Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 6 of 259
Found at i:1580359 original size:12 final size:12
Alignment explanation
Indices: 1580340--1580418 Score: 72
Period size: 12 Copynumber: 6.6 Consensus size: 12
1580330 GCGTCAACAG
*
1580340 TAATAATAGTAA
1 TAATAATACTAA
*
1580352 TTATAATACTAA
1 TAATAATACTAA
*
1580364 TACTAATACTAA
1 TAATAATACTAA
1580376 TAATAAATA-TAA
1 TAAT-AATACTAA
* *
1580388 TAATAGTAGTAA
1 TAATAATACTAA
*
1580400 AAATAAATAC-AA
1 TAAT-AATACTAA
1580412 TAATAAT
1 TAATAAT
1580419 CATAAAATTA
Statistics
Matches: 54, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
11 6 0.11
12 41 0.76
13 7 0.13
ACGTcount: A:0.58, C:0.05, G:0.04, T:0.33
Consensus pattern (12 bp):
TAATAATACTAA
Found at i:1580381 original size:3 final size:3
Alignment explanation
Indices: 1580340--1580482 Score: 53
Period size: 3 Copynumber: 47.0 Consensus size: 3
1580330 GCGTCAACAG
* * * * *
1580340 TAA TAA TAG TAA TTA TAA TAC TAA TAC TAA TAC TAA TAA TAA -ATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
* * * * *
1580385 TAA TAA TAG TAG TAA AAA TAA -ATA CAA TAA TAA TCA TAA -AA TTAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA -TAA
** * * *
1580430 T-A TAAA TAA TGTG TACA TGAA AAA TAA TAA TGA T-A TGA TAA TAA TAA
1 TAA T-AA TAA T-AA TA-A T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1580477 TAA TAA
1 TAA TAA
1580483 AACGAAAAAA
Statistics
Matches: 103, Mismatches: 25, Indels: 24
0.68 0.16 0.16
Matches are distributed among these distances:
2 8 0.08
3 85 0.83
4 9 0.09
5 1 0.01
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1580424 original size:24 final size:23
Alignment explanation
Indices: 1580340--1580439 Score: 69
Period size: 24 Copynumber: 4.2 Consensus size: 23
1580330 GCGTCAACAG
**
1580340 TAATAATAGTAATTAT-AATACTAA
1 TAATAATAGTAAAAATAAATA--AA
* * *
1580364 TACTAATACTAATAATAAATATAA
1 TAATAATAGTAAAAATAAATA-AA
*
1580388 TAATAGTAGTAAAAATAAATACAA
1 TAATAATAGTAAAAATAAATA-AA
*
1580412 TAATAATCA-TAAAATTAATATAAA
1 TAATAAT-AGTAAAAATAA-ATAAA
1580436 TAAT
1 TAAT
1580440 GTGTACATGA
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
24 55 0.87
25 8 0.13
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (23 bp):
TAATAATAGTAAAAATAAATAAA
Found at i:1588586 original size:15 final size:14
Alignment explanation
Indices: 1588546--1588588 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
1588536 ATTTGTTAAA
*
1588546 ATTTAATTATTTGT
1 ATTTAATTATTTTT
*
1588560 ATTTATTATATTTTT
1 ATTTAAT-TATTTTT
1588575 ATTTGAATTATTTT
1 ATTT-AATTATTTT
1588589 GAATATTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 6 0.25
15 16 0.67
16 2 0.08
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (14 bp):
ATTTAATTATTTTT
Found at i:1590358 original size:20 final size:19
Alignment explanation
Indices: 1590333--1590370 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1590323 TACAAAATAA
*
1590333 TTCAAAATAATTTTTAAAAT
1 TTCAAAAT-ATTTATAAAAT
1590353 TTCAAAATATTTATAAAA
1 TTCAAAATATTTATAAAA
1590371 ACTCCAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
TTCAAAATATTTATAAAAT
Found at i:1590371 original size:20 final size:20
Alignment explanation
Indices: 1590333--1590371 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1590323 TACAAAATAA
*
1590333 TTCAAAATAATTTTTAAAAT
1 TTCAAAATAATTTTAAAAAT
1590353 TTCAAAAT-ATTTATAAAAA
1 TTCAAAATAATTT-TAAAAA
1590372 CTCCAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
TTCAAAATAATTTTAAAAAT
Found at i:1593088 original size:3 final size:3
Alignment explanation
Indices: 1593075--1593402 Score: 131
Period size: 3 Copynumber: 107.0 Consensus size: 3
1593065 AATGGGTAAA
* *
1593075 AAT AA- AAT AAT AAT AAT -AT AAT AGT AAT AAT AAT GAT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
1593120 AGT AAT AAAT CAT AAT GAT AAT AAT GAT GAT AAT -AT AAGT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT
* * * * *
1593166 -AT AAGT AAAT ACAG AGAG AAT -AT GTAT AAT AA- CAT AAT AAT ACCT
1 AAT AA-T -AAT A-AT A-AT AAT AAT -AAT AAT AAT AAT AAT AAT A-AT
* * * * *
1593211 ATAT AA- AATT AATT AACCT AAT AAC AA- GAT GAT AAT ACT AGT AAT
1 A-AT AAT AA-T AA-T AA--T AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
1593256 AGT AAT AAGGT GGAA- AA- AAT AAT AAT AAT AAT -AT ATT AAT AAG AAT
1 AAT AAT AA--T --AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * * *
1593302 AAA AAT ATAT ATT TAT AAT AAC GAT AAAT AAT TAT AAT AAT GAT TAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT
*
1593349 GAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
1593397 AGT AAT
1 AAT AAT
1593403 GGTAATAGCA
Statistics
Matches: 247, Mismatches: 52, Indels: 52
0.70 0.15 0.15
Matches are distributed among these distances:
2 21 0.09
3 188 0.76
4 30 0.12
5 6 0.02
7 2 0.01
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1593134 original size:21 final size:23
Alignment explanation
Indices: 1593080--1593142 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
1593070 GTAAAAATAA
*
1593080 AATAATAATAATATAATAGTAAT
1 AATAATCATAATATAATAGTAAT
*
1593103 AATAATGATAATAATAA-AGTAAT
1 AATAATCATAAT-ATAATAGTAAT
1593126 -A-AATCATAATGATAATA
1 AATAATCATAAT-ATAATA
1593143 ATGATGATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 12 0.34
22 2 0.06
23 17 0.49
24 4 0.11
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (23 bp):
AATAATCATAATATAATAGTAAT
Found at i:1593407 original size:6 final size:6
Alignment explanation
Indices: 1593351--1593420 Score: 50
Period size: 6 Copynumber: 11.3 Consensus size: 6
1593341 ATGATTATGA
* * * * * * *
1593351 TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAATAG
1 TAATAG TAATAG TAATAG TAATAG TAATAG TAATAG TAATAG TAATAG
*
1593399 TAATGG TAATAG CATAATAG TA
1 TAATAG TAATAG --TAATAG TA
1593421 TTAGAAATAT
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
6 53 0.90
8 6 0.10
ACGTcount: A:0.59, C:0.01, G:0.07, T:0.33
Consensus pattern (6 bp):
TAATAG
Found at i:1593677 original size:20 final size:21
Alignment explanation
Indices: 1593639--1593690 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
1593629 AACAATAAAA
1593639 ATACA-ATAT-TAAAAGATGT
1 ATACATATATATAAAAGATGT
*
1593658 ATATATATATATAAAA-ATGT
1 ATACATATATATAAAAGATGT
1593678 ATACATA-ATATAA
1 ATACATATATATAA
1593691 TATTAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 10 0.34
20 14 0.48
21 5 0.17
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.35
Consensus pattern (21 bp):
ATACATATATATAAAAGATGT
Found at i:1593698 original size:24 final size:25
Alignment explanation
Indices: 1593660--1593795 Score: 91
Period size: 24 Copynumber: 5.4 Consensus size: 25
1593650 AAAGATGTAT
*
1593660 ATATATATATAAAAATGTATACATA
1 ATATATATATAAAAATATATACATA
* *
1593685 ATATA-ATATTAAAATATTTACATA
1 ATATATATATAAAAATATATACATA
* * *
1593709 GTATATACATAATAATAATAATA-ATA
1 ATATATATATAAAAAT-AT-ATACATA
*
1593735 ACTATTAATATTATATAAATATATACAT-
1 A-TA-T-ATA-TATAAAAATATATACATA
** *
1593763 ATATCCAT-TAAAGATATATACATA
1 ATATATATATAAAAATATATACATA
*
1593787 AGATATATA
1 ATATATATA
1593796 AATATATAAA
Statistics
Matches: 82, Mismatches: 19, Indels: 20
0.68 0.16 0.17
Matches are distributed among these distances:
23 13 0.16
24 26 0.32
25 13 0.16
26 6 0.07
27 6 0.07
28 5 0.06
29 7 0.09
30 6 0.07
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.38
Consensus pattern (25 bp):
ATATATATATAAAAATATATACATA
Found at i:1593766 original size:21 final size:21
Alignment explanation
Indices: 1593742--1593808 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
1593732 ATAACTATTA
1593742 ATATTATATAAATATATACAT
1 ATATTATATAAATATATACAT
*
1593763 ATATCCAT-TAAAGATATATACAT
1 ATAT-TATAT-AA-ATATATACAT
* *
1593786 A-AGATATATAAATATATAAAT
1 ATA-TTATATAAATATATACAT
1593807 AT
1 AT
1593809 TAATTGAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 11
0.71 0.08 0.22
Matches are distributed among these distances:
21 15 0.42
22 9 0.25
23 12 0.33
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (21 bp):
ATATTATATAAATATATACAT
Found at i:1595277 original size:20 final size:22
Alignment explanation
Indices: 1595244--1595292 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
1595234 AAGAATACTA
* *
1595244 TAATAATGATAATAT-GT-TAG
1 TAATAATAACAATATAGTATAG
1595264 TAATAATAACAATATAGTAATAG
1 TAATAATAACAATATAGT-ATAG
1595287 TAATAA
1 TAATAA
1595293 AAATAGTACT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 13 0.54
21 2 0.08
23 9 0.38
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.35
Consensus pattern (22 bp):
TAATAATAACAATATAGTATAG
Found at i:1595446 original size:3 final size:3
Alignment explanation
Indices: 1595425--1595512 Score: 79
Period size: 3 Copynumber: 28.0 Consensus size: 3
1595415 TAATGCTAAG
* *
1595425 ATA ATG ATA ATA GTA ATA ATA ATA ATA ATA ATA ATA ATA ATTCA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-T-A ATA
* * *
1595472 ATTCA ATA ATA GTA ATA ATG ACA ATA ATA GA-A ATA ATA ATA
1 A-T-A ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA
1595513 GTGTTTGAAT
Statistics
Matches: 69, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
2 1 0.01
3 59 0.86
4 5 0.07
5 4 0.06
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1600640 original size:5 final size:5
Alignment explanation
Indices: 1600630--1600661 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
1600620 TTGTGTGTTC
1600630 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1600662 TCACAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:1600644 original size:9 final size:9
Alignment explanation
Indices: 1600630--1600660 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
