Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008480.1 Hibiscus syriacus cultivar Beakdansim tig00111311_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: 2515485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 13
Found at i:1107964 original size:3 final size:3
Alignment explanation
Indices: 1107949--1107985 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
1107939 ACTATTAAAA
* *
1107949 ATT ATT GTT ATT ATT ATT ATT ACT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1107986 ACTAATAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1109338 original size:29 final size:29
Alignment explanation
Indices: 1109300--1109376 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
1109290 TGGGACAAAA
* *
1109300 TATATAACTTTTAAAAATTATATTTTGGTC
1 TATA-AACTTTTCAAAATTATACTTTGGTC
*
1109330 TATAAACTTTTCCAAATTTATACTTTGGTC
1 TATAAACTTTT-CAAAATTATACTTTGGTC
* *
1109360 -ACAAAGTTTTCAAAATT
1 TATAAACTTTTCAAAATT
1109377 TGCATTTTGG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 6 0.15
29 15 0.38
30 19 0.47
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (29 bp):
TATAAACTTTTCAAAATTATACTTTGGTC
Found at i:1109357 original size:30 final size:30
Alignment explanation
Indices: 1109300--1109377 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 30
1109290 TGGGACAAAA
* *
1109300 TATATAACTTTT-AAAAATTATATTTTGGTC
1 TATA-AACTTTTCAAAATTTATACTTTGGTC
*
1109330 TATAAACTTTTCCAAATTTATACTTTGGTC
1 TATAAACTTTTCAAAATTTATACTTTGGTC
* *
1109360 -ACAAAGTTTTCAAAATTT
1 TATAAACTTTTCAAAATTT
1109378 GCATTTTGGT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 22 0.54
30 19 0.46
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (30 bp):
TATAAACTTTTCAAAATTTATACTTTGGTC
Found at i:1109385 original size:29 final size:29
Alignment explanation
Indices: 1109305--1109390 Score: 84
Period size: 29 Copynumber: 3.0 Consensus size: 29
1109295 CAAAATATAT
* * *
1109305 AACTTTT-AAAAATTATATTTTGGTCTATA
1 AACTTTTCAAAATTTACATTTTGGTC-ACA
* * *
1109334 AACTTTTCCAAATTTATACTTTGGTCACA
1 AACTTTTCAAAATTTACATTTTGGTCACA
* *
1109363 AAGTTTTCAAAATTTGCATTTTGGTCAC
1 AACTTTTCAAAATTTACATTTTGGTCAC
1109391 TACCTAGAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
29 32 0.68
30 15 0.32
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (29 bp):
AACTTTTCAAAATTTACATTTTGGTCACA
Found at i:1110431 original size:2 final size:2
Alignment explanation
Indices: 1110424--1110474 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1110414 CACAATATTC
1110424 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1110466 AT AT AT AT A
1 AT AT AT AT A
1110475 AAATAGTAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1113758 original size:3 final size:3
Alignment explanation
Indices: 1113745--1113798 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
1113735 TATTATGAAG
* * * *
1113745 TAT TGT TAT TAT TAT TAT TAT TATT TAT TAT AAT TAT TAC TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
1113791 TAT TAT TA
1 TAT TAT TA
1113799 AAATAAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1121803 original size:21 final size:22
Alignment explanation
Indices: 1121778--1121818 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1121768 ATTTGTATTT
1121778 AAGTTTCATAT-TTACAAAAAA
1 AAGTTTCATATCTTACAAAAAA
*
1121799 AAGTTTCATATCTTTCAAAA
1 AAGTTTCATATCTTACAAAA
1121819 TCATTCTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.37
Consensus pattern (22 bp):
AAGTTTCATATCTTACAAAAAA
Found at i:1124601 original size:13 final size:15
Alignment explanation
Indices: 1124583--1124614 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
1124573 CCATTGCAAT
1124583 ATATTCC-AATTT-A
1 ATATTCCAAATTTGA
1124596 ATATTCCAAATTTGA
1 ATATTCCAAATTTGA
1124611 ATAT
1 ATAT
1124615 GAATCAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 5 0.29
15 5 0.29
ACGTcount: A:0.41, C:0.12, G:0.03, T:0.44
Consensus pattern (15 bp):
ATATTCCAAATTTGA
Found at i:1127725 original size:22 final size:22
Alignment explanation
Indices: 1127700--1127741 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1127690 ACCATTTTTC
1127700 TATTGATATAACTATTATTAAG
1 TATTGATATAACTATTATTAAG
* * *
1127722 TATTGTTATTATTATTATTA
1 TATTGATATAACTATTATTA
1127742 TTTATTATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (22 bp):
TATTGATATAACTATTATTAAG
Found at i:1127733 original size:3 final size:3
Alignment explanation
Indices: 1127712--1127772 Score: 59
Period size: 3 Copynumber: 19.7 Consensus size: 3
1127702 TTGATATAAC
* * * *
1127712 TAT TAT TAAG TAT TGT TAT TAT TAT TAT TATT TAT TAT AAT TAT TAC
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
*
1127759 TAC TAT TAT TAT TA
1 TAT TAT TAT TAT TA
1127773 ACTAATGATA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
3 43 0.90
4 5 0.10
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:1128408 original size:26 final size:24
Alignment explanation
Indices: 1128344--1128411 Score: 66
Period size: 26 Copynumber: 2.8 Consensus size: 24
1128334 GTTATAGATC
* *
1128344 ATTCTTTAAAATTATA-TTTGAAA
1 ATTCATTAAAAATATATTTTGAAA
* *
1128367 ATTCATTCGAATATATATTTTGAAA
1 ATTCATT-AAAAATATATTTTGAAA
1128392 ATATCATATAAAAATATATT
1 AT-TCAT-TAAAAATATATT
1128412 GGACAATCAC
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
23 6 0.17
24 6 0.17
25 9 0.26
26 13 0.37
27 1 0.03
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (24 bp):
ATTCATTAAAAATATATTTTGAAA
Found at i:1135124 original size:17 final size:15
Alignment explanation
Indices: 1135094--1135128 Score: 52
Period size: 17 Copynumber: 2.2 Consensus size: 15
1135084 CCGACCCGCT
1135094 GACCCGACATGACCC
1 GACCCGACATGACCC
1135109 GACCCGACTGATGACCC
1 GACCCGAC--ATGACCC
1135126 GAC
1 GAC
1135129 TGCCCGACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
17 10 0.56
ACGTcount: A:0.26, C:0.43, G:0.23, T:0.09
Consensus pattern (15 bp):
GACCCGACATGACCC
Found at i:1135214 original size:25 final size:25
Alignment explanation
Indices: 1135186--1135240 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
1135176 CAGTTGACTA
*
1135186 TTGACCGATCGTTGACCTTTGACCG
1 TTGACCGACCGTTGACCTTTGACCG
* * *
1135211 TTGACTGACCTTTTACCTTTGACCG
1 TTGACCGACCGTTGACCTTTGACCG
1135236 TTGAC
1 TTGAC
1135241 TTTGACAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.16, C:0.27, G:0.20, T:0.36
Consensus pattern (25 bp):
TTGACCGACCGTTGACCTTTGACCG
Found at i:1135219 original size:18 final size:18
Alignment explanation
Indices: 1135198--1135233 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1135188 GACCGATCGT
1135198 TGACCTTTGACCGTTGAC
1 TGACCTTTGACCGTTGAC
* *
1135216 TGACCTTTTACCTTTGAC
1 TGACCTTTGACCGTTGAC
1135234 CGTTGACTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.39
Consensus pattern (18 bp):
TGACCTTTGACCGTTGAC
Found at i:1136893 original size:3 final size:3
Alignment explanation
Indices: 1136879--1136942 Score: 74
Period size: 3 Copynumber: 20.7 Consensus size: 3
1136869 TTGATATAAC
* *
1136879 TAT TAT TAAT TAT TAT TGT TAT TAT TAT TAT TATT TAT TAT AAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
* *
1136926 TAC TAC TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
1136943 ACTAATAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
3 47 0.89
4 6 0.11
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1136907 original size:25 final size:25
Alignment explanation
Indices: 1136877--1136942 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 25
1136867 GATTGATATA
**
1136877 ACTATTATTAATTATTATTGTTATT
1 ACTATTATTAATTATTATAATTATT
* *
1136902 ATTATTATTATTTATTATAATTATT
1 ACTATTATTAATTATTATAATTATT
*
1136927 ACTACTATT-ATTATTA
1 ACTATTATTAATTATTA
1136943 ACTAATAATA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
24 6 0.18
25 28 0.82
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.59
Consensus pattern (25 bp):
ACTATTATTAATTATTATAATTATT
Found at i:1136919 original size:28 final size:28
Alignment explanation
Indices: 1136879--1136943 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
1136869 TTGATATAAC
* * * *
1136879 TATTATTAATTATTATTGTTATTATTAT
1 TATTATTAATTATAATTATTACTACTAT
*
1136907 TATTATTTATTATAATTATTACTACTAT
1 TATTATTAATTATAATTATTACTACTAT
1136935 TATTATTAA
1 TATTATTAA
1136944 CTAATAATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (28 bp):
TATTATTAATTATAATTATTACTACTAT
Found at i:1142654 original size:20 final size:20
Alignment explanation
Indices: 1142594--1142655 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
1142584 CACAATCAAA
*
1142594 CATGTTCTCCATGAACCCTAAT
