Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008488.1 Hibiscus syriacus cultivar Beakdansim tig00111330_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: 12876159
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 50 of 54
Found at i:11819437 original size:24 final size:23
Alignment explanation
Indices: 11819410--11819472 Score: 63
Period size: 26 Copynumber: 2.6 Consensus size: 23
11819400 TCTAAAAAGC
11819410 CTTAAACCCTAAAAAATTATAAAT
1 CTTAAACCCTAAAAAATTAT-AAT
* *
11819434 CTTAAAAATCCTAAATAATTATAAT
1 CTT--AAACCCTAAAAAATTATAAT
*
11819459 CCTAAACGCCTAAA
1 CTTAAAC-CCTAAA
11819473 TTGTTAACCT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
23 3 0.09
24 9 0.28
25 5 0.16
26 15 0.47
ACGTcount: A:0.51, C:0.19, G:0.02, T:0.29
Consensus pattern (23 bp):
CTTAAACCCTAAAAAATTATAAT
Found at i:11822536 original size:39 final size:39
Alignment explanation
Indices: 11822492--11822569 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
11822482 TCTTGAAGTT
* * *
11822492 CTCATGTCTGACTGTGTCTGACATATCCAAACACTAGTA
1 CTCATGTCTAACTGTGTCCGACACATCCAAACACTAGTA
11822531 CTCATGTCTAACTGTGTCCGACACATCCAAACACTAGTA
1 CTCATGTCTAACTGTGTCCGACACATCCAAACACTAGTA
11822570 TGGTGATACA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.28
Consensus pattern (39 bp):
CTCATGTCTAACTGTGTCCGACACATCCAAACACTAGTA
Found at i:11826005 original size:2 final size:2
Alignment explanation
Indices: 11825998--11826024 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11825988 TACGATAAAC
11825998 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 A
11826025 ACAAAATATC
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11827237 original size:15 final size:15
Alignment explanation
Indices: 11827217--11827254 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
11827207 CCGATTCGGT
*
11827217 TCGGGTTGGACCGAG
1 TCGGGTCGGACCGAG
*
11827232 TCGGGTCGGATCGAG
1 TCGGGTCGGACCGAG
11827247 TCGGGTCG
1 TCGGGTCG
11827255 AGTCTGGTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.11, C:0.21, G:0.47, T:0.21
Consensus pattern (15 bp):
TCGGGTCGGACCGAG
Found at i:11828155 original size:22 final size:22
Alignment explanation
Indices: 11828127--11828172 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
11828117 AGGGGGAAAA
11828127 GGATTCATCTTACTTTAGTTTT
1 GGATTCATCTTACTTTAGTTTT
11828149 GGATTCATCTTACTTTAGTTTT
1 GGATTCATCTTACTTTAGTTTT
11828171 GG
1 GG
11828173 TTAAAATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.13, G:0.17, T:0.52
Consensus pattern (22 bp):
GGATTCATCTTACTTTAGTTTT
Found at i:11831245 original size:6 final size:5
Alignment explanation
Indices: 11831221--11831255 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
11831211 TATAATTACA
11831221 AAAAT AAAAT AAAAT AAAAT AAAAAT AAAA- AAAAT
1 AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT
11831256 CTTATTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.14
5 19 0.68
6 5 0.18
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:11831685 original size:48 final size:48
Alignment explanation
Indices: 11831631--11831726 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 48
11831621 ATTTTTTTGG
*
11831631 GTTAAAATAGGTACTTAAAGTATATTATCTTTTTCATCTACTTAAAGT
1 GTTAAAATAGGTACTTAAAGTATATTATCTTTTTCATCTACCTAAAGT
* *
11831679 GTTAAAATAGGTACTTAAGGTATATTATCTTTTTCATTTACCTAAAGT
1 GTTAAAATAGGTACTTAAAGTATATTATCTTTTTCATCTACCTAAAGT
11831727 AGCCAGTCTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.44
Consensus pattern (48 bp):
GTTAAAATAGGTACTTAAAGTATATTATCTTTTTCATCTACCTAAAGT
Found at i:11831816 original size:29 final size:29
Alignment explanation
Indices: 11831784--11831861 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
11831774 GAGTACATTG
* *
11831784 AATACTTTAGGTTTTTGTTTTGACTAAAA
1 AATACTTTAGGTATTTATTTTGACTAAAA
* *
11831813 AATAGTTTAGGTATTTATTTTGATTAAAA
1 AATACTTTAGGTATTTATTTTGACTAAAA
* *
11831842 AATACTTTAAGTATCTATTT
1 AATACTTTAGGTATTTATTT
11831862 CGAACAAAGT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.49
Consensus pattern (29 bp):
AATACTTTAGGTATTTATTTTGACTAAAA
Found at i:11832734 original size:22 final size:22
Alignment explanation
Indices: 11832684--11832735 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
11832674 CACCAACATC
*
11832684 TATTATTTATATTTAATTAATT
1 TATTATTTATAATTAATTAATT
* *
11832706 TAATATTTATAATT-ATTATTT
1 TATTATTTATAATTAATTAATT
11832727 TATTTATTT
1 TA-TTATTT
11832736 TTTAAATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TATTATTTATAATTAATTAATT
Found at i:11839113 original size:20 final size:19
Alignment explanation
Indices: 11839078--11839121 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
11839068 TAATCTAAAA
*
11839078 ATATAA-ATATTAATTAATT
1 ATATAATATACTAATT-ATT
11839097 ATATAATATACTAATTATT
1 ATATAATATACTAATTATT
11839116 A-ATAAT
1 ATATAAT
11839122 TAAACTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 5 0.22
19 10 0.43
20 8 0.35
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
ATATAATATACTAATTATT
Found at i:11840459 original size:18 final size:19
Alignment explanation
Indices: 11840425--11840472 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
11840415 TATTAAGAAT
11840425 AATATTAAT-ATAATTA-TA
1 AATA-TAATAATAATTATTA
*
11840443 AATATAATAATATTTATTA
1 AATATAATAATAATTATTA
11840462 AATATATATAA
1 AATATA-ATAA
11840473 ACGTCACTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 4 0.15
18 10 0.38
19 8 0.31
20 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AATATAATAATAATTATTA
Found at i:11840707 original size:36 final size:37
Alignment explanation
Indices: 11840642--11840720 Score: 124
Period size: 36 Copynumber: 2.2 Consensus size: 37
11840632 TGATATGATC
* *
11840642 TTGCTTCACTACTCTTTTTGTGAAAGCTGATTTTGCA
1 TTGCTTCACTACTCATTTTGTGAAAGCTGAATTTGCA
*
11840679 TTGCTTCACTACT-ATTTTGTGAAGGCTGAATTTGCA
1 TTGCTTCACTACTCATTTTGTGAAAGCTGAATTTGCA
11840715 TTGCTT
1 TTGCTT
11840721 GTTTCCACTA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
36 26 0.67
37 13 0.33
ACGTcount: A:0.19, C:0.18, G:0.18, T:0.46
Consensus pattern (37 bp):
TTGCTTCACTACTCATTTTGTGAAAGCTGAATTTGCA
Found at i:11842884 original size:3 final size:3
Alignment explanation
Indices: 11842876--11842913 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
11842866 CCAAGGTTTC
11842876 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
11842914 AATGTTAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:11845975 original size:21 final size:19
Alignment explanation
Indices: 11845947--11845992 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
11845937 TCATTGAATC
11845947 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
11845967 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
11845986 ACTTAGT
1 A-TTAGT
11845993 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:11847355 original size:18 final size:18
Alignment explanation
Indices: 11847332--11847366 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
11847322 ACGTACAACC
11847332 CTGGTTGGAGACAACACT
1 CTGGTTGGAGACAACACT
11847350 CTGGTTGGAGACAACAC
1 CTGGTTGGAGACAACAC
11847367 CCAAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.23, G:0.29, T:0.20
Consensus pattern (18 bp):
CTGGTTGGAGACAACACT
Found at i:11847575 original size:21 final size:21
Alignment explanation
Indices: 11847551--11847594 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
11847541 TTATCCTTAC
11847551 AAGAATTCATGGCCTCGACAA
1 AAGAATTCATGGCCTCGACAA
* * *
11847572 AAGATTTCATGGCGTCTACAA
1 AAGAATTCATGGCCTCGACAA
11847593 AA
1 AA
11847595 TCCTTGATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (21 bp):
AAGAATTCATGGCCTCGACAA
Found at i:11856263 original size:21 final size:19
Alignment explanation
Indices: 11856235--11856280 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
11856225 TCATTGAATC
11856235 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
11856255 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
11856274 ACTTAGT
1 A-TTAGT
11856281 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:11861612 original size:17 final size:17
Alignment explanation
Indices: 11861590--11861638 Score: 80
Period size: 17 Copynumber: 2.9 Consensus size: 17
11861580 ATTGATCAAT
*
11861590 AACAAGAAATAAGAATC
1 AACAAGAAACAAGAATC
11861607 AACAAGAAACAAGAATC
1 AACAAGAAACAAGAATC
*
11861624 AACAAGAATCAAGAA
1 AACAAGAAACAAGAA
11861639 AGAATCAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.65, C:0.14, G:0.12, T:0.08
Consensus pattern (17 bp):
AACAAGAAACAAGAATC
Found at i:11861652 original size:10 final size:10
Alignment explanation
Indices: 11861600--11861646 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
11861590 AACAAGAAAT
11861600 AAGAATCAAC
1 AAGAATCAAC
11861610 AAG-A--AAC
1 AAGAATCAAC
11861617 AAGAATCAAC
1 AAGAATCAAC
*
11861627 AAGAATCAAGA
1 AAGAATCAA-C
11861638 AAGAATCAA
1 AAGAATCAA
11861647 AGAGAAAGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
7 6 0.19
8 1 0.03
9 1 0.03
10 15 0.47
11 9 0.28
ACGTcount: A:0.64, C:0.15, G:0.13, T:0.09
Consensus pattern (10 bp):
AAGAATCAAC
Found at i:11867055 original size:23 final size:22
Alignment explanation
Indices: 11867013--11867073 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 22
11867003 TTGCTGCAGA
* *
11867013 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCCTTGAAG
11867035 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-TTGAAG
11867058 GGGAACCGATTCCCCC
1 GGGAACCGATTCCCCC
11867074 CCCCCTGTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 14 0.39
23 22 0.61
ACGTcount: A:0.23, C:0.33, G:0.26, T:0.18
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTGAAG
Found at i:11868671 original size:18 final size:18
Alignment explanation
Indices: 11868636--11868671 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
11868626 ATAATCGCAC
*
11868636 GAGGAACAAGCTCCACCA
1 GAGGAACAAGCACCACCA
*
11868654 GAGGAACAAGCACGACCA