1600620 TTGTGTGTTC
1600630 TTTATTTTA
1 TTTATTTTA
1600639 TTTATTTTA
1 TTTATTTTA
1600648 TTTTATTTTA
1 -TTTATTTTA
1600658 TTT
1 TTT
1600661 TTCACAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:1605075 original size:5 final size:5
Alignment explanation
Indices: 1605061--1605092 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
1605051 TTGTGTGTTC
1605061 TTTA- TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1605093 TCACACAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:1605997 original size:19 final size:19
Alignment explanation
Indices: 1605962--1605999 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1605952 TGTTTTTTCC
*
1605962 TTCATTTTTTTTAATTTAT
1 TTCATTTTATTTAATTTAT
1605981 TTCATTTTAATTT-ATTTAT
1 TTCATTTT-ATTTAATTTAT
1606000 ATATTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (19 bp):
TTCATTTTATTTAATTTAT
Found at i:1607427 original size:367 final size:367
Alignment explanation
Indices: 1606953--1608059 Score: 2205
Period size: 367 Copynumber: 3.0 Consensus size: 367
1606943 CTCCATTCCC
1606953 GAAAGGAAGAACATGAATTCTTTTTTCTTTCCGCAGGGACCAAGAGATTGGATTTAGCCATAAGA
1 GAAAGGAAGAACATGAATTCTTTTTTCTTTCCGCAGGGACCAAGAGATTGGATTTAGCCATAAGA
1607018 AGAATGCTTGGCTAATAAATAATTCATTTATTGGTCTTCGACCTCCTCAGTCACTACGAACGCCC
66 AGAATGCTTGGCTAATAAATAATTCATTTATTGGTCTTCGACCTCCTCAGTCACTACGAACGCCC
1607083 TCGATCACTGTAATGGGATATGTCTATTTATCTATCTCTTGACTCGAAATGGGAGCAAGTTTGAA
131 TCGATCACTGTAATGGGATATGTCTATTTATCTATCTCTTGACTCGAAATGGGAGCAAGTTTGAA
1607148 AAAGATCTTAGAGTGTTTAGGGTTGGGCCAAGAGAGTCTCTTAACACCCTCTTTTTGTTTTTTCC
196 AAAGATCTTAGAGTGTTTAGGGTTGGGCCAAGAGAGTCTCTTAACACCCTCTTTTTGTTTTTTCC
1607213 CATCAGAGTTATTTCTTATTTCACAAATACTTGCCATGGTAAGGAAGAATGGGGGAACAAGCAAA
261 CATCAGAGTTATTTCTTATTTCACAAATACTTGCCATGGTAAGGAAGAATGGGGGAACAAGCAAA
1607278 CTTGAAGAGCACAATACAATGGAAAGTTGTATGCTGTGTTTG
326 CTTGAAGAGCACAATACAATGGAAAGTTGTATGCTGTGTTTG
1607320 GAAAGGAAGAACATGAATTCTTTTTTCTTTCCGCAGGGACCAAGAGATTGGATTTAGCCATAAGA
1 GAAAGGAAGAACATGAATTCTTTTTTCTTTCCGCAGGGACCAAGAGATTGGATTTAGCCATAAGA
1607385 AGAATGCTTGGCTAATAAATAATTCATTTATTGGTCTTCGACCTCCTCAGTCACTACGAACGCCC
66 AGAATGCTTGGCTAATAAATAATTCATTTATTGGTCTTCGACCTCCTCAGTCACTACGAACGCCC
1607450 TCGATCACTGTAATGGGATATGTCTATTTATCTATCTCTTGACTCGAAATGGGAGCAAGTTTGAA
131 TCGATCACTGTAATGGGATATGTCTATTTATCTATCTCTTGACTCGAAATGGGAGCAAGTTTGAA
1607515 AAAGATCTTAGAGTGTTTAGGGTTGGGCCAAGAGAGTCTCTTAACACCCTCTTTTTGTTTTTTCC
196 AAAGATCTTAGAGTGTTTAGGGTTGGGCCAAGAGAGTCTCTTAACACCCTCTTTTTGTTTTTTCC
1607580 CATCAGAGTTATTTCTTATTTCACAAATACTTGCCATGGTAAGGAAGAATGGGGGAACAAGCAAA
261 CATCAGAGTTATTTCTTATTTCACAAATACTTGCCATGGTAAGGAAGAATGGGGGAACAAGCAAA
1607645 CTTGAAGAGCACAATACAATGGAAAGTTGTATGCTGTGTTTG
326 CTTGAAGAGCACAATACAATGGAAAGTTGTATGCTGTGTTTG
1607687 GAAAGGAAGAACATGAATTCTTTTTTCTTTCCGCAGGGACCAAGAGATTGGATTTAGCCATAAGA
1 GAAAGGAAGAACATGAATTCTTTTTTCTTTCCGCAGGGACCAAGAGATTGGATTTAGCCATAAGA
1607752 AGAATGCTTGGCTAATAAATAATTCATTTATTGGTCTTCGACCTCCTCAGTCACTACGAACGCCC
66 AGAATGCTTGGCTAATAAATAATTCATTTATTGGTCTTCGACCTCCTCAGTCACTACGAACGCCC
1607817 TCGATCACTGTAATGGGATATGTCTATTTATCTATCTCTTGACTCGAAATGGGAGCAAGTTTGAA
131 TCGATCACTGTAATGGGATATGTCTATTTATCTATCTCTTGACTCGAAATGGGAGCAAGTTTGAA
1607882 AAAGATCTTAGAGTGTTTAGGGTTGGGCCAAGAGAGTCTCTTAACACCCTCTTTTTGTTTTTTCC
196 AAAGATCTTAGAGTGTTTAGGGTTGGGCCAAGAGAGTCTCTTAACACCCTCTTTTTGTTTTTTCC
1607947 CATCAGAGTTATTTCTTATTTCACAAATACTTGCCATGGTAAGGAAGAATGGGGGAACAAGCAAA
261 CATCAGAGTTATTTCTTATTTCACAAATACTTGCCATGGTAAGGAAGAATGGGGGAACAAGCAAA
1608012 CTTGAAGAGCACAATACAATGGAAAGTTGTATGCTGTGTTTG
326 CTTGAAGAGCACAATACAATGGAAAGTTGTATGCTGTGTTTG
1608054 AGAAAG
1 -GAAAG
1608060 ATGAATCACT
Statistics
Matches: 739, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
367 734 0.99
368 5 0.01
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.31
Consensus pattern (367 bp):
GAAAGGAAGAACATGAATTCTTTTTTCTTTCCGCAGGGACCAAGAGATTGGATTTAGCCATAAGA
AGAATGCTTGGCTAATAAATAATTCATTTATTGGTCTTCGACCTCCTCAGTCACTACGAACGCCC
TCGATCACTGTAATGGGATATGTCTATTTATCTATCTCTTGACTCGAAATGGGAGCAAGTTTGAA
AAAGATCTTAGAGTGTTTAGGGTTGGGCCAAGAGAGTCTCTTAACACCCTCTTTTTGTTTTTTCC
CATCAGAGTTATTTCTTATTTCACAAATACTTGCCATGGTAAGGAAGAATGGGGGAACAAGCAAA
CTTGAAGAGCACAATACAATGGAAAGTTGTATGCTGTGTTTG
Found at i:1616055 original size:5 final size:5
Alignment explanation
Indices: 1616047--1616072 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1616037 ACACTATGGT
1616047 AATAC AATAC AATAC AATAC AATAC A
1 AATAC AATAC AATAC AATAC AATAC A
1616073 TTATTTAGGT
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:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAC
Found at i:1616326 original size:38 final size:38
Alignment explanation
Indices: 1616268--1616344 Score: 120
Period size: 38 Copynumber: 2.0 Consensus size: 38
1616258 AATTGCCCCT
*
1616268 TTCTATTAAAAATTACATTCATTTCTACTATTAAAAAC
1 TTCTATTAAAAATTACATTCACTTCTACTATTAAAAAC
*
1616306 TTCTCTTAAAAATTTA-ATTCACTTCTACTATTAAAAAC
1 TTCTATTAAAAA-TTACATTCACTTCTACTATTAAAAAC
1616344 T
1 T
1616345 GCCATGACTG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 33 0.92
39 3 0.08
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (38 bp):
TTCTATTAAAAATTACATTCACTTCTACTATTAAAAAC
Found at i:1628894 original size:13 final size:13
Alignment explanation
Indices: 1628876--1628903 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1628866 AAATTCTCTT
1628876 GATAGACAAGCAA
1 GATAGACAAGCAA
1628889 GATAGACAAGCAA
1 GATAGACAAGCAA
1628902 GA
1 GA
1628904 GGTGGAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.14, G:0.25, T:0.07
Consensus pattern (13 bp):
GATAGACAAGCAA
Found at i:1631036 original size:24 final size:25
Alignment explanation
Indices: 1631009--1631060 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
1630999 AATATTTTCA
*
1631009 AAAATTAAATAT-TTAATTAATAAT
1 AAAATTAAATATGATAATTAATAAT
1631033 AAAATTAAATATGATAATTAATAAT
1 AAAATTAAATATGATAATTAATAAT
1631058 AAA
1 AAA
1631061 TATAATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 12 0.46
25 14 0.54
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (25 bp):
AAAATTAAATATGATAATTAATAAT
Found at i:1631042 original size:29 final size:29
Alignment explanation
Indices: 1631009--1631078 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
1630999 AATATTTTCA
1631009 AAAATTAAATATTTAATTAAT-AATAAAAT
1 AAAATTAAATATTTAA-TAATAAATAAAAT
* * * *
1631038 TAAA-TATGATAATTAATAATAAATATAAT
1 AAAATTA-AATATTTAATAATAAATAAAAT
1631067 AAAATTAAATAT
1 AAAATTAAATAT
1631079 GTTTAAAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
28 6 0.19
29 23 0.74
30 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (29 bp):
AAAATTAAATATTTAATAATAAATAAAAT
Found at i:1631075 original size:15 final size:15
Alignment explanation
Indices: 1631028--1631078 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 15
1631018 TATTTAATTA
1631028 ATAATAAAATTAAAT
1 ATAATAAAATTAAAT
*
1631043 ATGATAATTAATAATAAAT
1 ATAATAA--AAT--TAAAT
1631062 ATAATAAAATTAAAT
1 ATAATAAAATTAAAT
1631077 AT
1 AT
1631079 GTTTAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
15 13 0.43
17 6 0.20
19 11 0.37
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (15 bp):
ATAATAAAATTAAAT
Found at i:1638678 original size:20 final size:20
Alignment explanation
Indices: 1638615--1638741 Score: 67
Period size: 20 Copynumber: 6.3 Consensus size: 20
1638605 GCATCACAGA
* *
1638615 TGCATAACAGGAGCACTGAAG
1 TGCA-AACAGGGGCACCGAAG
* *
1638636 TGCAGACAGGGGCA-CAAATG
1 TGCAAACAGGGGCACCGAA-G
*
1638656 TGCAAACAGGGGCACCGTAG
1 TGCAAACAGGGGCACCGAAG
* * ***
1638676 TGCGAACAAGAAAACCGAAG
1 TGCAAACAGGGGCACCGAAG
* ** ** *
1638696 TGTATGCAAAGGCACCGGAG
1 TGCAAACAGGGGCACCGAAG
* *
1638716 TGCAAACAGAGGCAACGAAG
1 TGCAAACAGGGGCACCGAAG
1638736 TGCAAA
1 TGCAAA
1638742 TCTCGTACAA
Statistics
Matches: 76, Mismatches: 28, Indels: 5
0.70 0.26 0.05
Matches are distributed among these distances:
19 2 0.03
20 68 0.89
21 6 0.08
ACGTcount: A:0.39, C:0.20, G:0.31, T:0.10
Consensus pattern (20 bp):
TGCAAACAGGGGCACCGAAG
Found at i:1639122 original size:13 final size:14
Alignment explanation
Indices: 1639098--1639135 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1639088 AGTTTCACTG
1639098 AAAATGACTTTC-GA
1 AAAATGA-TTTCTGA
*
1639112 AAAATGATTTCTGG
1 AAAATGATTTCTGA
1639126 AAAATGATTT
1 AAAATGATTT
1639136 ACTTTTCTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.34
Consensus pattern (14 bp):
AAAATGATTTCTGA
Found at i:1639618 original size:15 final size:15
Alignment explanation
Indices: 1639598--1639663 Score: 55
Period size: 14 Copynumber: 4.3 Consensus size: 15
1639588 ACTACAAAAC
1639598 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
1639613 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
1639632 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
*
1639647 A-TTAATATTAA-AT
1 ATTTATTATTAATAT
1639660 ATTT
1 ATTT
1639664 TCAATAATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
13 3 0.07
14 11 0.26
15 10 0.24
16 1 0.02
17 7 0.17
18 1 0.02
19 9 0.21
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:1639770 original size:22 final size:22
Alignment explanation
Indices: 1639726--1639785 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
1639716 TTAAAATAAA
* *
1639726 ATTAAAAT-ATTAAGTA-ATTT
1 ATTAAAATAATAAATTATATTT
1639746 ATTAAAATAATAAATTATATTT
1 ATTAAAATAATAAATTATATTT
* * *
1639768 ATTATATTAATAAGTTAT
1 ATTAAAATAATAAATTAT
1639786 TATAAGACTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
20 8 0.24
21 6 0.18
22 19 0.58
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (22 bp):
ATTAAAATAATAAATTATATTT
Found at i:1640694 original size:4 final size:4
