 final size:82
Alignment explanation
Indices: 1323138--1323294 Score: 246
Period size: 81 Copynumber: 1.9 Consensus size: 82
1323128 ATTTTTCATT
*
1323138 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAATCGC-ACGCGATTTTCCAGC-TCG
1 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTAAAAATCGCGACGCGATTTTCCA-CTTCG
1323201 CGTTGCGATAGTTAAAAA
65 CGTTGCGATAGTTAAAAA
* * **
1323219 TCGCGTTGCGATTTTCCATTTCGCGTTGCGGTAGTTAAAAATCGCGTTGCGATTTTCCACTTCGC
1 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTAAAAATCGCGACGCGATTTTCCACTTCGC
1323284 GTTGCGATAGT
66 GTTGCGATAGT
1323295 CTACAGTTGT
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
81 43 0.62
82 26 0.38
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.34
Consensus pattern (82 bp):
TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTAAAAATCGCGACGCGATTTTCCACTTCGC
GTTGCGATAGTTAAAAA
Found at i:1323311 original size:22 final size:22
Alignment explanation
Indices: 1323283--1323395 Score: 103
Period size: 22 Copynumber: 5.4 Consensus size: 22
1323273 TTCCACTTCG
*
1323283 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTTTACAGTTGT
* **
1323305 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTTTACAGTTGT
* **
1323324 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTTTACAGTTGT
*
1323343 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTTTACAGTTGT
*
1323365 TGTTGCGATAGTTTACAGTTGT
1 CGTTGCGATAGTTTACAGTTGT
1323387 CGTTGCGAT
1 CGTTGCGAT
1323396 TTTCCAAATT
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
19 29 0.38
20 5 0.06
21 5 0.06
22 38 0.49
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.40
Consensus pattern (22 bp):
CGTTGCGATAGTTTACAGTTGT
Found at i:1323328 original size:19 final size:19
Alignment explanation
Indices: 1323304--1323351 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
1323294 TCTACAGTTG
1323304 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
1323323 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
1323342 TCGTTGCGAT
1 TCGTTGCGAT
1323352 AGTCTACAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.42
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:1323328 original size:82 final size:81
Alignment explanation
Indices: 1323141--1323413 Score: 238
Period size: 82 Copynumber: 3.3 Consensus size: 81
1323131 TTTCATTTCG
* * **
1323141 CGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAATCGC-ACGCGATTTTCCAGC-TCGCGT
1 CGTTGCGATTTTCCAATTC-CGTTGCGATAGTTAAAAATCGCGTTGCGATTTTCCA-CTTCGCGT
* * *
1323204 TGCGATAGTTAAAAATCG-
64 TGCGATAGTT-ACAGTTGT
* *
1323222 CGTTGCGATTTTCCATTTCGCGTTGCGGTAGTTAAAAATCGCGTTGCGATTTTCCACTTCGCGTT
1 CGTTGCGATTTTCCAATTC-CGTTGCGATAGTTAAAAATCGCGTTGCGATTTTCCACTTCGCGTT
1323287 GCGATAGTCTACAGTTGT
65 GCGATAGT-TACAGTTGT
* ** * * * * *
1323305 CGTTGCGATTTTCCAAATT-CGTTGCGAT-TTTCCAAAT-TCGTTGCGATAGTCTACAGTT-GTT
1 CGTTGCGATTTTCC-AATTCCGTTGCGATAGTTAAAAATCGCGTTGCGAT--TTTCCACTTCG-C
1323366 GTTGCGATAGTTTACAGTTGT
62 GTTGCGATAG-TTACAGTTGT
1323387 CGTTGCGATTTTCCAAATT-CGTTGCGA
1 CGTTGCGATTTTCC-AATTCCGTTGCGA
1323414 AAATTCGTTG
Statistics
Matches: 165, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
80 9 0.05
81 47 0.28
82 90 0.55
83 16 0.10
84 3 0.02
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (81 bp):
CGTTGCGATTTTCCAATTCCGTTGCGATAGTTAAAAATCGCGTTGCGATTTTCCACTTCGCGTTG
CGATAGTTACAGTTGT
Found at i:1324003 original size:6 final size:6
Alignment explanation
Indices: 1323994--1324026 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
1323984 GTCCGTCTCG
1323994 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1324027 AATATGTGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1324172 original size:20 final size:20
Alignment explanation
Indices: 1324147--1324198 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
1324137 ACTGTAGACT
1324147 ATCGCAACGCGAAATAAAAA
1 ATCGCAACGCGAAATAAAAA
**
1324167 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATAAAAA
*
1324187 ATCGTAACGCGA
1 ATCGCAACGCGA
1324199 TTTTCAACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (20 bp):
ATCGCAACGCGAAATAAAAA
Found at i:1328149 original size:18 final size:17
Alignment explanation
Indices: 1328124--1328157 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1328114 TGAAATATTT
1328124 TATTTTTTTATTAAAAC
1 TATTTTTTTATTAAAAC
*
1328141 TATTATTTTTTTTAAAA
1 TATT-TTTTTATTAAAA
1328158 TTAAAACGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTTTTTTATTAAAAC
Found at i:1331015 original size:21 final size:21
Alignment explanation
Indices: 1330991--1331043 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1330981 ATTCTGACTA
*
1330991 TCGCATTGTGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
1331012 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
1331033 TCGCAATGCGA
1 TCGCATTGCGA
1331044 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:1331293 original size:22 final size:22
Alignment explanation
Indices: 1331268--1331332 Score: 94
Period size: 22 Copynumber: 3.0 Consensus size: 22
1331258 GCGACATCCG
1331268 TCCCCATCTCCGACGAAATCAA
1 TCCCCATCTCCGACGAAATCAA
* * *
1331290 TCCCCATCGCCGACGATATCAG
1 TCCCCATCTCCGACGAAATCAA
*
1331312 TCTCCATCTCCGACGAAATCA
1 TCCCCATCTCCGACGAAATCA
1331333 TTCACGGTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.28, C:0.40, G:0.12, T:0.20
Consensus pattern (22 bp):
TCCCCATCTCCGACGAAATCAA
Found at i:1331725 original size:20 final size:20
Alignment explanation
Indices: 1331667--1331732 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
1331657 GCAATTCTAT
**
1331667 CGTTGCGATTTTC-ATTTCG
1 CGTTGCGATAGTCAATTTCG
*
1331686 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAATTTCG
* *
1331706 CGTTTCGATAGTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
*
1331726 TGTTGCG
1 CGTTGCG
1331733 GTTTTCATTT
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 11 0.29
20 27 0.71
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.41
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:1331764 original size:20 final size:20
Alignment explanation
Indices: 1331721--1331764 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1331711 CGATAGTCAT
* ** *
1331721 TTTCGTGTTGCGGTTTTCAT
1 TTTCGTGTTGCGATTTAAAG
1331741 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
1331761 TTTC
1 TTTC
1331765 AGAAACTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.11, C:0.14, G:0.23, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:1333656 original size:20 final size:20
Alignment explanation
Indices: 1333631--1333827 Score: 215
Period size: 20 Copynumber: 10.5 Consensus size: 20
1333621 AGAATAGTTT
*
1333631 ACTATCGCAATGCGAAAATA
1 ACTATCGCAATGCGAAAATG
*
1333651 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1333671 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
1333687 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
1333704 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
1333720 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
1333738 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