1 CATGTTTTCCATGAA-CC-AAT
* * *
1142616 CATGAATTT-CATCATCCAAT
1 CATG-TTTTCCATGAACCAAT
1142636 CATGTTTTCCATGAACCAAT
1 CATGTTTTCCATGAACCAAT
1142656 TATAGCAAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
19 3 0.10
20 16 0.52
21 2 0.06
22 8 0.26
23 2 0.06
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.34
Consensus pattern (20 bp):
CATGTTTTCCATGAACCAAT
Found at i:1144502 original size:18 final size:18
Alignment explanation
Indices: 1144481--1144528 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1144471 TAAGTGATCG
1144481 TTGACCGTTGACCGACCT
1 TTGACCGTTGACCGACCT
*
1144499 TTGACCATTGACCGACCT
1 TTGACCGTTGACCGACCT
1144517 TTGACCGTTGAC
1 TTGACCGTTGAC
1144529 TTTGACCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.19, C:0.31, G:0.21, T:0.29
Consensus pattern (18 bp):
TTGACCGTTGACCGACCT
Found at i:1146191 original size:3 final size:3
Alignment explanation
Indices: 1146170--1146230 Score: 59
Period size: 3 Copynumber: 19.7 Consensus size: 3
1146160 TTGATATAAC
* * * *
1146170 TAT TAT TAAT TAT TGT TAT TAT TAT TAT TAT TATT TAT AAT TAC TAC
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
*
1146217 TAC TAT TAT TAT TA
1 TAT TAT TAT TAT TA
1146231 ACTAATAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
3 44 0.88
4 6 0.12
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:1146223 original size:25 final size:25
Alignment explanation
Indices: 1146168--1146229 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 25
1146158 GATTGATATA
* ** * *
1146168 ACTATTATTAATTATTGTTATTATT
1 ACTATTATTATTTATAATTACTACT
*
1146193 ATTATTATTATTTATAATTACTACT
1 ACTATTATTATTTATAATTACTACT
1146218 ACTATTATTATT
1 ACTATTATTATT
1146230 AACTAATAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (25 bp):
ACTATTATTATTTATAATTACTACT
Found at i:1146835 original size:24 final size:25
Alignment explanation
Indices: 1146800--1146846 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
1146790 TCATTCTTTA
1146800 AAATTATATTCA-AAAAT-TCATTC
1 AAATTATATTCAGAAAATATCATTC
1146823 AAATATATATTCAGAAAATATCAT
1 AAAT-TATATTCAGAAAATATCAT
1146847 ATAAAAATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.19
24 8 0.38
25 5 0.24
26 4 0.19
ACGTcount: A:0.51, C:0.11, G:0.02, T:0.36
Consensus pattern (25 bp):
AAATTATATTCAGAAAATATCATTC
Found at i:1147633 original size:23 final size:23
Alignment explanation
Indices: 1147615--1147698 Score: 125
Period size: 23 Copynumber: 3.7 Consensus size: 23
1147605 CTCGTATAAA
1147615 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1147638 TGCACCGAAGTG-TAGCGTAGAAT
1 TGCACCGAAGTGCCA-CGTAGAAT
* *
1147661 TGCACCAAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
1147684 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
1147699 TATAAAATGT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
22 1 0.02
23 52 0.98
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1147820 original size:20 final size:20
Alignment explanation
Indices: 1147784--1147821 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1147774 CAAAAGACCT
*
1147784 CATATATGTTCCAAAGGATA
1 CATATATGTCCCAAAGGATA
*
1147804 CATATATGTCCCGAAGGA
1 CATATATGTCCCAAAGGA
1147822 CCGCGTAGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26
Consensus pattern (20 bp):
CATATATGTCCCAAAGGATA
Found at i:1155001 original size:11 final size:11
Alignment explanation
Indices: 1154985--1155026 Score: 75
Period size: 11 Copynumber: 3.8 Consensus size: 11
1154975 TCTGATTACT
*
1154985 CATCTTTATTG
1 CATCTTCATTG
1154996 CATCTTCATTG
1 CATCTTCATTG
1155007 CATCTTCATTG
1 CATCTTCATTG
1155018 CATCTTCAT
1 CATCTTCAT
1155027 AACTCCTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.19, C:0.26, G:0.07, T:0.48
Consensus pattern (11 bp):
CATCTTCATTG
Found at i:1157428 original size:23 final size:23
Alignment explanation
Indices: 1157372--1157432 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
1157362 CTCGTATAAA
* *
1157372 TGCACCCAAGTGCCATGTAGAAT
1 TGCACCAAAGTGCCACGTAGAAT
* *
1157395 TGC-CCTGAAGTGCCGCGTAGAAT
1 TGCACC-AAAGTGCCACGTAGAAT
1157418 TGCACCAAAGTGCCA
1 TGCACCAAAGTGCCA
1157433 TATAAAATGT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
22 2 0.06
23 27 0.87
24 2 0.06
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.20
Consensus pattern (23 bp):
TGCACCAAAGTGCCACGTAGAAT
Found at i:1159720 original size:21 final size:21
Alignment explanation
Indices: 1159679--1159720 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1159669 TTTTAACTTA
*
1159679 TTTCAAAATTGACCATATAGT
1 TTTCAAAATTGACAATATAGT
* *
1159700 TTTCAAAATTTACAATTTAGT
1 TTTCAAAATTGACAATATAGT
1159721 CACTAGCCCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (21 bp):
TTTCAAAATTGACAATATAGT
Found at i:1160828 original size:21 final size:22
Alignment explanation
Indices: 1160804--1160856 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
1160794 TGTTTTGACA
1160804 TGAACTG-ATATCGATCCGAA-C
1 TGAACTGAAT-TCGATCCGAACC
* *
1160825 TGAAATTAATTCGATCCGAACC
1 TGAACTGAATTCGATCCGAACC
1160847 TGAACTGAAT
1 TGAACTGAAT
1160857 CTGATGTCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (22 bp):
TGAACTGAATTCGATCCGAACC
Found at i:1161208 original size:24 final size:24
Alignment explanation
Indices: 1161176--1161237 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
1161166 GGTTGAGTGA
1161176 CTGGATTTAGTTTTAGACCTAAAT
1 CTGGATTTAGTTTTAGACCTAAAT
1161200 CTGGATTTAGTTTTAGACCTAAAT
1 CTGGATTTAGTTTTAGACCTAAAT
* *
1161224 CTAGATTTTGTTTT
1 CTGGATTTAGTTTT
1161238 GTTATGGTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (24 bp):
CTGGATTTAGTTTTAGACCTAAAT
Found at i:1167463 original size:13 final size:13
Alignment explanation
Indices: 1167445--1167481 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1167435 GATATAACTA
1167445 TTATTAATTATTG
1 TTATTAATTATTG
1167458 TTATT-ATTATTTG
1 TTATTAATTA-TTG
1167471 TTA-TAATTATT
1 TTATTAATTATT
1167482 ACTACTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 7 0.32
13 15 0.68
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (13 bp):
TTATTAATTATTG
Found at i:1168427 original size:14 final size:16
Alignment explanation
Indices: 1168398--1168435 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
1168388 CTACCAACAC
1168398 AATATAATTCTGATAA
1 AATATAATTCTGATAA
1168414 AATA-AATTCT-ATAA
1 AATATAATTCTGATAA
*
1168428 AAAATAAT
1 AATATAAT
1168436 CGATACTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 7 0.35
15 9 0.45
16 4 0.20
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (16 bp):
AATATAATTCTGATAA
Found at i:1168820 original size:24 final size:24
Alignment explanation
Indices: 1168790--1168835 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1168780 TTTTGTCCAT
1168790 TTTTAT-ATTAATTTCAACTTAACA
1 TTTTATAATT-ATTTCAACTTAACA
*
1168814 TTTTATAATTATTTCGACTTAA
1 TTTTATAATTATTTCAACTTAA
1168836 TCCCTCATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.35, C:0.11, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTTATAATTATTTCAACTTAACA
Found at i:1169983 original size:21 final size:21
Alignment explanation
Indices: 1169957--1169996 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1169947 ATAAAGACAA
1169957 TGAG-AAATAAATAAAATAAGG
1 TGAGAAAATAAA-AAAATAAGG
1169978 TGAGAAAATAAAAAAATAA
1 TGAGAAAATAAAAAAATAA
1169997 ATATAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.17
Consensus pattern (21 bp):
TGAGAAAATAAAAAAATAAGG
Found at i:1170297 original size:2 final size:2
Alignment explanation
Indices: 1170290--1170336 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1170280 TAAAATATTA
1170290 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1170332 AT AT A
1 AT AT A
1170337 CATACGTATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1172206 original size:69 final size:69
Alignment explanation
Indices: 1172105--1172273 Score: 227
Period size: 69 Copynumber: 2.4 Consensus size: 69
1172095 CGAAGGTTTG
*
1172105 GTGTTTCAAGAGAAACATTTTCAAAGATTTTTTTTGTGTTTCAAGAGAAACAATTTCAAAGG-TT
1 GTGTTTCAAGAGAAACATTCTCAAAGATTTTTTTTGTGTTTCAAGA-AAACAATTTCAAAGGTTT
1172169 TTTTT
65 TTTTT
* ***
1172174 GTGTTTCAAGAGAAAC-TGTCTCAAGGGATTTTTTTTGTGTTTCAAGAAAATTGTTTCAAAGGTT
1 GTGTTTCAAGAGAAACAT-TCTCAA-AGATTTTTTTTGTGTTTCAAGAAAACAATTTCAAAGG-T
1172238 TTTTTTT
63 TTTTTTT
1172245 GTGTTTCAAGAGAAACAATT-TCAAAGATT
1 GTGTTTCAAGAGAAAC-ATTCTCAAAGATT
1172274 AGTGCTTCAA
Statistics
Matches: 88, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
68 1 0.01
69 33 0.38
70 25 0.28
71 27 0.31
72 1 0.01
73 1 0.01