Alignment explanation
Indices: 1640685--1640716 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
1640675 TATTTTTATT
1640685 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1640717 CTTAGTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:1641788 original size:8 final size:9
Alignment explanation
Indices: 1641760--1641792 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
1641750 ATTCCCGCAA
1641760 AAAAACAGTC
1 AAAAA-AGTC
1641770 AAAAAAGTC
1 AAAAAAGTC
1641779 AAAAAA-TC
1 AAAAAAGTC
1641787 AAAAAA
1 AAAAAA
1641793 AGACGAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.35
9 10 0.43
10 5 0.22
ACGTcount: A:0.73, C:0.12, G:0.06, T:0.09
Consensus pattern (9 bp):
AAAAAAGTC
Found at i:1650985 original size:6 final size:6
Alignment explanation
Indices: 1650976--1651006 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
1650966 AATTCTGCTC
1650976 CTTTTA CTTTTA CTTTTA CTTTTA CTTTTA C
1 CTTTTA CTTTTA CTTTTA CTTTTA CTTTTA C
1651007 ACACTGTGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.19, G:0.00, T:0.65
Consensus pattern (6 bp):
CTTTTA
Found at i:1653322 original size:11 final size:10
Alignment explanation
Indices: 1653295--1653365 Score: 53
Period size: 10 Copynumber: 7.2 Consensus size: 10
1653285 GACTAAAAAA
1653295 AATATTT-A-
1 AATATTTAAT
1653303 AATAATTTAAT
1 AAT-ATTTAAT
*
1653314 AATATTTTAT
1 AATATTTAAT
*
1653324 AACTTTTTAA-
1 AA-TATTTAAT
1653334 AA-ATTTAAT
1 AATATTTAAT
1653343 GAA-ATTTAAT
1 -AATATTTAAT
1653353 AATAATTTAAT
1 AAT-ATTTAAT
1653364 AA
1 AA
1653366 GGTTACATGT
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
8 8 0.16
9 6 0.12
10 20 0.39
11 17 0.33
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (10 bp):
AATATTTAAT
Found at i:1653361 original size:29 final size:30
Alignment explanation
Indices: 1653297--1653362 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 30
1653287 CTAAAAAAAA
*
1653297 TATTTAAATAATTTAATAATATTTTATAAC
1 TATTTAAATAATTTAATAATATTTAATAAC
*
1653327 TTTTTAAA-AATTTAATGAA-ATTTAATAA-
1 TATTTAAATAATTTAAT-AATATTTAATAAC
1653355 TAATTTAA
1 T-ATTTAA
1653363 TAAGGTTACA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 1 0.03
29 21 0.68
30 9 0.29
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (30 bp):
TATTTAAATAATTTAATAATATTTAATAAC
Found at i:1654186 original size:3 final size:3
Alignment explanation
Indices: 1654178--1654205 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1654168 AGTGGAGCTG
1654178 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1654206 AGATGATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:1654213 original size:3 final size:3
Alignment explanation
Indices: 1654207--1654237 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1654197 TTCTTCTTCA
1654207 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1654238 GTAACAGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:1654722 original size:3 final size:3
Alignment explanation
Indices: 1654714--1654766 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
1654704 TGAGAAGCCA
* *
1654714 AAG AAG AAG ATG AAG AAA AAG AAG AAG AAG AAG AAG AAG AA- AACG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA-G
1654759 AAG AAG AA
1 AAG AAG AA
1654767 AGTGGAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 40 0.91
4 2 0.05
ACGTcount: A:0.68, C:0.02, G:0.28, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:1668930 original size:46 final size:46
Alignment explanation
Indices: 1668863--1668957 Score: 156
Period size: 46 Copynumber: 2.1 Consensus size: 46
1668853 TCTCCATACC
*
1668863 CTTAATATGTTTCTCTAGAACTTTTAGCCACTAGAGAAAAATGCAT
1 CTTAATATGTTTCTCTAGAACTTTCAGCCACTAGAGAAAAATGCAT
*
1668909 CTTAATATGTTTCTCCT-GAACTTTCAGCCACTAGAGAACAATGCAT
1 CTTAATATGTTTCT-CTAGAACTTTCAGCCACTAGAGAAAAATGCAT
1668955 CTT
1 CTT
1668958 TCTCACCCAA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 44 0.96
47 2 0.04
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.35
Consensus pattern (46 bp):
CTTAATATGTTTCTCTAGAACTTTCAGCCACTAGAGAAAAATGCAT
Found at i:1680727 original size:33 final size:29
Alignment explanation
Indices: 1680690--1680754 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 29
1680680 TATTATATAA
*
1680690 TTATATTAAAATTTTAAAATTAATAATAAATAT
1 TTATA-TAAAATTAT-AAATTAA-AATAAAT-T
*
1680723 TTATATGAAATTATAAATTAAAATAAATT
1 TTATATAAAATTATAAATTAAAATAAATT
1680752 TTA
1 TTA
1680755 AAACATTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 4 0.13
30 7 0.23
31 7 0.23
32 7 0.23
33 5 0.17
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (29 bp):
TTATATAAAATTATAAATTAAAATAAATT
Found at i:1681887 original size:16 final size:14
Alignment explanation
Indices: 1681856--1681894 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
1681846 TTATTTATTA
1681856 AATTAATTTTAATT
1 AATTAATTTTAATT
1681870 AATTAAATTTTCAATT
1 AATT-AATTTT-AATT
*
1681886 AAATAATTT
1 AATTAATTT
1681895 CTTAACTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 4 0.18
15 11 0.50
16 7 0.32
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (14 bp):
AATTAATTTTAATT
Found at i:1692490 original size:21 final size:24
Alignment explanation
Indices: 1692446--1692497 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 24
1692436 TATGTACATA
*
1692446 ACATATACTTAGTAATAATGTTGG
1 ACATATACTTAGTAATAATATTGG
1692470 ACATATAC-TA-T-ATAATATTGG
1 ACATATACTTAGTAATAATATTGG
*
1692491 AAATATA
1 ACATATA
1692498 TACACAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 15 0.58
22 1 0.04
23 2 0.08
24 8 0.31
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.37
Consensus pattern (24 bp):
ACATATACTTAGTAATAATATTGG
Found at i:1692986 original size:26 final size:25
Alignment explanation
Indices: 1692957--1693011 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
1692947 AAATATGCAT
*
1692957 ACAATATTACAAA-ATATATATAACTA
1 ACAATATTA-AAATATATACATAAC-A
1692983 ACAATATTAAAATATATACATAACA
1 ACAATATTAAAATATATACATAACA
1693008 ACAA
1 ACAA
1693012 AAGTATGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 8 0.30
26 19 0.70
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (25 bp):
ACAATATTAAAATATATACATAACA
Found at i:1695407 original size:75 final size:75
Alignment explanation
Indices: 1695284--1695451 Score: 237
Period size: 75 Copynumber: 2.2 Consensus size: 75
1695274 AGTAGAAATT
* * * *
1695284 AAAAACAGAATTTGAAAATACCTCAGCGTGTCCTGAGACTCAACTCACCTCTCGCAATATGAATT
1 AAAAATAGAATTTGAAAATACCTCAGCGTGCCCCGAGACCCAACTCACCTCTCGCAATATGAATT
1695349 GATTTTTTTG
66 GATTTTTTTG
* * * * *
1695359 AAAAATAGAAATTGAAATTACCTCAGCGTGCCCCGAGGCCCAACTCACCTCTCGTAATATGAGTT
1 AAAAATAGAATTTGAAAATACCTCAGCGTGCCCCGAGACCCAACTCACCTCTCGCAATATGAATT
1695424 GATTTTTTTG
66 GATTTTTTTG
* *
1695434 CAAAGTAGAATTTGAAAA
1 AAAAATAGAATTTGAAAA
1695452 ACAGAAATTG
Statistics
Matches: 80, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
75 80 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (75 bp):
AAAAATAGAATTTGAAAATACCTCAGCGTGCCCCGAGACCCAACTCACCTCTCGCAATATGAATT
GATTTTTTTG
Found at i:1695466 original size:89 final size:88
Alignment explanation
Indices: 1695355--1696127 Score: 877
Period size: 89 Copynumber: 8.9 Consensus size: 88
1695345 AATTGATTTT
* * * * * *
1695355 TTTGAAAAATAGAAATTGAAATTACCTCAGCGTGCCCCGAGGCCCAACTCACCTCTCGTAATATG
1 TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
* **
1695420 AGTTGATTTTTTTGCAAAGTAGA-A
66 AGTTGA--TTTTTGAAAAACAGACA
*
1695444 TTTGAAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
**
1695509 AGTTGATTTTTGAAAAGTAGA-A
66 AGTTGATTTTTGAAAAACAGACA
* * * *
1695531 ATTG-AAAACAGAAATTGAAATTACCTCAGCGTGTGAGCC-AATGCTCAACTCACCTCTCGCAAT
1 TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGT---CCTGAGGCTCAACTCACCTCTCGCAAT
* * *
1695594 ATGAGTTGATTTTTGAAAAATATAGA
63 ATGAGTTGATTTTTGAAAAACAGACA
* * *
1695620 TTGGAAAAAACAGAAATTGAAAATACATCAGCGTGTCCTGAGGCTCAACTCACCTCTCACAATAT
1 TTTG-AAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT
*
1695685 GAGTTGA---TTCAAAAACAGACA
65 GAGTTGATTTTTGAAAAACAGACA
* * *
1695706 -TT-AAGAACAAAAATTGAAAATACCTCAGCGTGTCCTAAGGCTCAACTCACCTCTCGCAATATG
1 TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
* * *
1695769 AGTTGATCTTTT-AAAAATATAGA
66 AGTTGAT-TTTTGAAAAACAGACA
*
1695792 TTGGAAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT
1 TTTG-AAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT
*
1695857 GAGTTGA---TTCAAAAACAGACA
65 GAGTTGATTTTTGAAAAACAGACA
*
1695878 -TT-AAGAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1695941 AGTTGATTTTTTG-AAAACATGA-A
66 AGTTGA-TTTTTGAAAAACA-GACA
** * * * * *
1695964 TTAAAAAAATAGAAATTGAAGATACCTCAGTATGTGAGCC-GAGGCTCAACTCACTTCTCGCAAT
1 TTTGAAAAACAGAAATTGAAAATACCTCAG--CGTG-TCCTGAGGCTCAACTCACCTCTCGCAAT
1696028 ATGAGTTGATTTTTG-AAAACAGA-A
63 ATGAGTTGATTTTTGAAAAACAGACA
** * * *
1696052 -TTGAAAAACAGAAATTGAAGTTACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCACAATATG
1 TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1696116 AGTTGACTTTTT
66 AGTTGA-TTTTT
1696128 TTTTCTCTTT
Statistics
Matches: 602, Mismatches: 55, Indels: 57
0.84 0.08 0.08
Matches are distributed among these distances:
83 128 0.21
84 2 0.00
85 39 0.06
86 68 0.11
87 51 0.08
88 72 0.12
89 177 0.29
90 35 0.06
91 30 0.05
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (88 bp):
TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTTTTGAAAAACAGACA
Found at i:1695812 original size:172 final size:168
Alignment explanation
Indices: 1695232--1696127 Score: 1008
Period size: 172 Copynumber: 5.2 Consensus size: 168
1695222 CATGTGACCC
* * * * *