1333758 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1333778 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
1333798 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
1333818 ACTATCGCAA
1 ACTATCGCAA
1333828 CGAAAGAATC
Statistics
Matches: 155, Mismatches: 8, Indels: 28
0.81 0.04 0.15
Matches are distributed among these distances:
14 14 0.09
16 10 0.06
17 8 0.05
18 5 0.03
19 7 0.05
20 111 0.72
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:1333776 original size:40 final size:35
Alignment explanation
Indices: 1333654--1333848 Score: 202
Period size: 40 Copynumber: 5.4 Consensus size: 35
1333644 GAAAATAACT
* *
1333654 ATCGCAACGCGAAAATGACTATCGCAACG-AGAGA
1 ATCGCAATGCGAAAATGACTATCGCAACGAAAAGA
**
1333688 ATCGCAATGCG-AAATGAAAATCGCAAC-AACAA-A
1 ATCGCAATGCGAAAATGACTATCGCAACGAA-AAGA
1333721 ATCGCAATGCGAAAATGACTATCGCAATGCGAAAATGA
1 ATCGCAATGCGAAAATGACTATCGCAA--CGAAAA-GA
1333759 CTATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGA
1 --ATCGCAATGCGAAAATGACTATCGCAA--CGAAAA-GA
**
1333799 CTATCGCAATGCGAATTTGACTATCGCAACG-AAAGA
1 --ATCGCAATGCGAAAATGACTATCGCAACGAAAAGA
1333835 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
1333849 TGAAAATCAC
Statistics
Matches: 141, Mismatches: 10, Indels: 20
0.82 0.06 0.12
Matches are distributed among these distances:
33 27 0.19
34 37 0.26
36 5 0.04
37 5 0.04
38 3 0.02
40 64 0.45
ACGTcount: A:0.42, C:0.22, G:0.20, T:0.16
Consensus pattern (35 bp):
ATCGCAATGCGAAAATGACTATCGCAACGAAAAGA
Found at i:1333899 original size:20 final size:20
Alignment explanation
Indices: 1333874--1333959 Score: 93
Period size: 20 Copynumber: 4.3 Consensus size: 20
1333864 GATTCTCTCG
*
1333874 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAATTTCGCA
* *
1333894 TTGCGATAGTCATTTTTGCA
1 TTGCGATAGTCAATTTCGCA
* * *
1333914 TTGCGATAATCATTTTCGCG
1 TTGCGATAGTCAATTTCGCA
**
1333934 TTGCGATTTTC-ATTTCGCA
1 TTGCGATAGTCAATTTCGCA
1333953 TTGCGAT
1 TTGCGAT
1333960 TCTCTCGTTG
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
19 13 0.23
20 43 0.77
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.41
Consensus pattern (20 bp):
TTGCGATAGTCAATTTCGCA
Found at i:1333932 original size:40 final size:40
Alignment explanation
Indices: 1333874--1334013 Score: 132
Period size: 40 Copynumber: 3.7 Consensus size: 40
1333864 GATTCTCTCG
** *
1333874 TTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTTGCA
1 TTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTTGCA
* ** *
1333914 TTGCGATAATCATTTTCGCGTTGCGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTTGCA
* * *
1333953 TTGCGAT--TC----TCTCGTTGCGATAGTTATTTTTGCG
1 TTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTTGCA
*
1333987 TTGCGATAGTCATTTTCGTGTTGCGAT
1 TTGCGATAGTCATTTTCGCGTTGCGAT
1334014 TTTAAGTTTC
Statistics
Matches: 78, Mismatches: 15, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
33 13 0.17
34 12 0.15
36 2 0.03
37 2 0.03
39 13 0.17
40 36 0.46
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.43
Consensus pattern (40 bp):
TTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTTGCA
Found at i:1333990 original size:20 final size:20
Alignment explanation
Indices: 1333965--1334013 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1333955 GCGATTCTCT
* *
1333965 CGTTGCGATAGTTATTTTTG
1 CGTTGCGATAGTCATTTTCG
1333985 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
1334005 TGTTGCGAT
1 CGTTGCGAT
1334014 TTTAAGTTTC
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:0.14, C:0.14, G:0.27, T:0.45
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1334535 original size:18 final size:19
Alignment explanation
Indices: 1334496--1334537 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
1334486 CTCACCTGTC
1334496 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
1334517 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
1334535 ATC
1 ATC
1334538 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:1334591 original size:42 final size:42
Alignment explanation
Indices: 1334491--1334601 Score: 109
Period size: 42 Copynumber: 2.6 Consensus size: 42
1334481 CCCGACTCAC
* * * *
1334491 CTGTCATCGTTCAAGAG-GCCTCCCCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCCCTTCCC-ACCGTTCAAGAGGCCA
* ** *
1334533 CTATCATCCCTCAAGAGTCCCTTCCCACCGTTTAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCTTCCCACCGTTCAAGAGGCCA
*
1334575 CTGTCATCGTTGAAGAGGTCCC-TCCCA
1 CTGTCATCGTTCAAGA-GTCCCTTCCCA
1334602 ACATTCTAGA
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
42 44 0.80
43 11 0.20
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCTTCCCACCGTTCAAGAGGCCA
Found at i:1335997 original size:14 final size:14
Alignment explanation
Indices: 1335978--1336013 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1335968 ATTGTTTAAT
1335978 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1335992 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1336006 TGATTTGT
1 TGATTTGT
1336014 TTAATTGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1336023 original size:13 final size:14
Alignment explanation
Indices: 1335965--1336026 Score: 51
Period size: 13 Copynumber: 4.6 Consensus size: 14
1335955 TTATTATTAT
*
1335965 TTGA-TTGTTTAA-
1 TTGATTTGTTAAAG
*
1335977 TTGATTTGTAAAAG
1 TTGATTTGTTAAAG
*
1335991 ATGATTTG-TAAATG
1 TTGATTTGTTAAA-G
*
1336005 TTGATTTGTTTAA-
1 TTGATTTGTTAAAG
1336018 TTGATTTGT
1 TTGATTTGT
1336027 ACATAATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
12 4 0.10
13 18 0.45
14 15 0.38
15 3 0.08
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.53
Consensus pattern (14 bp):
TTGATTTGTTAAAG
Found at i:1336169 original size:33 final size:34
Alignment explanation
Indices: 1336119--1336182 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 34
1336109 AAAACAGACT
**
1336119 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAACGCGGAAATGAAAATCGCAACGAGAGA
*
1336153 ATCGCAATGC-GAAATGAAAATCGCAACGAG
1 ATCGCAACGCGGAAATGAAAATCGCAACGAG
1336183 TCAATTCCGC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 18 0.67
34 9 0.33
ACGTcount: A:0.41, C:0.22, G:0.25, T:0.12
Consensus pattern (34 bp):
ATCGCAACGCGGAAATGAAAATCGCAACGAGAGA
Found at i:1336210 original size:20 final size:20
Alignment explanation
Indices: 1336181--1336226 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1336171 AATCGCAACG
1336181 AGTCAATTCCGCGTTGCGAT
1 AGTCAATTCCGCGTTGCGAT
* *
1336201 AGTCATTTCCGTGTTGCGAT
1 AGTCAATTCCGCGTTGCGAT
1336221 AGTCAA
1 AGTCAA
1336227 ATGAATGTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.33
Consensus pattern (20 bp):
AGTCAATTCCGCGTTGCGAT
Found at i:1338507 original size:24 final size:24
Alignment explanation
Indices: 1338473--1338526 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1338463 CTGAAAAATC
1338473 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1338497 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1338521 ATCAAA
1 ATCAAA