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.43
Consensus pattern (69 bp):
GTGTTTCAAGAGAAACATTCTCAAAGATTTTTTTTGTGTTTCAAGAAAACAATTTCAAAGGTTTT
TTTT
Found at i:1172267 original size:36 final size:36
Alignment explanation
Indices: 1172105--1172270 Score: 223
Period size: 35 Copynumber: 4.7 Consensus size: 36
1172095 CGAAGGTTTG
*
1172105 GTGTTTCAAGAGAAACATTTTCAAA-GATTTTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGGATTTTTTTT
1172140 GTGTTTCAAGAGAAACAATTTCAAAGG--TTTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGGATTTTTTTT
** * *
1172174 GTGTTTCAAGAGAAACTGTCTCAAGGGATTTTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGGATTTTTTTT
*** *
1172210 GTGTTTCAAGA-AAATTGTTTCAAAGGTTTTTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGGATTTTTTTT
1172245 GTGTTTCAAGAGAAACAATTTCAAAG
1 GTGTTTCAAGAGAAACAATTTCAAAG
1172271 ATTAGTGCTT
Statistics
Matches: 115, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
34 30 0.26
35 55 0.48
36 30 0.26
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (36 bp):
GTGTTTCAAGAGAAACAATTTCAAAGGATTTTTTTT
Found at i:1172414 original size:29 final size:29
Alignment explanation
Indices: 1172332--1172401 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
1172322 GGAGACGAAA
* * *
1172332 TTTGTTTCAAGGAATATAGATTCAAAGAT
1 TTTGTTTCAAGGAAGACAGGTTCAAAGAT
1172361 TTTGTTTCAAGGAAGACAGGTTCAAAGAT
1 TTTGTTTCAAGGAAGACAGGTTCAAAGAT
1172390 TTTGTTTCAAGG
1 TTTGTTTCAAGG
1172402 GAAACTGTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.37
Consensus pattern (29 bp):
TTTGTTTCAAGGAAGACAGGTTCAAAGAT
Found at i:1172442 original size:36 final size:36
Alignment explanation
Indices: 1172390--1172777 Score: 377
Period size: 36 Copynumber: 11.2 Consensus size: 36
1172380 GTTCAAAGAT
*
1172390 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
1172426 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
1172462 CTTAGTTCCAACAGAAACTGTCTCAAGGGAGACGAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
1172499 TTTGTTTCAAG-GAAAACAGAT-TC-A-A-AG----AT
1 TTTGTTTCAAGAG-AAACTG-TCTCAAGAGAGACAAAA
*
1172528 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
1172564 -TT-TTT-AAGAGAAAATGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
1172597 TTTGTTTTAAAAGAAACTGTCTCAAGGGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
1172633 TTTGTTTCAAG-GAAAACAGAT-TC-----A-A-ATAT
1 TTTGTTTCAAGAG-AAACTG-TCTCAAGAGAGACAAAA
* *
1172662 TTTGTTTCAAGGGAAACTCTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
1172698 TTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
1172734 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1172770 CTTTGTTT
1 -TTTGTTT
1172778 TGAGTAAATT
Statistics
Matches: 290, Mismatches: 35, Indels: 53
0.77 0.09 0.14
Matches are distributed among these distances:
28 2 0.01
29 38 0.13
30 4 0.01
31 2 0.01
32 2 0.01
33 28 0.10
34 6 0.02
35 9 0.03
36 160 0.55
37 39 0.13
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:1172454 original size:167 final size:169
Alignment explanation
Indices: 1172280--1172638 Score: 507
Period size: 167 Copynumber: 2.1 Consensus size: 169
1172270 GATTAGTGCT
*
1172280 TCAAGAGAGACAAAACTTTGTTCCAAAATAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGA
1 TCAAGAGAGACAAAACTTTGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGA
* * ** *
1172345 ATATAGATTCAAAGATTTTGTTTCAA-GGAAGACAGGT-TC-A-A-AG-ATTTTGTTTCAAGGGA
66 AAACAGATTCAAAGATTTTGTTTCAAGGGAA-AC-GGTCTCAAGAGAGAAAATT-TTT-AAGAGA
* *
1172404 AACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTC
127 AAATGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTC
* *
1172447 TCAAGAGAGACAAAACTTAGTTCCAACAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGA
1 TCAAGAGAGACAAAACTTTGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGA
*
1172512 AAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTTTAAGAGAAA
66 AAACAGATTCAAAGATTTTGTTTCAAGGGAAACGGTCTCAAGAGAG--AAAATTTTTAAGAGAAA
1172577 ATGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTC
129 ATGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTC
*
1172618 TCAAGGGAGACAAAA-TTTGTT
1 TCAAGAGAGACAAAACTTTGTT
1172639 TCAAGGAAAA
Statistics
Matches: 171, Mismatches: 13, Indels: 13
0.87 0.07 0.07
Matches are distributed among these distances:
166 2 0.01
167 90 0.53
168 5 0.03
169 1 0.01
170 7 0.04
171 60 0.35
172 3 0.02
173 3 0.02
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (169 bp):
TCAAGAGAGACAAAACTTTGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGA
AAACAGATTCAAAGATTTTGTTTCAAGGGAAACGGTCTCAAGAGAGAAAATTTTTAAGAGAAAAT
GTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTC
Found at i:1172656 original size:134 final size:136
Alignment explanation
Indices: 1172361--1172777 Score: 676
Period size: 134 Copynumber: 3.1 Consensus size: 136
1172351 ATTCAAAGAT
* *
1172361 TTTGTTTCAAGGAAGACAGGTTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * ** *
1172426 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAACAGAAACTGTCTCAAGGG
66 -TTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAA-TTTGTTTTAAAAGAAACTGTCTCAAGGG
*
1172491 AGACGAAA
129 AGACAAAA
1172499 TTTGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1172564 -T-TTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTCTCAAGGGAG
66 TTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTCTCAAGGGAG
1172627 ACAAAA
131 ACAAAA
* *
1172633 TTTGTTTCAAGGAAAACAGATTCAAATATTTTGTTTCAAGGGAAACTCTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
1172698 TTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGA
66 -TTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTCTCAAGGGA
1172763 GACAAAA
130 GACAAAA
1172770 CTTTGTTT
1 -TTTGTTT
1172778 TGAGTAAATT
Statistics
Matches: 263, Mismatches: 12, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
134 94 0.36
135 31 0.12
136 2 0.01
137 66 0.25
138 70 0.27
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (136 bp):
TTTGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
TTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTCTCAAGGGAG
ACAAAA
Found at i:1172693 original size:65 final size:65
Alignment explanation
Indices: 1172475--1172777 Score: 260
Period size: 65 Copynumber: 4.5 Consensus size: 65
1172465 AGTTCCAACA
* *
1172475 GAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAG-GAAAACAGATTCAAAGATTTTGTTTCAAG
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAAACAGATTCAAA-ATTTTGTTTCAAG
1172539 G
65 G
**
1172540 GAAACTGTCTCAAGAGAGACAAAA-TT-TTT-AAGAGAAAATGTCTCAAGAGAGACAAAA-TTTG
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAAA-----C---AGATTCAAAATTTTG
* **
1172601 TTTTAAAA
58 TTTCAAGG
*
1172609 GAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAG-GAAAACAGATTCAAATATTTTGTTTCAAG
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAAACAGATTCAAA-ATTTTGTTTCAAG
1172673 G
65 G
* * **
1172674 GAAACTCTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAA-TTTG
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAAA-----C---AGATTCAAAATTTTG
* *
1172738 TTTTAAGA
58 TTTCAAGG
1172746 GAAACTGTCTCAAGAGAGACAAAACTTTGTTT
1 GAAACTGTCTCAAGAGAGACAAAA-TTTGTTT
1172778 TGAGTAAATT
Statistics
Matches: 193, Mismatches: 21, Indels: 40
0.76 0.08 0.16
Matches are distributed among these distances:
62 3 0.02
63 15 0.08
64 3 0.02
65 63 0.33
66 6 0.03
68 1 0.01
69 32 0.17
70 3 0.02
71 16 0.08
72 36 0.19
73 8 0.04
74 7 0.04
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (65 bp):
GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAAACAGATTCAAAATTTTGTTTCAAGG
Found at i:1172746 original size:19 final size:19
Alignment explanation
Indices: 1172688--1172747 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
1172678 CTCTCTCAAG
1172688 AGAGACAAAATTTGTTTTA
1 AGAGACAAAATTTGTTTTA
**
1172707 AGAG--AAAA--TGTCTCAA
1 AGAGACAAAATTTGT-TTTA
1172723 GAGAGACAAAATTTGTTTTA
1 -AGAGACAAAATTTGTTTTA
1172743 AGAGA
1 AGAGA
1172748 AACTGTCTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 12
0.66 0.09 0.26
Matches are distributed among these distances:
15 3 0.10
16 2 0.06
17 8 0.26
19 13 0.42
20 2 0.06
21 3 0.10
ACGTcount: A:0.45, C:0.07, G:0.20, T:0.28
Consensus pattern (19 bp):
AGAGACAAAATTTGTTTTA
Found at i:1174318 original size:95 final size:95
Alignment explanation
Indices: 1174150--1174331 Score: 294
Period size: 95 Copynumber: 1.9 Consensus size: 95
1174140 ATATGTAAAT
* *
1174150 ACCTTTATCAGGTTAGCTGAATATTATCCATAAAGCCGAGGTGTTTAACCAATTACCTTAGAGGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGAGGCGTTTAACCAATTACCTTAGAGGG