1695232 GAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTTTGAAAAGTAGAAATT--AAAAACAGAAT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-AAAAATATAGATTGAAAAAACAGAAA
* * ****
1695295 TTGAAAATACCTCAGCGTGTCCTGAGACTCAACTCACCTCTCGCAATATGAATTGATT---TTTT
65 TTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCAAAAAC
* * * *
1695357 TG-A--AAAATAGAAATTGAAATTACCTCAGCGTGCCCC
130 AGAATTAAAACAGAAATTGAAATTACCTCAGCGTGTCCT
* * ** *
1695393 GAGGCCCAACTCACCTCTCGTAATATGAGTTGATTTTTTTGCAAA-GTAGAATTTG-AAAAACAG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTAAAAATATAG-A-TTGAAAAAACAG
* *
1695456 AAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
62 AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTC
**
1695521 AAAAGTAGAAATTGAAAACAGAAATTGAAATTACCTCAGCGTGTGAGCC-
124 AAAAACAG-AATT-AAAACAGAAATTGAAATTACCTCAGCGTGT---CCT
* *
1695570 AATGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAGATTGGAAAAAACAGAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-AAAAATATAGATT-GAAAAAACAGAA
* *
1695635 ATTGAAAATACATCAGCGTGTCCTGAGGCTCAACTCACCTCTCACAATATGAGTTGATTCAAAAA
64 ATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCAAAAA
* *
1695700 CAGACATTAAGAACAAAAATTGAAAATACCTCAGCGTGTCCT
129 CAGA-ATTAA-AACAGAAATTGAAATTACCTCAGCGTGTCCT
*
1695742 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATCTTTTAAAAATATAGATTGGAAAAAACAGAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGAT-TTTTAAAAATATAGATT-GAAAAAACAGAA
1695807 ATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCAAAAA
64 ATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCAAAAA
*
1695872 CAGACATTAAGAACAGAAATTGAAAATACCTCAGCGTGTCCT
129 CAGA-ATTAA-AACAGAAATTGAAATTACCTCAGCGTGTCCT
* * * *
1695914 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAT-GAATTAAAAAAATAGAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTAAAAATATAG-ATTGAAAAAACAGAA
* * * * *
1695978 ATTGAAGATACCTCAGTATGTGAGCC-GAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTT
64 ATTGAAAATACCTCAG--CGTG-TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTC
* * *
1696042 GAAAACAGAATTGAAAAACAGAAATTGAAGTTACCTCAGCGTGCCCT
124 AAAAACAGAATT--AAAACAGAAATTGAAATTACCTCAGCGTGTCCT
* *
1696089 GAGGCTCAACTCACTTCTCACAATATGAGTTGACTTTTT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTT
1696128 TTTTCTCTTT
Statistics
Matches: 644, Mismatches: 55, Indels: 58
0.85 0.07 0.08
Matches are distributed among these distances:
161 31 0.05
162 3 0.00
163 7 0.01
164 63 0.10
167 2 0.00
170 2 0.00
171 28 0.04
172 209 0.32
173 43 0.07
174 42 0.07
175 109 0.17
176 7 0.01
177 96 0.15
178 2 0.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (168 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAATATAGATTGAAAAAACAGAAAT
TGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCAAAAACA
GAATTAAAACAGAAATTGAAATTACCTCAGCGTGTCCT
Found at i:1696150 original size:349 final size:343
Alignment explanation
Indices: 1695113--1696129 Score: 1102
Period size: 349 Copynumber: 2.9 Consensus size: 343
1695103 AATAACATAA
* *
1695113 AGAAATTGAAAATAACTCAGTGCGTGATCC-AAGGCTCAACTCACCTCTCGCAATATGAGTTGGT
1 AGAAATTGAAAATACCTCA--GCGTG-TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT-G-
* *** ** * * *** * *
1695177 CTTTTTGAAACTTAATTTGAAAAGTAGGTTTTGAAAGTACCTC-GTCATGTGACCCGAGGCTCAA
61 ATTTCAAAAACAGAAATTGAAAA-CAGAAATTGAAAATACCTCAG-CGTGTG--CCGAGGCTCAA
* * *
1695241 CTCATCTCTCGCAATATGAGTTGATTTTTGAAAAGTAGAAATT-AAAAACAGAATTTGAAAATAC
122 CTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAG-AATTAAAAAACAGAAATTGAAAATAC
* *
1695305 CTCAGCGTGTCCTGAGACTCAACTCACCTCTCGCAATATGAATTGATTTTT---------TTGAA
186 CTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAACAGAATTGAA
* * * *
1695361 AAATAGAAATTGAAATTACCTCAGCGTGCCCCGAGGCCCAACTCACCTCTCGTAATATGAGTTGA
251 AAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
* **
1695426 TTTTTTTGCAAAGTAGAATTTG-AAAAAC
316 TTTTTTTACAATTTA-AATTTGAAAAAAC
*
1695454 AGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 AGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TT
* ** * * *
1695519 TGAAAAGTAGAAATTGAAAACAGAAATTGAAATTACCTCAGCGTGTGAGCCAATGCTCAACTCAC
64 TCAAAAACAGAAATTGAAAACAGAAATTGAAAATACCTCAGCGTGT--GCCGAGGCTCAACTCAC
* *
1695584 CTCTCGCAATATGAGTTGATTTTTGAAAAATATAGATTGGAAAAAACAGAAATTGAAAATACATC
127 CTCTCGCAATATGAGTTGATTTTTGAAAAATAGA-ATT--AAAAAACAGAAATTGAAAATACCTC
* ** *
1695649 AGCGTGTCCTGAGGCTCAACTCACCTCTCACAATATGAGTTGA-TTCAAAAACAGACATT-AAGA
189 AGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAACAGA-ATTGAAAA
* * * * *
1695712 ACAAAAATTGAAAATACCTCAGCGTGTCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATC
253 ACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
* * * * *
1695777 TTTTAAAAATATAGATTGGAAAAAAC
318 TTTTTACAATTTAAATTTGAAAAAAC
1695803 AGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTC
1 AGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTC
*
1695867 AAAAACAGACATT-AAGAACAGAAATTGAAAATACCTCAGCGTGT-CCTGAGGCTCAACTCACCT
66 AAAAACAGAAATTGAA-AACAGAAATTGAAAATACCTCAGCGTGTGCC-GAGGCTCAACTCACCT
* *
1695930 CTCGCAATATGAGTTGATTTTTTGAAAACAT-GAATTAAAAAAATAGAAATTGAAGATACCTCAG
129 CTCGCAATATGAGTTGA-TTTTTGAAAA-ATAGAATT-AAAAAACAGAAATTGAAAATACCTCAG
* * *
1695994 TATGTGAGCC-GAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAACAGAATTGAAA
191 --CGTG-TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-AAAACAGAATTGAAA
* * *
1696058 AACAGAAATTGAAGTTACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCACAATATGAGTTGAC
252 AACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
1696123 TTTTTTT
316 TTTTTTT
1696130 TTCTCTTTTT
Statistics
Matches: 568, Mismatches: 76, Indels: 57
0.81 0.11 0.08
Matches are distributed among these distances:
337 1 0.00
338 69 0.12
339 50 0.09
340 3 0.01
341 79 0.14
343 26 0.05
344 34 0.06
345 47 0.08
346 48 0.08
347 67 0.12
348 9 0.02
349 133 0.23
350 2 0.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (343 bp):
AGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTC
AAAAACAGAAATTGAAAACAGAAATTGAAAATACCTCAGCGTGTGCCGAGGCTCAACTCACCTCT
CGCAATATGAGTTGATTTTTGAAAAATAGAATTAAAAAACAGAAATTGAAAATACCTCAGCGTGT
CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAACAGAATTGAAAAACAGAAAT
TGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTACA
ATTTAAATTTGAAAAAAC
Found at i:1707898 original size:21 final size:24
Alignment explanation
Indices: 1707854--1707905 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 24
1707844 TATGTACATA
*
1707854 ACATATACTTAGTAATAATGTTGG
1 ACATATACTTAGTAATAATATTGG
1707878 ACATATAC-T-GT-ATAATATTGG
1 ACATATACTTAGTAATAATATTGG
*
1707899 AAATATA
1 ACATATA
1707906 TACACAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 15 0.58
22 2 0.08
23 1 0.04
24 8 0.31
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (24 bp):
ACATATACTTAGTAATAATATTGG
Found at i:1709795 original size:12 final size:12
Alignment explanation
Indices: 1709778--1709816 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
1709768 ACTAACAATC
1709778 ATTTATTAATAT
1 ATTTATTAATAT
1709790 ATTTATATAAATAT
1 ATTTAT-T-AATAT
*
1709804 ATTTTTTAATAT
1 ATTTATTAATAT
1709816 A
1 A
1709817 AAATATTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 12 0.50
13 2 0.08
14 10 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTATTAATAT
Found at i:1721205 original size:27 final size:27
Alignment explanation
Indices: 1721164--1721217 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
1721154 TGCTGTTAGC
* *
1721164 CCCAATACCCAGAGGGTCGTGGGCAAT
1 CCCAATACCCAGAGGGTCATGGACAAT
*
1721191 CCCAATACCCTGAGGGTCATGGACAAT
1 CCCAATACCCAGAGGGTCATGGACAAT
1721218 TATTTTACCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.17
Consensus pattern (27 bp):
CCCAATACCCAGAGGGTCATGGACAAT
Found at i:1724624 original size:131 final size:130
Alignment explanation
Indices: 1724479--1724911 Score: 376
Period size: 130 Copynumber: 3.3 Consensus size: 130
1724469 GAAATCACAA
* * * * * * *
1724479 CCAAGCACGATAGGGCATGATTCC-CGAATCGTCAAACACTGA-GTATTGCCTCCGTTTTAAAGG
1 CCAA-CACGTTAGGGCACGATTCCGCGAATCGCCAAACA-TCACATATCGCATCCGTTTTAAA-G
* ** * * *
1724542 ATTTTTAGAAGAGC-CGAGTGAAATTTTGAAGGGATATTTGATTATTTTAAAC-AATCGGGAAAT
63 A-TTTTAAAAGA-CACGAGCAAAATTTTAAAGGGATATTCGATTATTTTAAACAAAT-GCGAAAT
*
1724605 TGCTAC
125 TGCAAC
* * * * *
1724611 CCAACACGTTAGGGCACGATCCCGCGAATTGCCAAATATCACATATCGCATTCGTTTTAGAGATT
1 CCAACACGTTAGGGCACGATTCCGCGAATCGCCAAACATCACATATCGCATCCGTTTTAAAGATT
* *
1724676 TTAAAAGACACGAGCAAAATTTTAAAGTGATATTCGATTATTTTGAACAAATGCGAAATTGCAAC
66 TTAAAAGACACGAGCAAAATTTTAAAGGGATATTCGATTATTTTAAACAAATGCGAAATTGCAAC
* * * *
1724741 CCAACACGTTAGGGCACGATTCCGCGAATGGCCAAACATCA-A-ATCTCATCTTC-ATTTAAGGG
1 CCAACACGTTAGGGCACGATTCCGCGAATCGCCAAACATCACATATCGCATC--CGTTTTAA-AG
** * *** ** * * * * *
1724803 ATTTTAAAAGGTATGAATGAAATTTCGAAGGAAAATTCGATTATTTTGAGCAAATACGAAATTGC
63 ATTTTAAAAGACACGAGCAAAATTTTAAAGGGATATTCGATTATTTTAAACAAATGCGAAATTGC
1724868 AAC
128 AAC
* *
1724871 CCAACACGTTAGGGCACGATTCCGTGAATCGCCGAACATCA
1 CCAACACGTTAGGGCACGATTCCGCGAATCGCCAAACATCA
1724912 AATTTCGTCT
Statistics
Matches: 249, Mismatches: 45, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
128 6 0.02
129 6 0.02
130 185 0.74
131 23 0.09
132 29 0.12
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (130 bp):
CCAACACGTTAGGGCACGATTCCGCGAATCGCCAAACATCACATATCGCATCCGTTTTAAAGATT
TTAAAAGACACGAGCAAAATTTTAAAGGGATATTCGATTATTTTAAACAAATGCGAAATTGCAAC
Found at i:1724806 original size:130 final size:129
Alignment explanation
Indices: 1724562--1724923 Score: 406
Period size: 130 Copynumber: 2.8 Consensus size: 129
1724552 GAGCCGAGTG
* * * *
1724562 AAATTTTGAAGGGATATTTGATTATTTTAAAC-AATCGGGAAATTGCTACCCAACACGTTAGGGC
