Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009259.1 Hibiscus syriacus cultivar Beakdansim tig00112910_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: 1149570
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:987291 original size:16 final size:18
Alignment explanation
Indices: 987164--987292 Score: 89
Period size: 18 Copynumber: 7.3 Consensus size: 18
987154 TTGGTTATAT
987164 ATATAGTTTTGAAAATAA
1 ATATAGTTTTGAAAATAA
987182 ATATAGTTTTGAAATATATATA
1 ATATAGTTTTG-AA-A-ATA-A
987204 TATAGCATAGTTTTGAAAATAA
1 -AT---ATAGTTTTGAAAATAA
* *
987226 ATATAGTTTTGGAAA-AC
1 ATATAGTTTTGAAAATAA
*
987243 ATATA----T--ATAT-A
1 ATATAGTTTTGAAAATAA
987254 ATATAGTTTTGAAAATAA
1 ATATAGTTTTGAAAATAA
987272 ATATAGTTTT-AAAA-AA
1 ATATAGTTTTGAAAATAA
987288 ATATA
1 ATATA
987293 TATAATATAG
Statistics
Matches: 90, Mismatches: 5, Indels: 34
0.70 0.04 0.26
Matches are distributed among these distances:
11 7 0.08
13 1 0.01
15 1 0.01
16 7 0.08
17 13 0.14
18 34 0.38
19 2 0.02
20 1 0.01
21 5 0.06
22 2 0.02
23 5 0.06
24 1 0.01
25 2 0.02
26 9 0.10
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.40
Consensus pattern (18 bp):
ATATAGTTTTGAAAATAA
Found at i:987437 original size:3 final size:3
Alignment explanation
Indices: 987419--987468 Score: 79
Period size: 3 Copynumber: 17.7 Consensus size: 3
987409 TACATTTTCA
987419 TAT TA- TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
987464 TAT TA
1 TAT TA
987469 AAGGTCCAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 6 0.14
3 38 0.86
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:993840 original size:21 final size:21
Alignment explanation
Indices: 993816--993860 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
993806 AGAGTCCATC
* *
993816 AAACAATTTGAAGAA-AAATGT
1 AAACAACTAGAAGAATAAAT-T
993837 AAACAACTAGAAGAATAAATT
1 AAACAACTAGAAGAATAAATT
993858 AAA
1 AAA
993861 GCTATGAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.62, C:0.07, G:0.11, T:0.20
Consensus pattern (21 bp):
AAACAACTAGAAGAATAAATT
Found at i:1002122 original size:43 final size:43
Alignment explanation
Indices: 1002071--1002185 Score: 178
Period size: 44 Copynumber: 2.7 Consensus size: 43
1002061 TTTTGGTTAT
* *
1002071 ATATATATATGTATA-TTTGAAAATAAATATAGCTTTGGAAAAC
1 ATATATATA-ATATAGTTTGAAAATAAATATAGCTTTAGAAAAC
*
1002114 ATATATATAATATAGTTTTGAAAATAAATATAGTTTTAGAAAAC
1 ATATATATAATATAG-TTTGAAAATAAATATAGCTTTAGAAAAC
1002158 ATATATATAATATAGTTTGAAAATAAAT
1 ATATATATAATATAGTTTGAAAATAAAT
1002186 CTAGTATTAA
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
42 4 0.06
43 22 0.33
44 41 0.61
ACGTcount: A:0.50, C:0.03, G:0.10, T:0.38
Consensus pattern (43 bp):
ATATATATAATATAGTTTGAAAATAAATATAGCTTTAGAAAAC
Found at i:1002125 original size:26 final size:24
Alignment explanation
Indices: 1002096--1002180 Score: 81
Period size: 24 Copynumber: 3.6 Consensus size: 24
1002086 TTTGAAAATA
1002096 AATATAGCTTTGGAAAACATATATAT
1 AATATAG-TTT-GAAAACATATATAT
*
1002122 AATATAGTTTTG-AAA-ATAAATAT
1 AATATAG-TTTGAAAACATATATAT
* *
1002145 AGT-T--TTAGAAAACATATATAT
1 AATATAGTTTGAAAACATATATAT
1002166 AATATAGTTTGAAAA
1 AATATAGTTTGAAAA
1002181 TAAATCTAGT
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
19 3 0.06
20 3 0.06
21 9 0.19
22 2 0.04
23 9 0.19
24 10 0.21
25 1 0.02
26 10 0.21
ACGTcount: A:0.49, C:0.04, G:0.11, T:0.36
Consensus pattern (24 bp):
AATATAGTTTGAAAACATATATAT
Found at i:1002144 original size:25 final size:26
Alignment explanation
Indices: 1002096--1002145 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
1002086 TTTGAAAATA
*
1002096 AATATAGCTTTGGAAAACATATATAT
1 AATATAGCTTTGGAAAACAAATATAT
* *
1002122 AATATAG-TTTTGAAAATAAATATA
1 AATATAGCTTTGGAAAACAAATATA
1002146 GTTTTAGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.50, C:0.04, G:0.10, T:0.36
Consensus pattern (26 bp):
AATATAGCTTTGGAAAACAAATATAT
Found at i:1002163 original size:19 final size:18
Alignment explanation
Indices: 1002122--1002164 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
1002112 ACATATATAT
*
1002122 AATATAGTTTTGAAAATA
1 AATATAGTTTTGAAAACA
1002140 AATATAGTTTTAGAAAACA
1 AATATAGTTTT-GAAAACA
*
1002159 TATATA
1 AATATA
1002165 TAATATAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.37
Consensus pattern (18 bp):
AATATAGTTTTGAAAACA
Found at i:1002214 original size:43 final size:45
Alignment explanation
Indices: 1002069--1002214 Score: 169
Period size: 44 Copynumber: 3.3 Consensus size: 45
1002059 TATTTTGGTT
* *
1002069 ATATATATATATGTA-TATTTGAAAATAAATATAGCT-TTGGAAAAC
1 ATATATATATATATAGT-TTTGAAAATAAATATAG-TATTAGAAAAC
*
1002114 ATATATATA-ATATAGTTTTGAAAATAAATATAGTTTTAGAAAAC
1 ATATATATATATATAGTTTTGAAAATAAATATAGTATTAGAAAAC
* *
1002158 ATATATATA-ATATAG-TTTGAAAATAAATCTAGTATTA-AAAAT
1 ATATATATATATATAGTTTTGAAAATAAATATAGTATTAGAAAAC
* *
1002200 TTATATAGATATATA
1 ATATATATATATATA
1002215 ATATAATTTA
Statistics
Matches: 91, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
42 11 0.12
43 26 0.29
44 44 0.48
45 10 0.11
ACGTcount: A:0.49, C:0.03, G:0.09, T:0.39
Consensus pattern (45 bp):
ATATATATATATATAGTTTTGAAAATAAATATAGTATTAGAAAAC
Found at i:1002297 original size:3 final size:3
Alignment explanation
Indices: 1002289--1002329 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1002279 TACATTTTCA
1002289 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1002330 CTATATTGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1006805 original size:38 final size:38
Alignment explanation
Indices: 1006738--1006822 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 38
1006728 TCATTTCATT
* * *
1006738 CAAAAATTTTATTTAACTTGAGATTGTTTCTCTCGAAA
1 CAAAAATTTCATCTAACTTGAGATAGTTTCTCTCGAAA
* * *
1006776 CAAAAATTTCATCTCACTTTAGATAGTTTCTCTTGAAA
1 CAAAAATTTCATCTAACTTGAGATAGTTTCTCTCGAAA
*