*
1174215 ACAGCTCAAGCTTTATTGTATAGTATAATC
66 ACAACTCAAGCTTTATTGTATAGTATAATC
* * *
1174245 ACCTTTATCAGGCTAGTTGAATATTATCCATATAGCCGAGGCGTTTAACCAATT-GCTCTAGAGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGAGGCGTTTAACCAATTACCT-TAGAGG
1174309 GACAACTCAAGCTTTATTGTATA
65 GACAACTCAAGCTTTATTGTATA
1174332 TAAATAATAT
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
94 2 0.03
95 78 0.98
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (95 bp):
ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGAGGCGTTTAACCAATTACCTTAGAGGG
ACAACTCAAGCTTTATTGTATAGTATAATC
Found at i:1178267 original size:21 final size:20
Alignment explanation
Indices: 1178229--1178281 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
1178219 AGTGATTTGA
1178229 AAATAAAGATAATGAG-AAAT
1 AAATAAA-ATAATGAGAAAAT
1178249 AAATAAAATAAGGTGAGAAAAT
1 AAATAAAATAA--TGAGAAAAT
*
1178271 AAAAAAAATAA
1 AAATAAAATAA
1178282 ATATAATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 4 0.14
20 7 0.24
21 4 0.14
22 14 0.48
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (20 bp):
AAATAAAATAATGAGAAAAT
Found at i:1178430 original size:2 final size:2
Alignment explanation
Indices: 1178423--1178452 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1178413 AATAACGATA
1178423 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1178453 GTGTGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1178596 original size:2 final size:2
Alignment explanation
Indices: 1178589--1178629 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1178579 TAAAATATTA
1178589 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1178630 AATAATAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1178741 original size:28 final size:29
Alignment explanation
Indices: 1178679--1178760 Score: 73
Period size: 28 Copynumber: 2.8 Consensus size: 29
1178669 GAAAATAATT
*
1178679 TAATAT-ATATATATATACATATAAT-AATAA
1 TAATATCA-ATATA-ATAAATA-AATGAATAA
*
1178709 TAATATGAATAATAA-AAATAAATGAATAA
1 TAATATCAAT-ATAATAAATAAATGAATAA
*
1178738 -AATATCTATATAATAAATAAATG
1 TAATATCAATATAATAAATAAATG
1178761 GACTAAATCG
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
27 4 0.09
28 19 0.42
29 9 0.20
30 9 0.20
31 4 0.09
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (29 bp):
TAATATCAATATAATAAATAAATGAATAA
Found at i:1179781 original size:2 final size:2
Alignment explanation
Indices: 1179774--1179805 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1179764 CAAATAAATA
1179774 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1179806 CAATATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1183655 original size:80 final size:80
Alignment explanation
Indices: 1183445--1184702 Score: 1546
Period size: 80 Copynumber: 15.4 Consensus size: 80
1183435 TTGTTGACAA
* * * *
1183445 ATAGCCCTTCTCGCCTTAAGTTATGCTGTAAATTTGATGTGCCTTTGAGCTGAGTGTAATCGAAC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAA--TGATGTGCCTTTGAGCTGAGTGTAATCGAAC
* *
1183510 TCAAAGGTCTTTTGTTGGTAG
64 TCGAAGGTC---T-TTGGCAG
* * * * *
1183531 ATATCCCTTCTTGCCTTAAGCTATGCTGCAAATGATGTGTCTTTGAACTGAGTGTAATCAAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1183596 GAAGGTCTTTGGCAG
66 GAAGGTCTTTGGCAG
* * * *
1183611 ATAGCCCTTCTTGCCTTGAGCTAAGGTACAAATGATGTGCCTTTGAGCTGAGTGTAATCAAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
*
1183676 GAAGGTCTTTTGTTGGCAT
66 GAAGGTC---T-TTGGCAG
** * *
1183695 ATAGCCCTTCTTGCCTTGAGCTATGCTATAAATGGTGTGCCTTTGAGCTGAGTGTAATTGAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
*
1183760 GAAGGTATTGGTTGGCAG
66 GAAGGT-CT--TTGGCAG
* *
1183778 ATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
*
1183843 GAAGGACTTTGGCAG
66 GAAGGTCTTTGGCAG
* * * * *
1183858 ATAGCCCTTCCTGCCTTGAGCTTTACTACAAATGATGTGCCTTTGAGCTTAGTGTAATCGAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1183923 GAAGGTCTTTGGCAG
66 GAAGGTCTTTGGCAG
* * * *
1183938 ATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCAAACTT
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1184003 GAAGGTCTTTGGCAG
66 GAAGGTCTTTGGCAG
* *
1184018 ATAGCCCTTCTTACCTTGAGCTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1184083 GAAGGTCTTTGGCAG
66 GAAGGTCTTTGGCAG
* * *
1184098 GTAGCCCTTCCTGCCTTGAGCTATTCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1184163 GAAGGTCTTTGGCAG
66 GAAGGTCTTTGGCAG
* * * * * *
1184178 ATAGTCCTTCTTACCTTGAGCTATGCTGCAAATGATGTGTCTTTTAGCTGAGTGGAATCGTACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1184243 GAAGGTCTTTGTTGGCAG
66 GAAGGTC--T-TTGGCAG
* * * * *
1184261 ATAGCCCTTCTTGCCTTGAGGTATGCTACAAATGATGTTCCTTTGAGCTGCGTGTAATCAAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1184326 GAAGGTCTTTGGCAG
66 GAAGGTCTTTGGCAG
* * * ** * * *
1184341 ACATCCCTTCTTTCCTTGAGCTATATTGCAAATAATTTACCTTTGAGCTGAGTGTAATCGAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1184406 GAAGGTCTTTGTTGGCAG
66 GAAGGTC--T-TTGGCAG
* *
1184424 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATAATGTGCCTTTGAGCTGAGTGTAATCAAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
* *
1184489 AAAGGTCTTGGTTGGTAG
66 GAAGGTC-T--TTGGCAG
* * * *
1184507 ATAGCCCTTCTTGCCTTGAACTATGCTGCAGATGATGTGCCGTTGAGCTGAGTGTAATCGAAGTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
*
1184572 GAAGGTCTTTTGATGACAA
66 GAAGGTC-TTTG--G-CAG
* * * * * *
1184591 ATAACCCTTCTAGCCTTGAGTTATGCTGGAAATGATATGTCC-TTGAGCTGAGTGTAATCAAACT
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTG-CCTTTGAGCTGAGTGTAATCGAACT
* *
1184655 TGAAGGTCTTGGCTGACAG
65 CGAAGGTCTT---TGGCAG
* * *
1184674 ATAACCCTTCTTTCCTTGAGTTATGCTGC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGC
1184703 CAATAGTTCC
Statistics
Matches: 1027, Mismatches: 125, Indels: 43
0.86 0.10 0.04
Matches are distributed among these distances:
80 502 0.49
81 5 0.00
82 6 0.01
83 315 0.31
84 167 0.16
85 2 0.00
86 30 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (80 bp):
ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
GAAGGTCTTTGGCAG
Found at i:1186054 original size:99 final size:99
Alignment explanation
Indices: 1185882--1186079 Score: 274
Period size: 99 Copynumber: 2.0 Consensus size: 99
1185872 CAACTCAATA
* * * * *
1185882 TATAAACACCTTTATCATGTTAGCTGAATCTTATCCATAAAGCCGGGGCGTTTAACTAATTGCCT
1 TATAAACACCTCTATCAAGCTAGCTAAATCTTATCCATAAAGCCGGGGCGTTTAACCAATTGCCT
* *
1185947 TAGTGGGACAACTCAAGCTTTATTGTATAGATAT
66 TAGAGGGACAACTCAAGCTTTATTATATAGATAT
*
1185981 TATAATCACCTCTATCAAGCTAGCTAAATCTTATCCATAGAA-CCGGGGCGTTTAACCAATTG-C
1 TATAAACACCTCTATCAAGCTAGCTAAATCTTATCCATA-AAGCCGGGGCGTTTAACCAATTGCC
* *
1186044 TCTAGAGGGACAATTCAAGCTTTATTATATATATAT
65 T-TAGAGGGACAACTCAAGCTTTATTATATAGATAT
1186080 AATATTATAA
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
98 2 0.02
99 83 0.95
100 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (99 bp):
TATAAACACCTCTATCAAGCTAGCTAAATCTTATCCATAAAGCCGGGGCGTTTAACCAATTGCCT
TAGAGGGACAACTCAAGCTTTATTATATAGATAT
Found at i:1194305 original size:9 final size:9
Alignment explanation
Indices: 1194291--1194338 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
1194281 AAGGCAAAAG
1194291 TGACCGGTT
1 TGACCGGTT
1194300 TGACCGGTTT
1 TGACCGG-TT
* *
1194310 TGGAACTGTTT
1 T-G-ACCGGTT
1194321 TGACCGGTT
1 TGACCGGTT
1194330 TGACCGGTT
1 TGACCGGTT
1194339 ACAACCCGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
9 21 0.66
10 4 0.12
11 4 0.12
12 3 0.09
ACGTcount: A:0.12, C:0.19, G:0.31, T:0.38
Consensus pattern (9 bp):
TGACCGGTT
Found at i:1194397 original size:23 final size:23
Alignment explanation
Indices: 1194342--1194397 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
1194332 ACCGGTTACA
*
1194342 ACCCGACCCAACCCGTTCACCCG
1 ACCCGACCCGACCCGTTCACCCG
*
1194365 ACCCGACCCGACCCGTTGACCC-
1 ACCCGACCCGACCCGTTCACCCG
1194387 ACCCCGACCCG
1 A-CCCGACCCG
1194398 TTGACCGTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 1 0.03
23 29 0.97
ACGTcount: A:0.20, C:0.57, G:0.16, T:0.07
Consensus pattern (23 bp):
ACCCGACCCGACCCGTTCACCCG
Found at i:1197317 original size:32 final size:31
Alignment explanation
Indices: 1197244--1197320 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
1197234 CTAATGTGAC
* * *
1197244 TCTTAGGTAGGCTCTGTGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
** **
1197275 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGAT-CAT
1197307 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
1197321 CACAGCCCCG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.14, C:0.26, G:0.31, T:0.29
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