1 AAATTTTGAA-GGATATTCGATTATTTTGAACAAAT-GCGAAATTGCAACCCAACACGTTAGGGC
* * * * * *
1724626 ACGATCCCGCGAATTGCCAAATATCACATATCGCA--TTCGTTTTAGAGATTTTAAAAGACACGA
64 ACGATTCCGCGAATCGCCAAACATCA-A-ATCTCATCTTCATTTAAGAGATTTTAAAAGACACGA
*
1724689 GCA
127 ACA
*
1724692 AAATTTTAAAGTGATATTCGATTATTTTGAACAAATGCGAAATTGCAACCCAACACGTTAGGGCA
1 AAATTTTGAAG-GATATTCGATTATTTTGAACAAATGCGAAATTGCAACCCAACACGTTAGGGCA
* * ** * **
1724757 CGATTCCGCGAATGGCCAAACATCAAATCTCATCTTCATTTAAGGGATTTTAAAAGGTATGAATG
65 CGATTCCGCGAATCGCCAAACATCAAATCTCATCTTCATTTAAGAGATTTTAAAAGACACGAACA
* * * *
1724822 AAATTTCGAAGGAAAATTCGATTATTTTGAGCAAATACGAAATTGCAACCCAACACGTTAGGGCA
1 AAATTTTGAAGG-ATATTCGATTATTTTGAACAAATGCGAAATTGCAACCCAACACGTTAGGGCA
* * * *
1724887 CGATTCCGTGAATCGCCGAACATCAAATTTCGTCTTC
65 CGATTCCGCGAATCGCCAAACATCAAATCTCATCTTC
1724924 GTTTTGAAGA
Statistics
Matches: 199, Mismatches: 28, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
128 5 0.03
129 3 0.02
130 188 0.94
131 3 0.02
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (129 bp):
AAATTTTGAAGGATATTCGATTATTTTGAACAAATGCGAAATTGCAACCCAACACGTTAGGGCAC
GATTCCGCGAATCGCCAAACATCAAATCTCATCTTCATTTAAGAGATTTTAAAAGACACGAACA
Found at i:1727908 original size:44 final size:44
Alignment explanation
Indices: 1727845--1728262 Score: 658
Period size: 44 Copynumber: 9.5 Consensus size: 44
1727835 GTTTTTTGTA
* * *
1727845 AATACAAAGACGCCAAATCTGCTATCTTTGATCTGCTCTCCGCC
1 AATACAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCCGCC
*
1727889 AATACAGAGATGCCAAATCTGCTATCTTTGATCTGCTCTCCGCC
1 AATACAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCCGCC
* *
1727933 AATACAGAGATGCCAAATCTACGATCTTCGATCTGCTCTCCGCC
1 AATACAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCCGCC
* * * *
1727977 AATACAGAGATGCCAAATCTGCTATTTTCGACCTGTTCACCGCC
1 AATACAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCCGCC
*
1728021 AATACAGAGATGCCAAATATGCTATCTTCGATCTGCTCTCCGCC
1 AATACAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCCGCC
*
1728065 AATACAGAGATGCCAAATCTG-TGACCTTCGATCTGCTCTCCGCC
1 AATACAGAGATGCCAAATCTGCT-ATCTTCGATCTGCTCTCCGCC
* *
1728109 AATACAGAGATGCCAAATCTACTATCTTCGATCTGTTCTCCGCC
1 AATACAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCCGCC
*
1728153 AATACAGAGATGTCAAATCTGCTATCTTCGATCTGCTCTCCGCC
1 AATACAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCCGCC
1728197 AATACAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCCGCC
1 AATACAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCCGCC
** *
1728241 AATATGGAGACGCCAAATCTGC
1 AATACAGAGATGCCAAATCTGC
1728263 AGGATTTACC
Statistics
Matches: 344, Mismatches: 28, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
43 1 0.00
44 342 0.99
45 1 0.00
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (44 bp):
AATACAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCCGCC
Found at i:1729078 original size:3 final size:3
Alignment explanation
Indices: 1729070--1729102 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1729060 TTGGCCTCTC
*
1729070 CTT CTT CTT CTT CTT CTT CAT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1729103 TTTTTTTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:1740290 original size:130 final size:128
Alignment explanation
Indices: 1740058--1740424 Score: 407
Period size: 130 Copynumber: 2.8 Consensus size: 128
1740048 GAGCCGAGTG
* * * *
1740058 AAATTTTGAAGGGATATTTGATTATTTTAAAC-AAT-CGGGAAATTGCTACCCAACACGTTAAGG
1 AAATTTTGAA-GGATATTCGATTATTTTGAACAAATAC--GAAATTGCAACCCAACACGTTAGGG
* * * * *
1740121 CACGATCCCGCGAATTGCCAAATAACACATATCTC-CTTCATTTTAGATATTTTAAAAGACATGA
63 CACGATTCCGCGAATCGCCAAACATCA-A-ATCTCTCTTCATTTTAGAGATTTTAAAAGACATGA
*
1740185 GCA
126 ACA
*
1740188 AAATTTTAAAGTGATATTCGATTATTTTGAACAAATACGAAATTGCAACCCAACACGTTAGGGCA
1 AAATTTTGAAG-GATATTCGATTATTTTGAACAAATACGAAATTGCAACCCAACACGTTAGGGCA
* * * * **
1740253 CGATTCCGCGAATGGCCAAACATCAAATCTCATCTTCATTTAAGGGATTTTAAAAGATATGAATG
65 CGATTCCGCGAATCGCCAAACATCAAATCTC-TCTTCATTTTAGAGATTTTAAAAGACATGAACA
* * *
1740318 AAATTTCGAAGGAAAATTCGATTATTTTGAGCAAATACGAAATTGCAACCCAACACGTTAGGGCA
1 AAATTTTGAAGG-ATATTCGATTATTTTGAACAAATACGAAATTGCAACCCAACACGTTAGGGCA
* * * * *
1740383 CGACTCCGTGAATCGCCGAACATCAAATTTCGTCTTCGTTTT
65 CGATTCCGCGAATCGCCAAACATCAAATCTC-TCTTCATTTT
1740425 GAAGAATTTT
Statistics
Matches: 203, Mismatches: 28, Indels: 12
0.84 0.12 0.05
Matches are distributed among these distances:
128 5 0.02
129 3 0.01
130 191 0.94
131 3 0.01
132 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (128 bp):
AAATTTTGAAGGATATTCGATTATTTTGAACAAATACGAAATTGCAACCCAACACGTTAGGGCAC
GATTCCGCGAATCGCCAAACATCAAATCTCTCTTCATTTTAGAGATTTTAAAAGACATGAACA
Found at i:1743073 original size:43 final size:42
Alignment explanation
Indices: 1742994--1743122 Score: 125
Period size: 43 Copynumber: 3.0 Consensus size: 42
1742984 CATTAGGTTG
* * * * *
1742994 TCGAGATGTGATTACATGTAAGACCATGTATTGGACATTGGCA
1 TCGATATGTGATAACATGTAAGACCATATCTGGGACA-TGGCA
* ** * *
1743037 TCGTTAAT-TGATTTCGTGTAAGACCCTATCTGGGACAGTGGCA
1 TCGAT-ATGTGATAACATGTAAGACCATATCTGGGACA-TGGCA
*
1743080 TCGATATGTGATAACATGTAAGACCATATCTGGGATATGGCA
1 TCGATATGTGATAACATGTAAGACCATATCTGGGACATGGCA
1743122 T
1 T
1743123 TGTACGAGCT
Statistics
Matches: 69, Mismatches: 15, Indels: 5
0.78 0.17 0.06
Matches are distributed among these distances:
42 8 0.12
43 59 0.86
44 2 0.03
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.31
Consensus pattern (42 bp):
TCGATATGTGATAACATGTAAGACCATATCTGGGACATGGCA
Found at i:1745795 original size:23 final size:23
Alignment explanation
Indices: 1745769--1745812 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1745759 CTGATGGACA
*
1745769 GTAAGCTCTATTGAACTGAAACG
1 GTAAGCTCTAATGAACTGAAACG
*
1745792 GTAAGCTCTAATGAGCTGAAA
1 GTAAGCTCTAATGAACTGAAA
1745813 ATAGTAAGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (23 bp):
GTAAGCTCTAATGAACTGAAACG
Found at i:1745824 original size:24 final size:24
Alignment explanation
Indices: 1745766--1745834 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
1745756 GAGCTGATGG
* *
1745766 ACAGTAAGCTCTATTGAACTG-AA
1 ACAGTAAGCTCTAATGAGCTGAAA
*
1745789 ACGGTAAGCTCTAATGAGCTGAAA
1 ACAGTAAGCTCTAATGAGCTGAAA
* * *
1745813 ATAGTAAGCTCTTACGAGCTGA
1 ACAGTAAGCTCTAATGAGCTGA
1745835 TATATAGGCA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 18 0.47
24 20 0.53
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (24 bp):
ACAGTAAGCTCTAATGAGCTGAAA
Found at i:1748755 original size:5 final size:6
Alignment explanation
Indices: 1748740--1748789 Score: 55
Period size: 6 Copynumber: 7.8 Consensus size: 6
1748730 CGACTCTTCA
* *
1748740 TTTTTC TTTTTC TTTTTC GACTCTTC ATTTTTC TTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC --TTTTTC -TTTTTC TTTTTC TTTTTC TTTTT
1748790 AACATTTATG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
6 29 0.76
7 5 0.13
8 4 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTTTC
Found at i:1748766 original size:27 final size:27
Alignment explanation
Indices: 1748728--1748784 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
1748718 TATATACTGC
1748728 TTCGACTCTTCATTTTTCTTTTTCTTT
1 TTCGACTCTTCATTTTTCTTTTTCTTT
1748755 TTCGACTCTTCATTTTTCTTTTTCTTT
1 TTCGACTCTTCATTTTTCTTTTTCTTT
1748782 TTC
1 TTC
1748785 TTTTTAACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.07, C:0.23, G:0.04, T:0.67
Consensus pattern (27 bp):
TTCGACTCTTCATTTTTCTTTTTCTTT
Found at i:1748772 original size:15 final size:15
Alignment explanation
Indices: 1748728--1748772 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
1748718 TATATACTGC
1748728 TTCGACTCTTCATTT
1 TTCGACTCTTCATTT
* *
1748743 TTC--TTTTTC-TTT
1 TTCGACTCTTCATTT
1748755 TTCGACTCTTCATTT
1 TTCGACTCTTCATTT
1748770 TTC
1 TTC
1748773 TTTTTCTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 6
0.70 0.12 0.18
Matches are distributed among these distances:
12 6 0.26
13 4 0.17
14 4 0.17
15 9 0.39
ACGTcount: A:0.09, C:0.24, G:0.04, T:0.62
Consensus pattern (15 bp):
TTCGACTCTTCATTT
Found at i:1758110 original size:19 final size:19
Alignment explanation
Indices: 1758088--1758126 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1758078 TTTTAAATAG
*
1758088 ATACACATGTATTAATAAT
1 ATACACATGTATAAATAAT
1758107 ATACACATGTATAAATAAT
1 ATACACATGTATAAATAAT
1758126 A
1 A
1758127 AATAAGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.33
Consensus pattern (19 bp):
ATACACATGTATAAATAAT
Found at i:1758554 original size:15 final size:15
Alignment explanation
Indices: 1758531--1758608 Score: 95
Period size: 15 Copynumber: 5.3 Consensus size: 15
1758521 TATCAAATTT
1758531 ATATTGATTGAAATC
1 ATATTGATTGAAATC
* * *
1758546 ATTTTGATTGAATTT
1 ATATTGATTGAAATC
1758561 ATATTGATTGAAATC
1 ATATTGATTGAAATC
* * *
1758576 ATTTTGATTGAATTT
1 ATATTGATTGAAATC
1758591 ATATTGATTGAAAT-
1 ATATTGATTGAAATC
1758605 ATAT
1 ATAT
1758609 ATTATATATA
Statistics
Matches: 52, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
14 4 0.08
15 48 0.92
ACGTcount: A:0.36, C:0.03, G:0.13, T:0.49
Consensus pattern (15 bp):
ATATTGATTGAAATC
Found at i:1758560 original size:30 final size:30
Alignment explanation
Indices: 1758526--1758604 Score: 158
Period size: 30 Copynumber: 2.6 Consensus size: 30
1758516 GAATTTATCA
1758526 AATTTATATTGATTGAAATCATTTTGATTG
1 AATTTATATTGATTGAAATCATTTTGATTG
1758556 AATTTATATTGATTGAAATCATTTTGATTG
1 AATTTATATTGATTGAAATCATTTTGATTG
1758586 AATTTATATTGATTGAAAT
1 AATTTATATTGATTGAAAT
1758605 ATATATTATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.49
Consensus pattern (30 bp):
AATTTATATTGATTGAAATCATTTTGATTG
Found at i:1759132 original size:23 final size:23