1338527 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1338540 original size:24 final size:24
Alignment explanation
Indices: 1338473--1338540 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1338463 CTGAAAAATC
* * *
1338473 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
1338497 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1338521 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1338541 TAGTACTCAC
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:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1339393 original size:20 final size:20
Alignment explanation
Indices: 1339368--1339414 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1339358 AAATTCAGTA
*
1339368 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
1339388 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
1339408 TTGCGAT
1 TTGCGAT
1339415 TTACGTATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:1339424 original size:20 final size:20
Alignment explanation
Indices: 1339401--1339554 Score: 218
Period size: 20 Copynumber: 7.7 Consensus size: 20
1339391 CGATAGTCAG
*
1339401 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1339421 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1339441 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
1339461 ATTCGCATTGAGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
1339481 ATTCGCATTTCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * * **
1339501 AATCGCATTGTGATTTTTCAA
1 ATTCGCATTGCGA-TTTACGT
*
1339522 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1339542 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1339555 ATTAGGAAAA
Statistics
Matches: 116, Mismatches: 17, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
20 102 0.88
21 14 0.12
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1339577 original size:21 final size:21
Alignment explanation
Indices: 1339551--1339596 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1339541 TATTCGCATT
1339551 GCGAATTAGGAAAATCACAAC
1 GCGAATTAGGAAAATCACAAC
* * * *
1339572 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCACAAC
1339593 GCGA
1 GCGA
1339597 TAGTCAGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCACAAC
Found at i:1339995 original size:22 final size:23
Alignment explanation
Indices: 1339970--1340016 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
1339960 ATAAAGTACA
*
1339970 ATAACATACTAGGTAGCGC-TAT
1 ATAACATAATAGGTAGCGCTTAT
**
1339992 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
1340015 AT
1 AT
1340017 TTACCTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1341709 original size:198 final size:199
Alignment explanation
Indices: 1340919--1341828 Score: 1677
Period size: 199 Copynumber: 4.6 Consensus size: 199
1340909 TCATTTAGCT
* *
1340919 CGGTAAAATTGTACCAGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
1 CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
*
1340984 TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACTCTGTTTTCCATTCATTC
66 TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTC
1341049 TGGAAAACAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATA
131 TGGAAAACAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATA
*
1341114 AAAT
196 AAAC
**
1341118 AAGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
1 CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
1341183 TTGGGATCGACAC-TTTT-TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTC
66 TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTC
1341246 TGGAAAAC-AA-ATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATA
131 TGGAAAACAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATA
*
1341309 AAAT
196 AAAC
**
1341313 AAGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
1 CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
*
1341378 TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCATCCTGTTTTCCATTCATTC
66 TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTC
1341443 TGGAAAACAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATA
131 TGGAAAACAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATA
1341508 AAAC
196 AAAC
1341512 CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
1 CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
1341577 TTGGGATCGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTC
66 TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTC
*
1341641 TGGAAAACAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATA
131 TGGAAAACAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATA
1341706 AAAC
196 AAAC
1341710 CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
1 CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
1341775 TTGGGATCGACACTTTGTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
66 TTGGGATCGACACTTT-TTATATATGGATCGACACTTTATGGGTGCACCCTGTT
1341829 GGCCATATTG
Statistics
Matches: 694, Mismatches: 11, Indels: 11
0.97 0.02 0.02
Matches are distributed among these distances:
195 135 0.19
196 6 0.01
197 106 0.15
198 202 0.29
199 208 0.30
200 37 0.05
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (199 bp):
CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTC
TGGAAAACAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATA
AAAC
Found at i:1341979 original size:19 final size:19
Alignment explanation
Indices: 1341947--1341993 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
1341937 TTATATTCAC
1341947 ATACAAAA--ATAAATCGT
1 ATACAAAATTATAAATCGT
*
1341964 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1341983 ATACAAAATTA
1 ATACAAAATTA
1341994 ACCCTACATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 8 0.30
19 19 0.70
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1343823 original size:33 final size:33
Alignment explanation
Indices: 1343786--1343851 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1343776 CATCTTAATA
* *
1343786 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCATTCACCACT
* *
1343819 TCACCCCTCAACACCTCTACTTCATTCACCACT
1 TCACCCCTCAACACCCCAACTTCATTCACCACT
1343852 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.48, G:0.00, T:0.27
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCATTCACCACT
Found at i:1343910 original size:21 final size:21
Alignment explanation
Indices: 1343885--1343928 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1343875 CCCCTTATGC
*
1343885 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTGTATCTACGACT
* *
1343906 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTGTATCTACGACT
1343927 CT
1 CT
1343929 TGATTGTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.32, G:0.16, T:0.39
Consensus pattern (21 bp):
CTCTCGAGTGTATCTACGACT
Found at i:1346181 original size:17 final size:18
Alignment explanation
Indices: 1346159--1346201 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
1346149 ATATATCCGG
1346159 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
1346176 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
1346196 TATCAT
1 TATCAT