Found at i:1198302 original size:22 final size:22
Alignment explanation
Indices: 1198277--1198329 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
1198267 TTGATATAAC
*
1198277 TATTATTAATTATTGTTATTAT
1 TATTATTAATTATTATTATTAT
*
1198299 TATTATTTATTATTATTATTAT
1 TATTATTAATTATTATTATTAT
1198321 TATTATTAA
1 TATTATTAA
1198330 CTAAGAGTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TATTATTAATTATTATTATTAT
Found at i:1198348 original size:3 final size:3
Alignment explanation
Indices: 1198277--1198328 Score: 77
Period size: 3 Copynumber: 16.7 Consensus size: 3
1198267 TTGATATAAC
*
1198277 TAT TAT TAAT TAT TGT TAT TAT TAT TATT TAT TAT TAT TAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
1198324 TAT TA
1 TAT TA
1198329 ACTAAGAGTA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 39 0.87
4 6 0.13
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1206276 original size:19 final size:19
Alignment explanation
Indices: 1206248--1206286 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1206238 TAACCGCACT
*
1206248 ACCCTTATAATCAT-AAGCA
1 ACCCTAATAAT-ATAAAGCA
1206267 ACCCTAATAATATAAAGCA
1 ACCCTAATAATATAAAGCA
1206286 A
1 A
1206287 AACCAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.49, C:0.23, G:0.05, T:0.23
Consensus pattern (19 bp):
ACCCTAATAATATAAAGCA
Found at i:1208063 original size:19 final size:19
Alignment explanation
Indices: 1208037--1208077 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1208027 ATTCGCACAA
1208037 AAACATTTATTT-CGAGAC
1 AAACATTTATTTACGAGAC
*
1208055 AAACTATTTATTTATGAGAC
1 AAAC-ATTTATTTACGAGAC
1208075 AAA
1 AAA
1208078 ATATATATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 8 0.40
20 8 0.40
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (19 bp):
AAACATTTATTTACGAGAC
Found at i:1209136 original size:19 final size:19
Alignment explanation
Indices: 1209112--1209150 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1209102 GAAACCCCTT
*
1209112 TGAAAACACATGATTTTAA
1 TGAAAACACATAATTTTAA
*
1209131 TGAAAATACATAATTTTAA
1 TGAAAACACATAATTTTAA
1209150 T
1 T
1209151 AAAGATAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.36
Consensus pattern (19 bp):
TGAAAACACATAATTTTAA
Found at i:1214628 original size:31 final size:30
Alignment explanation
Indices: 1214584--1214651 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 30
1214574 TTGATATAAC
** *
1214584 TATTATTAATTATTATTGTTATTATTATTAT
1 TATTA-TAATTATTATAATTATTACTATTAT
1214615 TATTATAATTTATTATAATTATTACTATTAT
1 TATTATAA-TTATTATAATTATTACTATTAT
1214646 TATTAT
1 TATTAT
1214652 TAACTAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 3 0.09
31 30 0.91
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (30 bp):
TATTATAATTATTATAATTATTACTATTAT
Found at i:1214673 original size:3 final size:3
Alignment explanation
Indices: 1214584--1214653 Score: 86
Period size: 3 Copynumber: 22.7 Consensus size: 3
1214574 TTGATATAAC
* *
1214584 TAT TAT TAAT TAT TAT TGT TAT TAT TAT TAT TAT TAT AATT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
* *
1214631 AAT TAT TAC TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
1214654 ACTAATAATA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
3 52 0.91
4 5 0.09
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1217172 original size:19 final size:19
Alignment explanation
Indices: 1217148--1217186 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1217138 GAAACCCCTT
*
1217148 TGAAAACACATGATTTTAA
1 TGAAAACACATAATTTTAA
*
1217167 TGAAAATACATAATTTTAA
1 TGAAAACACATAATTTTAA
1217186 T
1 T
1217187 AAAGATAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.36
Consensus pattern (19 bp):
TGAAAACACATAATTTTAA
Found at i:1218694 original size:3 final size:3
Alignment explanation
Indices: 1218608--1218674 Score: 71
Period size: 3 Copynumber: 21.7 Consensus size: 3
1218598 TTGATATAAC
* * * *
1218608 TAT TAT TAAT TAT TGT TGT TGT TAT TAT TAT TAT TATT TAT TAT AAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
*
1218655 TAT TAC TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
1218675 ACTAATAATA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
3 50 0.89
4 6 0.11
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1223672 original size:19 final size:19
Alignment explanation
Indices: 1223632--1223703 Score: 117
Period size: 19 Copynumber: 3.7 Consensus size: 19
1223622 AACGCGATAG
1223632 TCAAATTCGCAACGTGGAATT
1 TCAAATTCGCAAC-T-GAATT
1223653 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
1223672 TCAAGTTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
1223691 TCAAATTCGCAAC
1 TCAAATTCGCAAC
1223704 AGGTTTTTGT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 35 0.71
20 1 0.02
21 13 0.27
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:1223895 original size:16 final size:15
Alignment explanation
Indices: 1223860--1223898 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1223850 TCCCCATCTC
*
1223860 TAATTTTTTTTTACA
1 TAATTTTTTTCTACA
*
1223875 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
1223891 TAATTTTT
1 TAATTTTT
1223899 CAATGATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:1224408 original size:12 final size:12
Alignment explanation
Indices: 1224387--1224420 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1224377 ACCACATTTC
*
1224387 CAATACCAAACA
1 CAATATCAAACA
1224399 CAATATCAAACA
1 CAATATCAAACA
*
1224411 CAATCTCAAA
1 CAATATCAAA
1224421 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1226156 original size:20 final size:20
Alignment explanation
Indices: 1226144--1226206 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
1226134 AAACTTAAAT
1226144 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
1226164 TCACAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
1226184 TCGCAACGCGAAACT-AAAA
1 TCGCAACGCGAAAATGAAAA
1226203 TCGC
1 TCGC
1226207 GTTGTGATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 8 0.20
20 32 0.80
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:1226725 original size:20 final size:19
Alignment explanation
Indices: 1226697--1226827 Score: 122
Period size: 20 Copynumber: 6.6 Consensus size: 19
1226687 ACATTTGTCT
* *
1226697 TTCGCGTTGCAAATTTGAC
1 TTCGTGTTGCGAATTTGAC
1226716 TTCTGTGTTGCG-ATTT-AC
1 TTC-GTGTTGCGAATTTGAC
* *
1226734 AAATTCGCGTTGCAAATTTGAC
1 ---TTCGTGTTGCGAATTTGAC
1226756 TTTCGTGTTGCGAATTTGAC
1 -TTCGTGTTGCGAATTTGAC
* *
1226776 TATCGCGTTGTGAATTTGAC
1 T-TCGTGTTGCGAATTTGAC
*
1226796 TTTGTGTTGCGAATTTGAC
1 TTCGTGTTGCGAATTTGAC
1226815 TATCGTGTTGCGA
1 T-TCGTGTTGCGA
1226828 TTTACAAATT
Statistics
Matches: 91, Mismatches: 13, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
18 2 0.02
19 24 0.26
20 56 0.62
21 7 0.08
22 2 0.02
ACGTcount: A:0.19, C:0.16, G:0.24, T:0.41
Consensus pattern (19 bp):
TTCGTGTTGCGAATTTGAC
Found at i:1226752 original size:40 final size:39
Alignment explanation
Indices: 1226697--1226814 Score: 150
Period size: 40 Copynumber: 2.9 Consensus size: 39
1226687 ACATTTGTCT
1226697 TTCGCGTTGCAAATTTGACTTCTGTGTTGCGATTT-ACAAA
1 TTCGCGTTGCAAATTTGACTT-TGTGTTGCGATTTGAC-AA
*
1226737 TTCGCGTTGCAAATTTGACTTTCGTGTTGCGAATTTGACTA
1 TTCGCGTTGCAAATTTGACTTT-GTGTTGCG-ATTTGACAA
**
1226778 -TCGCGTTGTGAATTTGACTTTGTGTTGCGAATTTGAC
1 TTCGCGTTGCAAATTTGACTTTGTGTTGCG-ATTTGAC
1226815 TATCGTGTTG
Statistics
Matches: 72, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
39 17 0.24
40 48 0.67
41 5 0.07
42 2 0.03
ACGTcount: A:0.19, C:0.16, G:0.23, T:0.42
Consensus pattern (39 bp):
TTCGCGTTGCAAATTTGACTTTGTGTTGCGATTTGACAA
Found at i:1226844 original size:20 final size:20
Alignment explanation
Indices: 1226821--1226867 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
1226811 TGACTATCGT
1226821 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
*
1226841 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAAATTCGC
1226861 GTTGCGA
1 GTTGCGA
1226868 ATTTGGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:1227104 original size:18 final size:18
Alignment explanation
Indices: 1227083--1227127 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
1227073 TGATTCGCAC
* *
1227083 AAAAATATTTTTTTCGAG
1 AAAAATATTTATTTAGAG
*
1227101 AAAAACTATTTATTTATAG
1 AAAAA-TATTTATTTAGAG
1227120 AAAAATAT
1 AAAAATAT
1227128 ATAACTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40
Consensus pattern (18 bp):
AAAAATATTTATTTAGAG
Found at i:1227454 original size:3 final size:3
Alignment explanation
Indices: 1227446--1227470 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1227436 AATTATCCTG