Alignment explanation
Indices: 1759104--1759161 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
1759094 TAATATTCCG
1759104 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTTGGATATTCT
1759127 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTTGGATATTCT
*
1759150 AGTGTGTTTGGG
1 GGTGTGTTTGGG
1759162 AGGAATCCGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.09, C:0.03, G:0.41, T:0.47
Consensus pattern (23 bp):
GGTGTGTTTGGGTTGGATATTCT
Found at i:1759287 original size:18 final size:19
Alignment explanation
Indices: 1759266--1759306 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1759256 AATGAAATGA
1759266 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
1759284 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
1759303 GAAA
1 GAAA
1759307 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:1760475 original size:58 final size:58
Alignment explanation
Indices: 1760405--1760521 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
1760395 ATTATGTCAA
1760405 TGTGACATCGTTTACTCGCATTGATTATCGGATCAAGTAAAAAAACATTACATGACAT
1 TGTGACATCGTTTACTCGCATTGATTATCGGATCAAGTAAAAAAACATTACATGACAT
1760463 TGTGACATCGTTTACTCGCATTGATTATCGGATCAAGTAAAAAAACATTACATGACAT
1 TGTGACATCGTTTACTCGCATTGATTATCGGATCAAGTAAAAAAACATTACATGACAT
1760521 T
1 T
1760522 TTGATAATGT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (58 bp):
TGTGACATCGTTTACTCGCATTGATTATCGGATCAAGTAAAAAAACATTACATGACAT
Found at i:1761224 original size:24 final size:24
Alignment explanation
Indices: 1761192--1761238 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
1761182 CGATTGTATC
1761192 TCGAGTCAACTTTGAGCTTAAAAT
1 TCGAGTCAACTTTGAGCTTAAAAT
1761216 TCGAGTCAACTTTGAGCTTAAAA
1 TCGAGTCAACTTTGAGCTTAAAA
1761239 ATTGATGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (24 bp):
TCGAGTCAACTTTGAGCTTAAAAT
Found at i:1772600 original size:14 final size:14
Alignment explanation
Indices: 1772577--1772616 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1772567 ATAGAAAAGT
*
1772577 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
1772591 AAATCATTTTACGG
1 AAAACATTTTACAG
1772605 AAAACATTTTAC
1 AAAACATTTTAC
1772617 TGCCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:1772608 original size:34 final size:35
Alignment explanation
Indices: 1772542--1772608 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
1772532 CAAACACCAG
* * *
1772542 AAAATATTTTCCAGTAAGTCATTTTATAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
1772577 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
1772609 CATTTTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 15 0.54
35 13 0.46
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:1773285 original size:23 final size:23
Alignment explanation
Indices: 1773240--1773286 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1773230 CACAAGTGCA
*
1773240 CCATGGTTGCGGGCTCCCGTGCG
1 CCATGGTTGCGGGCTCCCATGCG
**
1773263 CCATGGTTGCGGGCTGTCATGCG
1 CCATGGTTGCGGGCTCCCATGCG
1773286 C
1 C
1773287 AACCCATGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.06, C:0.32, G:0.38, T:0.23
Consensus pattern (23 bp):
CCATGGTTGCGGGCTCCCATGCG
Found at i:1774972 original size:12 final size:12
Alignment explanation
Indices: 1774931--1774972 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
1774921 TTTAATTCTT
*
1774931 TTATTTTTTTAC
1 TTATTTTTTTTC
1774943 ATTATTTCTTTTTC
1 -TTATTT-TTTTTC
1774957 -TATTTTTTTTC
1 TTATTTTTTTTC
1774968 TTATT
1 TTATT
1774973 CCTTTATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 6 0.23
12 9 0.35
13 6 0.23
14 5 0.19
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (12 bp):
TTATTTTTTTTC
Found at i:1775281 original size:18 final size:17
Alignment explanation
Indices: 1775260--1775296 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
1775250 AATTTCATTT
1775260 ATTTTAAATATTTTATAA
1 ATTTTAAATATTTT-TAA
*
1775278 ATTTTTAATATTTTTAA
1 ATTTTAAATATTTTTAA
1775295 AT
1 AT
1775297 ATATAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTAAATATTTTTAA
Found at i:1777855 original size:59 final size:57
Alignment explanation
Indices: 1777740--1777858 Score: 139
Period size: 59 Copynumber: 2.1 Consensus size: 57
1777730 TATTAAGGTC
* ***
1777740 TAAATTTTTTTACCCAAGTTAATCTCTAAACTTAATAATTATTTTTGTATCAGGGCT
1 TAAATTTTTTTACCCAAGTTAATCTCTAAACTTAATAATTATTCTCACATCAGGGCT
* * * **
1777797 TAAACTTTTATTTATCCAAGTTAATCTCTAAACTTGATAATTGTTCTCACATTGGGGCT
1 TAAA-TTTT-TTTACCCAAGTTAATCTCTAAACTTAATAATTATTCTCACATCAGGGCT
1777856 TAA
1 TAA
1777859 GCTTAATAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
57 4 0.08
58 4 0.08
59 43 0.84
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (57 bp):
TAAATTTTTTTACCCAAGTTAATCTCTAAACTTAATAATTATTCTCACATCAGGGCT
Found at i:1780959 original size:27 final size:28
Alignment explanation
Indices: 1780916--1780968 Score: 65
Period size: 27 Copynumber: 1.9 Consensus size: 28
1780906 TAAAAATTCA
* *
1780916 AAAAAATTATAACTAAATATTTAAAAAT
1 AAAAAATTATAACTAAAAATTCAAAAAT
1780944 AAAAAA-TATATA-TAAAAATTCAAAA
1 AAAAAATTATA-ACTAAAAATTCAAAA
1780969 GTTATTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 15 0.68
28 7 0.32
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (28 bp):
AAAAAATTATAACTAAAAATTCAAAAAT
Found at i:1784399 original size:22 final size:22
Alignment explanation
Indices: 1784371--1784421 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1784361 AGCACACGGT
1784371 CGTGTGGTGGCTCGAGTGAGGC
1 CGTGTGGTGGCTCGAGTGAGGC
*
1784393 CGTGTGGTGGCTCGATTGAGGC
1 CGTGTGGTGGCTCGAGTGAGGC
1784415 CGTGTGG
1 CGTGTGG
1784422 GCCACACGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.08, C:0.18, G:0.49, T:0.25
Consensus pattern (22 bp):
CGTGTGGTGGCTCGAGTGAGGC
Found at i:1786056 original size:14 final size:14
Alignment explanation
Indices: 1786032--1786071 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
1786022 TGTTAAGTTT
1786032 GTTTTAAAAAATAA
1 GTTTTAAAAAATAA
* *
1786046 TTTTTAGAAAATAA
1 GTTTTAAAAAATAA
1786060 GTTTTAAAAAAT
1 GTTTTAAAAAAT
1786072 TTGCACAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (14 bp):
GTTTTAAAAAATAA
Found at i:1793829 original size:22 final size:22
Alignment explanation
Indices: 1793801--1793851 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1793791 AGCACACGGT
1793801 CGTGTGGTGGCTCGAGTGAGGC
1 CGTGTGGTGGCTCGAGTGAGGC
*
1793823 CGTGTGGTGGCTCGATTGAGGC
1 CGTGTGGTGGCTCGAGTGAGGC
1793845 CGTGTGG
1 CGTGTGG
1793852 GCCACACGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.08, C:0.18, G:0.49, T:0.25
Consensus pattern (22 bp):
CGTGTGGTGGCTCGAGTGAGGC
Found at i:1795486 original size:14 final size:14
Alignment explanation
Indices: 1795462--1795501 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
1795452 TGTTAAGTTT
1795462 GTTTTAAAAAATAA
1 GTTTTAAAAAATAA
* *
1795476 TTTTTAGAAAATAA
1 GTTTTAAAAAATAA
1795490 GTTTTAAAAAAT
1 GTTTTAAAAAAT
1795502 TTGCACAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (14 bp):
GTTTTAAAAAATAA
Found at i:1797387 original size:8 final size:9
Alignment explanation
Indices: 1797344--1797398 Score: 53
Period size: 9 Copynumber: 6.3 Consensus size: 9
1797334 GAAATTATAA
1797344 AAAAATTATT
1 AAAAATTA-T
1797354 AAAAATT-T
1 AAAAATTAT
* *
1797362 -TAAATTAA
1 AAAAATTAT
1797370 AAAAATTAT
1 AAAAATTAT
1797379 AAAAA-TAT
1 AAAAATTAT
*
1797387 AAAAGTTAT
1 AAAAATTAT
1797396 AAA
1 AAA
1797399 TGAGATAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
7 5 0.14
8 8 0.22
9 17 0.46
10 7 0.19
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:1797637 original size:26 final size:25
Alignment explanation
Indices: 1797607--1797704 Score: 67
Period size: 26 Copynumber: 3.8 Consensus size: 25
1797597 AAAATCTATG
1797607 TTTTTATAGATATTTTATAATTATTTA
1 TTTTTA-A-ATATTTTATAATTATTTA
* *
1797634 TTTTTTATAAT-TTTAATATTTATTGTAA
1 -TTTTTA-AATATTTTATAATTATT-T-A
*
1797662 TTTTTAAATATTTT-TAATGATTT-
1 TTTTTAAATATTTTATAATTATTTA
** *
1797685 TTTTTTTATTTTTTATAATT
1 TTTTTAAATATTTTATAATT
1797705 TCAAAATGAA
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
23 11 0.19
24 4 0.07
25 1 0.02
26 20 0.35
27 12 0.21
28 9 0.16
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (25 bp):
TTTTTAAATATTTTATAATTATTTA
Found at i:1800225 original size:22 final size:22
Alignment explanation
Indices: 1800184--1800242 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
1800174 GTTTTAAGAA
* *
1800184 TTGTTTTAGTA-TCATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
1800205 TTGTTTTAATATTTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
1800227 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
1800243 GATTTATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 7 0.21
21 16 0.48
22 10 0.30
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.68
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:1800241 original size:20 final size:22
Alignment explanation
Indices: 1800197--1800242 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
1800187 TTTTAGTATC
* *
1800197 ATTTTTATTTGTTTTAATATTT
1 ATTTTTATGTGTTTTAATATAT
1800219 ATTTTTATGT-TTTTAA-ATAT
1 ATTTTTATGTGTTTTAATATAT
1800239 ATTT
1 ATTT
1800243 GATTTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
21 6 0.27
22 9 0.41
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (22 bp):
ATTTTTATGTGTTTTAATATAT
Found at i:1800259 original size:26 final size:24
Alignment explanation
Indices: 1800213--1800260 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
1800203 ATTTGTTTTA
*
1800213 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTTAAAT
1800237 ATATTTGATTTATTATATTTTTAA
1 ATATTT-ATTT-TTATATTTTTAA