1 GAGGAACAAGCACCACCA
11868672 AAAGATCAAA
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:0.42, C:0.31, G:0.25, T:0.03
Consensus pattern (18 bp):
GAGGAACAAGCACCACCA
Found at i:11874660 original size:15 final size:15
Alignment explanation
Indices: 11874635--11874672 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
11874625 TTATTCTAGT
11874635 AATTT-TAATATCTA
1 AATTTATAATATCTA
*
11874649 AATTTATAATATTTA
1 AATTTATAATATCTA
*
11874664 AATTCATAA
1 AATTTATAA
11874673 AAATATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTTATAATATCTA
Found at i:11877515 original size:15 final size:16
Alignment explanation
Indices: 11877487--11877519 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
11877477 TACATTCCCT
*
11877487 TTAACCCTAGCACATA
1 TTAACCCTAACACATA
11877503 TTAA-CCTAACACATA
1 TTAACCCTAACACATA
11877518 TT
1 TT
11877520 CTATTAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.39, C:0.27, G:0.03, T:0.30
Consensus pattern (16 bp):
TTAACCCTAACACATA
Found at i:11878845 original size:18 final size:16
Alignment explanation
Indices: 11878819--11878865 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
11878809 ACTGCATCCA
*
11878819 TGCACCATGCACCTACAG
1 TGCATCATGCACCT--AG
11878837 TGCATCATGCA-CTAG
1 TGCATCATGCACCTAG
11878852 TGCATCGATGCACC
1 TGCATC-ATGCACC
11878866 CCTGCAGTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 8 0.31
16 5 0.19
17 3 0.12
18 10 0.38
ACGTcount: A:0.26, C:0.34, G:0.19, T:0.21
Consensus pattern (16 bp):
TGCATCATGCACCTAG
Found at i:11878855 original size:15 final size:16
Alignment explanation
Indices: 11878835--11878864 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11878825 ATGCACCTAC
11878835 AGTGCATC-ATGCACT
1 AGTGCATCGATGCACT
11878850 AGTGCATCGATGCAC
1 AGTGCATCGATGCAC
11878865 CCCTGCAGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (16 bp):
AGTGCATCGATGCACT
Found at i:11879325 original size:34 final size:33
Alignment explanation
Indices: 11879286--11879356 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
11879276 TTTTGTAAAG
*
11879286 GGGAAAGGTTCTAGCTAAACCCATGTAAAAGCTA
1 GGGAAAGGTTCTAGCTAAACCCATG-AAAAACTA
* * *
11879320 GGGAAAGGTTCTAGTTTAACCCGTGAAAAACTA
1 GGGAAAGGTTCTAGCTAAACCCATGAAAAACTA
11879353 GGGA
1 GGGA
11879357 GTTGTAAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 11 0.33
34 22 0.67
ACGTcount: A:0.37, C:0.15, G:0.27, T:0.21
Consensus pattern (33 bp):
GGGAAAGGTTCTAGCTAAACCCATGAAAAACTA
Found at i:11885503 original size:23 final size:21
Alignment explanation
Indices: 11885451--11885512 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
11885441 TTTTGGTGCA
*
11885451 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
11885471 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
11885492 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
11885513 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:11885520 original size:21 final size:21
Alignment explanation
Indices: 11885494--11885533 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11885484 CCCCCTTTGA
*
11885494 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
11885515 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
11885534 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:11885925 original size:26 final size:25
Alignment explanation
Indices: 11885894--11885943 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
11885884 AGAATTTTCC
11885894 AAAAAATT-TTAAATTTTCGAAATTAA
1 AAAAAATTGTT-AATTTTC-AAATTAA
11885920 AAAAAATTGTTAATTTTCAAATTA
1 AAAAAATTGTTAATTTTCAAATTA
11885944 TTGTGTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 6 0.26
26 15 0.65
27 2 0.09
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (25 bp):
AAAAAATTGTTAATTTTCAAATTAA
Found at i:11887823 original size:43 final size:43
Alignment explanation
Indices: 11887773--11887859 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
11887763 TGTGTTTTGA
11887773 GTGTGTTTTAAAATGATAAATGGAAGAAGTGTTAAAGTAAGGG
1 GTGTGTTTTAAAATGATAAATGGAAGAAGTGTTAAAGTAAGGG
*
11887816 GTGTGTTTTAAAATGATAAATGGGAGAAGTGTTAAAGTAAGGG
1 GTGTGTTTTAAAATGATAAATGGAAGAAGTGTTAAAGTAAGGG
11887859 G
1 G
11887860 GAGTAATTTC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.30
Consensus pattern (43 bp):
GTGTGTTTTAAAATGATAAATGGAAGAAGTGTTAAAGTAAGGG
Found at i:11887851 original size:24 final size:24
Alignment explanation
Indices: 11887780--11887851 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 24
11887770 TGAGTGTGTT
*
11887780 TTAAAATGATAAATGGAAGAAGTG
1 TTAAAATGATAAATGGGAGAAGTG
* * * *
11887804 TT-AAA-G-T-AAGGGGTG-TGTT
1 TTAAAATGATAAATGGGAGAAGTG
11887823 TTAAAATGATAAATGGGAGAAGTG
1 TTAAAATGATAAATGGGAGAAGTG
11887847 TTAAA
1 TTAAA
11887852 GTAAGGGGGA
Statistics
Matches: 34, Mismatches: 9, Indels: 10
0.64 0.17 0.19
Matches are distributed among these distances:
19 4 0.12
20 8 0.24
21 2 0.06
22 2 0.06
23 9 0.26
24 9 0.26
ACGTcount: A:0.43, C:0.00, G:0.28, T:0.29
Consensus pattern (24 bp):
TTAAAATGATAAATGGGAGAAGTG
Found at i:11889802 original size:15 final size:15
Alignment explanation
Indices: 11889771--11889801 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
11889761 GATGATGGTG
11889771 AATGAAGATGAAGAA
1 AATGAAGATGAAGAA
11889786 AATGAAGA-GAAGAA
1 AATGAAGATGAAGAA
11889800 AA
1 AA
11889802 ACAAGAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.65, C:0.00, G:0.26, T:0.10
Consensus pattern (15 bp):
AATGAAGATGAAGAA
Found at i:11891492 original size:21 final size:21
Alignment explanation
Indices: 11891466--11891505 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
11891456 TAAAAATTGG
11891466 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
*
11891487 TAACAATTGATATCTTTTT
1 TAACAATTGATATCATTTT
11891506 CATTAAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:11891928 original size:20 final size:22
Alignment explanation
Indices: 11891890--11891929 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
11891880 TTTTAGTAGA
11891890 AAAACCATCCCCAAATGGCTCC
1 AAAACCATCCCCAAATGGCTCC
11891912 AAAA-CATCCCC-AATGGCT
1 AAAACCATCCCCAAATGGCT
11891930 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAACCATCCCCAAATGGCTCC
Found at i:11892201 original size:34 final size:33
Alignment explanation
Indices: 11892142--11892214 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 33
11892132 CCTTTTGTAA
11892142 AGGGAAAAGGTTCTAGGTAAGCCCGTGTA-AAAGCT
1 AGGG-AAAGGTTCTAGGTAAGCCCGTG-AGAAA-CT
*
11892177 AGGGAAAGGTTCTAGTTTAA-CCCGTGAGAAACT
1 AGGGAAAGGTTCTAG-GTAAGCCCGTGAGAAACT
11892210 AGGGA
1 AGGGA
11892215 GTTGTAAAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
33 8 0.23
34 20 0.57
35 7 0.20
ACGTcount: A:0.34, C:0.14, G:0.32, T:0.21
Consensus pattern (33 bp):
AGGGAAAGGTTCTAGGTAAGCCCGTGAGAAACT
Found at i:11894107 original size:2 final size:2
Alignment explanation
Indices: 11894100--11894136 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
11894090 TGTCTATACC
11894100 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 A
11894137 CTTAGTGACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11894422 original size:32 final size:32
Alignment explanation
Indices: 11894321--11894424 Score: 145
Period size: 33 Copynumber: 3.2 Consensus size: 32
11894311 AAAAAGGACT
* *
11894321 CAAGGCACACTAAGTCAATAGGGATTTTATAGC
1 CAAGGCGCACAAAGTCAATAGGG-TTTTATAGC
11894354 CAAGGCGCACAAAGTCAATAGGGGTTTTATAGC
1 CAAGGCGCACAAAGTCAATA-GGGTTTTATAGC
* * *
11894387 CAAGTCGCACAAAGTCAATAGGGTTTTACAAC
1 CAAGGCGCACAAAGTCAATAGGGTTTTATAGC
11894419 CAAGGC
1 CAAGGC
11894425 ACAAGCAAGA
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
32 15 0.23
33 46 0.72
34 3 0.05
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (32 bp):
CAAGGCGCACAAAGTCAATAGGGTTTTATAGC
Found at i:11896163 original size:26 final size:26
Alignment explanation
Indices: 11896148--11896208 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
11896138 TTTGCATTTC
11896148 ACAATTTTATAAAAAATTTGTCATAA
1 ACAATTTTATAAAAAATTTGTCATAA
*
11896174 ACAATTTTATAAAAAAATTGTCATAA
1 ACAATTTTATAAAAAATTTGTCATAA
11896200 ACAATTTTA
1 ACAATTTTA
11896209 AAGTGTGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (26 bp):
ACAATTTTATAAAAAATTTGTCATAA
Found at i:11896173 original size:14 final size:14
Alignment explanation
Indices: 11896156--11896206 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
11896146 TCACAATTTT
11896156 ATAAAAAATTTGTC
1 ATAAAAAATTTGTC
*
11896170 ATAAACAATTT-T-
1 ATAAAAAATTTGTC
*
11896182 ATAAAAAAATTGTC
1 ATAAAAAATTTGTC
*
11896196 ATAAACAATTT
1 ATAAAAAATTT
11896207 TAAAGTGTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
12 9 0.30
13 2 0.07
14 19 0.63
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (14 bp):
ATAAAAAATTTGTC
Found at i:11899789 original size:120 final size:120
Alignment explanation
Indices: 11899550--11899782 Score: 285
Period size: 120 Copynumber: 2.0 Consensus size: 120
11899540 TATATTAATT
* * *
11899550 TATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGGTGCCT
1 TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGGTGCCT
*** *
11899615 TAAGACAGTTTTTTTCTTCGATATTAAAAAATAAATAAATATTTAAAACAATTAA
66 TAAGACAGTCCCTTTCTTCAATATTAAAAAATAAATAAATATTTAAAACAATTAA
** * * *
11899670 TATATA-ATTTATAAAATAGGATATTTATTTATTTAAAAATATTAGAAAATGGACATCCAGTTGT
1 TATATATATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAA-GGACATCCAGGTGC
* * *
11899734 TTTAAGACTG-CCCTTTCTT-AATATTGAAAAATAAATAAATA-TTAAAACA
64 CTTAAGACAGTCCCTTTCTTCAATATTAAAAAATAAATAAATATTTAAAACA
11899783 TGATTAAAAT
Statistics
Matches: 96, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
118 8 0.08
119 26 0.27
120 44 0.46
121 18 0.19
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.39
Consensus pattern (120 bp):
TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGGTGCCT
TAAGACAGTCCCTTTCTTCAATATTAAAAAATAAATAAATATTTAAAACAATTAA
Found at i:11899847 original size:21 final size:20