1227446 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1227471 TTACATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1229398 original size:22 final size:21
Alignment explanation
Indices: 1229358--1229398 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1229348 ATTTATATTT
1229358 AAGTTTCATATCTTTAAAAAA
1 AAGTTTCATATCTTTAAAAAA
*
1229379 AAGTTTCATATCTTTTAAAA
1 AAGTTTCATATCTTTAAAAA
1229399 TCATTCTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (21 bp):
AAGTTTCATATCTTTAAAAAA
Found at i:1231433 original size:24 final size:25
Alignment explanation
Indices: 1231382--1231472 Score: 148
Period size: 25 Copynumber: 3.7 Consensus size: 25
1231372 ATTTGTATTT
1231382 AAGTTTCATATCTTTTACAAAAAAA
1 AAGTTTCATATCTTTTACAAAAAAA
1231407 AAGTTTCATATCTTTTAC-AAAAAA
1 AAGTTTCATATCTTTTACAAAAAAA
*
1231431 AAGTTTAATATCTTTTACAAAAAAA
1 AAGTTTCATATCTTTTACAAAAAAA
* *
1231456 AAGTTTTACATCTTTTA
1 AAGTTTCATATCTTTTA
1231473 AAATCATTCT
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
24 23 0.37
25 39 0.63
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.40
Consensus pattern (25 bp):
AAGTTTCATATCTTTTACAAAAAAA
Found at i:1231667 original size:13 final size:13
Alignment explanation
Indices: 1231651--1231682 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
1231641 TAACTTTTAT
1231651 TTTTTAAAATTAA
1 TTTTTAAAATTAA
1231664 -TTTTAAAATTAA
1 TTTTTAAAATTAA
1231676 TTTTTAA
1 TTTTTAA
1231683 TATAAAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTTAAAATTAA
Found at i:1232605 original size:20 final size:20
Alignment explanation
Indices: 1232576--1232621 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1232566 AATAATAAGC
*
1232576 AAACCTGATAATATAAAGAA
1 AAACCAGATAATATAAAGAA
*
1232596 AAACCAGATAATATAAAGCA
1 AAACCAGATAATATAAAGAA
1232616 AAACCA
1 AAACCA
1232622 AAACAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.61, C:0.15, G:0.09, T:0.15
Consensus pattern (20 bp):
AAACCAGATAATATAAAGAA
Found at i:1234810 original size:30 final size:30
Alignment explanation
Indices: 1234767--1234837 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 30
1234757 CAAAATATAT
* *
1234767 AACTTTTAAAAA-TTATATTCTTAGTCCCAA
1 AACTTTTAAAAATTTATACT-TTAGTCACAA
** *
1234797 AACTTTTCCAAATTTATACTTTGGTCACAA
1 AACTTTTAAAAATTTATACTTTAGTCACAA
*
1234827 AACTTTCAAAA
1 AACTTTTAAAA
1234838 CATGCATTTT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
30 26 0.81
31 6 0.19
ACGTcount: A:0.39, C:0.18, G:0.04, T:0.38
Consensus pattern (30 bp):
AACTTTTAAAAATTTATACTTTAGTCACAA
Found at i:1238509 original size:24 final size:24
Alignment explanation
Indices: 1238482--1238546 Score: 112
Period size: 24 Copynumber: 2.7 Consensus size: 24
1238472 ATTTGTATTT
1238482 AAGTTTCATATCTTTTACAAAAAA
1 AAGTTTCATATCTTTTACAAAAAA
*
1238506 AAGTTTCATATCTTTTATAAAAAA
1 AAGTTTCATATCTTTTACAAAAAA
*
1238530 AAGTTTTATATCTTTTA
1 AAGTTTCATATCTTTTA
1238547 AAATCATTCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.45
Consensus pattern (24 bp):
AAGTTTCATATCTTTTACAAAAAA
Found at i:1243065 original size:60 final size:60
Alignment explanation
Indices: 1242978--1243096 Score: 229
Period size: 60 Copynumber: 2.0 Consensus size: 60
1242968 TAAAATTAAC
*
1242978 TCGATCCGAACCCGAATTGAATTTGATGTCAAATCAACCAAAAAATGACCTGAACTGATA
1 TCGATCCGAACCCGAATTGAATCTGATGTCAAATCAACCAAAAAATGACCTGAACTGATA
1243038 TCGATCCGAACCCGAATTGAATCTGATGTCAAATCAACCAAAAAATGACCTGAACTGAT
1 TCGATCCGAACCCGAATTGAATCTGATGTCAAATCAACCAAAAAATGACCTGAACTGAT
1243097 TTTACCCAGA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.23
Consensus pattern (60 bp):
TCGATCCGAACCCGAATTGAATCTGATGTCAAATCAACCAAAAAATGACCTGAACTGATA
Found at i:1244597 original size:24 final size:24
Alignment explanation
Indices: 1244565--1244653 Score: 151
Period size: 24 Copynumber: 3.7 Consensus size: 24
1244555 ATATGTATTT
*
1244565 AAGTTTCATATCTTTCACAAAAAA
1 AAGTTTCATATCTTTTACAAAAAA
1244589 AAGTTTCATATCTTTTACAAAAAA
1 AAGTTTCATATCTTTTACAAAAAA
*
1244613 AAGTTTAATATCTTTTACAAAAAA
1 AAGTTTCATATCTTTTACAAAAAA
*
1244637 AAGTTTTATATCTTTTA
1 AAGTTTCATATCTTTTA
1244654 AAATCATTCT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.40
Consensus pattern (24 bp):
AAGTTTCATATCTTTTACAAAAAA
Found at i:1245363 original size:20 final size:20
Alignment explanation
Indices: 1245338--1245384 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
1245328 TAATAATAAG
1245338 AAAACCAGATAATATAAAGC
1 AAAACCAGATAATATAAAGC
1245358 AAAACCAGATAATATAAAGC
1 AAAACCAGATAATATAAAGC
1245378 AAAACCA
1 AAAACCA
1245385 AAACAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.62, C:0.17, G:0.09, T:0.13
Consensus pattern (20 bp):
AAAACCAGATAATATAAAGC
Found at i:1248450 original size:13 final size:13
Alignment explanation
Indices: 1248432--1248458 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1248422 CGACCTGAAT
1248432 TTTGAACGTGGTA
1 TTTGAACGTGGTA
1248445 TTTGAACGTGGTA
1 TTTGAACGTGGTA
1248458 T
1 T
1248459 GTGGTGGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.30, T:0.41
Consensus pattern (13 bp):
TTTGAACGTGGTA
Found at i:1249945 original size:13 final size:13
Alignment explanation
Indices: 1249929--1249960 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
1249919 AACTTTTATT
1249929 TTTTTAAAATTAA
1 TTTTTAAAATTAA
1249942 TTTTT-AAATTAA
1 TTTTTAAAATTAA
1249954 TTTTTAA
1 TTTTTAA
1249961 TATAAAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTTTAAAATTAA
Found at i:1251016 original size:19 final size:19
Alignment explanation
Indices: 1250988--1251026 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1250978 CAACCGCACT
*
1250988 ACCCTTATAATCAT-AAGCA
1 ACCCTAATAAT-ATAAAGCA
1251007 ACCCTAATAATATAAAGCA
1 ACCCTAATAATATAAAGCA
1251026 A
1 A
1251027 AACCAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.49, C:0.23, G:0.05, T:0.23
Consensus pattern (19 bp):
ACCCTAATAATATAAAGCA
Found at i:1253933 original size:19 final size:19
Alignment explanation
Indices: 1253909--1253947 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1253899 GAAACCCCTT
*
1253909 TGAAAACACATGATTTTAA
1 TGAAAACACATAATTTTAA
*
1253928 TGAAAATACATAATTTTAA
1 TGAAAACACATAATTTTAA
1253947 T
1 T
1253948 AAAGATAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.36
Consensus pattern (19 bp):
TGAAAACACATAATTTTAA
Found at i:1255454 original size:3 final size:3
Alignment explanation
Indices: 1255389--1255434 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
1255379 ATTGTTGTTC
* *
1255389 TTA TTA TTA TTA TTA TTTA TTA TAA TTA TTA CTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1255435 ACTAATAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1257953 original size:19 final size:19
Alignment explanation
Indices: 1257929--1257967 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1257919 GAAACCCCTT
*
1257929 TGAAAACACATGATTTTAA
1 TGAAAACACATAATTTTAA
*
1257948 TGAAAATACATAATTTTAA
1 TGAAAACACATAATTTTAA
1257967 T
1 T
1257968 AAAGATAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.36
Consensus pattern (19 bp):
TGAAAACACATAATTTTAA
Found at i:1259429 original size:31 final size:31
Alignment explanation
Indices: 1259391--1259461 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
1259381 TTGATATAAC
* ** * *
1259391 TATTATTAATTATTGTTGTTGTTATTATTAT
1 TATTATTAATTATTATAATTATTAATATTAT
*
1259422 TATTATTATTTATTATAATTATTAATATTAT
1 TATTATTAATTATTATAATTATTAATATTAT
1259453 TATTATTAA
1 TATTATTAA
1259462 CTAATAATAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (31 bp):
TATTATTAATTATTATAATTATTAATATTAT
Found at i:1259469 original size:22 final size:22
Alignment explanation
Indices: 1259425--1259483 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
1259415 TTATTATTAT
* *
1259425 TATTATTTATTA-TAATTATTAA
1 TATTA-TTATTATTAACTAATAA
1259447 TATTATTATTATTAACTAATAA
1 TATTATTATTATTAACTAATAA
*
1259469 TAATATTATTATTAA
1 TATTATTATTATTAA
1259484 AATAAATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 6 0.18
22 27 0.82
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
TATTATTATTATTAACTAATAA
Found at i:1259472 original size:25 final size:24
Alignment explanation
Indices: 1259422--1259482 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 24
1259412 TTATTATTAT
*
1259422 TATTATTATTTATTATAATTATTAA
1 TATTATTA-TTATTATAATTAATAA
1259447 TATTATTATTATTAACTAA-TAATAA
1 TATTATTATTATT-A-TAATTAATAA
1259472 TATTATTATTA
1 TATTATTATTA
1259483 AAATAAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
24 5 0.15
25 25 0.76
26 3 0.09