1346202 ATTTTTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:1346358 original size:20 final size:20
Alignment explanation
Indices: 1346332--1346377 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
1346322 CACTTTTAAA
1346332 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
1346351 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
1346372 TTTACC
1 TTTACC
1346378 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:1352661 original size:2 final size:2
Alignment explanation
Indices: 1352642--1352686 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
1352632 GAGCTAGTGC
*
1352642 AT AT A- AT AT -T AA 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
1352682 A- AT AT
1 AT AT AT
1352687 TAAAAAATCC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
1 3 0.08
2 35 0.92
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1353134 original size:2 final size:2
Alignment explanation
Indices: 1353127--1353185 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1353117 TTACGCTTGA
1353127 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
1353169 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
1353186 ACTGTTGAAC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1359663 original size:17 final size:17
Alignment explanation
Indices: 1359632--1359665 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1359622 TAATTACAAA
1359632 GTTTAATAATAAATAAT
1 GTTTAATAATAAATAAT
1359649 GTTTAGATAAT-AATAAT
1 GTTTA-ATAATAAATAAT
1359666 AATAATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (17 bp):
GTTTAATAATAAATAAT
Found at i:1360140 original size:19 final size:19
Alignment explanation
Indices: 1360116--1360165 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
1360106 ACATATTAAT
1360116 TTTTTTTTAATTTTTCTGA
1 TTTTTTTTAATTTTTCTGA
*
1360135 TTTTTTATAATTTTTCTGA
1 TTTTTTTTAATTTTTCTGA
*
1360154 TTTTTTTAAATT
1 TTTTTTTTAATT
1360166 CAATTAGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.72
Consensus pattern (19 bp):
TTTTTTTTAATTTTTCTGA
Found at i:1365416 original size:72 final size:72
Alignment explanation
Indices: 1365305--1365454 Score: 219
Period size: 72 Copynumber: 2.1 Consensus size: 72
1365295 CTACGACTGT
* * **
1365305 GTCGAACGGTGGCAGTGATACTCGGAACAACGACAGGATCATGATGGGCGTGGTGGTGAAGGTCA
1 GTCGAACAGTGGCAGTGATACTCGAAACAACGACAGGATCATGATGGGCGTGGCAGTGAAGGTCA
*
1365370 CGACGGC
66 CGACGAC
* * *
1365377 GTCGAACAGTGGCAGTGATACTCGAAACAACGACGGGATCGTGATGGGCGTGGCAGTGAAGGTTA
1 GTCGAACAGTGGCAGTGATACTCGAAACAACGACAGGATCATGATGGGCGTGGCAGTGAAGGTCA
*
1365442 TGACGAC
66 CGACGAC
1365449 GTCGAA
1 GTCGAA
1365455 TGGCTCCAAT
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 69 1.00
ACGTcount: A:0.27, C:0.19, G:0.37, T:0.17
Consensus pattern (72 bp):
GTCGAACAGTGGCAGTGATACTCGAAACAACGACAGGATCATGATGGGCGTGGCAGTGAAGGTCA
CGACGAC
Found at i:1365832 original size:83 final size:84
Alignment explanation
Indices: 1365720--1365956 Score: 307
Period size: 83 Copynumber: 2.8 Consensus size: 84
1365710 TTGAAAAACA
* ** *
1365720 CCACTATGGATGAACCCTATTGCGGCATTTACATAAAAACGCCGCTAAAGTACTACTCTGTCACG
1 CCACTATGGATGAACCCTATTGCGACATTTGTATAAAAACGCCGCTAAAGTACTACTATGTCACG
1365785 ACGTTTATTG-AAAAAATG
66 ACGTTTATTGAAAAAAATG
* ** * *
1365803 CCACTATGGATAAACCCTATTATGACATTTGTATAAAACCGCCACTAAAGTACTACTATGTCACG
1 CCACTATGGATGAACCCTATTGCGACATTTGTATAAAAACGCCGCTAAAGTACTACTATGTCACG
*
1365868 ACGTTTGTTGAAAAAAATG
66 ACGTTTATTGAAAAAAATG
* * * ** * *
1365887 CCACTATGGATGAA-CGTATTGCAACGTTTGTATAAAAACTTCGCTAAAGTACTACTTTGTAACG
1 CCACTATGGATGAACCCTATTGCGACATTTGTATAAAAACGCCGCTAAAGTACTACTATGTCACG
1365951 ACGTTT
66 ACGTTT
1365957 TGTATAAAAT
Statistics
Matches: 131, Mismatches: 22, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
83 110 0.84
84 21 0.16
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (84 bp):
CCACTATGGATGAACCCTATTGCGACATTTGTATAAAAACGCCGCTAAAGTACTACTATGTCACG
ACGTTTATTGAAAAAAATG
Found at i:1366654 original size:64 final size:65
Alignment explanation
Indices: 1366531--1366662 Score: 187
Period size: 64 Copynumber: 2.0 Consensus size: 65
1366521 ATCAAGTCTC
* * *
1366531 AAATCAACACAAGATGTTCATATTAAAAATACTACACAAGAGTATCAAATTTCAACAACACAATA
1 AAATCAACACAAGATGTTCAAAATAAAAATACCACACAAGAGTATCAAATTTCAACAACACAATA
* * *
1366596 AAATCAACACAAGATGTTCAAAAT-AAAATACCACATAAGAGTATCAAGTCTT-AACAACATAAT
1 AAATCAACACAAGATGTTCAAAATAAAAATACCACACAAGAGTATCAAAT-TTCAACAACACAAT
1366659 A
65 A
1366660 AAA
1 AAA
1366663 GAGATAGTAG
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
64 36 0.60
65 24 0.40
ACGTcount: A:0.54, C:0.17, G:0.07, T:0.22
Consensus pattern (65 bp):
AAATCAACACAAGATGTTCAAAATAAAAATACCACACAAGAGTATCAAATTTCAACAACACAATA
Found at i:1368315 original size:19 final size:17
Alignment explanation
Indices: 1368291--1368325 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
1368281 TATTTTAATC
1368291 AATTTAAACTTTTAAATTG
1 AATTTAAA--TTTAAATTG
1368310 AATTTAAATTTAAATT
1 AATTTAAATTTAAATT
1368326 AGAGTTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (17 bp):
AATTTAAATTTAAATTG
Found at i:1368468 original size:20 final size:20
Alignment explanation
Indices: 1368443--1368512 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
1368433 TATCGAAAAT
*
1368443 GGTGAGTTGAGTGATGTGCA
1 GGTGAGTTGAGTGTTGTGCA
* *
1368463 GGTGAGTTGGGTGTTGTGTA
1 GGTGAGTTGAGTGTTGTGCA
* * *
1368483 AGTGAGCTGGGTGTTGTGCA
1 GGTGAGTTGAGTGTTGTGCA
1368503 GGTGAGTTGA
1 GGTGAGTTGA
1368513 CTTTGTACAT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.16, C:0.04, G:0.47, T:0.33
Consensus pattern (20 bp):
GGTGAGTTGAGTGTTGTGCA
Found at i:1368808 original size:14 final size:13
Alignment explanation
Indices: 1368777--1368831 Score: 56
Period size: 13 Copynumber: 3.9 Consensus size: 13
1368767 TATATTTTTA
1368777 TTTTTTATTAAAG
1 TTTTTTATTAAAG
*
1368790 TTTTTTATTAAGG
1 TTTTTTATTAAAG
1368803 TATTTTCATTATTAAAG
1 --TTTT--TTATTAAAG
*
1368820 TTTTCTATTAAA
1 TTTTTTATTAAA
1368832 ATATTTTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
13 19 0.54
15 8 0.23
17 8 0.23
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.58
Consensus pattern (13 bp):
TTTTTTATTAAAG
Found at i:1368837 original size:30 final size:30
Alignment explanation
Indices: 1368781--1368838 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1368771 TTTTTATTTT
* **
1368781 TTATTAAAGTTTTTTATTAAGGTATTTTCA
1 TTATTAAAGTTTTCTATTAAAATATTTTCA
1368811 TTATTAAAGTTTTCTATTAAAATATTTT
1 TTATTAAAGTTTTCTATTAAAATATTTT
1368839 TTATTTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (30 bp):
TTATTAAAGTTTTCTATTAAAATATTTTCA
Found at i:1370092 original size:227 final size:225
Alignment explanation
Indices: 1369693--1370139 Score: 788
Period size: 227 Copynumber: 2.0 Consensus size: 225
1369683 GTAAATTATC
* * *
1369693 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
1369758 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
1369823 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
1369888 AAACATAAATTACATAACTTTCAAAAAAGTA
196 AAACATAAATTACATAACTTT-AAAAAAGTA
*