1006814 CACAAATTT
1 CAAAAATTT
1006823 TGAAATTGTT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.40
Consensus pattern (38 bp):
CAAAAATTTCATCTAACTTGAGATAGTTTCTCTCGAAA
Found at i:1006873 original size:67 final size:67
Alignment explanation
Indices: 1006755--1006890 Score: 157
Period size: 67 Copynumber: 2.0 Consensus size: 67
1006745 TTTATTTAAC
* * * *
1006755 TTGAGATTGTTTCTCTCGAAACAAAAATTTCATCTCACTTTAGATAGTTTCTCTTGAAACACAAA
1 TTGAAATTGTTTCTCTCGAAACAAAAATTTCATCCCACTTGAGATAGTTTCTCTTAAAACACAAA
1006820 TT
66 TT
* ** * * * *
1006822 TTGAAATTGTTTCAT-TTGAAACAAAGTTTTTATCCCACTTGAGATATTTTCTCTTAAAATACGA
1 TTGAAATTGTTTC-TCTCGAAACAAAAATTTCATCCCACTTGAGATAGTTTCTCTTAAAACACAA
1006886 ATT
65 ATT
1006889 TT
1 TT
1006891 AAGATCATTT
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
67 56 0.98
68 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.42
Consensus pattern (67 bp):
TTGAAATTGTTTCTCTCGAAACAAAAATTTCATCCCACTTGAGATAGTTTCTCTTAAAACACAAA
TT
Found at i:1006899 original size:167 final size:167
Alignment explanation
Indices: 1006574--1007042 Score: 606
Period size: 167 Copynumber: 2.8 Consensus size: 167
1006564 CTTAAAAATG
* * * * * ** * *
1006574 AAAATTTTCATCTCACTTGAGATTGTTTGTCT-TAAA-ATAAGTTTCATCTTGCTTGAGACAGTT
1 AAAATTTT-ATCTAACTTGAGATTGTTTCTCTCAAAACAAAAATTTCATCTCACTTTAGATAGTT
* * * * * * *
1006637 TCCCTTGAAACAAAAAGTTTGAAATCGTTTCACTCGAAACAAAGTTTTTTTCTTACTTGAGATGT
65 TCTCTTGAAACACAAATTTTGAAATTGTTTCACTCGAAACAAAGTTTTTATCTCACTTGAGATAT
**
1006702 TTTCTCTTAAAATACGAATTTTGGGATCATTTCATTCA
130 TTTCTCTTAAAATACGAATTTTAAGATCATTTCATTCA
* *
1006740 AAAATTTTATTTAACTTGAGATTGTTTCTCTCGAAACAAAAATTTCATCTCACTTTAGATAGTTT
1 AAAATTTTATCTAACTTGAGATTGTTTCTCTCAAAACAAAAATTTCATCTCACTTTAGATAGTTT
* * *
1006805 CTCTTGAAACACAAATTTTGAAATTGTTTCATTTGAAACAAAGTTTTTATCCCACTTGAGATATT
66 CTCTTGAAACACAAATTTTGAAATTGTTTCACTCGAAACAAAGTTTTTATCTCACTTGAGATATT
1006870 TTCTCTTAAAATACGAATTTTAAGATCATTTCATTCA
131 TTCTCTTAAAATACGAATTTTAAGATCATTTCATTCA
*
1006907 AAACA-TTTATCTAACTTGAGATGGTTTCTCTCAAAAC-AAAATGTTCATCTCACTTGT-GATAG
1 AAA-ATTTTATCTAACTTGAGATTGTTTCTCTCAAAACAAAAAT-TTCATCTCACTT-TAGATAG
* * *
1006969 TTTCTCTTGAAACACAAATTTTGACATTGTTTCACTCGAAAGAAATTTTTTTATCTCACTTGAGA
63 TTTCTCTTGAAACACAAATTTTGAAATTGTTTCACTCGAAACAAA-GTTTTTATCTCACTTGAGA
1007034 TTATTTTCT
127 -TATTTTCT
1007043 TAAAACAAAA
Statistics
Matches: 265, Mismatches: 31, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
165 20 0.08
166 16 0.06
167 202 0.76
168 19 0.07
169 8 0.03
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (167 bp):
AAAATTTTATCTAACTTGAGATTGTTTCTCTCAAAACAAAAATTTCATCTCACTTTAGATAGTTT
CTCTTGAAACACAAATTTTGAAATTGTTTCACTCGAAACAAAGTTTTTATCTCACTTGAGATATT
TTCTCTTAAAATACGAATTTTAAGATCATTTCATTCA
Found at i:1006902 original size:67 final size:67
Alignment explanation
Indices: 1006772--1006904 Score: 151
Period size: 67 Copynumber: 2.0 Consensus size: 67
1006762 TGTTTCTCTC
* * * **
1006772 GAAACAAAAATTTCATCTCACTTTAGATAGTTTCTCTTGAAACACAAATTTTGAAATTGTTTCAT
1 GAAACAAAAATTTCATCCCACTTGAGATAGTTTCTCTTAAAACACAAATTTTGAAATCATTTCAT
1006837 TT
66 TT
** * * * *
1006839 GAAACAAAGTTTTTATCCCACTTGAGATATTTTCTCTTAAAATACGAATTTT-AAGATCATTTCA
1 GAAACAAAAATTTCATCCCACTTGAGATAGTTTCTCTTAAAACACAAATTTTGAA-ATCATTTCA
1006903 TT
65 TT
1006905 CAAAACATTT
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
66 2 0.04
67 52 0.96
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (67 bp):
GAAACAAAAATTTCATCCCACTTGAGATAGTTTCTCTTAAAACACAAATTTTGAAATCATTTCAT
TT
Found at i:1007086 original size:144 final size:145
Alignment explanation
Indices: 1006922--1007197 Score: 414
Period size: 144 Copynumber: 1.9 Consensus size: 145
1006912 TTTATCTAAC
* * *** * *
1006922 TTGAGATGGTTTCTCTCAAAA-CAAAATGTTCATCTCACTTGTGATAGTTTCTCTTGAAACACAA
1 TTGAGATCGTTTCTCTCAAAATAAAAAAAAT-ATCTCACTTGAGATAGTTTCTCTTAAAACACAA
* *
1006986 ATTTTGACATTGTTTCACTCGAAA-GAAATTTTTTTATCTCACTTGAGATT-ATTTTCTTAAAAC
65 ATTTTGAAATTGTTTCACTCGAAATGAAA-TTTTTTATCTCACTTGAGATTGATTTTATTAAAAC
1007049 AAAATATTTTATCACTT
129 AAAATATTTTATCACTT
1007066 TTGAGATCGTTTCTCTCAAAATAAAAAAAATATCTCACTTGAGATAGTTTCTCTTAAAACACAAA
1 TTGAGATCGTTTCTCTCAAAATAAAAAAAATATCTCACTTGAGATAGTTTCTCTTAAAACACAAA
*
1007131 TTTTGAAATTGTTTCACTCGAAATTGAAATTTTTTATCTCACTTGAGATTGTTTTTATTAAAACA
66 TTTTGAAATTGTTTCACTCGAAA-TGAAATTTTTTATCTCACTTGAGATTGATTTTATTAAAACA
1007196 AA
130 AA
1007198 TTTCATCTAA
Statistics
Matches: 118, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
144 74 0.63
145 26 0.22
146 18 0.15
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (145 bp):
TTGAGATCGTTTCTCTCAAAATAAAAAAAATATCTCACTTGAGATAGTTTCTCTTAAAACACAAA
TTTTGAAATTGTTTCACTCGAAATGAAATTTTTTATCTCACTTGAGATTGATTTTATTAAAACAA
AATATTTTATCACTT
Found at i:1007618 original size:5 final size:5
Alignment explanation
Indices: 1007605--1007651 Score: 62
Period size: 5 Copynumber: 9.6 Consensus size: 5
1007595 GGAAAATGGA
*
1007605 AAAAA AAAAT AAAA- AATAA- AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1007652 GAAATATTAG
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
4 4 0.10
5 35 0.90
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:1007619 original size:19 final size:19
Alignment explanation
Indices: 1007604--1007651 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
1007594 TGGAAAATGG
1007604 AAAAAA-AAAATAAAAAAT
1 AAAAAATAAAATAAAAAAT
1007622 AAAAAATAAAATAAAATAA-
1 AAAAAATAAAATAAAA-AAT
1007641 AATAAAATAAA
1 AA-AAAATAAA
1007652 GAAATATTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 6 0.22
19 11 0.41
20 10 0.37
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (19 bp):
AAAAAATAAAATAAAAAAT
Found at i:1011876 original size:12 final size:12
Alignment explanation
Indices: 1011859--1011914 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
1011849 ACATCAATTT