Alignment explanation
Indices: 11899808--11899848 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
11899798 AAAAGTAATT
11899808 AAATAATATTTTAATAAATA
1 AAATAATATTTTAATAAATA
11899828 AAAT-ATATTATTATATAAATA
1 AAATAATATT-TTA-ATAAATA
11899849 TATATAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 7 0.37
21 7 0.37
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATAATATTTTAATAAATA
Found at i:11901167 original size:3 final size:3
Alignment explanation
Indices: 11901152--11901209 Score: 80
Period size: 3 Copynumber: 19.3 Consensus size: 3
11901142 TAAATAATGT
* * * *
11901152 ATA ATA TTA ATA ATA ATA ATA ATA ATT ATA ATA ATA ATA ATT TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
11901200 ATA ATA ATA A
1 ATA ATA ATA A
11901210 ATTTAAATTT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
ATA
Found at i:11901631 original size:76 final size:76
Alignment explanation
Indices: 11901347--11901603 Score: 460
Period size: 76 Copynumber: 3.4 Consensus size: 76
11901337 GAAATGTTGA
* * * *
11901347 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
11901412 ATGCTTTTTGG
66 AGGCTTTTTGG
11901423 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
11901488 AGGCATTTTGG
66 AGGCTTTTTGG
11901499 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
11901564 AGGCTTTTTGG
66 AGGCTTTTTGG
11901575 AAACATCATGCACTGTAGGACTTACAGAT
1 AAACATCATGCACTGTAGGACTTACAGAT
11901604 ATGGGAAATA
Statistics
Matches: 174, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 174 1.00
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:11901860 original size:76 final size:76
Alignment explanation
Indices: 11901729--11902095 Score: 644
Period size: 76 Copynumber: 4.8 Consensus size: 76
11901719 TCAAAATAAC
*
11901729 AACATCAAAAAGCTCCCGAAGGCTTTTTTTTGGAAACGTCATGCACTGTAGGACTTACAGATGAC
1 AACATCAAAAAGCTCCCGAAGGC---TTTTTGGAAACATCATGCACTGTAGGACTTACAGATGAC
11901794 CCTAAGGCTTTGAA
63 CCTAAGGCTTTGAA
* * *
11901808 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCGCTGTAGGACTTATAGATGACCAT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
11901873 AAGGCTTTGAA
66 AAGGCTTTGAA
* *
11901884 AACATCAAAAAGCTCCCGAAGGTTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCG
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
11901949 AAGGCTTTGAA
66 AAGGCTTTGAA
11901960 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
11902025 AAGGCTTTGAA
66 AAGGCTTTGAA
*
11902036 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATG
11902096 TGGGAAATAG
Statistics
Matches: 276, Mismatches: 12, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
76 253 0.92
79 23 0.08
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (76 bp):
AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
AAGGCTTTGAA
Found at i:11902372 original size:166 final size:166
Alignment explanation
Indices: 11902098--11902422 Score: 551
Period size: 166 Copynumber: 2.0 Consensus size: 166
11902088 TACAGATGTG
*
11902098 GGAAATAGTTTACTAAGTAAAAAAAACTAAGGAAATCATTTTCTTACTTTTCAACAATTTCATTT
1 GGAAATAGTTTACTAAGTAAAAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTT
** *
11902163 TAGAAAAGATTGAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAATAACATGTTGA
66 TAGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAATAACATGTCGA
*
11902228 TTGGGTAACATGCCCCAATCTCAAGATAAGGCTGTT
131 TTAGGTAACATGCCCCAATCTCAAGATAAGGCTGTT
* * *
11902264 GGAAATAGTTTACTAAGTAAAAAAAACTAAGAAAATCCTTTTCTTATTTTTCGACAATTTCATTT
1 GGAAATAGTTTACTAAGTAAAAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTT
* *
11902329 TAGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCGAAATAACATGTCGA
66 TAGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAATAACATGTCGA
*
11902394 TTAGGTAGCATGCCCCAATCTCAAGATAA
131 TTAGGTAACATGCCCCAATCTCAAGATAA
11902423 TGCTCATATT
Statistics
Matches: 148, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
166 148 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.34
Consensus pattern (166 bp):
GGAAATAGTTTACTAAGTAAAAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTT
TAGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAATAACATGTCGA
TTAGGTAACATGCCCCAATCTCAAGATAAGGCTGTT
Found at i:11902962 original size:22 final size:22
Alignment explanation
Indices: 11902937--11902995 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
11902927 AATAAAGCTT
*
11902937 TCATTTTTGAAAAGATAATCTA
1 TCATCTTTGAAAAGATAATCTA
*
11902959 TCATCTTTAAAAAGATAATCTA
1 TCATCTTTGAAAAGATAATCTA
11902981 TCATCTTTGAAAAGA
1 TCATCTTTGAAAAGA
11902996 GTGTAGATGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.37
Consensus pattern (22 bp):
TCATCTTTGAAAAGATAATCTA
Found at i:11913418 original size:31 final size:29
Alignment explanation
Indices: 11913370--11913428 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 29
11913360 ATTTCAAAAT
11913370 TATAATTATGAAAAAAATATATTAATTTATA
1 TATAATTATGAAAAAAATAT-TT-ATTTATA
*
11913401 TATATTTAT-AAATAAAATATTTATTTAT
1 TATAATTATGAAA-AAAATATTTATTTAT
11913429 TTAGAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 6 0.23
30 5 0.19
31 15 0.58
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
TATAATTATGAAAAAAATATTTATTTATA
Found at i:11913523 original size:20 final size:19
Alignment explanation
Indices: 11913484--11913525 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
11913474 TTTCTTCGAT
11913484 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
11913503 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
11913523 ATT
1 ATT
11913526 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:11913636 original size:120 final size:120
Alignment explanation
Indices: 11913397--11913629 Score: 312
Period size: 120 Copynumber: 2.0 Consensus size: 120
11913387 TATATTAATT
* * *
11913397 TATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGGTGCCT
1 TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGGTGCCT
* *
11913462 TAAGACAGCTCTTTTCTTCGATATTAAAAAATAAATAAATAATTAAAACAATTAA
66 TAAGACAGCTCCTTTCTTCAATATTAAAAAATAAATAAATAATTAAAACAATTAA
** * *
11913517 TATATA-ATTTATAAAATAGGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAGTTGT
1 TATATATATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAA-GGACATCCAGGTGC
* * *
11913581 TTTAAGACTGC-CCTTTCTT-AATATTGAAAAATAAATAAAT-ATTAAAACA
64 CTTAAGACAGCTCCTTTCTTCAATATTAAAAAATAAATAAATAATTAAAACA
11913630 TGATTAAAAT
Statistics
Matches: 99, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
118 9 0.09
119 25 0.25
120 46 0.46
121 19 0.19
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.37
Consensus pattern (120 bp):
TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGGTGCCT
TAAGACAGCTCCTTTCTTCAATATTAAAAAATAAATAAATAATTAAAACAATTAA
Found at i:11915034 original size:12 final size:12
Alignment explanation
Indices: 11914986--11915041 Score: 50
Period size: 11 Copynumber: 5.0 Consensus size: 12
11914976 TTGGGCTTTG
*
11914986 TAATATTTAATA
1 TAATAATTAATA
11914998 -AATAA-T-ATA
1 TAATAATTAATA
11915007 TAAT-ATTAATA
1 TAATAATTAATA
*
11915018 TTAATAATTATTA
1 -TAATAATTAATA
11915031 TAATAA-TAATA
1 TAATAATTAATA
11915042 ATTTTAATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
9 4 0.11
10 5 0.14
11 11 0.31
12 10 0.28
13 6 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAATAATTAATA
Found at i:11915036 original size:3 final size:3
Alignment explanation
Indices: 11914993--11915060 Score: 64
Period size: 3 Copynumber: 22.0 Consensus size: 3
11914983 TTGTAATATT
* * * *
11914993 TAA TAAA TAA TATA TAA TAT TAA TAT TAA TAA TTA TTA TAA TAA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
11915040 TAA TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
11915061 ATTTAAATTT
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
3 47 0.89
4 6 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:11915040 original size:18 final size:18
Alignment explanation
Indices: 11914986--11915066 Score: 80
Period size: 18 Copynumber: 4.5 Consensus size: 18
11914976 TTGGGCTTTG
11914986 TAATATTTAATAAATAATATA
1 TAAT-TTTAAT-AATAATA-A
*
11915007 TAATATTAAT-AT--TAA
1 TAATTTTAATAATAATAA
11915022 TAATTATT-ATAATAATAA
1 TAATT-TTAATAATAATAA
11915040 TAATTTTAATAATAATAA
1 TAATTTTAATAATAATAA
*
11915058 TAAATTTAA
1 TAATTTTAA
11915067 ATTTAAAATG
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
15 7 0.13
16 6 0.12
17 2 0.04
18 28 0.54
20 5 0.10
21 4 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAATTTTAATAATAATAA
Found at i:11916036 original size:41 final size:42
Alignment explanation
Indices: 11915988--11916071 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 42
11915978 ATTTAATCTG
*
11915988 GCAAAAATATT-AATGTGTAAACTTTTGTAAGGTTTGGAGAC
1 GCAAAAATATTAAATATGTAAACTTTTGTAAGGTTTGGAGAC
11916029 GCAAAAATATTAAAATATGTAAACTTTTGTAAGGTTTGGAGAC
1 GCAAAAATATT-AAATATGTAAACTTTTGTAAGGTTTGGAGAC
11916072 AGGTGGGGTA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
41 11 0.28
43 29 0.73
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.33
Consensus pattern (42 bp):
GCAAAAATATTAAATATGTAAACTTTTGTAAGGTTTGGAGAC
Found at i:11918709 original size:2 final size:2
Alignment explanation
Indices: 11918702--11918756 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
11918692 GTCAACATGA
11918702 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
11918744 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
11918757 GAAGATAAAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11920736 original size:94 final size:94
Alignment explanation
Indices: 11920575--11920767 Score: 325
Period size: 94 Copynumber: 2.1 Consensus size: 94
11920565 TAATTATTAT
11920575 ATCATTCGAAGTTAGCATCATCAGTTACAGTACAATCATAACAAGCAAGAGAATTAGTCAGGTAA
1 ATCATTCGAAGTTAGCATCATCAGTTACAGTACAATCATAACAAGCAAGAGAATTAGTCAGGTAA
*
11920640 CAGAATTGGCAAGTTCTGAGTATGCAAGA
66 CAGAATTGGCAAGTTCTGAGCATGCAAGA
* * *
11920669 ATCATTGGAAGTTAGTATCATCAGTTACAGTACAATCATAACAAGCAAGAGAATTAGT-TGGCTA