1369919 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
1369984 TTAATATTGTTAAATTT-AAATGCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAAT
65 TTAATATTGTTAAATTTAAAAT-CTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAAT
* *
1370048 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
129 TTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAT
1370113 TGAAACATAAATTACATAACTTTAAAA
194 TGAAACATAAATTACATAACTTTAAAA
1370140 GCAGTTTTAA
Statistics
Matches: 211, Mismatches: 8, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
226 44 0.21
227 167 0.79
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (225 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTA
Found at i:1370228 original size:20 final size:19
Alignment explanation
Indices: 1370205--1370250 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
1370195 CGATATACCA
1370205 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
1370225 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
1370245 GGTAAA
1 GGTAAA
1370251 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1370393 original size:20 final size:19
Alignment explanation
Indices: 1370370--1370416 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1370360 CGATATAACA
*
1370370 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAAAC
*
1370390 GGTATCAAAATGATAAAAAC
1 GGTA-AAAAATGATAAAAAC
1370410 GGTAAAA
1 GGTAAAA
1370417 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAAAC
Found at i:1372769 original size:33 final size:33
Alignment explanation
Indices: 1372727--1372792 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1372717 AAATAGATGG
*
1372727 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
1372760 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1372793 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1374607 original size:19 final size:19
Alignment explanation
Indices: 1374583--1374631 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1374573 AATGTCGAGT
1374583 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1374602 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
1374621 TATTTTTGTAT
1 TAATTTTGTAT
1374632 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1375319 original size:198 final size:199
Alignment explanation
Indices: 1374750--1376515 Score: 3272
Period size: 198 Copynumber: 8.9 Consensus size: 199
1374740 CAATATGGCC
*
1374750 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAAC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAAC
*
1374815 CCAAAAGTATAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
1374880 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
**
1374945 TTAAA
195 TGGAA
1374950 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAAC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAAC
*
1375015 CCAAAAGTATAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
1375080 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
**
1375145 TTAAA
195 TGGAA
1375150 AACAAGGTGCACCCATAAAGTGTCGATCCATATA-AAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
1375214 CAAAAGTATAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
1375279 AATAAGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
**
1375343 TAAA
196 GGAA
1375347 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1375412 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
1375477 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
**
1375542 TCAA
196 GGAA
1375546 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAAC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
1375611 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
* **
1375676 GGATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTCCCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
1375741 TGGAA
195 TGGAA
* *
1375746 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAGAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1375811 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
1375876 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
1375940 GGAA
196 GGAA
*
1375944 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1376009 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
1376074 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
1376138 GGAA
196 GGAA
* *
1376142 AACAGGGTGCACTCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1376206 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
1376271 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
1376336 GGAA
196 GGAA
1376340 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1376405 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
1376470 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
1376516 CTAATTTAAA
Statistics
Matches: 1541, Mismatches: 20, Indels: 11
0.98 0.01 0.01
Matches are distributed among these distances:
197 196 0.13
198 584 0.38
199 336 0.22
200 425 0.28
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (199 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
GGAA
Found at i:1377995 original size:18 final size:18
Alignment explanation
Indices: 1377974--1378035 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
1377964 AGCGGTCGCA
1377974 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* * *
1377992 GAAGATGACGATGATGAT
1 GAAGATGAAGCTGACGAT
* *
1378010 GACGATGAAGCTGGCGAT
1 GAAGATGAAGCTGACGAT
1378028 GAAGATGA
1 GAAGATGA
1378036 TGACGATGAT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.37, C:0.10, G:0.35, T:0.18
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:1377998 original size:6 final size:6
Alignment explanation
Indices: 1377974--1378065 Score: 67
Period size: 6 Copynumber: 15.3 Consensus size: 6
1377964 AGCGGTCGCA
* * * * * *
1377974 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
** * * * * *
1378022 GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
1378066 TGATCCAAAC
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:1378009 original size:3 final size:3
Alignment explanation
Indices: 1377989--1378069 Score: 72
Period size: 3 Copynumber: 27.0 Consensus size: 3
1377979 TGAAGCTGAC
* * * * * ** *
1377989 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
1378037 GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1378070 CCAAACAAGT
Statistics
Matches: 59, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.36, C:0.06, G:0.35, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:1378028 original size:36 final size:36
Alignment explanation
Indices: 1377977--1378053 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
1377967 GGTCGCAGAA
*
1377977 GATGAAGCTGACGATGAAGATGACGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
* * *
1378013 GATGAAGCTGGCGATGAAGATGATGACGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
1378049 GATGA
1 GATGA
1378054 TGATGAAGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.35, C:0.09, G:0.35, T:0.21
Consensus pattern (36 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGAC
Found at i:1378069 original size:12 final size:12