1800261 TTTTTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 4 0.19
26 11 0.52
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTTAAAT
Found at i:1800518 original size:25 final size:25
Alignment explanation
Indices: 1800489--1800538 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1800479 TACTCAACCA
1800489 AAACTTTATTTAATTTTATTATTTT
1 AAACTTTATTTAATTTTATTATTTT
1800514 AAACTTTATTTAATTTTATTATTTT
1 AAACTTTATTTAATTTTATTATTTT
1800539 CCGTTAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (25 bp):
AAACTTTATTTAATTTTATTATTTT
Found at i:1814840 original size:22 final size:23
Alignment explanation
Indices: 1814815--1814860 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1814805 ATTTAAATAT
*
1814815 AAAAAATAAA-TAAATATACTTA
1 AAAAAATAAAGGAAATATACTTA
*
1814837 AAAAAATAAAGGAAATATATTTA
1 AAAAAATAAAGGAAATATACTTA
1814860 A
1 A
1814861 TGCACTATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.26
Consensus pattern (23 bp):
AAAAAATAAAGGAAATATACTTA
Found at i:1814974 original size:20 final size:19
Alignment explanation
Indices: 1814922--1814975 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
1814912 AGTGAAAGAT
1814922 TTATAAATAAATACTAATAA
1 TTATAAATAAATA-TAATAA
* ** *
1814942 TTTTATTTCAATATAATTAA
1 TTATAAATAAATATAA-TAA
1814962 TTATAAATAAATAT
1 TTATAAATAAATAT
1814976 TAAAACTCCG
Statistics
Matches: 25, Mismatches: 8, Indels: 2
0.71 0.23 0.06
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (19 bp):
TTATAAATAAATATAATAA
Found at i:1818591 original size:15 final size:15
Alignment explanation
Indices: 1818573--1818627 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
1818563 AAAAAGTATA
*
1818573 TAATTTTAGTTTCAT
1 TAATTGTAGTTTCAT
*
1818588 TAATTGTA-TAT-A-
1 TAATTGTAGTTTCAT
*
1818600 TAATTTTAGTTTCAT
1 TAATTGTAGTTTCAT
1818615 TAATTGTAGTTTC
1 TAATTGTAGTTTC
1818628 TTATTCCACA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
12 7 0.22
13 3 0.09
14 3 0.09
15 19 0.59
ACGTcount: A:0.29, C:0.05, G:0.09, T:0.56
Consensus pattern (15 bp):
TAATTGTAGTTTCAT
Found at i:1818606 original size:27 final size:27
Alignment explanation
Indices: 1818569--1818622 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
1818559 AATTAAAAAG
1818569 TATATAATTTTAGTTTCATTAATTGTA
1 TATATAATTTTAGTTTCATTAATTGTA
1818596 TATATAATTTTAGTTTCATTAATTGTA
1 TATATAATTTTAGTTTCATTAATTGTA
1818623 GTTTCTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56
Consensus pattern (27 bp):
TATATAATTTTAGTTTCATTAATTGTA
Found at i:1818664 original size:26 final size:26
Alignment explanation
Indices: 1818614--1818665 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1818604 TTTAGTTTCA
*
1818614 TTAATTGTAGTTTCTTATTCCACAAG
1 TTAATTGTAGTTTCTTATGCCACAAG
*
1818640 TTAATTTTAGTTTCTTA-GCCTACAAG
1 TTAATTGTAGTTTCTTATGCC-ACAAG
1818666 AATAAAACCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 2 0.09
26 21 0.91
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (26 bp):
TTAATTGTAGTTTCTTATGCCACAAG
Found at i:1820068 original size:15 final size:15
Alignment explanation
Indices: 1820048--1820078 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1820038 ATAAAAGCAC
*
1820048 TTAATTTTAGTTTCT
1 TTAATTATAGTTTCT
1820063 TTAATTATAGTTTCT
1 TTAATTATAGTTTCT
1820078 T
1 T
1820079 ATTCTACAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.65
Consensus pattern (15 bp):
TTAATTATAGTTTCT
Found at i:1826870 original size:2 final size:2
Alignment explanation
Indices: 1826863--1826889 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1826853 AATTTTCAAA
1826863 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1826890 AAAAAGTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1828355 original size:8 final size:8
Alignment explanation
Indices: 1828342--1828373 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
1828332 AATCAAGACT
1828342 CTTCATCA
1 CTTCATCA
1828350 CTTCATCA
1 CTTCATCA
1828358 CTTCATCA
1 CTTCATCA
1828366 CTTCATCA
1 CTTCATCA
1828374 TACGTGAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.25, C:0.38, G:0.00, T:0.38
Consensus pattern (8 bp):
CTTCATCA
Found at i:1830092 original size:9 final size:9
Alignment explanation
Indices: 1830079--1830139 Score: 86
Period size: 9 Copynumber: 6.8 Consensus size: 9
1830069 TTTGGTTAAA
*
1830079 AATTACCCA
1 AATTACCCG
*
1830088 AATTACCTG
1 AATTACCCG
1830097 AATTACCCG
1 AATTACCCG
1830106 AATTACCCG
1 AATTACCCG
*
1830115 AATTAACCG
1 AATTACCCG
*
1830124 AATTAACCG
1 AATTACCCG
1830133 AATTACC
1 AATTACC
1830140 GAAAAATACC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 47 1.00
ACGTcount: A:0.39, C:0.28, G:0.08, T:0.25
Consensus pattern (9 bp):
AATTACCCG
Found at i:1831215 original size:25 final size:25
Alignment explanation
Indices: 1831180--1831230 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
1831170 TCATCTATAT
*
1831180 TTACTTGATTGATATGAAGATTTTG
1 TTACTTAATTGATATGAAGATTTTG
1831205 TTACTTAATTGATATGAAGATTTTG
1 TTACTTAATTGATATGAAGATTTTG
1831230 T
1 T
1831231 GACTAACATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.04, G:0.18, T:0.49
Consensus pattern (25 bp):
TTACTTAATTGATATGAAGATTTTG
Found at i:1845188 original size:18 final size:19
Alignment explanation
Indices: 1845143--1845190 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
1845133 CATGATATAC
1845143 ATAACATATATATAAAAACA
1 ATAACATA-ATATAAAAACA
* *
1845163 ATAA-ATAATATGAAAATA
1 ATAACATAATATAAAAACA
1845181 A-AACATAATA
1 ATAACATAATA
1845191 AAGATTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 2 0.08
18 16 0.64
19 3 0.12
20 4 0.16
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.25
Consensus pattern (19 bp):
ATAACATAATATAAAAACA
Found at i:1845317 original size:27 final size:26
Alignment explanation
Indices: 1845281--1845337 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
1845271 TATAAGTAAT
* *
1845281 TAATAAATATAATATATGTGAAAAT-A
1 TAATAAATATAAAAGATGT-AAAATAA
1845307 TAATAATATATAAAAGATGTAAAATAA
1 TAATAA-ATATAAAAGATGTAAAATAA
1845334 TAAT
1 TAAT
1845338 TTAAGGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 11 0.41
27 16 0.59
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (26 bp):
TAATAAATATAAAAGATGTAAAATAA
Found at i:1845388 original size:20 final size:20
Alignment explanation
Indices: 1845352--1845389 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1845342 GGAAAATAAT
*
1845352 ATATATAATAAGTAATAACA
1 ATATATAATAAGAAATAACA
1845372 ATATATAATTAA-AAATAA
1 ATATATAA-TAAGAAATAA
1845390 TACTCATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (20 bp):
ATATATAATAAGAAATAACA
Found at i:1847701 original size:19 final size:19
Alignment explanation
Indices: 1847676--1847766 Score: 134
Period size: 19 Copynumber: 4.9 Consensus size: 19
1847666 ATAATCTTCA
1847676 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
1847695 GTGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
1847714 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
1847731 ATGAT-TCCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
1847749 ATGATATACAATCTTAGA
1 ATGATATGCAATCTTAGA
1847767 AGATATGATT
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.24
18 16 0.24
19 34 0.52
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:1847716 original size:14 final size:15
Alignment explanation
Indices: 1847697--1847752 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 15
1847687 TCTTAGATGT
1847697 GATATG-CAATCTTA
1 GATATGACAATCTTA
1847711 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
1847728 GATATGATTCCAATCTTA
1 GATATGA---CAATCTTA
1847746 GATATGA
1 GATATGA
1847753 TATACAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.17
15 1 0.03
17 14 0.39
18 15 0.42
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:1847748 original size:35 final size:37
Alignment explanation
Indices: 1847684--1847766 Score: 125
Period size: 35 Copynumber: 2.3 Consensus size: 37
1847674 CAATGATATG
* *
1847684 CAATCTTAGATGTGATATGCAATCTTAGATATG-ATA
1 CAATCTTAGATATGATATCCAATCTTAGATATGAATA
1847720 CAATCTTAGATATGAT-TCCAATCTTAGATATGATATA
1 CAATCTTAGATATGATATCCAATCTTAGATATGA-ATA
1847757 CAATCTTAGA
1 CAATCTTAGA
1847767 AGATATGATT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
35 15 0.35
36 15 0.35
37 13 0.30
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.36
Consensus pattern (37 bp):
CAATCTTAGATATGATATCCAATCTTAGATATGAATA
Found at i:1851900 original size:21 final size:21
Alignment explanation
Indices: 1851876--1851920 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1851866 TTTATTATTT
1851876 AAAAAAATTAATAATTTAAAA
1 AAAAAAATTAATAATTTAAAA
* * * *
1851897 AAAAGAATTATTACTTTAATA
1 AAAAAAATTAATAATTTAAAA
1851918 AAA
1 AAA
1851921 CTCTAAGTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (21 bp):
AAAAAAATTAATAATTTAAAA
Found at i:1854614 original size:25 final size:25
Alignment explanation
Indices: 1854585--1854632 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1854575 GCACTCTTTC
*
1854585 GAGCCATAAAACAGGATGCTTATAT
1 GAGCCATAAAACAGGAAGCTTATAT
**
1854610 GAGCCATGTAACAGGAAGCTTAT
1 GAGCCATAAAACAGGAAGCTTAT
1854633 CCTGGCTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.23
Consensus pattern (25 bp):
GAGCCATAAAACAGGAAGCTTATAT
Found at i:1856944 original size:17 final size:17
Alignment explanation
Indices: 1856924--1856956 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1856914 GATTAATGTT
1856924 TGGCACTGATTTTCTTA
1 TGGCACTGATTTTCTTA
1856941 TGGCACTGATTTTCTT
1 TGGCACTGATTTTCTT
1856957 GTGATGGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.18, G:0.18, T:0.48
Consensus pattern (17 bp):