1011859 AGTTAGGTAGAG
1 AGTTAGGTAGAG
*
1011871 AGTTAGG-CGAAG
1 AGTTAGGTAG-AG
* * *
1011883 AATTAGATAAAG
1 AGTTAGGTAGAG
1011895 AGTTAGGT-GAG
1 AGTTAGGTAGAG
1011906 AGTTAGGTA
1 AGTTAGGTA
1011915 TTTGTATATT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
11 11 0.33
12 22 0.67
ACGTcount: A:0.38, C:0.02, G:0.36, T:0.25
Consensus pattern (12 bp):
AGTTAGGTAGAG
Found at i:1013713 original size:19 final size:19
Alignment explanation
Indices: 1013691--1013733 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
1013681 GCCTGAAAGC
1013691 TTGCTACAAAGATGCATCA
1 TTGCTACAAAGATGCATCA
**
1013710 TTGCTTTAAAGATGCATCA
1 TTGCTACAAAGATGCATCA
1013729 TTGCT
1 TTGCT
1013734 TTGGCATCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (19 bp):
TTGCTACAAAGATGCATCA
Found at i:1013734 original size:19 final size:19
Alignment explanation
Indices: 1013698--1013735 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1013688 AGCTTGCTAC
1013698 AAAGATGCATCATTGCTTT
1 AAAGATGCATCATTGCTTT
1013717 AAAGATGCATCATTGCTTT
1 AAAGATGCATCATTGCTTT
1013736 GGCATCTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (19 bp):
AAAGATGCATCATTGCTTT
Found at i:1016515 original size:12 final size:12
Alignment explanation
Indices: 1016498--1016553 Score: 69
Period size: 12 Copynumber: 4.8 Consensus size: 12
1016488 ACATCAATTT
1016498 AGTTAGGTAAAG
1 AGTTAGGTAAAG
*
1016510 AGTTAGGTGAAG
1 AGTTAGGTAAAG
* *
1016522 AATTAGGTGAAG
1 AGTTAGGTAAAG
*
1016534 AGTTAGGT-GAG
1 AGTTAGGTAAAG
1016545 AGTTAGGTA
1 AGTTAGGTA
1016554 TTTGTATATT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
11 10 0.26
12 29 0.74
ACGTcount: A:0.36, C:0.00, G:0.38, T:0.27
Consensus pattern (12 bp):
AGTTAGGTAAAG
Found at i:1016534 original size:24 final size:23
Alignment explanation
Indices: 1016500--1016553 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 23
1016490 ATCAATTTAG
1016500 TTAGGTAAAGAGTTAGGTGAAGAA
1 TTAGGTAAAGAGTTAGGTG-AGAA
* *
1016524 TTAGGTGAAGAGTTAGGTGAGAG
1 TTAGGTAAAGAGTTAGGTGAGAA
1016547 TTAGGTA
1 TTAGGTA
1016554 TTTGTATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 9 0.33
24 18 0.67
ACGTcount: A:0.35, C:0.00, G:0.37, T:0.28
Consensus pattern (23 bp):
TTAGGTAAAGAGTTAGGTGAGAA
Found at i:1019870 original size:26 final size:26
Alignment explanation
Indices: 1019832--1019883 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
1019822 AAGTGAAAAG
1019832 AAAAAATACTACTTGTAAATTGTTTT
1 AAAAAATACTACTTGTAAATTGTTTT
*
1019858 AAAAAATATTACTTGTAAATTGTTTT
1 AAAAAATACTACTTGTAAATTGTTTT
1019884 CTTTATTACG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (26 bp):
AAAAAATACTACTTGTAAATTGTTTT
Found at i:1023823 original size:19 final size:19
Alignment explanation
Indices: 1023801--1023841 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1023791 ACCGATTCAA
*
1023801 ACCGATCTGAACCGATTTG
1 ACCGATCCGAACCGATTTG
* *
1023820 ACCGGTCCGAACCGGTTTG
1 ACCGATCCGAACCGATTTG
1023839 ACC
1 ACC
1023842 CGACCCGACC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.22, C:0.32, G:0.24, T:0.22
Consensus pattern (19 bp):
ACCGATCCGAACCGATTTG
Found at i:1023961 original size:58 final size:56
Alignment explanation
Indices: 1023854--1023963 Score: 141
Period size: 58 Copynumber: 1.9 Consensus size: 56
1023844 ACCCGACCTA
*
1023854 ATGACATTTTCGGATTTTTTACAAACAGTGACATTCTGGTAATTGTTTTTAAAACG
1 ATGACATTTTCGGATTTTTTACAAACAGTGACATTCTGGTAATTATTTTTAAAACG
* * * *
1023910 ATGACATTTTGGGAATTATTTGTA-AAACGGTGATATTTTGGTAATTATTTTTAA
1 ATGACATTTTCGG-ATT-TTT-TACAAACAGTGACATTCTGGTAATTATTTTTAA
1023964 TAAAGGTGAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
56 12 0.26
57 3 0.07
58 29 0.63
59 2 0.04
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (56 bp):
ATGACATTTTCGGATTTTTTACAAACAGTGACATTCTGGTAATTATTTTTAAAACG
Found at i:1023974 original size:30 final size:29
Alignment explanation
Indices: 1023869--1023985 Score: 126
Period size: 29 Copynumber: 4.0 Consensus size: 29
1023859 ATTTTCGGAT
* * *
1023869 TTTTTACAAACAGTGACATTCTGGTAATTG
1 TTTTTA-AAACGGTGACATTTTGGTAATTA
* *
1023899 TTTTTAAAACGATGACATTTTGGGAATTA
1 TTTTTAAAACGGTGACATTTTGGTAATTA
* *
1023928 TTTGTAAAACGGTGATATTTTGGTAATTA
1 TTTTTAAAACGGTGACATTTTGGTAATTA
* * *
1023957 TTTTTAATAAAGGTGATATTTTTGTAATT
1 TTTTTAA-AACGGTGACATTTTGGTAATT
1023986 TTTGAATGTG
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
29 49 0.66
30 25 0.34
ACGTcount: A:0.32, C:0.06, G:0.17, T:0.45
Consensus pattern (29 bp):
TTTTTAAAACGGTGACATTTTGGTAATTA
Found at i:1027012 original size:16 final size:16
Alignment explanation
Indices: 1026991--1027021 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1026981 CTTCTAATTT
1026991 CTTTTTGAGTTCAAGC
1 CTTTTTGAGTTCAAGC
1027007 CTTTTTGAGTTCAAG
1 CTTTTTGAGTTCAAG
1027022 TTTCAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.45
Consensus pattern (16 bp):
CTTTTTGAGTTCAAGC
Found at i:1028927 original size:18 final size:18
Alignment explanation
Indices: 1028860--1028928 Score: 66
Period size: 18 Copynumber: 3.6 Consensus size: 18
1028850 TCAGTATTCG
* *
1028860 TCCCGTAGGACCACTATG
1 TCCCGAAGGACCACTATA
*
1028878 TTCCGAAGGACCACTGTATA
1 TCCCGAAGGACCAC--TATA
*
1028898 TGTCCCGTAGGACCACTATA
1 --TCCCGAAGGACCACTATA
1028918 TCCCGAAGGAC
1 TCCCGAAGGAC
1028929 TACTCCTTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
18 22 0.54
20 7 0.17
22 12 0.29
ACGTcount: A:0.26, C:0.30, G:0.22, T:0.22
Consensus pattern (18 bp):
TCCCGAAGGACCACTATA
Found at i:1030017 original size:26 final size:26
Alignment explanation
Indices: 1029966--1030018 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
1029956 TTACTTATGT
* * *
1029966 CTTATATCACATATTTATATTATAAA
1 CTTATATAACACATATATATTATAAA
1029992 CTTATATAACACATATACTATT-TAAA
1 CTTATATAACACATATA-TATTATAAA
1030018 C
1 C