Alignment explanation
Indices: 1377977--1378065 Score: 88
Period size: 12 Copynumber: 7.4 Consensus size: 12
1377967 GGTCGCAGAA
*
1377977 GATGAAGCTGAC
1 GATGAAGATGAC
1377989 GATGAAGATGAC
1 GATGAAGATGAC
*
1378001 GATGATGATGAC
1 GATGAAGATGAC
* *
1378013 GATGAAGCTGGC
1 GATGAAGATGAC
*
1378025 GATGAAGATGAT
1 GATGAAGATGAC
* * *
1378037 GACGATGATGAT
1 GATGAAGATGAC
* *
1378049 GATGATGATGAA
1 GATGAAGATGAC
1378061 GATGA
1 GATGA
1378066 TGATCCAAAC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 65 1.00
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.21
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:1378069 original size:18 final size:18
Alignment explanation
Indices: 1377974--1378065 Score: 76
Period size: 18 Copynumber: 5.1 Consensus size: 18
1377964 AGCGGTCGCA
*
1377974 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGACGAT
* *
1377992 GAAGATGACGATGATGAT
1 GAAGATGAAGATGACGAT
* * *
1378010 GACGATGAAGCTGGCGAT
1 GAAGATGAAGATGACGAT
* * *
1378028 GAAGATGATGACGATGAT
1 GAAGATGAAGATGACGAT
* * *
1378046 GATGATGATGATGAAGAT
1 GAAGATGAAGATGACGAT
1378064 GA
1 GA
1378066 TGATCCAAAC
Statistics
Matches: 57, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 57 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.21
Consensus pattern (18 bp):
GAAGATGAAGATGACGAT
Found at i:1379850 original size:184 final size:183
Alignment explanation
Indices: 1379541--1379883 Score: 560
Period size: 184 Copynumber: 1.9 Consensus size: 183
1379531 CTTTCAACAT
* *
1379541 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATAAAATAGATAAATTTGCAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
* *
1379606 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAA-AAA
*
1379671 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
130 AATGTGTCGATACCATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
** * * *
1379725 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATAAAATAGATAAATTTGCAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
***
1379790 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAATTGA
66 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAAAAA
1379855 ATGTGTCGATACCATTTAAAAAAGTGTCG
131 ATGTGTCGATACCATTTAAAAAAGTGTCG
1379884 GTAATTTGAA
Statistics
Matches: 146, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
183 29 0.20
184 117 0.80
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (183 bp):
ATTATAATAAAATAGATAAATTTGCAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAAAAA
ATGTGTCGATACCATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:1382455 original size:23 final size:23
Alignment explanation
Indices: 1382424--1382487 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
1382414 ATAGGTGAAC
*
1382424 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
1382447 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
1382470 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
1382488 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:1382494 original size:23 final size:23
Alignment explanation
Indices: 1382424--1382496 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
1382414 ATAGGTGAAC
* **
1382424 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
1382447 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
1382470 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
1382493 ATAT
1 ATAT
1382497 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:1382885 original size:23 final size:23
Alignment explanation
Indices: 1382854--1382917 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
1382844 ATAGGTAAAC
*
1382854 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
1382877 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
1382900 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
1382918 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:1382924 original size:23 final size:23
Alignment explanation
Indices: 1382854--1382926 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
1382844 ATAGGTAAAC
* **
1382854 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
1382877 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
1382900 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
1382923 ATAT
1 ATAT
1382927 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:1383225 original size:25 final size:25
Alignment explanation
Indices: 1383191--1383241 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1383181 ACAACAAATC
*
1383191 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
1383216 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
1383241 A
1 A
1383242 TTTGGATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:1383511 original size:18 final size:18
Alignment explanation
Indices: 1383490--1383526 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1383480 GTAATTGGAG
1383490 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
1383508 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
1383526 T
1 T
1383527 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:1383534 original size:24 final size:24
Alignment explanation
Indices: 1383482--1383528 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1383472 TTTCATATGT
* *
1383482 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
1383506 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
1383529 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:1383827 original size:39 final size:39
Alignment explanation
Indices: 1383784--1383870 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
1383774 TCCGATGCTC
*
1383784 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
*
1383823 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
1383862 ATCAAAATC
1 ATCAAAATC
1383871 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:1384303 original size:23 final size:23
Alignment explanation
Indices: 1384272--1384335 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
1384262 ATAGGTAAAC
*
1384272 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
1384295 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
1384318 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
1384336 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:1384342 original size:23 final size:23
Alignment explanation
Indices: 1384272--1384344 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
1384262 ATAGGTAAAC
* **
1384272 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
1384295 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
1384318 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
1384341 ATAT
1 ATAT
1384345 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:1393897 original size:27 final size:26
Alignment explanation
Indices: 1393855--1393922 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 26
1393845 CTGTAGGAAT
1393855 TATAGAG-ATGATTTGTTACAATTCC
1 TATAGAGAATGATTTGTTACAATTCC
* *
1393880 TATAGAGATATGATTTGTTACCATTTC
1 TATAGAGA-ATGATTTGTTACAATTCC
1393907 TATAGAGACATGATTT