TGGCACTGATTTTCTTA
Found at i:1861448 original size:23 final size:23
Alignment explanation
Indices: 1861408--1861471 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
1861398 TTTTTCACTT
* **
1861408 AAATTTTTTAGAATTTTTTTTTTAA
1 AAATTTATTA-AA-TTTTTTTCGAA
*
1861433 AAATTTATTATATTTTTTTCGAA
1 AAATTTATTAAATTTTTTTCGAA
*
1861456 AATTTTATTAAATTTT
1 AAATTTATTAAATTTT
1861472 CTTAAAATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 23 0.70
24 1 0.03
25 9 0.27
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (23 bp):
AAATTTATTAAATTTTTTTCGAA
Found at i:1861479 original size:21 final size:21
Alignment explanation
Indices: 1861424--1861479 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 21
1861414 TTTAGAATTT
* *
1861424 TTTTTTTAAAAATTTATTATA
1 TTTTTTTAAAATTTTATTAAA
1861445 TTTTTTTCGAAAATTTTATTAAA
1 TTTTTTT--AAAATTTTATTAAA
*
1861468 TTTTCTTAAAAT
1 TTTTTTTAAAAT
1861480 ATTAAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 12 0.40
23 18 0.60
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTTTTAAAATTTTATTAAA
Found at i:1862301 original size:23 final size:23
Alignment explanation
Indices: 1862275--1862326 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
1862265 TTATCTATTA
1862275 TTTTTGTTTTTATTT-TTATTTCT
1 TTTTTGTTTTT-TTTCTTATTTCT
* *
1862298 TTTTTCTTTTTTTTCTTTTTTCT
1 TTTTTGTTTTTTTTCTTATTTCT
1862321 TTTTTG
1 TTTTTG
1862327 GATGTTCTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 3 0.12
23 22 0.88
ACGTcount: A:0.04, C:0.08, G:0.04, T:0.85
Consensus pattern (23 bp):
TTTTTGTTTTTTTTCTTATTTCT
Found at i:1862324 original size:16 final size:16
Alignment explanation
Indices: 1862281--1862325 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
1862271 ATTATTTTTG
*
1862281 TTTTTATTTTTATTTCT
1 TTTTTCTTTTT-TTTCT
1862298 TTTTTCTTTTTTTTCT
1 TTTTTCTTTTTTTTCT
1862314 TTTTTCTTTTTT
1 TTTTTCTTTTTT
1862326 GGATGTTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
16 17 0.63
17 10 0.37
ACGTcount: A:0.04, C:0.09, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTTCTTTTTTTTCT
Found at i:1862360 original size:23 final size:22
Alignment explanation
Indices: 1862309--1862371 Score: 76
Period size: 23 Copynumber: 2.9 Consensus size: 22
1862299 TTTTCTTTTT
1862309 TTTCTTTT-TTCTT-TTTTGGA
1 TTTCTTTTCTTCTTCTTTTGGA
*
1862329 TGTTCTTTTCTTCTTCTTCTTGGG
1 T-TTCTTTTCTTCTTCTT-TTGGA
*
1862353 TTTCTTTTCTTTTTCTTTT
1 TTTCTTTTCTTCTTCTTTT
1862372 AAAAACAGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
20 1 0.03
21 7 0.19
22 7 0.19
23 17 0.46
24 5 0.14
ACGTcount: A:0.02, C:0.16, G:0.10, T:0.73
Consensus pattern (22 bp):
TTTCTTTTCTTCTTCTTTTGGA
Found at i:1862916 original size:21 final size:21
Alignment explanation
Indices: 1862892--1862947 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
1862882 GTGGCTAACC
**
1862892 CACACGGGCGTGTGTTTTGGA
1 CACACGGGCGTGTGTGGTGGA
* * * *
1862913 CACACGGCCATGTCTGGTGGG
1 CACACGGGCGTGTGTGGTGGA
1862934 CACACGGGCGTGTG
1 CACACGGGCGTGTG
1862948 AGACCCTCAT
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.14, C:0.25, G:0.39, T:0.21
Consensus pattern (21 bp):
CACACGGGCGTGTGTGGTGGA
Found at i:1863075 original size:22 final size:22
Alignment explanation
Indices: 1863047--1863089 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1863037 GGCTCACACG
1863047 GGCGTGTGCCTCTCTTTACAGA
1 GGCGTGTGCCTCTCTTTACAGA
*
1863069 GGCGTGTGCCTTTCTTTACAG
1 GGCGTGTGCCTCTCTTTACAG
1863090 GGGCATTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.12, C:0.26, G:0.28, T:0.35
Consensus pattern (22 bp):
GGCGTGTGCCTCTCTTTACAGA
Found at i:1868226 original size:58 final size:60
Alignment explanation
Indices: 1868164--1868288 Score: 155
Period size: 58 Copynumber: 2.1 Consensus size: 60
1868154 GAATAGCTGA
* * *
1868164 GTGACTATCTTGTAATTTTTCATAACTAGGTGACC-AAAAA-AAATTTACTAATAGTCAG
1 GTGACTATCTTGTAACTTCTCATAACTAGGTGACCAAAAAACAAATTCACTAATAGTCAG
* * * * **
1868222 GTGACCATTTTGTAACTTCTCATAATTGGGTGACCAAAAAACAAATTCACTAATAGTTGG
1 GTGACTATCTTGTAACTTCTCATAACTAGGTGACCAAAAAACAAATTCACTAATAGTCAG
1868282 GTGACTA
1 GTGACTA
1868289 CTAGTGTAGT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
58 29 0.53
59 5 0.09
60 21 0.38
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (60 bp):
GTGACTATCTTGTAACTTCTCATAACTAGGTGACCAAAAAACAAATTCACTAATAGTCAG
Found at i:1874220 original size:22 final size:20
Alignment explanation
Indices: 1874183--1874229 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1874173 TAGGAGACCG
* *
1874183 AAATTAAATTGTAATTTTTAA
1 AAATTAAATT-AAAATTTTAA
1874204 ATAATTAAATTAAAATTTTAA
1 A-AATTAAATTAAAATTTTAA
1874225 AAATT
1 AAATT
1874230 TTAAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.17
21 10 0.43
22 9 0.39
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
AAATTAAATTAAAATTTTAA
Found at i:1874229 original size:9 final size:9
Alignment explanation
Indices: 1874215--1874243 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
1874205 TAATTAAATT
1874215 AAAATTTTA
1 AAAATTTTA
1874224 AAAATTTTA
1 AAAATTTTA
1874233 AAAATTTTA
1 AAAATTTTA
1874242 AA
1 AA
1874244 GGGTTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
AAAATTTTA
Found at i:1884166 original size:206 final size:204
Alignment explanation
Indices: 1883812--1884219 Score: 559
Period size: 206 Copynumber: 2.0 Consensus size: 204
1883802 ATTTGATTGG
* * * * *
1883812 ATATTTCTCGTTAAAAGTTGTTTTGTGGACAAAAACACTCTTGGCTCATTAATTGGCTTCATCAT
1 ATATTTCTCGTTAAAAGTTGTTGTGTAGACAAAAACACTCTTGGCTCATTAATTGACCTCATCAC
* * * * * *
1883877 ATTAGTGTCGCAACATTGATGGTAGTCTACTAGTCTTATGCATGTCTTCAAGGTTGTGTTGTGAC
66 ATCAGTGTCGCAACATTGATAGCAGTCTACTAGTCTTAGGCATGTCTTCAAGGTTGTGCTGCGAC
* *
1883942 ACTGAAGGCATACTACTCCTTTTTTGAGTACTCTGTTCACTGTGTTGCGACATCGAAGCTCCGTG
131 ACTAAAGGCAGACTACTCC--TTTTGAGTACTCTGTTCACTGTGTTGCGACATCGAAGCTCCGTG
1884007 TTGCAACATCA
194 TTGCAACATCA
** * *
1884018 ATATTTC-CTGTTAAAAGTTGTTGTGTAGATGAAAACACTCTTGGCTTATTAATTGACCTCATTA
1 ATATTTCTC-GTTAAAAGTTGTTGTGTAGACAAAAACACTCTTGGCTCATTAATTGACCTCATCA
* *
1884082 CGTCAGTGTTGCAACATTGATAGCAGTCTACTAGTCTTAGGCATGTCTTCAAGGTTGTGCCT-CG
65 CATCAGTGTCGCAACATTGATAGCAGTCTACTAGTCTTAGGCATGTCTTCAAGGTTGTG-CTGCG
* * * *
1884146 ACACTAAAGGCAGACTACTCCTTTTGAGTACTTTGTTCACTGTGTTGCGATATTGAAGCTCTGTG
129 ACACTAAAGGCAGACTACTCCTTTTGAGTACTCTGTTCACTGTGTTGCGACATCGAAGCTCCGTG
1884211 TTGCAACAT
194 TTGCAACAT
1884220 TACAGGTAGT
Statistics
Matches: 177, Mismatches: 23, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
204 49 0.28
205 1 0.01
206 126 0.71
207 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (204 bp):
ATATTTCTCGTTAAAAGTTGTTGTGTAGACAAAAACACTCTTGGCTCATTAATTGACCTCATCAC
ATCAGTGTCGCAACATTGATAGCAGTCTACTAGTCTTAGGCATGTCTTCAAGGTTGTGCTGCGAC
ACTAAAGGCAGACTACTCCTTTTGAGTACTCTGTTCACTGTGTTGCGACATCGAAGCTCCGTGTT
GCAACATCA
Found at i:1885313 original size:5 final size:5
Alignment explanation
Indices: 1885303--1885341 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
1885293 TTCTGATACG
*
1885303 TATGA TATGA TATGA TACGA TATGA TATGA TATGA TATG
1 TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATG
1885342 TGGTGATGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (5 bp):
TATGA
Found at i:1892737 original size:25 final size:25
Alignment explanation
Indices: 1892682--1892730 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
1892672 TGTTCCTAAG
*
1892682 ATAACATCAAATTCAATAAAAAGGT
1 ATAACATCAAATTCAACAAAAAGGT
1892707 AGTAACATCAAA-TCAACAAGAAAG
1 A-TAACATCAAATTCAACAA-AAAG
1892731 TCATAACCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.57, C:0.14, G:0.10, T:0.18
Consensus pattern (25 bp):
ATAACATCAAATTCAACAAAAAGGT
Found at i:1897051 original size:25 final size:24
Alignment explanation
Indices: 1897015--1897103 Score: 87
Period size: 24 Copynumber: 3.8 Consensus size: 24
1897005 TTCTAACGAG
*
1897015 AAGCTCA-TAAGAGCCATAATCAGA
1 AAGCTCACAAAGAGCCAT-ATCAGA
* *
1897039 AAGTTCACAAAGAACCATATC-GA
1 AAGCTCACAAAGAGCCATATCAGA
*
1897062 GAAGCTCACGAAA-AGCC-TATCAGG
1 -AAGCTCAC-AAAGAGCCATATCAGA
1897086 AAGCTCACAAAGAGCCAT
1 AAGCTCACAAAGAGCCAT
1897104 GTAACGGGAA
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
22 3 0.06
23 18 0.34
24 21 0.40
25 11 0.21
ACGTcount: A:0.44, C:0.24, G:0.18, T:0.15
Consensus pattern (24 bp):
AAGCTCACAAAGAGCCATATCAGA
Found at i:1897095 original size:47 final size:48
Alignment explanation
Indices: 1897011--1897103 Score: 118
Period size: 47 Copynumber: 2.0 Consensus size: 48
1897001 AGCTTTCTAA
* * *
1897011 CGAGAAGCTCATAAGAGCCATAATCAGAAAGTTCACAAAGAACCATAT
1 CGAGAAGCTCAGAAAAGCCATAATCAGAAAGCTCACAAAGAACCATAT
* *
1897059 CGAGAAGCTCACGAAAAGCC-T-ATCAGGAAGCTCACAAAGAGCCAT
1 CGAGAAGCTCA-GAAAAGCCATAATCAGAAAGCTCACAAAGAACCAT
1897104 GTAACGGGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
47 21 0.54
48 12 0.31
49 6 0.15
ACGTcount: A:0.43, C:0.24, G:0.19, T:0.14
Consensus pattern (48 bp):
CGAGAAGCTCAGAAAAGCCATAATCAGAAAGCTCACAAAGAACCATAT
Found at i:1902848 original size:16 final size:16
Alignment explanation
Indices: 1902827--1902857 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1902817 TGTATTTTGT
1902827 ACTTGAATGTGCATGA
1 ACTTGAATGTGCATGA
*
1902843 ACTTGAATTTGCATG
1 ACTTGAATGTGCATG
1902858 CTTTGTGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (16 bp):
ACTTGAATGTGCATGA
Found at i:1904118 original size:12 final size:12
Alignment explanation
Indices: 1904101--1904125 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1904091 TGTGAAAAAT
1904101 AAAATAAAATAA
1 AAAATAAAATAA
1904113 AAAATAAAATAA
1 AAAATAAAATAA
1904125 A
1 A
1904126 GAACACACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAATAAAATAA
Done.