1 ATCATTCGAAGTTAGCATCATCAGTTACAGTACAATCATAACAAGCAAGAGAATTAGTCAGG-TA
*
11920733 ACAGAATTGGTAAGTTCTGAGCATGCAAGA
65 ACAGAATTGGCAAGTTCTGAGCATGCAAGA
11920763 ATCAT
1 ATCAT
11920768 CTTAACTTCA
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
93 2 0.02
94 91 0.98
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (94 bp):
ATCATTCGAAGTTAGCATCATCAGTTACAGTACAATCATAACAAGCAAGAGAATTAGTCAGGTAA
CAGAATTGGCAAGTTCTGAGCATGCAAGA
Found at i:11935612 original size:13 final size:12
Alignment explanation
Indices: 11935582--11935614 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
11935572 CCAGTCTGTT
11935582 TATTTTTCTTTC
1 TATTTTTCTTTC
11935594 TATTTTTCTTTC
1 TATTTTTCTTTC
11935606 TATTTTTCT
1 TATTTTTCT
11935615 GTCCGTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (12 bp):
TATTTTTCTTTC
Found at i:11942236 original size:18 final size:20
Alignment explanation
Indices: 11942213--11942258 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
11942203 TTTTTTGTAC
11942213 CGATACTC-ATGG-GAGTAT
1 CGATACTCAATGGAGAGTAT
11942231 CGATAC-CAATGGTAGAGTAT
1 CGATACTCAATGG-AGAGTAT
*
11942251 CAATACTC
1 CGATACTC
11942259 CCAATAGGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 1 0.04
18 10 0.43
20 11 0.48
21 1 0.04
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.26
Consensus pattern (20 bp):
CGATACTCAATGGAGAGTAT
Found at i:11943069 original size:21 final size:21
Alignment explanation
Indices: 11943043--11943121 Score: 149
Period size: 21 Copynumber: 3.8 Consensus size: 21
11943033 ACTAGTGGCA
*
11943043 GGTGCATGGATGCACTTCAGG
1 GGTGCATGGATGCACTGCAGG
11943064 GGTGCATGGATGCACTGCAGG
1 GGTGCATGGATGCACTGCAGG
11943085 GGTGCATGGATGCACTGCAGG
1 GGTGCATGGATGCACTGCAGG
11943106 GGTGCATGGATGCACT
1 GGTGCATGGATGCACT
11943122 TTGACACCCT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.19, C:0.19, G:0.41, T:0.22
Consensus pattern (21 bp):
GGTGCATGGATGCACTGCAGG
Found at i:11944754 original size:20 final size:20
Alignment explanation
Indices: 11944731--11944770 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
11944721 AAACCTAACT
11944731 CTTAAATAATAAACCCTAAA
1 CTTAAATAATAAACCCTAAA
* **
11944751 CTTAACTCTTAAACCCTAAA
1 CTTAAATAATAAACCCTAAA
11944771 TCCTAAGTCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (20 bp):
CTTAAATAATAAACCCTAAA
Found at i:11944776 original size:27 final size:27
Alignment explanation
Indices: 11944684--11944763 Score: 133
Period size: 27 Copynumber: 2.9 Consensus size: 27
11944674 ACCTCAAGCT
*
11944684 ATAAACCCTAAATCTCAACTCTTAAATA
1 ATAAACCCTAAA-CTTAACTCTTAAATA
*
11944712 ATAAACCCTAAACCTAACTCTTAAATA
1 ATAAACCCTAAACTTAACTCTTAAATA
11944739 ATAAACCCTAAACTTAACTCTTAAA
1 ATAAACCCTAAACTTAACTCTTAAA
11944764 CCCTAAATCC
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
27 37 0.76
28 12 0.24
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (27 bp):
ATAAACCCTAAACTTAACTCTTAAATA
Found at i:11954963 original size:35 final size:35
Alignment explanation
Indices: 11954856--11954963 Score: 98
Period size: 35 Copynumber: 3.0 Consensus size: 35
11954846 TTTTAGGGAT
*
11954856 CAAATATGGAATTCCCATGTTCAAAGTTTGGCCAC
1 CAAATATGAAATTCCCATGTTCAAAGTTTGGCCAC
* * *
11954891 CTACCAA-A-GAATTTTCCAATGTGT-ACAAG-TTAGCCAC
1 C-A--AATATGAA-ATTCCCATGT-TCA-AAGTTTGGCCAC
11954928 CAAATATGAAATTCCCATGTTCAAAGTTTGGCCAC
1 CAAATATGAAATTCCCATGTTCAAAGTTTGGCCAC
11954963 C
1 C
11954964 GACTAAGATG
Statistics
Matches: 56, Mismatches: 7, Indels: 20
0.67 0.08 0.24
Matches are distributed among these distances:
34 6 0.11
35 19 0.34
36 7 0.12
37 18 0.32
38 6 0.11
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (35 bp):
CAAATATGAAATTCCCATGTTCAAAGTTTGGCCAC
Found at i:11955188 original size:28 final size:28
Alignment explanation
Indices: 11955147--11955213 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
11955137 CCTATATATA
** *
11955147 TACAATATTTTTATTAATAAGAGGTGAT
1 TACAATATAATTATTAATAAGAGGTAAT
*
11955175 TACAATATAATTATTAGTAAGAGGTAAT
1 TACAATATAATTATTAATAAGAGGTAAT
*
11955203 TATAATATAAT
1 TACAATATAAT
11955214 ATTTATTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.40
Consensus pattern (28 bp):
TACAATATAATTATTAATAAGAGGTAAT
Found at i:11955690 original size:43 final size:41
Alignment explanation
Indices: 11955628--11955711 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 41
11955618 TCCTACTGTA
* *
11955628 CCAGTTAATTTCATGGATGAACGATGTTGTGCCAAATCTTGAT
1 CCAGTTAATTTCATCGATGAACGATG--CTGCCAAATCTTGAT
*
11955671 CCAGTTAATTTCGTCGATGAACGATGCTGCCAAATCTTGAT
1 CCAGTTAATTTCATCGATGAACGATGCTGCCAAATCTTGAT
11955712 GTTTGTTTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 14 0.37
43 24 0.63
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.33
Consensus pattern (41 bp):
CCAGTTAATTTCATCGATGAACGATGCTGCCAAATCTTGAT
Found at i:11956027 original size:17 final size:16
Alignment explanation
Indices: 11955997--11956028 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
11955987 TGATAGAACC
11955997 AAATAAAAATAAAATA
1 AAATAAAAATAAAATA
11956013 AAATAAAACATAAAAT
1 AAATAAAA-ATAAAAT
11956029 TTAAGATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (16 bp):
AAATAAAAATAAAATA
Found at i:11958839 original size:3 final size:3
Alignment explanation
Indices: 11958831--11958855 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
11958821 AAATGTAAAT
11958831 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
11958856 CGTATAGAAA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:11959393 original size:137 final size:137
Alignment explanation
Indices: 11959099--11959463 Score: 462
Period size: 137 Copynumber: 2.7 Consensus size: 137
11959089 TTGTCTAAGG
* * * * **
11959099 GTGACACGGCTCCTACGTAATGAGGAGATCTGGTCGGTGGATGAAACGGTTTCTACGCGATGAGG
1 GTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACAGTTCCTACATGATGAGG
* *
11959164 ACGGCTGGCCATCTTTAGGAATAAATATAGATAACACGACTCCTACATGATGAGGACGACTGGTT
66 ACGGCTGGCCATCTTTAGGGAT-AATATAGATAACACGACTCCTACATGATGAGGACGACTGATT
* *
11959229 ATCTAAGG
130 ATCCAAGA
* * *
11959237 GTGACACGGCTCCTACGTGATGAGGAAATCTGGTCGGTGGATGACACAGTTCCTACATGGTAAGG
1 GTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACAGTTCCTACATGATGAGG
* * * * *
11959302 ACGACTGGCCATCTTTAGGGATAATATAGATAACATG-CTTTCTACGTGATGAGGATGACTGATT
66 ACGGCTGGCCATCTTTAGGGATAATATAGATAACACGAC-TCCTACATGATGAGGACGACTGATT
11959366 ATCCAAGA
130 ATCCAAGA
* ** * * * * *
11959374 TTGACGTGGCTCCTACGTGATGAGGAGATTTGGTCGATAGATGACACAGTTCCTACCTGATGAGA
1 GTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACAGTTCCTACATGATGAGG
*
11959439 ACGGCTGGCCATCTTTAAGGATAAT
66 ACGGCTGGCCATCTTTAGGGATAAT
11959464 TTGTTTCAAG
Statistics
Matches: 195, Mismatches: 31, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
136 1 0.01
137 118 0.61
138 76 0.39
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.26
Consensus pattern (137 bp):
GTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACAGTTCCTACATGATGAGG
ACGGCTGGCCATCTTTAGGGATAATATAGATAACACGACTCCTACATGATGAGGACGACTGATTA
TCCAAGA
Found at i:11959505 original size:36 final size:35
Alignment explanation
Indices: 11959465--11959559 Score: 118
Period size: 36 Copynumber: 2.6 Consensus size: 35
11959455 AAGGATAATT
*
11959465 TGTTTCAAGAGAAACAGTCTCAAGCGAGACAAAATA
1 TGTTTCAAGAGAAACA-TCTCAAGAGAGACAAAATA
* * *
11959501 TGTTTCAATAGAAATTATCTCAGGAGAGACAAAATA
1 TGTTTCAAGAGAAA-CATCTCAAGAGAGACAAAATA
*
11959537 TGTTTCAAGGGAAACAATCTCAA
1 TGTTTCAAGAGAAAC-ATCTCAA
11959560 TGTTTTTATG
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
36 48 0.98
37 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.24
Consensus pattern (35 bp):
TGTTTCAAGAGAAACATCTCAAGAGAGACAAAATA
Found at i:11959588 original size:31 final size:32
Alignment explanation
Indices: 11959535--11959598 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
11959525 AGAGACAAAA
* *
11959535 TATGTTTCAAGGGAAACAATCTC-AATGTTTT
1 TATGTTTCAAGAGAAACAATCTCGAAGGTTTT
* *
11959566 TATGTTTCAAGATAAACTATCTCGAAGGTTTT
1 TATGTTTCAAGAGAAACAATCTCGAAGGTTTT
11959598 T
1 T
11959599 TTTATTCCAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 20 0.71
32 8 0.29
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (32 bp):
TATGTTTCAAGAGAAACAATCTCGAAGGTTTT
Found at i:11959691 original size:36 final size:35
Alignment explanation
Indices: 11959609--11959720 Score: 127
Period size: 36 Copynumber: 3.1 Consensus size: 35
11959599 TTTATTCCAC
* **
11959609 AGAAACTGTCTCTAGAGAGACAAAATTTGTTTCAA
1 AGAAACTGTCTCAAGAGAGACAAAATTTGTTTTTA
*
11959644 GAGAAAATGTCTCAAGA-AGGACAAAATTTGTTTTTA
1 -AGAAACTGTCTCAAGAGA-GACAAAATTTGTTTTTA
* * *
11959680 AGAAATCTGTCTCAAGTGAGACAAACTCTGTTTTTA
1 AGAAA-CTGTCTCAAGAGAGACAAAATTTGTTTTTA
11959716 AGAAA
1 AGAAA
11959721 ATAATCTCTA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
35 6 0.09
36 58 0.89
37 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.29
Consensus pattern (35 bp):
AGAAACTGTCTCAAGAGAGACAAAATTTGTTTTTA
Found at i:11959734 original size:36 final size:36
Alignment explanation
Indices: 11959663--11959736 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 36
11959653 TCTCAAGAAG
* **
11959663 GACAAAATTTGTTTTTAAGAAATCTGTCTCAAGTGA
1 GACAAAATCTGTTTTTAAGAAATCAATCTCAAGTGA
* *
11959699 GACAAACTCTGTTTTTAAGAAAAT-AATCTCTAGTGA
1 GACAAAATCTGTTTTTAAG-AAATCAATCTCAAGTGA
11959735 GA
1 GA
11959737 TGAATTTTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
36 28 0.88
37 4 0.12
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (36 bp):
GACAAAATCTGTTTTTAAGAAATCAATCTCAAGTGA
Found at i:11960043 original size:37 final size:37
Alignment explanation
Indices: 11959951--11960154 Score: 220
Period size: 36 Copynumber: 5.6 Consensus size: 37
11959941 TATCTCAAAG
* * *
11959951 GAAAAATGTCTCAAGCGAGACGAAATTTGTTTTGAGA
1 GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTTAGA
*
11959988 G-AAATTGTCTCAAGCGAGACAAAATTTGTTTTTAGA
1 GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTTAGA
* * *
11960024 GAAAACTGTCTCAAGCGAG--ATAATTTTTTTTTATA
1 GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTTAGA
* * * *
11960059 -AAGAACTTTCTCAAGTGAGACGAAGTTT-TTTTTAGA
1 GAA-AACTGTCTCAAGCGAGACAAAATTTGTTTTTAGA
* * * *
11960095 GAAAAATATATCAAGTGAGACAAAATTTGTTTTTAGA
1 GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTTAGA
*
11960132 GAAAACTGTCTCAAGTGAGACAA
1 GAAAACTGTCTCAAGCGAGACAA
11960155 TTTATTTCGA
Statistics
Matches: 140, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
34 2 0.01
35 27 0.19
36 60 0.43
37 51 0.36
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (37 bp):
GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTTAGA
Found at i:11960157 original size:108 final size:108
Alignment explanation
Indices: 11959959--11960157 Score: 301
Period size: 108 Copynumber: 1.8 Consensus size: 108
11959949 AGGAAAAATG
* * *
11959959 TCTCAAGCGAGACGAAATTTGTTTTGAGAGAAATTGTCTCAAGCGAGACAAAATTTGTTTTTAGA
1 TCTCAAGCGAGACGAAATTTGTTTTGAGAGAAAATATATCAAGCGAGACAAAATTTGTTTTTAGA
*
11960024 GAAAACTGTCTCAAGCGAGATAATTTTTTTTTATAAAGAACTT
66 GAAAACTGTCTCAAGCGAGACAATTTTTTTTTATAAAGAACTT
* * * *
11960067 TCTCAAGTGAGACGAAGTTT-TTTTTAGAGAAAAATATATCAAGTGAGACAAAATTTGTTTTTAG
1 TCTCAAGCGAGACGAAATTTGTTTTGAGAG-AAAATATATCAAGCGAGACAAAATTTGTTTTTAG
*
11960131 AGAAAACTGTCTCAAGTGAGACAATTT
65 AGAAAACTGTCTCAAGCGAGACAATTT
11960158 ATTTCGAAAT
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
107 8 0.10
108 73 0.90
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.34
Consensus pattern (108 bp):
TCTCAAGCGAGACGAAATTTGTTTTGAGAGAAAATATATCAAGCGAGACAAAATTTGTTTTTAGA
GAAAACTGTCTCAAGCGAGACAATTTTTTTTTATAAAGAACTT
Found at i:11972444 original size:11 final size:11
Alignment explanation
Indices: 11972430--11972471 Score: 59
Period size: 11 Copynumber: 3.7 Consensus size: 11
11972420 TCTTTTTTTG
11972430 TTTTCTTTGTT
1 TTTTCTTTGTT
11972441 TTTT-TCTTGTT
1 TTTTCT-TTGTT
11972452 TTTTCTTTGTCT
1 TTTTCTTTGT-T
11972464 TTTTCTTT
1 TTTTCTTT
11972472 TCTATTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 1 0.04
11 17 0.61
12 10 0.36
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (11 bp):
TTTTCTTTGTT
Found at i:11972445 original size:12 final size:12
Alignment explanation
Indices: 11972413--11972471 Score: 68
Period size: 12 Copynumber: 4.9 Consensus size: 12
11972403 CTTGATCTGT
*
11972413 TTTTCTTTCTTTT
1 TTTT-TTTCTTTG
11972426 TTTGTTTTCTTTG
1 TTT-TTTTCTTTG
11972439 TTTTTTTC-TTG
1 TTTTTTTCTTTG
11972450 -TTTTTTCTTTG
1 TTTTTTTCTTTG
*
11972461 TCTTTTTCTTT
1 TTTTTTTCTTT
11972472 TCTATTCTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
10 7 0.17
11 6 0.15
12 14 0.34
13 13 0.32
14 1 0.02
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (12 bp):
TTTTTTTCTTTG
Found at i:11972467 original size:39 final size:39
Alignment explanation
Indices: 11972412--11972498 Score: 113
Period size: 39 Copynumber: 2.2 Consensus size: 39
11972402 ACTTGATCTG
* * * *
11972412 TTTTTCTTTCTTTTTTTGTTTTCT-TTGTTTTTTTCTTGT
1 TTTTTCTTTCTCTTTTTCTTTTCTATTCTTTTTCTCTT-T
*
11972451 TTTTTCTTTGTCTTTTTCTTTTCTATTCTTTTTCTCTTT
1 TTTTTCTTTCTCTTTTTCTTTTCTATTCTTTTTCTCTTT
11972490 TTTTTCTTT
1 TTTTTCTTT
11972499 TTGTCCTCGC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
39 31 0.74
40 11 0.26
ACGTcount: A:0.01, C:0.14, G:0.05, T:0.80
Consensus pattern (39 bp):
TTTTTCTTTCTCTTTTTCTTTTCTATTCTTTTTCTCTTT
Found at i:11972479 original size:22 final size:22
Alignment explanation
Indices: 11972432--11972496 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
11972422 TTTTTTTGTT
* *
11972432 TTCTTTGTTTTTTTCTTGTT-TT
1 TTCTTTGTCTTTTTCTT-TTCTA
11972454 TTCTTTGTCTTTTTCTTTTCTA
1 TTCTTTGTCTTTTTCTTTTCTA
*
11972476 TTCTTTTTCTCTTTT-TTTTCT
1 TTCTTTGTCT-TTTTCTTTTCT
11972497 TTTTGTCCTC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 2 0.05
22 32 0.84
23 4 0.11
ACGTcount: A:0.02, C:0.15, G:0.05, T:0.78
Consensus pattern (22 bp):
TTCTTTGTCTTTTTCTTTTCTA
Found at i:11972480 original size:16 final size:17
Alignment explanation
Indices: 11972461--11972500 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
11972451 TTTTTCTTTG
11972461 TCTTTTTCT-TTTCTAT
1 TCTTTTTCTCTTTCTAT
* *
11972477 TCTTTTTCTCTTTTTTT
1 TCTTTTTCTCTTTCTAT
11972494 TCTTTTT
1 TCTTTTT
11972501 GTCCTCGCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (17 bp):
TCTTTTTCTCTTTCTAT
Found at i:11979583 original size:4 final size:4
Alignment explanation
Indices: 11979574--11979939 Score: 232
Period size: 4 Copynumber: 91.0 Consensus size: 4
11979564 CTAACCCCTT
* * *
11979574 CATA CATA CATG CATA CATG TATA CATGCA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CAT--A CATA CATA CATA CATA CATA
* * * * * * * * * * * *
11979624 CATG CACA CATG CACA CATG CACA CATG CACA CATG CACA CATG CACA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * * * * *
11979672 CATG CACA CATG CATA CATG CATT CATG CATT TATT CATA CATG CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * *
11979720 CATG CATT CATA CATA TATT CATA CATA TATA CATA CATT CATT CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
11979768 CATA CAT- -ATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * *
11979814 CATA CATG CATG CATA TGCATA CATA CATA CATA TATA CATG CATG CATG
1 CATA CATA CATA CATA --CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * * *
11979864 CATG CATG CATA CATG CATA CATG CATT CATA CATT CATG CATT CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * *
11979912 CATT CATT CATA CATG CATA CATG CATA
1 CATA CATA CATA CATA CATA CATA CATA
11979940 TTTGGCCATC
Statistics
Matches: 279, Mismatches: 77, Indels: 12
0.76 0.21 0.03
Matches are distributed among these distances:
2 2 0.01
4 269 0.96
6 8 0.03
ACGTcount: A:0.39, C:0.25, G:0.08, T:0.28
Consensus pattern (4 bp):
CATA
Found at i:11979591 original size:8 final size:8
Alignment explanation
Indices: 11979578--11979939 Score: 292
Period size: 8 Copynumber: 44.5 Consensus size: 8
11979568 CCCCTTCATA
11979578 CATACATG
1 CATACATG
11979586 CATACATG
1 CATACATG
*
11979594 TATACATG
1 CATACATG
*
11979602 CACATACATA
1 --CATACATG
*
11979612 CATACATA
1 CATACATG
11979620 CATACATG
1 CATACATG
*
11979628 CACACATG
1 CATACATG
*
11979636 CACACATG
1 CATACATG
*
11979644 CACACATG
1 CATACATG
*
11979652 CACACATG
1 CATACATG
*
11979660 CACACATG
1 CATACATG
*
11979668 CACACATG
1 CATACATG
*
11979676 CACACATG
1 CATACATG
11979684 CATACATG
1 CATACATG
*
11979692 CATTCATG
1 CATACATG
** *
11979700 CATTTATT
1 CATACATG
11979708 CATACATG
1 CATACATG
11979716 CATACATG
1 CATACATG
* *
11979724 CATTCATA
1 CATACATG
* *
11979732 CATATATT
1 CATACATG
*
11979740 CATACATA
1 CATACATG
* *
11979748 TATACATA
1 CATACATG
* *
11979756 CATTCATT
1 CATACATG
*
11979764 CATACATA
1 CATACATG
*
11979772 CATATACATA
1 C--ATACATG
*
11979782 CATACATA
1 CATACATG
*
11979790 CATACATA
1 CATACATG
*
11979798 CATACATA
1 CATACATG
*
11979806 CATACATA
1 CATACATG
11979814 CATACATG
1 CATACATG
*
11979822 CATGCATATG
1 CAT--ACATG
*
11979832 CATACATA
1 CATACATG
*
11979840 CATACATA
1 CATACATG
*
11979848 TATACATG
1 CATACATG
*
11979856 CATGCATG
1 CATACATG
*
11979864 CATGCATG
1 CATACATG
11979872 CATACATG
1 CATACATG
11979880 CATACATG
1 CATACATG
* *
11979888 CATTCATA
1 CATACATG
*
11979896 CATTCATG
1 CATACATG
* *
11979904 CATTCATA
1 CATACATG
* *
11979912 CATTCATT
1 CATACATG
11979920 CATACATG
1 CATACATG
11979928 CATACATG
1 CATACATG
11979936 CATA
1 CATA
11979940 TTTGGCCATC
Statistics
Matches: 307, Mismatches: 41, Indels: 12
0.85 0.11 0.03
Matches are distributed among these distances:
8 286 0.93
10 21 0.07
ACGTcount: A:0.39, C:0.25, G:0.08, T:0.28
Consensus pattern (8 bp):
CATACATG
Found at i:11981536 original size:41 final size:40
Alignment explanation
Indices: 11981471--11981550 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 40
11981461 CCAACGATGC
* * *
11981471 TGAACATTGCACATGAATGTACCAAAGCTGAACTGATAAT
1 TGAACATTGCACACGAATGCACCAAAGCTAAACTGATAAT
*
11981511 TGAACATTGATACACGAATGCACCAAAGCTAAACTGATAA
1 TGAACATTG-CACACGAATGCACCAAAGCTAAACTGATAA
11981551 GTACTCACTT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
40 9 0.26
41 26 0.74
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (40 bp):
TGAACATTGCACACGAATGCACCAAAGCTAAACTGATAAT
Found at i:11981706 original size:18 final size:18
Alignment explanation
Indices: 11981651--11981713 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
11981641 TATTAATGTG
11981651 TATCTAATAACTAT-TAAA-
1 TATCTAATAA-T-TGTAAAT
* *
11981669 TATCTTATATTTGT-AAT
1 TATCTAATAATTGTAAAT
11981686 TATCTAATAATTGTAAAT
1 TATCTAATAATTGTAAAT
11981704 TATCTAATAA
1 TATCTAATAA
11981714 CAGAAAATCA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
16 3 0.08
17 14 0.37
18 21 0.55
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (18 bp):
TATCTAATAATTGTAAAT
Found at i:11981721 original size:18 final size:18
Alignment explanation
Indices: 11981683--11981739 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
11981673 TTATATTTGT
* *
11981683 AATTATCTAATAATTGTA
1 AATTATCTAATAACTGAA
*
11981701 AATTATCTAATAACAGAA
1 AATTATCTAATAACTGAA
* *
11981719 AATCATCTGATAACTGAA
1 AATTATCTAATAACTGAA
11981737 AAT
1 AAT
11981740 ATTTAGAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.33
Consensus pattern (18 bp):
AATTATCTAATAACTGAA
Found at i:11981946 original size:3 final size:3
Alignment explanation
Indices: 11981938--11982024 Score: 174
Period size: 3 Copynumber: 29.0 Consensus size: 3
11981928 CTTTAACACT
11981938 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
11981986 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
11982025 AATCAAAATA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 84 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:11984036 original size:5 final size:5
Alignment explanation
Indices: 11984026--11984072 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
11984016 TGAACGGTCT
* *