1 TATAGAGA-ATGATTT
1393923 TGTAAATAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
25 7 0.18
27 31 0.82
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.41
Consensus pattern (26 bp):
TATAGAGAATGATTTGTTACAATTCC
Found at i:1397640 original size:27 final size:27
Alignment explanation
Indices: 1397598--1397665 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
1397588 GTGTAGGAAT
1397598 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
1397623 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
1397650 TATAGAGATATGATTT
1 TATAGAGATATGATTT
1397666 TGTAAATAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 7 0.17
27 34 0.83
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:1407607 original size:2 final size:2
Alignment explanation
Indices: 1407600--1407628 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1407590 TTCCAATTCT
1407600 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 T
1407629 GAGTTCTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1408918 original size:38 final size:38
Alignment explanation
Indices: 1408876--1408991 Score: 187
Period size: 38 Copynumber: 3.1 Consensus size: 38
1408866 ATTCAACAGC
**
1408876 CTAAGCTTCATAATAGCAAGCAGGCCAATATGATCAAA
1 CTAAGCTTCCGAATAGCAAGCAGGCCAATATGATCAAA
1408914 CTAAGCTTCCGAATAGCAAGCAGGCCAATATGATCAAA
1 CTAAGCTTCCGAATAGCAAGCAGGCCAATATGATCAAA
* * *
1408952 CTAAGCTTCCGAATAACAAGCCGGCCAATATGATCTAA
1 CTAAGCTTCCGAATAGCAAGCAGGCCAATATGATCAAA
1408990 CT
1 CT
1408992 TAGAATGGCA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 73 1.00
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.21
Consensus pattern (38 bp):
CTAAGCTTCCGAATAGCAAGCAGGCCAATATGATCAAA
Found at i:1411118 original size:35 final size:35
Alignment explanation
Indices: 1411052--1411118 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
1411042 AGCAATAGCA
**
1411052 TGGGTTGTTGCTTCATCTTCTTCCTTACTTTACCC
1 TGGGTTGTTGCTTCATCTTCGACCTTACTTTACCC
*
1411087 TGGGTTGTTGTTTCATCTTCGACTCTT-CTTTA
1 TGGGTTGTTGCTTCATCTTCGAC-CTTACTTTA
1411119 GCCCCATTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 25 0.89
36 3 0.11
ACGTcount: A:0.09, C:0.24, G:0.16, T:0.51
Consensus pattern (35 bp):
TGGGTTGTTGCTTCATCTTCGACCTTACTTTACCC
Found at i:1412331 original size:32 final size:32
Alignment explanation
Indices: 1412290--1412354 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
1412280 AATGTTATTC
1412290 CTCAAATTTAGCATAATATTTCCACATTTGTA
1 CTCAAATTTAGCATAATATTTCCACATTTGTA
1412322 CTCAAATTTAGCATAATATTTCCACATTTGTA
1 CTCAAATTTAGCATAATATTTCCACATTTGTA
1412354 C
1 C
1412355 ACTATCGATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (32 bp):
CTCAAATTTAGCATAATATTTCCACATTTGTA
Found at i:1420902 original size:20 final size:21
Alignment explanation
Indices: 1420877--1420925 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
1420867 AACGGACCAT
*
1420877 AAGATTATC-GGTGAGAATAA
1 AAGATTATCTAGTGAGAATAA
1420897 AAGATTA-CTAGTGAGAATAA
1 AAGATTATCTAGTGAGAATAA
1420917 AAGATTATC
1 AAGATTATC
1420926 CGGGAATAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 1 0.04
20 24 0.92
21 1 0.04
ACGTcount: A:0.47, C:0.06, G:0.20, T:0.27
Consensus pattern (21 bp):
AAGATTATCTAGTGAGAATAA
Found at i:1421118 original size:20 final size:20
Alignment explanation
Indices: 1421093--1421142 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1421083 AACGGAACAT
*
1421093 AAGATTATTAATGAGAATAA
1 AAGATTATCAATGAGAATAA
* *
1421113 AAGATTACCAGTGAGAATAA
1 AAGATTATCAATGAGAATAA
1421133 AAGATTATCA
1 AAGATTATCA
1421143 GGGAATATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.52, C:0.06, G:0.16, T:0.26
Consensus pattern (20 bp):
AAGATTATCAATGAGAATAA
Found at i:1421166 original size:216 final size:216
Alignment explanation
Indices: 1420785--1421229 Score: 748
Period size: 216 Copynumber: 2.1 Consensus size: 216
1420775 GGAAATTTAT
*
1420785 TTAAAATTAATAAATAAGGATAAACTATTGTCTATAGTATTTGGGTAAGTTTCTATTTTTACCAT
1 TTAAAATTAATAAATAAGGATAAACTATTGTCCATAGTATTTGGGTAAGTTTCTATTTTTACCAT
* ** *
1420850 TTAGGGTGCGTTTGGTTAACGGACCATAAGATTATCGGTGAGAATAAAAGATTACTAGTGAGAAT
66 TTAGGGTGCGTTTGGTTAACGGAACATAAGATTATCAATGAGAATAAAAGATTACCAGTGAGAAT
* *
1420915 AAAAGATTATCCGGGAATAGGATTACTGGGAATGTTGTATTTTATATTTGGTTGGTTTAGAATAA
131 AAAAGATTATCAGGGAATAGGATTACTGAGAATGTTGTATTTTATATTTGGTTGGTTTAGAATAA
*
1420980 ATGTAAGATTACCGTGTTTGG
196 ATGTAAGATTACAGTGTTTGG
*
1421001 TTAAAATTAATAAATAAGGATAAACTATTGTCCATAGTATTTGGGTAAGTTTCTCTTTTTACCAT
1 TTAAAATTAATAAATAAGGATAAACTATTGTCCATAGTATTTGGGTAAGTTTCTATTTTTACCAT
* *
1421066 TTATGGTGCGTTTGGTTAACGGAACATAAGATTATTAATGAGAATAAAAGATTACCAGTGAGAAT
66 TTAGGGTGCGTTTGGTTAACGGAACATAAGATTATCAATGAGAATAAAAGATTACCAGTGAGAAT
* * *
1421131 AAAAGATTATCAGGGAATATGATTACTGAGAATGTTGTATTTTGTGTTTGGTTGGTTTAGAATAA
131 AAAAGATTATCAGGGAATAGGATTACTGAGAATGTTGTATTTTATATTTGGTTGGTTTAGAATAA
1421196 ATGTAAGATTACAGTGTTTGG
196 ATGTAAGATTACAGTGTTTGG
*
1421217 TT-AAATGAATAAA
1 TTAAAATTAATAAA
1421230 AGATTATTAG
Statistics
Matches: 214, Mismatches: 15, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
215 10 0.05
216 204 0.95
ACGTcount: A:0.35, C:0.07, G:0.21, T:0.37
Consensus pattern (216 bp):
TTAAAATTAATAAATAAGGATAAACTATTGTCCATAGTATTTGGGTAAGTTTCTATTTTTACCAT
TTAGGGTGCGTTTGGTTAACGGAACATAAGATTATCAATGAGAATAAAAGATTACCAGTGAGAAT
AAAAGATTATCAGGGAATAGGATTACTGAGAATGTTGTATTTTATATTTGGTTGGTTTAGAATAA
ATGTAAGATTACAGTGTTTGG
Found at i:1421371 original size:36 final size:37
Alignment explanation
Indices: 1421301--1421372 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
1421291 TGGAAAATAA
*
1421301 TTATATATTTTCTTTAAAGAATTTAAATTCATAAAAT
1 TTATATATTTTCTTTAAAGAATTTAAAATCATAAAAT
*
1421338 TTATATAATTTT-TTTACA-AATTTGAAAAT-ATAAAA
1 TTATAT-ATTTTCTTTAAAGAATTT-AAAATCATAAAA
1421373 AGGTTTAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
36 11 0.35
37 15 0.48
38 5 0.16
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (37 bp):
TTATATATTTTCTTTAAAGAATTTAAAATCATAAAAT
Found at i:1422146 original size:18 final size:16
Alignment explanation
Indices: 1422103--1422147 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 16
1422093 AACATTCCCA
1422103 GTAATTTTATTCTCTG
1 GTAATTTTATTCTCTG
1422119 GTAATCTTTTATTCTCACTG
1 GTAA--TTTTATTCT--CTG
1422139 GTAATTTTA
1 GTAATTTTA
1422148 CATTCCGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.16
18 14 0.56
20 7 0.28
ACGTcount: A:0.22, C:0.13, G:0.11, T:0.53
Consensus pattern (16 bp):
GTAATTTTATTCTCTG
Found at i:1424018 original size:42 final size:42
Alignment explanation
Indices: 1423956--1424039 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
1423946 CATTAATTTG
*
1423956 GATTGGGTTATCTAACCTGGGTTCTTCAAAG-TTCTGGTTTTT
1 GATTGGATTATCTAACCTGGGTTCTTCAAAGTTTC-GGTTTTT
*
1423998 GATTGGATTATCTAATCTGGGTTCTTCAAAGTTTCGGTTTTT
1 GATTGGATTATCTAACCTGGGTTCTTCAAAGTTTCGGTTTTT
1424040 TGTCTGTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
42 36 0.92
43 3 0.08
ACGTcount: A:0.18, C:0.13, G:0.23, T:0.46
Consensus pattern (42 bp):
GATTGGATTATCTAACCTGGGTTCTTCAAAGTTTCGGTTTTT