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
TATTATTATTATTATAATTAATAA
Found at i:1259480 original size:3 final size:3
Alignment explanation
Indices: 1259391--1259460 Score: 77
Period size: 3 Copynumber: 22.7 Consensus size: 3
1259381 TTGATATAAC
* * *
1259391 TAT TAT TAAT TAT TGT TGT TGT TAT TAT TAT TAT TAT TATT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
* *
1259438 AAT TAT TAA TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
1259461 ACTAATAATA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
3 53 0.90
4 6 0.10
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1262619 original size:20 final size:22
Alignment explanation
Indices: 1262594--1262634 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1262584 CAATGTTCTG
1262594 TCTTTTC-GT-GTGATATTTTT
1 TCTTTTCTGTGGTGATATTTTT
*
1262614 TCTTTTCTTTGGTGATATTTT
1 TCTTTTCTGTGGTGATATTTT
1262635 GATGGTCGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 1 0.06
22 10 0.56
ACGTcount: A:0.10, C:0.10, G:0.15, T:0.66
Consensus pattern (22 bp):
TCTTTTCTGTGGTGATATTTTT
Found at i:1263989 original size:19 final size:19
Alignment explanation
Indices: 1263961--1263999 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1263951 CAACCGCACT
*
1263961 ACCCTTATAATCAT-AAGCA
1 ACCCTAATAAT-ATAAAGCA
1263980 ACCCTAATAATATAAAGCA
1 ACCCTAATAATATAAAGCA
1263999 A
1 A
1264000 AACCAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.49, C:0.23, G:0.05, T:0.23
Consensus pattern (19 bp):
ACCCTAATAATATAAAGCA
Found at i:1266283 original size:20 final size:20
Alignment explanation
Indices: 1266258--1266350 Score: 111
Period size: 20 Copynumber: 4.7 Consensus size: 20
1266248 TTGACAGAAG
*
1266258 TCAAATTCACAACGCGATAT
1 TCAAATTCGCAACGCGATAT
*
1266278 TCAAATTCGCAACGCGATAG
1 TCAAATTCGCAACGCGATAT
1266298 TCAAATTCGCAACGCGGA-ATT
1 TCAAATTCGCAACGC-GATA-T
*
1266319 TCAAATTCGCAAC-TGA-ATT
1 TCAAATTCGCAACGCGATA-T
1266338 TCAAATTCGCAAC
1 TCAAATTCGCAAC
1266351 AGGTTTTAGT
Statistics
Matches: 67, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
19 18 0.27
20 34 0.51
21 15 0.22
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.25
Consensus pattern (20 bp):
TCAAATTCGCAACGCGATAT
Found at i:1266533 original size:16 final size:16
Alignment explanation
Indices: 1266508--1266544 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1266498 CCCTATCTCT
*
1266508 ATTTTTTTTTTACATA
1 ATTTTATTTTTACATA
*
1266524 ATTTTATTTTTATATA
1 ATTTTATTTTTACATA
1266540 ATTTT
1 ATTTT
1266545 TCAATGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (16 bp):
ATTTTATTTTTACATA
Found at i:1267284 original size:24 final size:24
Alignment explanation
Indices: 1267257--1267310 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1267247 GTATTCAAAA
*
1267257 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGGCAATACCCGGAC
* * *
1267281 TTTGATCTTGGGGAATACTCGGAT
1 TTTGATCTTGGGCAATACCCGGAC
1267305 TTTGAT
1 TTTGAT
1267311 GATGTGATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (24 bp):
TTTGATCTTGGGCAATACCCGGAC
Found at i:1269101 original size:19 final size:19
Alignment explanation
Indices: 1269050--1269103 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
1269040 AGAAGTTTCT
*
1269050 GAAACTTAAATTCGCAACGC
1 GAAAC-TAAAATCGCAACGC
*
1269070 GAAAATGAAAATCGCAACGC
1 GAAACT-AAAATCGCAACGC
1269090 GAAACTAAAATCGC
1 GAAACTAAAATCGC
1269104 GTTGTGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.30
20 21 0.70
ACGTcount: A:0.46, C:0.22, G:0.17, T:0.15
Consensus pattern (19 bp):
GAAACTAAAATCGCAACGC
Found at i:1269611 original size:20 final size:20
Alignment explanation
Indices: 1269586--1269712 Score: 129
Period size: 19 Copynumber: 6.5 Consensus size: 20
1269576 GCGTAAAAAC
1269586 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
1269606 ATTTGACTATCGCATTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
1269626 ATTTGA-TTTATGTGTTGCG-
1 ATTTGACTTT-CGCGTTGCGA
*
1269645 ATTT-ACAAATTCGCGTTGCGA
1 ATTTGAC--TTTCGCGTTGCGA
*
1269666 ATTTGAC-TTCGTGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
1269685 ATTTGACTTT-GTGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
1269704 ATTTGACTT
1 ATTTGACTT
1269713 CTATGTTGCG
Statistics
Matches: 90, Mismatches: 10, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
18 1 0.01
19 42 0.47
20 39 0.43
21 6 0.07
22 2 0.02
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.43
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:1269643 original size:40 final size:39
Alignment explanation
Indices: 1269586--1269747 Score: 145
Period size: 40 Copynumber: 4.1 Consensus size: 39
1269576 GCGTAAAAAC
* *
1269586 ATTTGACTTTCGCGTTGCGAATTTGACTATCGCATTGCGA
1 ATTTGACTTT-GTGTTGCGAATTTGACTATCGCGTTGCGA
* *
1269626 ATTTGATTTATGTGTTGCG-ATTT-ACAAATTCGCGTTGCGA
1 ATTTGACTT-TGTGTTGCGAATTTGAC-TA-TCGCGTTGCGA
* * *
1269666 ATTTGACTTCGTGTTGCGAATTTGACT-TTGTGTTGCGA
1 ATTTGACTTTGTGTTGCGAATTTGACTATCGCGTTGCGA
* *
1269704 ATTTGACTTCTATGTTGCG-ATTT-ACAGATTCGCGTTGCGA
1 ATTTGACTT-TGTGTTGCGAATTTGAC-TA-TCGCGTTGCGA
1269744 ATTT
1 ATTT
1269748 AGAAAAGCGT
Statistics
Matches: 99, Mismatches: 14, Indels: 18
0.76 0.11 0.14
Matches are distributed among these distances:
37 2 0.02
38 24 0.24
39 20 0.20
40 50 0.51
41 3 0.03
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (39 bp):
ATTTGACTTTGTGTTGCGAATTTGACTATCGCGTTGCGA
Found at i:1269681 original size:19 final size:19
Alignment explanation
Indices: 1269586--1269723 Score: 127
Period size: 20 Copynumber: 7.0 Consensus size: 19
1269576 GCGTAAAAAC
*
1269586 ATTTGACTTTCGCGTTGCGA
1 ATTTGAC-TTCGTGTTGCGA
**
1269606 ATTTGACTATCGCATTGCGA
1 ATTTGACT-TCGTGTTGCGA
* *
1269626 ATTTGATTTATGTGTTGCG-
1 ATTTGACTT-CGTGTTGCGA
*
1269645 ATTT-ACAAATTCGCGTTGCGA
1 ATTTGAC---TTCGTGTTGCGA
1269666 ATTTGACTTCGTGTTGCGA
1 ATTTGACTTCGTGTTGCGA
*
1269685 ATTTGACTTTGTGTTGCGA
1 ATTTGACTTCGTGTTGCGA
*
1269704 ATTTGACTTCTATGTTGCGA
1 ATTTGACTTC-GTGTTGCGA
1269724 TTTACAGATT
Statistics
Matches: 98, Mismatches: 12, Indels: 16
0.78 0.10 0.13
Matches are distributed among these distances:
18 1 0.01
19 44 0.45
20 45 0.46
21 6 0.06
22 2 0.02
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (19 bp):
ATTTGACTTCGTGTTGCGA
Found at i:1269720 original size:78 final size:80
Alignment explanation
Indices: 1269586--1269747 Score: 238
Period size: 78 Copynumber: 2.0 Consensus size: 80
1269576 GCGTAAAAAC
* *
1269586 ATTTGACTTTCGCGTTGCGAATTTGACTATCGCATTGCGAATTTGATTTATGTGTTGCGATTTAC
1 ATTTGACTTTCGCGTTGCGAATTTGACTATCGCATTGCGAATTTGACTTATATGTTGCGATTTAC
1269651 AAATTCGCGTTGCGA
66 AAATTCGCGTTGCGA
* * ** *
1269666 ATTTGAC-TTCGTGTTGCGAATTTGACT-TTGTGTTGCGAATTTGACTTCTATGTTGCGATTTAC
1 ATTTGACTTTCGCGTTGCGAATTTGACTATCGCATTGCGAATTTGACTTATATGTTGCGATTTAC
*
1269729 AGATTCGCGTTGCGA
66 AAATTCGCGTTGCGA
1269744 ATTT
1 ATTT
1269748 AGAAAAGCGT
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
78 48 0.65
79 19 0.26
80 7 0.09
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (80 bp):
ATTTGACTTTCGCGTTGCGAATTTGACTATCGCATTGCGAATTTGACTTATATGTTGCGATTTAC
AAATTCGCGTTGCGA
Found at i:1270331 original size:3 final size:3
Alignment explanation
Indices: 1270323--1270350 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1270313 AATTATCCTG
1270323 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1270351 TTACATTAAT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1272280 original size:22 final size:21
Alignment explanation
Indices: 1272240--1272280 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1272230 ATTTGTATTT
1272240 AAGTTTCATATCTTTAAAAAA
1 AAGTTTCATATCTTTAAAAAA
*
1272261 AAGTTTCATATCTTTTAAAA
1 AAGTTTCATATCTTTAAAAA
1272281 TCATTCTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (21 bp):
AAGTTTCATATCTTTAAAAAA
Found at i:1276438 original size:24 final size:24
Alignment explanation
Indices: 1276387--1276476 Score: 144
Period size: 24 Copynumber: 3.7 Consensus size: 24
1276377 ATTTGTATTT
1276387 AAGTTTCATATCTTTTACAAAAAAA
1 AAGTTTCATATCTTTTAC-AAAAAA
1276412 AAGTTTCATATCTTTTACAAAAAA
1 AAGTTTCATATCTTTTACAAAAAA
*
1276436 AAGTTTAATATCTTTTACAAAAAA
1 AAGTTTCATATCTTTTACAAAAAA
* *
1276460 AAGTTTTACATCTTTTA
1 AAGTTTCATATCTTTTA
1276477 AAATCATTCT
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
24 44 0.71
25 18 0.29
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.40
Consensus pattern (24 bp):
AAGTTTCATATCTTTTACAAAAAA
Found at i:1276672 original size:13 final size:13
Alignment explanation
Indices: 1276656--1276687 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