11984026 GACCC GACCC GA-CC GACCC GACCC GA-CC GATCC AACCC GACCC GACC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACC
11984073 GTTGACCGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
4 8 0.22
5 29 0.78
ACGTcount: A:0.23, C:0.55, G:0.19, T:0.02
Consensus pattern (5 bp):
GACCC
Found at i:11984045 original size:14 final size:14
Alignment explanation
Indices: 11984026--11984072 Score: 67
Period size: 14 Copynumber: 3.3 Consensus size: 14
11984016 TGAACGGTCT
11984026 GACCCGACCCGACC
1 GACCCGACCCGACC
11984040 GACCCGACCCGACC
1 GACCCGACCCGACC
* *
11984054 GATCCAACCCGACCC
1 GACCCGACCCGA-CC
11984069 GACC
1 GACC
11984073 GTTGACCGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 24 0.83
15 5 0.17
ACGTcount: A:0.23, C:0.55, G:0.19, T:0.02
Consensus pattern (14 bp):
GACCCGACCCGACC
Found at i:11984050 original size:19 final size:20
Alignment explanation
Indices: 11984026--11984072 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
11984016 TGAACGGTCT
*
11984026 GACCCGACCCGA-CCGACCC
1 GACCCGACCCGATCCAACCC
11984045 GACCCGA-CCGATCCAACCC
1 GACCCGACCCGATCCAACCC
11984064 GACCCGACC
1 GACCCGACC
11984073 GTTGACCGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 4 0.16
19 20 0.80
20 1 0.04
ACGTcount: A:0.23, C:0.55, G:0.19, T:0.02
Consensus pattern (20 bp):
GACCCGACCCGATCCAACCC
Found at i:11991309 original size:5 final size:5
Alignment explanation
Indices: 11991299--11991344 Score: 56
Period size: 5 Copynumber: 8.8 Consensus size: 5
11991289 GAACCGGTCT
* *
11991299 GACCC GACCC GACCC GACCC GACCGTT GACCC GACCC GACTC GACC
1 GACCC GACCC GACCC GACCC GACC--C GACCC GACCC GACCC GACC
11991345 GTTGACCGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
5 31 0.89
7 4 0.11
ACGTcount: A:0.20, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:11991329 original size:22 final size:22
Alignment explanation
Indices: 11991304--11991351 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
11991294 GGTCTGACCC
11991304 GACCCGACCCGACCCGACCGTT
1 GACCCGACCCGACCCGACCGTT
*
11991326 GACCCGACCCGACTCGACCGTT
1 GACCCGACCCGACCCGACCGTT
11991348 GACC
1 GACC
11991352 GTTGACTTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.19, C:0.48, G:0.23, T:0.10
Consensus pattern (22 bp):
GACCCGACCCGACCCGACCGTT
Found at i:12000384 original size:11 final size:11
Alignment explanation
Indices: 12000368--12000394 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
12000358 CTGTATATAT
12000368 ATTTTGTTTGA
1 ATTTTGTTTGA
12000379 ATTTTGTTTGA
1 ATTTTGTTTGA
12000390 ATTTT
1 ATTTT
12000395 TAAACTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.15, T:0.67
Consensus pattern (11 bp):
ATTTTGTTTGA
Found at i:12004215 original size:257 final size:257
Alignment explanation
Indices: 12003759--12004273 Score: 1030
Period size: 257 Copynumber: 2.0 Consensus size: 257
12003749 ATTCTGAAAT
12003759 CATGAATCAATTTGACCGAAAGAGTTTAATGAATATGTTTAATCTGTAAAATCAAAGCCTATATT
1 CATGAATCAATTTGACCGAAAGAGTTTAATGAATATGTTTAATCTGTAAAATCAAAGCCTATATT
12003824 GGTGCAACACAGATACTTATCGCTTTTGTTTTATCTGCTTCCTCGTTTATGAACCTGGAAGAATT
66 GGTGCAACACAGATACTTATCGCTTTTGTTTTATCTGCTTCCTCGTTTATGAACCTGGAAGAATT
12003889 TAAATTTTATTCAATGATCTTACTCTTTTCTCTCTTCTTCAGGGATCTATGAAGACTGTAGTCAA
131 TAAATTTTATTCAATGATCTTACTCTTTTCTCTCTTCTTCAGGGATCTATGAAGACTGTAGTCAA
12003954 CTGCCTTTTAGCACTAAAAATACATTTCATATCATCTGTAGAGGACTTATCTGCCATAAGTA
196 CTGCCTTTTAGCACTAAAAATACATTTCATATCATCTGTAGAGGACTTATCTGCCATAAGTA
12004016 CATGAATCAATTTGACCGAAAGAGTTTAATGAATATGTTTAATCTGTAAAATCAAAGCCTATATT
1 CATGAATCAATTTGACCGAAAGAGTTTAATGAATATGTTTAATCTGTAAAATCAAAGCCTATATT
12004081 GGTGCAACACAGATACTTATCGCTTTTGTTTTATCTGCTTCCTCGTTTATGAACCTGGAAGAATT
66 GGTGCAACACAGATACTTATCGCTTTTGTTTTATCTGCTTCCTCGTTTATGAACCTGGAAGAATT
12004146 TAAATTTTATTCAATGATCTTACTCTTTTCTCTCTTCTTCAGGGATCTATGAAGACTGTAGTCAA
131 TAAATTTTATTCAATGATCTTACTCTTTTCTCTCTTCTTCAGGGATCTATGAAGACTGTAGTCAA
12004211 CTGCCTTTTAGCACTAAAAATACATTTCATATCATCTGTAGAGGACTTATCTGCCATAAGTA
196 CTGCCTTTTAGCACTAAAAATACATTTCATATCATCTGTAGAGGACTTATCTGCCATAAGTA
12004273 C
1 C
12004274 CATTACGAAA
Statistics
Matches: 258, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
257 258 1.00
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.37
Consensus pattern (257 bp):
CATGAATCAATTTGACCGAAAGAGTTTAATGAATATGTTTAATCTGTAAAATCAAAGCCTATATT
GGTGCAACACAGATACTTATCGCTTTTGTTTTATCTGCTTCCTCGTTTATGAACCTGGAAGAATT
TAAATTTTATTCAATGATCTTACTCTTTTCTCTCTTCTTCAGGGATCTATGAAGACTGTAGTCAA
CTGCCTTTTAGCACTAAAAATACATTTCATATCATCTGTAGAGGACTTATCTGCCATAAGTA
Found at i:12011365 original size:2 final size:2
Alignment explanation
Indices: 12011351--12011392 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
12011341 CGGATTAAAC
*
12011351 TA TA TA AA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12011392 T
1 T
12011393 CATACTATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12012889 original size:15 final size:15
Alignment explanation
Indices: 12012869--12012907 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
12012859 TTTTTTTAAT
12012869 TGAAATTGAAACTGC
1 TGAAATTGAAACTGC
12012884 TGAAATTGAAACTGC
1 TGAAATTGAAACTGC
*
12012899 TGGAATTGA
1 TGAAATTGA
12012908 GTACTTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.28
Consensus pattern (15 bp):
TGAAATTGAAACTGC
Found at i:12016109 original size:75 final size:73
Alignment explanation
Indices: 12015970--12016276 Score: 255
Period size: 75 Copynumber: 4.3 Consensus size: 73
12015960 TTCGAAAACA
* * * *
12015970 TTTTGAAAATATATATATTATATAGTTTTGAAAT-TTTTTGAAAACATT-TATAATGTATAGTTT
1 TTTTGGAAATATATATAATATATAGTTTTGAAATCTTTTTGAAAAC-TTATATAATATATA-ATT
* *
12016033 TTTAAGATCC
64 TTTAAAATAC
*
12016043 TTTTGGAAATATATATAATATATAGTTTTGAAATCGTTATTGAAAACTTATATAATATATAATTT
1 TTTTGGAAATATATATAATATATAGTTTTGAAATC-TTTTTGAAAACTTATATAATATATAATTT
*
12016108 TTAAAATAT
65 TTAAAATAC
* * * * *
12016117 TTTTTGAAAAATTATATGATATATAGTTTTAAAAACAATTTTTGAAAACTTAT-T--TA-AT-AT
1 TTTTGGAAATA-TATATAATATATAGTTTTGAAATC--TTTTTGAAAACTTATATAATATATAAT
* *
12016177 TTTTAAATTAA
63 TTTTAAAATAC
* * **
12016188 TTTT-GAAA-ACTATATAATATATAGTTTTGAAAGCTTTTT-AAAA--AATATAATATAT-GGTT
1 TTTTGGAAATA-TATATAATATATAGTTTTGAAATCTTTTTGAAAACTTATATAATATATAATTT
*
12016247 TAAAAATA-
65 TTAAAATAC
* *
12016255 TTTTTGAAATATATATTATATA
1 TTTTGGAAATATATATAATATA
12016277 ATTTATACTA
Statistics
Matches: 196, Mismatches: 27, Indels: 27
0.78 0.11 0.11
Matches are distributed among these distances:
64 2 0.01
65 1 0.01
66 4 0.02
67 11 0.06
68 24 0.12
69 23 0.12
70 4 0.02
71 15 0.08
72 2 0.01
73 34 0.17
74 20 0.10
75 42 0.21
76 14 0.07
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (73 bp):
TTTTGGAAATATATATAATATATAGTTTTGAAATCTTTTTGAAAACTTATATAATATATAATTTT
TAAAATAC
Found at i:12016133 original size:38 final size:38
Alignment explanation
Indices: 12015970--12016215 Score: 133
Period size: 38 Copynumber: 6.8 Consensus size: 38
12015960 TTCGAAAACA
* * *
12015970 TTTTG-AAAATATATATATTATAT-AGTTTT-GAA-ATT
1 TTTTGAAAAAT-TATATAATATATAATTTTTAAAATATT
* * * **
12016005 TTTTGAAAACATT-TATAATGTATAGTTTTTTAAGATCCT
1 TTTTGAAAA-ATTATATAATATATA-ATTTTTAAAATATT
* * * * **
12016044 TTTGGAAATA-TATATAATATAT-AGTTTTGAAATCGT
1 TTTTGAAAAATTATATAATATATAATTTTTAAAATATT
* *
12016080 TATTGAAAACTTATATAATATATAATTTTTAAAATATT
1 TTTTGAAAAATTATATAATATATAATTTTTAAAATATT
* * * * *
12016118 TTTTGAAAAATTATATGATATATAGTTTTAAAAACAAT
1 TTTTGAAAAATTATATAATATATAATTTTTAAAATATT
* * *
12016156 TTTTGAAAACTTAT-T--TA-AT-ATTTTTAAATTA-A
1 TTTTGAAAAATTATATAATATATAATTTTTAAAATATT
* *
12016188 TTTTG-AAAACTATATAATATATAGTTTT
1 TTTTGAAAAATTATATAATATATAATTTT
12016216 GAAAGCTTTT
Statistics
Matches: 157, Mismatches: 40, Indels: 27
0.70 0.18 0.12
Matches are distributed among these distances:
31 6 0.04
32 6 0.04
33 8 0.05
34 4 0.03
35 17 0.11
36 23 0.15
37 20 0.13
38 65 0.41
39 8 0.05
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (38 bp):
TTTTGAAAAATTATATAATATATAATTTTTAAAATATT
Found at i:12016259 original size:33 final size:33
Alignment explanation
Indices: 12016199--12016281 Score: 85
Period size: 33 Copynumber: 2.5 Consensus size: 33
12016189 TTTGAAAACT
** *
12016199 ATATAATATATAGTTTTGAAAGCTTTTTAAAAA
1 ATATAATATATAGTTTAAAAAGATTTTTAAAAA
* * * *
12016232 ATATAATATATGGTTTAAAAATATTTTTGAAAT
1 ATATAATATATAGTTTAAAAAGATTTTTAAAAA
* *
12016265 ATATATTATATAATTTA
1 ATATAATATATAGTTTA
12016282 TACTATATTA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.46
Consensus pattern (33 bp):
ATATAATATATAGTTTAAAAAGATTTTTAAAAA
Found at i:12017709 original size:25 final size:25
Alignment explanation
Indices: 12017656--12017713 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 25
12017646 TTCATTTAAT
12017656 TTTTATTTTATTATTATTTTTTATA
1 TTTTATTTTATTATTATTTTTTATA
*
12017681 TTTTATATTT-TTATTACTTTTTT-TC
1 TTTTAT-TTTATTATTA-TTTTTTATA
12017706 TTTTATTT
1 TTTTATTT
12017714 ATCTATGTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 2 0.07
25 19 0.63
26 9 0.30
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (25 bp):
TTTTATTTTATTATTATTTTTTATA
Found at i:12019106 original size:104 final size:105
Alignment explanation
Indices: 12018919--12019112 Score: 354
Period size: 104 Copynumber: 1.9 Consensus size: 105
12018909 CCACCCGCTC
*
12018919 CTGAGACCCCCCAGGTTACCTTAGCAAGCTTCGTCGGTATTGAGTTTCAAGCTAACCGATCTCGG
1 CTGAGACCCCCCAAGTTACCTTAGCAAGCTTCGTCGGTATTGAGTTTCAAGCTAACCGATCTCGG
12018984 CGGTGTCCATGCTATAGTGAGATTGTTTTGTGGGTTGATG
66 CGGTGTCCATGCTATAGTGAGATTGTTTTGTGGGTTGATG
**
12019024 CTGAGA-CCCCCAAGTTACCTTAGCAAGCTTCGTCGGTATTGAGTTTCAAGCTCCCCGATCTCGG
1 CTGAGACCCCCCAAGTTACCTTAGCAAGCTTCGTCGGTATTGAGTTTCAAGCTAACCGATCTCGG
12019088 CGGTGTCCATGCTATAGTGAGATTG
66 CGGTGTCCATGCTATAGTGAGATTG
12019113 CAGGTTGATG
Statistics
Matches: 86, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
104 80 0.93
105 6 0.07
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (105 bp):
CTGAGACCCCCCAAGTTACCTTAGCAAGCTTCGTCGGTATTGAGTTTCAAGCTAACCGATCTCGG