Found at i:1428435 original size:21 final size:19
Alignment explanation
Indices: 1428411--1428449 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
1428401 CAATGGCCTG
1428411 AAATTACAAGACAACACAAAC
1 AAATTACAA-ACAAC-CAAAC
1428432 AAATTACAAACAACCAAA
1 AAATTACAAACAACCAAA
1428450 ATTGCCTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 5 0.28
21 9 0.50
ACGTcount: A:0.64, C:0.23, G:0.03, T:0.10
Consensus pattern (19 bp):
AAATTACAAACAACCAAAC
Found at i:1429222 original size:93 final size:93
Alignment explanation
Indices: 1429063--1429250 Score: 358
Period size: 93 Copynumber: 2.0 Consensus size: 93
1429053 TCTAATTTTT
1429063 GGCTTGAAATAGGTCCATGTTCTTTTGAAATTATGCAAGTTGGCCACTCCCAATGTTTAATCCTA
1 GGCTTGAAATAGGTCCATGTTCTTTTGAAATTATGCAAGTTGGCCACTCCCAATGTTTAATCCTA
1429128 GTTCGTCCCTACATACCCTCCCTACATC
66 GTTCGTCCCTACATACCCTCCCTACATC
*
1429156 GGCTTGAAATAGGTCCCTGTTCTTTTGAAATTATGCAAGTTGGCCACTCCCAATGTTTAATCCTA
1 GGCTTGAAATAGGTCCATGTTCTTTTGAAATTATGCAAGTTGGCCACTCCCAATGTTTAATCCTA
*
1429221 GTTCGTCCCTATATACCCTCCCTACATC
66 GTTCGTCCCTACATACCCTCCCTACATC
1429249 GG
1 GG
1429251 ATGCTAGCCG
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 93 1.00
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.34
Consensus pattern (93 bp):
GGCTTGAAATAGGTCCATGTTCTTTTGAAATTATGCAAGTTGGCCACTCCCAATGTTTAATCCTA
GTTCGTCCCTACATACCCTCCCTACATC
Found at i:1430705 original size:19 final size:19
Alignment explanation
Indices: 1430681--1430722 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1430671 AATATACTCT
*
1430681 TAAATTATA-CCTAAATTCC
1 TAAATTATATCCCAAA-TCC
1430700 TAAATTATATCCCAAATCC
1 TAAATTATATCCCAAATCC
1430719 TAAA
1 TAAA
1430723 CCCCAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAATTATATCCCAAATCC
Found at i:1431917 original size:15 final size:16
Alignment explanation
Indices: 1431897--1431935 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1431887 GTTTACTTCA
*
1431897 GAATGATT-AAGCGCT
1 GAATGATTCAAACGCT
*
1431912 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
1431928 GAATGATT
1 GAATGATT
1431936 TAGAGGCTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:1432028 original size:27 final size:27
Alignment explanation
Indices: 1431990--1432054 Score: 130
Period size: 27 Copynumber: 2.4 Consensus size: 27
1431980 ATAATGACTC
1431990 TGAATCATTCATAATGTACTTCTATGT
1 TGAATCATTCATAATGTACTTCTATGT
1432017 TGAATCATTCATAATGTACTTCTATGT
1 TGAATCATTCATAATGTACTTCTATGT
1432044 TGAATCATTCA
1 TGAATCATTCA
1432055 ACACTGTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (27 bp):
TGAATCATTCATAATGTACTTCTATGT
Found at i:1436998 original size:31 final size:31
Alignment explanation
Indices: 1436925--1436992 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
1436915 TTATGATAAT
* *
1436925 TATAAAATTTTAATAAATTTAATGATTATTT
1 TATAATATTTTAATAAATTTAATGATTATTC
*
1436956 TATAATATTTTAATAAACTTTAAT-AGTTGTTC
1 TATAATATTTTAATAAA-TTTAATGA-TTATTC
1436988 TATAA
1 TATAA
1436993 CTTTTACAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 17 0.53
32 15 0.47
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (31 bp):
TATAATATTTTAATAAATTTAATGATTATTC
Found at i:1464317 original size:19 final size:19
Alignment explanation
Indices: 1464293--1464340 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1464283 TTCTTTAAAA
1464293 TTTAAAATTATCGTATATT-
1 TTTAAAATTAT-GTATATTC
* *
1464312 TTTAAAAATATGTATTTTC
1 TTTAAAATTATGTATATTC
1464331 TGTTAAAATT
1 T-TTAAAATT
1464341 TTATTTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 6 0.25
19 11 0.46
20 7 0.29
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (19 bp):
TTTAAAATTATGTATATTC
Found at i:1466192 original size:2 final size:2
Alignment explanation
Indices: 1466185--1466277 Score: 51
Period size: 2 Copynumber: 51.0 Consensus size: 2
1466175 TCGGGTCGAG
* * * *
1466185 TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA T- TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
1466224 TA TA TA TA T- TA -A TT TA AA T- TA AA TT TA T- TA -A TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1466260 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
1466278 ATAATTATTT
Statistics
Matches: 66, Mismatches: 16, Indels: 18
0.66 0.16 0.18
Matches are distributed among these distances:
1 9 0.14
2 57 0.86
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1468150 original size:2 final size:2
Alignment explanation
Indices: 1468143--1468170 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1468133 TTTGTTTTTC
1468143 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
1468171 GAATTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1479477 original size:31 final size:31
Alignment explanation
Indices: 1479379--1479503 Score: 110
Period size: 31 Copynumber: 4.0 Consensus size: 31
1479369 GTCGAGGGTA
*
1479379 TACCTATGTTCTACGGAACATATGGACAGAAT
1 TACCTATGTTCTACGGAACATATGGACAG-TT
* * * * *
1479411 TACTTAT-ATCTTTC-GAGACATATGGACAATA
1 TACCTATGTTC-TACGGA-ACATATGGACAGTT
* *
1479442 TACCTATGTTCTAAGGAACATATGAACAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
* * *
1479473 TACCTAGGTTCTTCGGAACCTATGGACAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
1479504 GCCAAGGATC
Statistics
Matches: 71, Mismatches: 18, Indels: 9
0.72 0.18 0.09
Matches are distributed among these distances:
31 48 0.68
32 23 0.32
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAGTT
Found at i:1483912 original size:31 final size:31
Alignment explanation
Indices: 1483825--1483951 Score: 141
Period size: 31 Copynumber: 4.1 Consensus size: 31
1483815 AGAGTCGAGG
1483825 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * *
1483856 GAATTACTTATG-TCTTTC-GAGACATATGGACA
1 GTA-TACCTATGTTC-TACGGA-ACATATGGACA
*
1483888 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * * *
1483919 GTTTACCTAGGTTCTTCGGAACCTATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
1483950 GT
1 GT
1483952 TGCCAAGGAT
Statistics
Matches: 79, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
31 53 0.67
32 26 0.33
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Consensus pattern (31 bp):
GTATACCTATGTTCTACGGAACATATGGACA
Found at i:1486460 original size:110 final size:111
Alignment explanation
Indices: 1486266--1486478 Score: 365
Period size: 110 Copynumber: 1.9 Consensus size: 111
1486256 ATTACAAAAA
* * * * *
1486266 TTAATTCTTAATCTAATAATCATGTATTAAATGAATCAACTAATTATTAATAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
1486331 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAAATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAAATAT
*
1486377 TTAATTATTAATATAATAATCATGCATTAAATAAAT-AACTAAATATTACTAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
1486441 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGT
1486479 AGAGATATAT
Statistics
Matches: 96, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
110 64 0.67
111 32 0.33
ACGTcount: A:0.46, C:0.09, G:0.08, T:0.37
Consensus pattern (111 bp):
TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAAATAT
Done.