1030019 CAATTCACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.43, C:0.15, G:0.00, T:0.42
Consensus pattern (26 bp):
CTTATATAACACATATATATTATAAA
Found at i:1030544 original size:64 final size:63
Alignment explanation
Indices: 1030411--1030567 Score: 158
Period size: 64 Copynumber: 2.4 Consensus size: 63
1030401 TAATGAAGGT
* * * * *
1030411 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTATAGGG
1 ATGCATCGATGCA-TACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
* *
1030475 ATGCATCGATGCATGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATT-TTAAA-A
1 ATGCATCGATGCAT-ACTAATGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATTAAAGA
1030537 G
63 G
* *
1030538 AGTGCATCAATGCATTACCAATGCATCGAT
1 A-TGCATCGATGCA-TACTAATGCATCGAT
1030568 ACACCTTCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
63 3 0.04
64 68 0.86
65 8 0.10
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCATACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
Found at i:1032404 original size:30 final size:29
Alignment explanation
Indices: 1032340--1032443 Score: 147
Period size: 29 Copynumber: 3.6 Consensus size: 29
1032330 GTATAGTTTT
* *
1032340 GAAAAAAATCA-AGCTTAAGTACTAAAACG
1 GAAAAAAATGATAG-TTAGGTACTAAAACG
1032369 GAAAAAAATGATAGTTAGGTACTAAAACG
1 GAAAAAAATGATAGTTAGGTACTAAAACG
*
1032398 GAAAAAAATGATAGTTAGGTACTAAAATG
1 GAAAAAAATGATAGTTAGGTACTAAAACG
*
1032427 GAACAAAAGTGATAGTT
1 GAA-AAAAATGATAGTT
1032444 TATGTATTAA
Statistics
Matches: 69, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
29 55 0.80
30 14 0.20
ACGTcount: A:0.52, C:0.08, G:0.19, T:0.21
Consensus pattern (29 bp):
GAAAAAAATGATAGTTAGGTACTAAAACG
Found at i:1033421 original size:7 final size:7
Alignment explanation
Indices: 1033401--1033489 Score: 90
Period size: 7 Copynumber: 12.7 Consensus size: 7
1033391 GTTAGAATAT
1033401 ACCCTAA
1 ACCCTAA
**
1033408 ACTATAA
1 ACCCTAA
*
1033415 ACCATAA
1 ACCCTAA
*
1033422 ACTCTAA
1 ACCCTAA
*
1033429 A-TCTCAA
1 ACCCT-AA
1033436 ACCCTAA
1 ACCCTAA
* *
1033443 ACCTTAT
1 ACCCTAA
*
1033450 GCCCTAA
1 ACCCTAA
1033457 ACCCTAA
1 ACCCTAA
1033464 ACCCTAA
1 ACCCTAA
1033471 ACCCTAA
1 ACCCTAA
1033478 ACCCTAA
1 ACCCTAA
1033485 ACCCT
1 ACCCT
1033490 TAATCTTATT
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
6 3 0.04
7 63 0.93
8 2 0.03
ACGTcount: A:0.42, C:0.37, G:0.01, T:0.20
Consensus pattern (7 bp):
ACCCTAA
Found at i:1046341 original size:77 final size:79
Alignment explanation
Indices: 1046198--1046349 Score: 202
Period size: 77 Copynumber: 1.9 Consensus size: 79
1046188 TGAATATAGT
* *
1046198 AAATAAACATTAAAAGAATGTAATTCTGACTACAACTCTTTTAATGGATATTTAATTCAGAATAA
1 AAATAAACATTAAAAGAATGTAATTCGGACTACAACTCTTTTAATAGATATTTAATTCAGAATAA
1046263 TTAAATAAGAGTCC
66 TTAAATAAGAGTCC
* * * * * *
1046277 AAATAAACGTT-AAAGATTGTAATTCGGATTATAAGTC-TTTAATAGATATTTAATT-TGAATTA
1 AAATAAACATTAAAAGAATGTAATTCGGACTACAACTCTTTTAATAGATATTTAATTCAGAA-TA
1046339 ATTAAATAAGA
65 ATTAAATAAGA
1046350 ATTTAATTAA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
76 3 0.05
77 30 0.47
78 21 0.33
79 10 0.16
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36
Consensus pattern (79 bp):
AAATAAACATTAAAAGAATGTAATTCGGACTACAACTCTTTTAATAGATATTTAATTCAGAATAA
TTAAATAAGAGTCC
Found at i:1050738 original size:33 final size:33
Alignment explanation
Indices: 1050701--1050764 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
1050691 TGGTTCTTGA
* *
1050701 TTGTTGATGTTTTGCCAGCGTATCTGTTGATAT
1 TTGTTAATATTTTGCCAGCGTATCTGTTGATAT
*
1050734 TTGTTAATATTTTTCCAGCGTATCTGTTGAT
1 TTGTTAATATTTTGCCAGCGTATCTGTTGAT
1050765 GATGAAAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.17, C:0.12, G:0.20, T:0.50
Consensus pattern (33 bp):
TTGTTAATATTTTGCCAGCGTATCTGTTGATAT
Found at i:1053783 original size:18 final size:18
Alignment explanation
Indices: 1053756--1053804 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
1053746 GCTATACAAG
*
1053756 TGTGATTATTCTAAGACT
1 TGTGACTATTCTAAGACT
1053774 TGTGACTATTCTAAGACT
1 TGTGACTATTCTAAGACT
*
1053792 TGTGCCTATTCTA
1 TGTGACTATTCTA
1053805 GATATAAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.43
Consensus pattern (18 bp):
TGTGACTATTCTAAGACT
Found at i:1054372 original size:15 final size:16
Alignment explanation
Indices: 1054330--1054371 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
1054320 CAAGGTCTAG
*
1054330 CAGCCATTTTTCACTT
1 CAGCCGTTTTTCACTT
1054346 CAGCCGTTTTTCACTT
1 CAGCCGTTTTTCACTT
*
1054362 CAGGCGTTTT
1 CAGCCGTTTT
1054372 CTCAAAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.14, C:0.29, G:0.14, T:0.43
Consensus pattern (16 bp):
CAGCCGTTTTTCACTT
Found at i:1065256 original size:20 final size:20
Alignment explanation
Indices: 1065219--1065257 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1065209 CTTTGGCTTT
*
1065219 CTAAATTTCACTGTTCTAAG
1 CTAAATTTCACTGATCTAAG
**
1065239 CTAAATTTCTTTGATCTAA
1 CTAAATTTCACTGATCTAA
1065258 AATATGAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.18, G:0.08, T:0.44
Consensus pattern (20 bp):
CTAAATTTCACTGATCTAAG
Found at i:1070090 original size:54 final size:54
Alignment explanation
Indices: 1069918--1070459 Score: 675
Period size: 54 Copynumber: 10.1 Consensus size: 54
1069908 AAGGTGGAGG
* *** *
1069918 CGAAACGGTTATTCATCCACATAGGATGAATTCTGTGGGTTGCACACATAGTGC
1 CGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGC
* * * * *
1069972 TTG-TATGGTTATTCATCTACATAGAATGAATTCC-TGAAATGCAC-CTTTAGTGC
1 -CGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACAC-TTAGTGC
1070025 CGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCAC-CTTTAGTGC
1 CGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACAC-TTAGTGC
* *
1070079 CGAAACAGTTATTCATCCATATAGGATGAATTCCGTGAAATGCAC-CTTTAGTGC
1 CGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACAC-TTAGTGC