1276646 TAACTTTTAT
1276656 TTTTTAAAATTAA
1 TTTTTAAAATTAA
1276669 -TTTTAAAATTAA
1 TTTTTAAAATTAA
1276681 TTTTTAA
1 TTTTTAA
1276688 TATAAAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTTAAAATTAA
Found at i:1277610 original size:20 final size:20
Alignment explanation
Indices: 1277577--1277626 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1277567 TTATAATAAT
*
1277577 AAGC-AAACCTGATAATATA
1 AAGCAAAACCAGATAATATA
1277596 AAGCAAAACCAGATAATATA
1 AAGCAAAACCAGATAATATA
1277616 AAGCAAAACCA
1 AAGCAAAACCA
1277627 AAACAAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 4 0.14
20 25 0.86
ACGTcount: A:0.58, C:0.18, G:0.10, T:0.14
Consensus pattern (20 bp):
AAGCAAAACCAGATAATATA
Found at i:1278911 original size:21 final size:21
Alignment explanation
Indices: 1278887--1278954 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
1278877 TTCATGCAAT
1278887 TTCAACCATCATAACATCAAA
1 TTCAACCATCATAACATCAAA
* *
1278908 TTCAATC-T-A-AATTCATGCAAT
1 TTCAACCATCATAA--CAT-CAAA
1278929 TTCAACCATCATAACATCAAA
1 TTCAACCATCATAACATCAAA
1278950 TTCAA
1 TTCAA
1278955 TCCAAATTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
18 2 0.05
19 1 0.03
20 4 0.11
21 23 0.62
22 4 0.11
23 1 0.03
24 2 0.05
ACGTcount: A:0.44, C:0.25, G:0.01, T:0.29
Consensus pattern (21 bp):
TTCAACCATCATAACATCAAA
Found at i:1278972 original size:42 final size:42
Alignment explanation
Indices: 1278873--1278964 Score: 175
Period size: 42 Copynumber: 2.2 Consensus size: 42
1278863 CTCCTATGAT
1278873 CAAATTCATGCAATTTCAACCATCATAACATCAAATTCAATC
1 CAAATTCATGCAATTTCAACCATCATAACATCAAATTCAATC
*
1278915 TAAATTCATGCAATTTCAACCATCATAACATCAAATTCAATC
1 CAAATTCATGCAATTTCAACCATCATAACATCAAATTCAATC
1278957 CAAATTCA
1 CAAATTCA
1278965 ACCAATTTAC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.43, C:0.25, G:0.02, T:0.29
Consensus pattern (42 bp):
CAAATTCATGCAATTTCAACCATCATAACATCAAATTCAATC
Found at i:1279858 original size:30 final size:30
Alignment explanation
Indices: 1279815--1279885 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 30
1279805 CAAAATATAT
* *
1279815 AACTTTTAAAAA-TTATATTCTTAGTCCCAA
1 AACTTTTAAAAATTTATACT-TTAGTCACAA
** *
1279845 AACTTTTCCAAATTTATACTTTGGTCACAA
1 AACTTTTAAAAATTTATACTTTAGTCACAA
*
1279875 AACTTTCAAAA
1 AACTTTTAAAA
1279886 CATGCATTTT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
30 26 0.81
31 6 0.19
ACGTcount: A:0.39, C:0.18, G:0.04, T:0.38
Consensus pattern (30 bp):
AACTTTTAAAAATTTATACTTTAGTCACAA
Found at i:1280209 original size:3 final size:3
Alignment explanation
Indices: 1280147--1280188 Score: 75
Period size: 3 Copynumber: 13.7 Consensus size: 3
1280137 TTGATATAAC
1280147 TAT TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1280189 ACTATAATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1283580 original size:24 final size:25
Alignment explanation
Indices: 1283536--1283601 Score: 116
Period size: 24 Copynumber: 2.7 Consensus size: 25
1283526 ATTTGTATTT
1283536 AAGTTTCATATCTTTTACAAAAAAA
1 AAGTTTCATATCTTTTACAAAAAAA
1283561 AAGTTTCATAT-TTTTACAAAAAAA
1 AAGTTTCATATCTTTTACAAAAAAA
*
1283585 AAGTTTTATATCTTTTA
1 AAGTTTCATATCTTTTA
1283602 AAATCATTCT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
24 23 0.59
25 16 0.41
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (25 bp):
AAGTTTCATATCTTTTACAAAAAAA
Found at i:1286575 original size:3 final size:3
Alignment explanation
Indices: 1286492--1286555 Score: 74
Period size: 3 Copynumber: 20.7 Consensus size: 3
1286482 TTGATATAAC
* * * *
1286492 TAT TAT TAAT TAT TGT TGT TAT TAT TAT TATT TAT TAT AAT TAT TAC
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
1286539 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
1286556 ACTAATAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
3 47 0.89
4 6 0.11
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1288407 original size:60 final size:60
Alignment explanation
Indices: 1288320--1288438 Score: 220
Period size: 60 Copynumber: 2.0 Consensus size: 60
1288310 TGAAATTAAC
*
1288320 TCGATCCGAACCCGAATTGAATCTGATGTCAAATCAACCAAAAAATGACCTGAACTGATA
1 TCGATCCGAACCCGAATTGAATATGATGTCAAATCAACCAAAAAATGACCTGAACTGATA
*
1288380 TCGATTCGAACCCGAATTGAATATGATGTCAAATCAACCAAAAAATGACCTGAACTGAT
1 TCGATCCGAACCCGAATTGAATATGATGTCAAATCAACCAAAAAATGACCTGAACTGAT
1288439 TTTACCCAGA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.23
Consensus pattern (60 bp):
TCGATCCGAACCCGAATTGAATATGATGTCAAATCAACCAAAAAATGACCTGAACTGATA
Found at i:1289938 original size:24 final size:24
Alignment explanation
Indices: 1289906--1289994 Score: 133
Period size: 24 Copynumber: 3.7 Consensus size: 24
1289896 ATATGTATTT
*
1289906 AAGTTTCATATCTTTCACAAAAAA
1 AAGTTTCATATCTTTTACAAAAAA
*
1289930 AAGTTTCATATCTTTTACAATAAA
1 AAGTTTCATATCTTTTACAAAAAA
*
1289954 AAGTTTAATATCTTTTACAAAAAA
1 AAGTTTCATATCTTTTACAAAAAA
* *
1289978 AAGTTTTATACCTTTTA
1 AAGTTTCATATCTTTTA
1289995 AAATCATTCT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.40
Consensus pattern (24 bp):
AAGTTTCATATCTTTTACAAAAAA
Found at i:1290194 original size:13 final size:13
Alignment explanation
Indices: 1290178--1290214 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
1290168 AACTTTTATT
1290178 TTTTTAAATATAA
1 TTTTTAAATATAA
1290191 TTTTTAAAT-TAA
1 TTTTTAAATATAA
1290203 TTTTT-AATATAA
1 TTTTTAAATATAA
1290215 AACATAGGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 3 0.13
12 11 0.48
13 9 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTTTAAATATAA
Found at i:1291074 original size:20 final size:20
Alignment explanation
Indices: 1291041--1291090 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1291031 TTATAATAAT
*
1291041 AAGC-AAACCTGATAATATA
1 AAGCAAAACCAGATAATATA
1291060 AAGCAAAACCAGATAATATA
1 AAGCAAAACCAGATAATATA
1291080 AAGCAAAACCA
1 AAGCAAAACCA
1291091 AAACAAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 4 0.14
20 25 0.86
ACGTcount: A:0.58, C:0.18, G:0.10, T:0.14
Consensus pattern (20 bp):
AAGCAAAACCAGATAATATA
Found at i:1297060 original size:19 final size:19
Alignment explanation
Indices: 1297032--1297070 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1297022 CAACCGCACT
*
1297032 ACCCTTATAATCAT-AAGCA
1 ACCCTAATAAT-ATAAAGCA
1297051 ACCCTAATAATATAAAGCA
1 ACCCTAATAATATAAAGCA
1297070 A
1 A
1297071 AACGAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.49, C:0.23, G:0.05, T:0.23
Consensus pattern (19 bp):
ACCCTAATAATATAAAGCA
Found at i:1298850 original size:19 final size:19
Alignment explanation
Indices: 1298822--1298862 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
1298812 ATTCGCACAA
1298822 AAACATTTATTT-TGAGAC
1 AAACATTTATTTATGAGAC
1298840 AAACTATTTATTTATGAGAC
1 AAAC-ATTTATTTATGAGAC
1298860 AAA
1 AAA
1298863 ATATAGATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 4 0.19
19 8 0.38
20 9 0.43
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.37
Consensus pattern (19 bp):
AAACATTTATTTATGAGAC
Found at i:1301465 original size:34 final size:34
Alignment explanation
Indices: 1301414--1301482 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
1301404 GATTGATATA
* **
1301414 ACTATTATTAATTATTGTTGTTATTATTATTATT
1 ACTATTATTAATAATTGTTACTATTATTATTATT
1301448 ACTATTTATT-ATAATTGTTACTATTATTATTATT
1 ACTA-TTATTAATAATTGTTACTATTATTATTATT
1301482 A
1 A
1301483 ACTAATAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 26 0.84
35 5 0.16
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.59
Consensus pattern (34 bp):
ACTATTATTAATAATTGTTACTATTATTATTATT
Found at i:1301500 original size:22 final size:22
Alignment explanation
Indices: 1301472--1301527 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
1301462 TTGTTACTAT
1301472 TATTATTATTAACTAATAATAA
1 TATTATTATTAACTAATAATAA
1301494 TATTATTATTAACTAATAATAA
1 TATTATTATTAACTAATAATAA
1301516 TATTATTATTAA
1 TATTATTATTAA
1301528 AATAAATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (22 bp):
TATTATTATTAACTAATAATAA
Found at i:1301524 original size:3 final size:3
Alignment explanation
Indices: 1301416--1301482 Score: 62
Period size: 3 Copynumber: 21.7 Consensus size: 3
1301406 TTGATATAAC
* * * *
1301416 TAT TAT TAAT TAT TGT TGT TAT TAT TAT TAT TAC TATT TAT TAT AAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
* *
1301463 TGT TAC TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
1301483 ACTAATAATA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
3 47 0.90
4 5 0.10
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.61
Consensus pattern (3 bp):
TAT
Done.