CGGTGTCCATGCTATAGTGAGATTGTTTTGTGGGTTGATG
Found at i:12020643 original size:30 final size:32
Alignment explanation
Indices: 12020585--12020643 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 32
12020575 AAAAGATAGA
* *
12020585 AAAAAATAGAAAAATCAAAAAGAGAGAGATTC
1 AAAAAATACAAAAATCAAAAAGAAAGAGATTC
*
12020617 AAAAAAT-CAAAAA-CAAAAATAAAGAGA
1 AAAAAATACAAAAATCAAAAAGAAAGAGA
12020644 GAAAGAGAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 12 0.50
31 5 0.21
32 7 0.29
ACGTcount: A:0.71, C:0.07, G:0.12, T:0.10
Consensus pattern (32 bp):
AAAAAATACAAAAATCAAAAAGAAAGAGATTC
Found at i:12029444 original size:21 final size:20
Alignment explanation
Indices: 12029412--12029451 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
12029402 GTATCAATCT
*
12029412 TTTGCATCTACATTTACATC
1 TTTGCATCTACATCTACATC
*
12029432 TTTGCATTTTACATCTACAT
1 TTTGCA-TCTACATCTACAT
12029452 TTCATTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.25, C:0.23, G:0.05, T:0.47
Consensus pattern (20 bp):
TTTGCATCTACATCTACATC
Found at i:12030623 original size:13 final size:14
Alignment explanation
Indices: 12030568--12030626 Score: 59
Period size: 13 Copynumber: 4.1 Consensus size: 14
12030558 AGATCAAGTT
12030568 AAAACAAAGA-AAA
1 AAAACAAAGAGAAA
* *
12030581 AAAATAAAGATCAAAGA
1 AAAACAAAGA--GAA-A
12030598 AAAACAAAGAGAAA
1 AAAACAAAGAGAAA
12030612 AAAACAAA-AGAAA
1 AAAACAAAGAGAAA
12030625 AA
1 AA
12030627 GAGGACAAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
13 16 0.41
14 9 0.23
15 2 0.05
16 2 0.05
17 10 0.26
ACGTcount: A:0.80, C:0.07, G:0.10, T:0.03
Consensus pattern (14 bp):
AAAACAAAGAGAAA
Found at i:12031858 original size:39 final size:37
Alignment explanation
Indices: 12031815--12031946 Score: 108
Period size: 36 Copynumber: 3.5 Consensus size: 37
12031805 ACAAAGTGTC
* *
12031815 GTCTCGCTAGAGACAGTTTTT-TTCTAAAAAATAAATTTT
1 GTCTCGCTTGAGACA-TTTTTCTT-T-AAAAACAAATTTT
* *
12031854 GTCTCGTTTGAGACATTTTTCTTTAAAAACAAGTTTT
1 GTCTCGCTTGAGACATTTTTCTTTAAAAACAAATTTT
* * * * *
12031891 -TCTCGCTTGAGACA-ATTTCTCTCAAAGCAAATTTC
1 GTCTCGCTTGAGACATTTTTCTTTAAAAACAAATTTT
* *
12031926 ATCTCACTTGAGACAATTTTT
1 GTCTCGCTTGAGAC-ATTTTT
12031947 ACTTGAAACA
Statistics
Matches: 76, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
35 15 0.20
36 25 0.33
37 12 0.16
38 9 0.12
39 15 0.20
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (37 bp):
GTCTCGCTTGAGACATTTTTCTTTAAAAACAAATTTT
Found at i:12032042 original size:66 final size:67
Alignment explanation
Indices: 12031927--12032221 Score: 386
Period size: 66 Copynumber: 4.5 Consensus size: 67
12031917 GCAAATTTCA
* * **
12031927 TCTCACTTGAGACAATTTTTACTTGAAACAAAAGTCTTTGAGCCTGTTTCTTTTGAAACAAAGTT
1 TCTCTCTTGAGACAATTTCT-CTTGAAACAAAAGTCTTTGAGCCTGTTTCCCTTGAAACAAAGTT
12031992 TTG
65 TTG
* * * **
12031995 TCTCTCTTGATACAATTTTTCTTTTAAA-AAAA-TCTTTGAGTTTGTTTCCCTTGAAAC-AAGTT
1 TCTCTCTTGAGACAATTTCTC-TTGAAACAAAAGTCTTTGAGCCTGTTTCCCTTGAAACAAAGTT
12032057 TTG
65 TTG
* * * *
12032060 TCTCCCTTGAGACAGTTCCTCTTGAAA-AAAA-TCTTTGAGTCTGTTTCCCTTGAAACAAAGTTT
1 TCTCTCTTGAGACAATTTCTCTTGAAACAAAAGTCTTTGAGCCTGTTTCCCTTGAAACAAAGTTT
12032123 TG
66 TG
* * *
12032125 TCTCTCTTGAGATAGTTTCTCTTGAAACAAAAGTCTTTGAGCCTGTTTCCCTTGAAATAAA-TTT
1 TCTCTCTTGAGACAATTTCTCTTGAAACAAAAGTCTTTGAGCCTGTTTCCCTTGAAACAAAGTTT
12032189 TG
66 TG
12032191 TCTCTCTTGAGACAATTTCTCTTGAAACAAA
1 TCTCTCTTGAGACAATTTCTCTTGAAACAAA
12032222 CCCCTAAAGA
Statistics
Matches: 202, Mismatches: 21, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
64 33 0.16
65 56 0.28
66 59 0.29
67 31 0.15
68 23 0.11
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (67 bp):
TCTCTCTTGAGACAATTTCTCTTGAAACAAAAGTCTTTGAGCCTGTTTCCCTTGAAACAAAGTTT
TG
Found at i:12032213 original size:131 final size:132
Alignment explanation
Indices: 12031918--12032221 Score: 389
Period size: 131 Copynumber: 2.3 Consensus size: 132
12031908 TCTCTCAAAG
** * **
12031918 CAAATTTCATCTCACTTGAGACAATTTTTACTTGAAACAAAAGTCTTTGAGCCTGTTTCTTTTGA
1 CAAATTTTGTCTCACTTGAGACAATTTCT-CTTGAAACAAAAGTCTTTGAGCCTGTTTCCCTTGA
* * * **
12031983 AACAAAGTTTTGTCTCTCTTGATACAATTTTTCTTTTAAAAAAATCTTTGAGTTTGTTTCCCTTG
65 AACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTTGAAAAAAATCTTTGAGCCTGTTTCCCTTG
12032048 AAA
130 AAA
* * * * *
12032051 CAAGTTTTGTCTCCCTTGAGACAGTTCCTCTTGAAA-AAAA-TCTTTGAGTCTGTTTCCCTTGAA
1 CAAATTTTGTCTCACTTGAGACAATTTCTCTTGAAACAAAAGTCTTTGAGCCTGTTTCCCTTGAA
* *
12032114 ACAAAGTTTTGTCTCTCTTGAGATAGTTTCTC-TTGAAACAAAAGTCTTTGAGCCTGTTTCCCTT
66 ACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTTGAAA-AAAA-TCTTTGAGCCTGTTTCCCTT
12032178 GAAA
129 GAAA
* *
12032182 TAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAA
1 CAAATTTTGTCTCACTTGAGACAATTTCTCTTGAAACAAA
12032222 CCCCTAAAGA
Statistics
Matches: 146, Mismatches: 22, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
129 5 0.03
130 52 0.36
131 57 0.39
132 10 0.07
133 22 0.15
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.40
Consensus pattern (132 bp):
CAAATTTTGTCTCACTTGAGACAATTTCTCTTGAAACAAAAGTCTTTGAGCCTGTTTCCCTTGAA
ACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTTGAAAAAAATCTTTGAGCCTGTTTCCCTTGA
AA
Found at i:12032465 original size:131 final size:130
Alignment explanation
Indices: 12032242--12032701 Score: 505
Period size: 131 Copynumber: 3.5 Consensus size: 130
12032232 TGGCCAGCTG
* * * *
12032242 TCCTCATCGCGTAAGAATCGTGTCATCCACCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCA
1 TCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTTCTCATCACGTAGGAGCCGTGTCA
* * * * *
12032307 ACCTTAGATAACCAACTGTCCTCATCACGTAGTAACTGTGTTATCATCCCTAAAGATGGTATGGC
66 CCCTTAGATAACCAGCAGTCCT-ATCACGTAGGAACCGTGTTATCATCCCTAAAGATGGTATGGC
12032372 A
130 A
* * * * **
12032373 TCCTCATCATGTAGGAACTGTGTCATCCCCCGACCAGATCTTCTCATCATGTAGGAGCCACGTCA
1 TCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTTCTCATCACGTAGGAGCCGTGTCA
*
12032438 CCCTTAGATAACCAGCAGTCCGTATCACGTAGGAACCGTGTTATCATCCCTAAAGATGGTATGTC
66 CCCTTAGATAACCAGCAGTCC-TATCACGTAGGAACCGTGTTATCATCCCTAAAGATGGTATGGC
12032503 A
130 A
* * * *
12032504 TCCTCATCACGTAGGAACCATGTCATCCACCGACCAGA-CTTCCCCATCACGTAGGAACCGTGTA
1 TCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTT-CTCATCACGTAGGAGCCGTGTC
* * *
12032568 ACCCCTAGATAACCAG-ACGTCCTTATCGCGTAGGAACCGTGTTATCACCCTTCCTAAAGATGGC
65 ACCCTTAGATAACCAGCA-GTCC-TATCACGTAGGAACCGTGTTATCA---TCCCTAAAGATGG-
* *
12032632 CA--GCTG
124 TATGGC-A
* ** * * * * *
12032638 TCCTTATTGCGTAGGAACCGTGTCATCCACCGACCATATCTCCACATCACGTAGTAGTCGTGTC
1 TCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTTCTCATCACGTAGGAGCCGTGTC
12032702 TTCCTTAAAA
Statistics
Matches: 276, Mismatches: 44, Indels: 15
0.82 0.13 0.04
Matches are distributed among these distances:
130 4 0.01
131 205 0.74
132 1 0.00
133 1 0.00
134 62 0.22
135 3 0.01
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.25
Consensus pattern (130 bp):
TCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTTCTCATCACGTAGGAGCCGTGTCA
CCCTTAGATAACCAGCAGTCCTATCACGTAGGAACCGTGTTATCATCCCTAAAGATGGTATGGCA
Found at i:12037218 original size:12 final size:12
Alignment explanation
Indices: 12037203--12037234 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
12037193 AAGTAAGTAT
*
12037203 ACAAGTTGGTAC
1 ACAACTTGGTAC
12037215 ACAACTTGGTAC
1 ACAACTTGGTAC
12037227 ACAACTTG
1 ACAACTTG
12037235 TTTCATTGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (12 bp):
ACAACTTGGTAC
Found at i:12039708 original size:22 final size:22
Alignment explanation
Indices: 12039680--12039724 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
12039670 TTTCTCACAT
12039680 AAATTAAGGT-GGACACAAATGA
1 AAATTAAGGTAGGA-ACAAATGA
*
12039702 AAATTAAGGTAGGAATAAATGA
1 AAATTAAGGTAGGAACAAATGA
12039724 A
1 A
12039725 TGAGGATGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.53, C:0.04, G:0.22, T:0.20
Consensus pattern (22 bp):
AAATTAAGGTAGGAACAAATGA
Found at i:12055142 original size:54 final size:54
Alignment explanation
Indices: 12055039--12055358 Score: 147
Period size: 54 Copynumber: 6.0 Consensus size: 54
12055029 ACAACTACAA
*** *
12055039 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATTAATCAATAC
1 TAATAAATTATTTAAAATAAATCAATCCATAAACTAAAATAAATAAATCAATAC
** *
12055093 TAATAAATTATTTAAAATAAATCAATTTATACAACTACAAT-AATAAATCAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-AACTAAAATAAATAAATCAATAC
* * *
12055146 -CAT--A-T-TTTAAAATAAATCAATTCATACTA-TAAATTATTTAAAATAAATCAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-AACTAAA--A--T-AAATAAATCAATAC
* * *
12055199 -CAT--ATT-TTAAAAATAAATCAATCTATACTAA-TAAATTATTTAAAATAAATCAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA--AACTAAA--A--T-AAATAAATCAATAC
* * * *** * *
12055254 -CATACAACTA--CAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATA-AATTATTTAA-AATAAATCAATCCATAAACTAAAATAAATAAATCAATAC
* *
12055307 TAATAAATTATTTAAAACAAATCAATCCATACAACTACAAT-AATAAATCAAT
1 TAATAAATTATTTAAAATAAATCAATCCATA-AACTAAAATAAATAAATCAAT
12055359 CCATATTTTA
Statistics
Matches: 213, Mismatches: 33, Indels: 40
0.74 0.12 0.14
Matches are distributed among these distances:
47 3 0.01
48 22 0.10
49 2 0.01
50 1 0.00
51 1 0.00
52 12 0.06
53 23 0.11
54 85 0.40
55 41 0.19
57 6 0.03
58 17 0.08
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATAAACTAAAATAAATAAATCAATAC
Found at i:12055178 original size:22 final size:22
Alignment explanation
Indices: 12055105--12055178 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 22
12055095 ATAAATTATT
*
12055105 TAAAATAAATCAATTTATACAACTA
1 TAAAATAAATCAATTCAT---ACTA
* * * *
12055130 CAATAATAAATCAATCCATATTT
1 TAA-AATAAATCAATTCATACTA
12055153 TAAAATAAATCAATTCATACTA
1 TAAAATAAATCAATTCATACTA
12055175 TAAA
1 TAAA
12055179 TTATTTAAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
22 20 0.51
23 4 0.10
25 2 0.05
26 13 0.33
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (22 bp):
TAAAATAAATCAATTCATACTA