* * * *
1070133 CGAAACGGTTATTCATCAACATAGGATGAATTCCATGAAAAGCACACTTAGTAC
1 CGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGC
* *
1070187 CGAAACGGTTATTCATCCACATAGGATAAATTTCGTGAAATGCACACTTAGTGC
1 CGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGC
* * * *
1070241 CGAAATGGTTATTCATCCGCATAGAATGAATTCCGTGAAATGCACACTTAGTGT
1 CGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGC
* * *
1070295 CGAAACGGTTATTCATCCATATAAGATGAATTCCATGAAATGCAC-CTTTAGTGC
1 CGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACAC-TTAGTGC
* ** *
1070349 CGAAACAGTTATTCATCCACATAGGATGAATTTTGTGAAATGTAC-CTTTAGTGC
1 CGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACAC-TTAGTGC
* * ** *
1070403 CAAAACAGTTATTCATCCATGTAGGATGAATTCTGTGAAATGCACACTTAGTGC
1 CGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGC
1070457 CGA
1 CGA
1070460 TTTGGTAATC
Statistics
Matches: 426, Mismatches: 55, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
52 2 0.00
53 41 0.10
54 380 0.89
55 3 0.01
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.30
Consensus pattern (54 bp):
CGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGC
Found at i:1074615 original size:44 final size:44
Alignment explanation
Indices: 1074477--1074621 Score: 218
Period size: 45 Copynumber: 3.2 Consensus size: 44
1074467 ATAATGCACC
* * *
1074477 ATTATACATTTTCATTTATGGCAACTGTCATGCCTTTTTATACACT
1 ATTATACA-TTTCATTTATGGCATCTTTCATGCC-TTTTATACTCT
* *
1074523 AATATACATTTCATTTATGGCATGCTTTCATGCCTTTTATACTAT
1 ATTATACATTTCATTTATGGCAT-CTTTCATGCCTTTTATACTCT
1074568 ATTATACATTTCATTTATGGCATCTTTCATGCCTTTTATACTCT
1 ATTATACATTTCATTTATGGCATCTTTCATGCCTTTTATACTCT
1074612 ATTATACATT
1 ATTATACATT
1074622 GTTATACATT
Statistics
Matches: 91, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
44 30 0.33
45 45 0.49
46 16 0.18
ACGTcount: A:0.26, C:0.19, G:0.08, T:0.48
Consensus pattern (44 bp):
ATTATACATTTCATTTATGGCATCTTTCATGCCTTTTATACTCT
Found at i:1075046 original size:54 final size:54
Alignment explanation
Indices: 1074998--1075821 Score: 1181
Period size: 54 Copynumber: 15.3 Consensus size: 54
1074988 TAGTGCATGT
**
1074998 ACGGTTATTCATCCACATAGGATGAATTATGTGAAATGCACCTTTAGTGCCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACCTTTAGTGCCGAA
* * *
1075052 ACGATTATTCATCCACATAGGATGAATTCTGTGAAATGCATCTTTAGTGCCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACCTTTAGTGCCGAA
*
1075106 ACGATTATTCATCCACATAGGATGAATTCCGTGAAATGCACCTTTAGTGCCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACCTTTAGTGCCGAA
** ** * *
1075160 ACAATTATTCATCCACATAGGATGAATTATGTGAAATGCAAAC-TTAGTGTCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGC-ACCTTTAGTGCCGAA
* * *
1075214 ACGGTTATTCATCCACATATGATGAATTTCGTGAAATGCACACTTT-GTGTCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCAC-CTTTAGTGCCGAA
** * * * *
1075268 ACGGTTATTCATCTGCTTAGAATGAATTCCGTGAAATGAACAC-TTAGTGTCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCAC-CTTTAGTGCCGAA
* * * *
1075322 ACGGTTATTAATCCACATAGGATGAATTCCTTGAAATGCACCTTTACTGCAGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACCTTTAGTGCCGAA
* *
1075376 ACGATTATTCATCCACATAGGATGAATTCCGTGAAATGCACCTTTAGTGCTGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACCTTTAGTGCCGAA
* *
1075430 ATGGTTATTCATTCACATAGGATGAATTCCGTGAAATGCACCTTTAGTGCCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACCTTTAGTGCCGAA
* *
1075484 ACGGTTATTCATTCACATAGGATGAATTCCGTGAAATGCACCTTTAGTGTCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACCTTTAGTGCCGAA
* * *
1075538 ACAGTTATTCATCCACATAGGATGAATTCCTTGAAATGCACCTTTAGTGCCAAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACCTTTAGTGCCGAA
* *
1075592 ATGGTTATTCATCCACATAGGATGAATTCCATGAAATGCACCTTTAGTGCCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACCTTTAGTGCCGAA
*
1075646 ATGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACCTTTAGTGCCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACCTTTAGTGCCGAA
* * * *
1075700 ATGATTAAT-AACCACATAGGATGAATTCCGTGAAATGCACCTTTAGTGCCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACCTTTAGTGCCGAA
* * **
1075753 ACGATTAATCA-CCACATAGGATGAATTCCGTGAAATGCACCTTTAGTGTTGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACCTTTAGTGCCGAA
1075806 ACGGTTATTCATCCAC
1 ACGGTTATTCATCCAC
1075822 GTATATGAAT
Statistics
Matches: 701, Mismatches: 62, Indels: 14
0.90 0.08 0.02
Matches are distributed among these distances:
53 104 0.15
54 593 0.85
55 4 0.01
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (54 bp):
ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACCTTTAGTGCCGAA
Found at i:1079046 original size:17 final size:18
Alignment explanation
Indices: 1079024--1079057 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1079014 ATTTTTATTG
1079024 AATAAA-ATAATATTTTT
1 AATAAATATAATATTTTT
*
1079041 AATAAATATATTATTTT
1 AATAAATATAATATTTT
1079058 GGATCAAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AATAAATATAATATTTTT
Found at i:1094309 original size:46 final size:44
Alignment explanation
Indices: 1094179--1094302 Score: 178
Period size: 46 Copynumber: 2.8 Consensus size: 44
1094169 GTAAGTATGC
* *
1094179 AAATAAGCTTACGAGCTTATGAAT-AATGGCAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGAATAAATGGTAAGTATTTTGATA
*
1094222 AAATAAGCTTACGAGCTTATGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGAA--TAAATGGTAAGTATTTTGATA
*
1094268 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTAT-GAATAAATGGTAAG
1094303 AGATTTTATA
Statistics
Matches: 73, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
43 23 0.32
45 12 0.16
46 36 0.49
47 2 0.03
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGAATAAATGGTAAGTATTTTGATA
Found at i:1094726 original size:21 final size:21
Alignment explanation
Indices: 1094702--1094757 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
1094692 ATGCTTAAAG
1094702 GGAATCGATTCCCCTGCTACA
1 GGAATCGATTCCCCTGCTACA
1094723 GGAATCGATTCCCCTGCTACA
1 GGAATCGATTCCCCTGCTACA
1094744 GGAATCGATTCCCC
1 GGAATCGATTCCCC
1094758 CACTGTTCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.23
Consensus pattern (21 bp):
GGAATCGATTCCCCTGCTACA
Found at i:1094779 original size:13 final size:13
Alignment explanation
Indices: 1094761--1094794 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1094751 ATTCCCCCAC
*
1094761 TGTTCATTGTTAA
1 TGTTCACTGTTAA
*
1094774 TGTTCACTGTTAC
1 TGTTCACTGTTAA
1094787 TGTTCACT
1 TGTTCACT
1094795 ATTCATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.50
Consensus pattern (13 bp):
TGTTCACTGTTAA
Found at i:1096807 original size:16 final size:18
Alignment explanation
Indices: 1096777--1096812 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1096767 CTCCTCGAAA
1096777 ATTTAAAATTA-TTTTAT
1 ATTTAAAATTATTTTTAT
1096794 ATTTAAAA-TATTTTTAT
1 ATTTAAAATTATTTTTAT
1096811 AT
1 AT
1096813 ACTTTTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 2 0.11
17 16 0.89
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTAAAATTATTTTTAT
Found at i:1097244 original size:61 final size:59
Alignment explanation
Indices: 1097167--1097335 Score: 182
Period size: 60 Copynumber: 2.8 Consensus size: 59
1097157 GTATATACAT
* *
1097167 ATAGTTTGGGATGAAATTGGAATGTTCAAAATGTTTGAGGATCAATTTAGAATGA-AGGTC
1 ATAGTTTGGGATGAAATTGGAATATTCAAAA-GTTTGAGGATCAATTTAGAATCATA-GTC
* *
1097227 ATAGTTTGGGGATGAAATTGAAATATTCAAAAGTTTGAAGA-CTAATTTAGAATCATAGTC
1 ATAGTTT-GGGATGAAATTGGAATATTCAAAAGTTTGAGGATC-AATTTAGAATCATAGTC
* * * * *
1097287 ATAGTCTAGAGATAAAATTGGAACATTAAAAAGTTT-ATGGATCAATTTA
1 ATAGT-TTGGGATGAAATTGGAATATTCAAAAGTTTGA-GGATCAATTTA
1097336 AAACAAGATT
Statistics
Matches: 92, Mismatches: 11, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
59 2 0.02
60 65 0.71
61 25 0.27
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (59 bp):
ATAGTTTGGGATGAAATTGGAATATTCAAAAGTTTGAGGATCAATTTAGAATCATAGTC
Found at i:1120234 original size:2 final size:2
Alignment explanation
Indices: 1120227--1120251 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1120217 AATGAAAATA
1120227 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 A
1120252 ATAAAACATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1122213 original size:85 final size:85
Alignment explanation
Indices: 1122067--1122729 Score: 868
Period size: 85 Copynumber: 7.8 Consensus size: 85
1122057 CGCTGTCAAC
* * * * * *
1122067 GAGCTGAATGGAATCGAAATCAAAAGTTTTCGTTGACAGATAACCCTTCTCGCCTTGAGCTATAC
1 GAGCTGAATGGAATCGAACTCAAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGC
**
1122132 TGTAAATTTGATATGCCCTT
66 TGCGAATTTGATATGCCCTT
* * * * * *
1122152 GAGCTGAATGAAATCGAACTCTAAGGTTTTTGTTAACAGATAGTCCTTCTCACTTTTAGCTATGC
1 GAGCTGAATGGAATCGAACTCAAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGC
1122217 TGCGAATTTGATATGCCCTT
66 TGCGAATTTGATATGCCCTT
* * * *
1122237 GAGCTAAATGGAATCGAACTCTAAGGTTTTTGTTGATAGATAGCCCTTCTCTCCTTGAGCTATGC
1 GAGCTGAATGGAATCGAACTCAAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGC
1122302 TGCGAATTTGATATGCCCTT
66 TGCGAATTTGATATGCCCTT
* * * * * * *
1122322 GAGTTGAATGAAATCGAACTCGAAGGTTTTTATTGACAGATAGCTCTTCTCACTTTGAGTTATGC
1 GAGCTGAATGGAATCGAACTCAAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGC
*
1122387 TGCAAATTTGATATGCCCTT
66 TGCGAATTTGATATGCCCTT
* ** * * *
1122407 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGAGGGATAACCCTTCTCGCGTTGAGCTATGC
1 GAGCTGAATGGAATCGAACTCAAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGC
*
1122472 TACGAATTTGATATGCCCTT
66 TGCGAATTTGATATGCCCTT
* *
1122492 -AGCTGAATGGAATCGAACT-ATAAAGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
1 GAGCTGAATGGAATCGAACTCA-AAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATG
* *
1122555 CTACAAATTTGATATGCCCTT
65 CTGCGAATTTGATATGCCCTT
* * *
1122576 GAGCTAAATGGAATCGAACTCAAAGGTTTTTGTTGACAGATTGCCCTTCTCACCTTGAGTTATGC
1 GAGCTGAATGGAATCGAACTCAAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGC
*
1122641 TGCGAATTTGATATGCCTTT
66 TGCGAATTTGATATGCCCTT
* * * * *
1122661 GAGCTGAATGGAATCAAACTCAAAGGTTTTT-TT-ACGGATAGTCCTTCTCGCCTTGAG-TATGT
1 GAGCTGAATGGAATCGAACTCAAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGC
1122723 TGCGAAT
66 TGCGAAT
1122730 AGTTTTTTTA
Statistics
Matches: 508, Mismatches: 67, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
82 11 0.02
83 20 0.04
84 78 0.15
85 398 0.78
86 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (85 bp):
GAGCTGAATGGAATCGAACTCAAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGC
TGCGAATTTGATATGCCCTT
Found at i:1122614 original size:254 final size:254
Alignment explanation
Indices: 1122067--1122721 Score: 929
Period size: 254 Copynumber: 2.6 Consensus size: 254
1122057 CGCTGTCAAC
* * * * * * *
1122067 GAGCTGAATGGAATCGAAATCAAAAGTTTTCGTTGACAGATAACCCTTCTCGCCTTGAGCTATAC
1 GAGCTGAATGGAATCGAACTCAAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGTTATGC
* * * *
1122132 TGTAAATTTGATATGCCCTTGAGCTGAATGAAATCGAACTCTAAGGTTTTTGTTAACAGATAGTC
66 TGCAAATTTGATATGCCCTTGAGCTGAATGGAATCGAACTCAAAGGTTTTTGTT-ACGGATAGTC
* * * * * *
1122197 CTTCTCACTTTTAGCTATGCTGCGAATTTGATATGCCCTTGAGCTAAATGGAATCGAACTCTAAG
130 CTTCTCGCCTTGAGCTATGCTACGAATTTGATATGCCCTTGAGCTAAATGGAATCGAACTATAAA
* * * *
1122262 GTTTTTGTTGATAGATAGCCCTTCTCTCCTTGAGCTATGCTGCGAATTTGATATGCCCTT
195 GTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTACAAATTTGATATGCCCTT
* * * * * *
1122322 GAGTTGAATGAAATCGAACTCGAAGGTTTTTATTGACAGATAGCTCTTCTCACTTTGAGTTATGC
1 GAGCTGAATGGAATCGAACTCAAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGTTATGC
* * **
1122387 TGCAAATTTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGAGGGATAACC
66 TGCAAATTTGATATGCCCTTGAGCTGAATGGAATCGAACTCAAAGGTTTTTGTT-ACGGATAGTC
* *
1122452 CTTCTCGCGTTGAGCTATGCTACGAATTTGATATGCCCTT-AGCTGAATGGAATCGAACTATAAA
130 CTTCTCGCCTTGAGCTATGCTACGAATTTGATATGCCCTTGAGCTAAATGGAATCGAACTATAAA
1122516 GTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTACAAATTTGATATGCCCTT
195 GTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTACAAATTTGATATGCCCTT
* *
1122576 GAGCTAAATGGAATCGAACTCAAAGGTTTTTGTTGACAGATTGCCCTTCTCACCTTGAGTTATGC
1 GAGCTGAATGGAATCGAACTCAAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGTTATGC
* * *
1122641 TGCGAATTTGATATGCCTTTGAGCTGAATGGAATCAAACTCAAAGGTTTTT-TTACGGATAGTCC
66 TGCAAATTTGATATGCCCTTGAGCTGAATGGAATCGAACTCAAAGGTTTTTGTTACGGATAGTCC
1122705 TTCTCGCCTTGAG-TATG
131 TTCTCGCCTTGAGCTATG
1122722 TTGCGAATAG
Statistics
Matches: 352, Mismatches: 48, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
251 4 0.01
252 20 0.06
253 2 0.01
254 181 0.51
255 145 0.41
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (254 bp):
GAGCTGAATGGAATCGAACTCAAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGTTATGC
TGCAAATTTGATATGCCCTTGAGCTGAATGGAATCGAACTCAAAGGTTTTTGTTACGGATAGTCC
TTCTCGCCTTGAGCTATGCTACGAATTTGATATGCCCTTGAGCTAAATGGAATCGAACTATAAAG
TTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTACAAATTTGATATGCCCTT
Found at i:1124939 original size:20 final size:20
Alignment explanation
Indices: 1124909--1124989 Score: 60
Period size: 21 Copynumber: 4.0 Consensus size: 20
1124899 ACATAATAGA
1124909 AAAAAAGAGATACAAAAAATG
1 AAAAAA-AGATACAAAAAATG
*
1124930 AAAAAAAGATAACAAATAA--
1 AAAAAAAGAT-ACAAAAAATG
* * *
1124949 AAATAAATATA-ACAAAAATA
1 AAAAAAAGATACA-AAAAATG
*
1124969 AAAAAAATATACCAAAAAATG
1 AAAAAAAGATA-CAAAAAATG
1124990 TAGCTAAGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
17 1 0.02
18 5 0.10
19 8 0.17
20 14 0.29
21 19 0.40
22 1 0.02
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.14
Consensus pattern (20 bp):
AAAAAAAGATACAAAAAATG
Found at i:1124962 original size:19 final size:18
Alignment explanation
Indices: 1124925--1124984 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
1124915 GAGATACAAA
* *
1124925 AAATGAAAAAAAGATAAC
1 AAATAAAAAAAATATAAC
1124943 AAATAAAAATAAATATAAC
1 AAATAAAAA-AAATATAAC
*
1124962 AAAAATAAAAAAAATATACC
1 --AAATAAAAAAAATATAAC
1124982 AAA
1 AAA
1124985 AAATGTAGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 11 0.31
19 8 0.22
20 8 0.22
21 9 0.25
ACGTcount: A:0.75, C:0.07, G:0.03, T:0.15
Consensus pattern (18 bp):
AAATAAAAAAAATATAAC
Found at i:1124988 original size:21 final size:21
Alignment explanation
Indices: 1124923--1124986 Score: 73
Period size: 20 Copynumber: 3.2 Consensus size: 21
1124913 AAGAGATACA
* *
1124923 AAAAATGAAAA-AAAGATAAC
1 AAAAATAAAAATAAATATAAC
1124943 --AAATAAAAATAAATATAAC
1 AAAAATAAAAATAAATATAAC
*
1124962 AAAAATAAAAA-AAATATACC
1 AAAAATAAAAATAAATATAAC
1124982 AAAAA
1 AAAAA
1124987 ATGTAGCTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
18 8 0.21
19 8 0.21
20 13 0.34
21 9 0.24
ACGTcount: A:0.77, C:0.06, G:0.03, T:0.14
Consensus pattern (21 bp):
AAAAATAAAAATAAATATAAC
Found at i:1125094 original size:30 final size:30
Alignment explanation
Indices: 1125038--1125136 Score: 85
Period size: 32 Copynumber: 3.2 Consensus size: 30
1125028 AATTAACATG
*
1125038 AAAATGAAACAAAATAAAAT-ATAAAACCCTAA
1 AAAAT-AAA-AAAAT-AAATGAAAAAACCCTAA
*
1125070 AAAATAAAAAAATAAATGAAAAAACCATATAA
1 AAAATAAAAAAATAAATGAAAAAACC--CTAA
* * *
1125102 AAAATAAGAAAGTAAA-GAAAAAACCCCCAA
1 AAAATAAAAAAATAAATGAAAAAA-CCCTAA
1125132 AAAAT
1 AAAAT
1125137 TAACTAAATT
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
29 4 0.07
30 19 0.33
31 10 0.18
32 24 0.42
ACGTcount: A:0.71, C:0.11, G:0.05, T:0.13
Consensus pattern (30 bp):
AAAATAAAAAAATAAATGAAAAAACCCTAA
Found at i:1125122 original size:31 final size:32
Alignment explanation
Indices: 1125067--1125126 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
1125057 TATAAAACCC
1125067 TAAAAAATAAAAAAATAAATGAAAAAACCATA
1 TAAAAAATAAAAAAATAAATGAAAAAACCATA
* *
1125099 TAAAAAATAAGAAAGTAAA-GAAAAAACC
1 TAAAAAATAAAAAAATAAATGAAAAAACC
1125127 CCCAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 9 0.35
32 17 0.65
ACGTcount: A:0.73, C:0.07, G:0.07, T:0.13
Consensus pattern (32 bp):
TAAAAAATAAAAAAATAAATGAAAAAACCATA
Found at i:1125135 original size:31 final size:32
Alignment explanation
Indices: 1125038--1125126 Score: 87
Period size: 32 Copynumber: 2.8 Consensus size: 32
1125028 AATTAACATG
*
1125038 AAAATGAAACAAAATAAAAT-ATAAAACC-C-TAA
1 AAAAT-AAA-AAAAT-AAATGAAAAAACCACATAA
*
1125070 AAAATAAAAAAATAAATGAAAAAACCATATAA
1 AAAATAAAAAAATAAATGAAAAAACCACATAA
* *
1125102 AAAATAAGAAAGTAAA-GAAAAAACC
1 AAAATAAAAAAATAAATGAAAAAACC
1125127 CCCAAAAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
29 4 0.08
30 12 0.24
31 12 0.24
32 22 0.44
ACGTcount: A:0.72, C:0.09, G:0.06, T:0.13
Consensus pattern (32 bp):
AAAATAAAAAAATAAATGAAAAAACCACATAA
Found at i:1127012 original size:36 final size:36
Alignment explanation
Indices: 1126971--1127043 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
1126961 TTCATGCCAA
1126971 AGGCATTTAACCTTTCATAAAACTTGCATTATTGGC
1 AGGCATTTAACCTTTCATAAAACTTGCATTATTGGC
*
1127007 AGGCATTTAACCTTTCATATAACTTGCATTATTGGC
1 AGGCATTTAACCTTTCATAAAACTTGCATTATTGGC
1127043 A
1 A
1127044 ACTTTCTGCC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (36 bp):
AGGCATTTAACCTTTCATAAAACTTGCATTATTGGC
Found at i:1127103 original size:81 final size:81
Alignment explanation
Indices: 1127011--1127649 Score: 864
Period size: 81 Copynumber: 7.9 Consensus size: 81
1127001 ATTGGCAGGC
* * * * * ** **
1127011 ATTTAACCTTTCATATAACTTGCATTATTGGCAACTTTCTGCCAAATGCACAGTTAGGCAATTAA
1 ATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTATCAAATGCACAACTAGGCAATTAA
*
1127076 TATTTTACTCAAAGGT
66 TCTTTTACTCAAAGGT
* * * * * *
1127092 ATTTAACCTTTCATCTAACTGGCATGATTGATACCTTTCTGTCAAATGCATAGCTAAGCAATTAG
1 ATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTATCAAATGCACAACTAGGCAATTAA
1127157 TCTTTTACTCAAAGGT
66 TCTTTTACTCAAAGGT
* *
1127173 ATTTAACCTTTCATCTAACTGGCATGATTGACATCTTTCTATCAAATGCACAACTAGGCAATTAG
1 ATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTATCAAATGCACAACTAGGCAATTAA
*
1127238 TCTTTTTCTCAAAGGT
66 TCTTTTACTCAAAGGT
* * * * * * *
1127254 GTTTAACCTTTCATGTAATTGACATGATTGGCACCTTTCTATCAAATGCACAGCTAGACAATTAA
1 ATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTATCAAATGCACAACTAGGCAATTAA
1127319 TCTTTTACTCAAAGGT
66 TCTTTTACTCAAAGGT
* * *
1127335 ATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTATGTCAAATGCACAACTAGGCAATTAA
1 ATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTATCAAATGCACAACTAGGCAATTAA
*
1127400 TCTTTTACTCAGAGGT
66 TCTTTTACTCAAAGGT
** * * * * *
1127416 ATTTAACCTTTCATCTAACTAACATGATTGACACCTTTATGTCAAATGGACAGCTAGGCAATTAG
1 ATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTATCAAATGCACAACTAGGCAATTAA
1127481 TCTTTTACTCAAAGGT
66 TCTTTTACTCAAAGGT
* * * * *
1127497 ATTCAACATTTCATCTAACTGGCATGGTTGACACCTTTCTATCAAATGCATAACTAGGCAATTAG
1 ATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTATCAAATGCACAACTAGGCAATTAA
1127562 TCTTTTACTCAAAGGT
66 TCTTTTACTCAAAGGT
* * *
1127578 ATTTAACCTTTCATCTAACTGGCATGATTGACACATTTTTATCAAATGCACAACTAAGCAATTAA
1 ATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTATCAAATGCACAACTAGGCAATTAA
*
1127643 TATTTTA
66 TCTTTTA
1127650 TTTTAAAACA
Statistics
Matches: 492, Mismatches: 66, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 492 1.00
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.36
Consensus pattern (81 bp):
ATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTATCAAATGCACAACTAGGCAATTAA
TCTTTTACTCAAAGGT
Found at i:1128194 original size:94 final size:95
Alignment explanation
Indices: 1128057--1128237 Score: 276
Period size: 94 Copynumber: 1.9 Consensus size: 95
1128047 ACCATGGTAT
* * * * *
1128057 CGATACTTCTATATTGTGGTACCAATACTCCCTTGCAGTATCGATACCATTTCTACATTAT-GTA
1 CGATACTTCTATACTATGGTACAAATACTCCCTTGCAGTATCGATACCATTTCGACATTATGGAA
*
1128121 TCCATGGTATCGATACTTTCCTCCTAGTAC
66 TCCATGATATCGATACTTTCCTCCTAGTAC
*
1128151 CGATACTTCTATACTATGGTACAAATACTCCCATT-CAGTATCGATACCATTTCGACATTCTGGA
1 CGATACTTCTATACTATGGTACAAATACTCCC-TTGCAGTATCGATACCATTTCGACATTATGGA
1128215 ATCCATGATATCGATACTTTCCT
65 ATCCATGATATCGATACTTTCCT
1128238 TTTTTGTATC
Statistics
Matches: 78, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
94 53 0.68
95 25 0.32
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.36
Consensus pattern (95 bp):
CGATACTTCTATACTATGGTACAAATACTCCCTTGCAGTATCGATACCATTTCGACATTATGGAA
TCCATGATATCGATACTTTCCTCCTAGTAC
Found at i:1130079 original size:10 final size:10
Alignment explanation
Indices: 1130064--1130089 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1130054 TTGCTATTTT
1130064 AAAAAAAACA
1 AAAAAAAACA
1130074 AAAAAAAACA
1 AAAAAAAACA
1130084 AAAAAA
1 AAAAAA
1130090 GCCGAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:1130107 original size:17 final size:17
Alignment explanation
Indices: 1130076--1130113 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
1130066 AAAAAACAAA
1130076 AAAAAACAAAAAAAGCC
1 AAAAAACAAAAAAAGCC
1130093 GAAAAAAC-AAAAAAGCC
1 -AAAAAACAAAAAAAGCC
1130110 AAAA
1 AAAA
1130114 TTTCAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 4 0.20
17 9 0.45
18 7 0.35
ACGTcount: A:0.76, C:0.16, G:0.08, T:0.00
Consensus pattern (17 bp):
AAAAAACAAAAAAAGCC
Found at i:1137089 original size:5 final size:5
Alignment explanation
Indices: 1137079--1137104 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1137069 TATTCAACGG
1137079 TCCGA TCCGA TCCGA TCCGA TCCGA T
1 TCCGA TCCGA TCCGA TCCGA TCCGA T
1137105 AATTCTCCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.38, G:0.19, T:0.23
Consensus pattern (5 bp):
TCCGA
Found at i:1139771 original size:163 final size:164
Alignment explanation
Indices: 1139499--1139810 Score: 450
Period size: 163 Copynumber: 1.9 Consensus size: 164
1139489 TATTGCTTTA
* **
1139499 GTTCTTATGAAAAGATCTTGGACTTTTCATTCAACTTTCTAGTTCATATATTAAAACCCTGTTGT
1 GTTCTTATGAAAAGATCTTGGACTTTTCATGCAACTTTCTAGTTCATATATTAAAACCCTGTCAT
* ** * *
1139564 TATATGTGATTATGTATTCTGGACTATGATGAAGATCGAAAGCTTTCATTCTTTGTGTTTTCTGA
66 TATA-GTGATTATGTATTCAGGACTATGATGAAGATCGAAAGCTTTCATTCTCGGAGTTCTCTGA
1139629 ATTAATTAATGCTTTTGGCGATAGATTGTCATCTT
130 ATTAATTAATGCTTTTGGCGATAGATTGTCATCTT
* * * *
1139664 GTTCTTATGACATGATCTTGTGGACTTTTCATGCAACTTTCTAGTTCATGTATT-AAA-GCTGTC
1 GTTCTTATGAAAAGATC-T-TGGACTTTTCATGCAACTTTCTAGTTCATATATTAAAACCCTGTC
*
1139727 ATTATA-TGATTATGTATTCAGGACTATGATGAAGATGGAAAGCTTTCATTCTCGGAGTTCTCTG
64 ATTATAGTGATTATGTATTCAGGACTATGATGAAGATCGAAAGCTTTCATTCTCGGAGTTCTCTG
*
1139791 AGTTAATTAATGCTTTTGGC
129 AATTAATTAATGCTTTTGGC
1139811 AATAAAGTGG
Statistics
Matches: 131, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
163 71 0.54
165 24 0.18
166 4 0.03
167 32 0.24
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.43
Consensus pattern (164 bp):
GTTCTTATGAAAAGATCTTGGACTTTTCATGCAACTTTCTAGTTCATATATTAAAACCCTGTCAT
TATAGTGATTATGTATTCAGGACTATGATGAAGATCGAAAGCTTTCATTCTCGGAGTTCTCTGAA
TTAATTAATGCTTTTGGCGATAGATTGTCATCTT
Found at i:1142416 original size:20 final size:21
Alignment explanation
Indices: 1142377--1142417 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1142367 CAGTCTGAAT
1142377 GCTGAACGGTTCAACATTCAGC
1 GCTGAACGGTTC-ACATTCAGC
*
1142399 GCTGAATGGTTC-CATTCAG
1 GCTGAACGGTTCACATTCAG
1142418 AGCCAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (21 bp):
GCTGAACGGTTCACATTCAGC
Done.