Found at i:12055187 original size:31 final size:30
Alignment explanation
Indices: 12055151--12055516 Score: 123
Period size: 26 Copynumber: 13.4 Consensus size: 30
12055141 CAATCCATAT
12055151 TTTAAAATAAATCAATTCATACTATAAATTA
1 TTTAAAATAAATCAA-TCATACTATAAATTA
12055182 TTTAAAATAAATCAATC---C-AT--ATT-
1 TTTAAAATAAATCAATCATACTATAAATTA
*
12055205 TTAAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATC-ATACT-ATAAATTA
*
12055237 TTTAAAATAAATCAATC---C-ATACAACTA
1 TTTAAAATAAATCAATCATACTATA-AATTA
* * *
12055264 --CAATAATAAATCAATCCATATTTTAAA--A
1 TTTAA-AATAAATCAAT-CATACTATAAATTA
*
12055292 --T-AAATCAATC---CATACTAATAAATTA
1 TTTAAAATAAATCAATCATACT-ATAAATTA
* *
12055317 TTTAAAACAAATCAATC---C-ATACAACTA
1 TTTAAAATAAATCAATCATACTATA-AATTA
* * *
12055344 --CAATAATAAATCAATCCATATTTTAAA--A
1 TTTAA-AATAAATCAAT-CATACTATAAATTA
* *
12055372 --T-ACATCAATC--T-ATACTAATAAATTA
1 TTTAAAATAAATCAATCATACT-ATAAATTA
12055397 TTTAAAATAAATCAATC---C-AT--A-T-
1 TTTAAAATAAATCAATCATACTATAAATTA
12055419 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATC-ATACT-ATAAATTA
12055451 TTTAAAATAAATCAATC---C-AT--A-T-
1 TTTAAAATAAATCAATCATACTATAAATTA
12055473 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATC-ATACT-ATAAATTA
12055505 TTTAAAATAAAT
1 TTTAAAATAAAT
12055517 TATTTTAAAA
Statistics
Matches: 250, Mismatches: 24, Indels: 121
0.63 0.06 0.31
Matches are distributed among these distances:
22 43 0.17
23 26 0.10
24 6 0.02
25 6 0.02
26 48 0.19
27 16 0.06
28 24 0.10
29 2 0.01
30 9 0.04
31 25 0.10
32 45 0.18
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (30 bp):
TTTAAAATAAATCAATCATACTATAAATTA
Found at i:12055312 original size:80 final size:80
Alignment explanation
Indices: 12055187--12055417 Score: 426
Period size: 80 Copynumber: 2.9 Consensus size: 80
12055177 AATTATTTAA
12055187 AATAAATCAATCCATATTTTAAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAA
1 AATAAATCAATCCATATTTT-AAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAA
12055252 TCCATACAACTACAAT
65 TCCATACAACTACAAT
* *
12055268 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAACAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
12055333 CCATACAACTACAAT
66 CCATACAACTACAAT
*
12055348 AATAAATCAATCCATATTTTAAAATACATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
12055413 CCATA
66 CCATA
12055418 TTTTAAAATA
Statistics
Matches: 145, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
80 125 0.86
81 20 0.14
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (80 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
CCATACAACTACAAT
Found at i:12055314 original size:22 final size:23
Alignment explanation
Indices: 12055239--12055313 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
12055229 ATAAATTATT
12055239 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
12055261 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
12055287 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
12055310 TAAA
1 TAAA
12055314 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:12055401 original size:32 final size:32
Alignment explanation
Indices: 12055365--12055516 Score: 155
Period size: 32 Copynumber: 5.4 Consensus size: 32
12055355 CAATCCATAT
*
12055365 TTTAAAATACATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACTAATAAATTA
12055397 TTTAAAATAAATCAATC----C--AT--A-T-
1 TTTAAAATAAATCAATCTATACTAATAAATTA
12055419 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACTAATAAATTA
12055451 TTTAAAATAAATCAATC----C--AT--A-T-
1 TTTAAAATAAATCAATCTATACTAATAAATTA
12055473 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACTAATAAATTA
12055505 TTTAAAATAAAT
1 TTTAAAATAAAT
12055517 TATTTTAAAA
Statistics
Matches: 99, Mismatches: 1, Indels: 40
0.71 0.01 0.29
Matches are distributed among these distances:
22 34 0.34
23 2 0.02
24 2 0.02
26 6 0.06
28 6 0.06
30 2 0.02
31 2 0.02
32 45 0.45
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.38
Consensus pattern (32 bp):
TTTAAAATAAATCAATCTATACTAATAAATTA
Found at i:12055417 original size:54 final size:54
Alignment explanation
Indices: 12055134--12055516 Score: 441
Period size: 54 Copynumber: 7.1 Consensus size: 54
12055124 CAACTACAAT
12055134 AATAAATCAATCCATATTTTAAAATAAATCAAT-TCATACT-ATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCT-ATACTAATAAATTATTTAA
12055187 AATAAATCAATCCATATTTTAAAAATAAATCAATCTATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTT-AAAATAAATCAATCTATACTAATAAATTATTTAA
*** * * * *
12055242 AATAAATCAATCCATACAACTACAAT-AATAAATCAAT-C-CAT--A-T-TTTAA
1 AATAAATCAATCCATA-TTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
** * * * * *
12055290 AATAAATCAATCCATACTAATAAATTATTTAAAACAAATCAAT-C-CATACAACTA--CAA
1 AATAAATCAATCCATA-TTTTAAA--A--TAAATC-AATCTATACTAATA-AATTATTTAA
*
12055347 TAATAAATCAATCCATATTTTAAAATACATCAATCTATACTAATAAATTATTTAA
1 -AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
12055402 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
12055456 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
12055510 AATAAAT
1 AATAAAT
12055517 TATTTTAAAA
Statistics
Matches: 288, Mismatches: 22, Indels: 39
0.83 0.06 0.11
Matches are distributed among these distances:
48 26 0.09
49 1 0.00
50 2 0.01
52 9 0.03
53 32 0.11
54 155 0.54
55 37 0.13
56 1 0.00
57 8 0.03
58 17 0.06
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.34
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
Found at i:12055428 original size:214 final size:214
Alignment explanation
Indices: 12055054--12055471 Score: 750
Period size: 214 Copynumber: 2.0 Consensus size: 214
12055044 AATTATTTAA
* *
12055054 AATAAATCAATCCATATTTTAAAATAAATTAATCAATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCAATACTAATAAATTATTTAAAACAAATCAAT
**
12055119 TTATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTATAAATTATT
66 CCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTATAAATTATT
12055184 TAAAATAAATCAATCCATATTTTAAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAAT
131 TAAAATAAATCAATCCATATTTTAAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAAT
12055249 CAATCCATACAACTACAAT
196 CAATCCATACAACTACAAT
*
12055268 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAACAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCAATACTAATAAATTATTTAAAACAAATCAAT
*
12055333 CCATACAACTACAATAATAAATCAATCCATATTTTAAAATACATCAA-TCTATACTAATAAATTA
66 CCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATTC-ATACT-ATAAATTA
12055397 TTTAAAATAAATCAATCCATATTTT-AAAATAAATCAATCTATACTAATAAATTATTTAAAATAA
129 TTTAAAATAAATCAATCCATATTTTAAAAATAAATCAATCTATACTAATAAATTATTTAAAATAA
12055461 ATCAATCCATA
194 ATCAATCCATA
12055472 TTTTAAAATA
Statistics
Matches: 196, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
213 2 0.01
214 161 0.82
215 33 0.17
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (214 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCAATACTAATAAATTATTTAAAACAAATCAAT
CCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTATAAATTATT
TAAAATAAATCAATCCATATTTTAAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAAT
CAATCCATACAACTACAAT
Found at i:12055448 original size:22 final size:22
Alignment explanation
Indices: 12055399--12055447 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
12055389 ATAAATTATT
**
12055399 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
12055421 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
12055444 TAAA
1 TAAA
12055448 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:12055477 original size:22 final size:22
Alignment explanation
Indices: 12055451--12055553 Score: 80
Period size: 22 Copynumber: 4.5 Consensus size: 22
12055441 TAATAAATTA
12055451 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
12055473 TTTAAAATAAATCAATCTATACT
1 TTTAAAATAAATCAATCCATA-T
** * ** * **
12055496 AATAAATTATTTAAAATAAATTAT
1 TTTAAAATAAAT-CAATCCA-TAT
*
12055520 TTTAAAATAAAGCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
12055542 TTTATAATAAAT
1 TTTAAAATAAAT
12055554 TATTTTAAAA
Statistics
Matches: 58, Mismatches: 20, Indels: 6
0.69 0.24 0.07
Matches are distributed among these distances:
22 33 0.57
23 12 0.21
24 11 0.19
25 2 0.03
ACGTcount: A:0.51, C:0.09, G:0.01, T:0.39
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:12055525 original size:15 final size:15
Alignment explanation
Indices: 12055496--12055568 Score: 67
Period size: 15 Copynumber: 4.5 Consensus size: 15
12055486 AATCTATACT
12055496 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
12055510 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
12055525 AATAAAGCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
12055547 AATAAATTATTTTAA
1 AATAAATTATTTTAA
12055562 AATAAAT
1 AATAAAT
12055569 AACCTTATTA
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
14 9 0.18
15 22 0.45
17 1 0.02
18 3 0.06
19 3 0.06
20 1 0.02
22 10 0.20
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.41
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:12055552 original size:37 final size:36
Alignment explanation
Indices: 12055442--12055567 Score: 129
Period size: 37 Copynumber: 3.6 Consensus size: 36
12055432 AATCTATACT
12055442 AATAAATTA-TTTAAAATAAATCAATCCATATTTTAA
1 AATAAATTATTTTAAAATAAA-CAATCCATATTTTAA
* * * * *
12055478 AATAAATCAATCTATACTAATA-AAT---TA-TTTAA
1 AATAAATTATTTTAAAATAA-ACAATCCATATTTTAA
*
12055510 AATAAATTATTTTAAAATAAAGCAATCCATATTTTAT
1 AATAAATTATTTTAAAATAAA-CAATCCATATTTTAA
12055547 AATAAATTATTTTAAAATAAA
1 AATAAATTATTTTAAAATAAA
12055568 TAACCTTATT
Statistics
Matches: 72, Mismatches: 10, Indels: 15
0.74 0.10 0.15
Matches are distributed among these distances:
31 1 0.01
32 20 0.28
33 5 0.07
36 13 0.18
37 32 0.44
38 1 0.01
ACGTcount: A:0.53, C:0.07, G:0.01, T:0.39
Consensus pattern (36 bp):
AATAAATTATTTTAAAATAAACAATCCATATTTTAA
Found at i:12066771 original size:12 final size:12
Alignment explanation
Indices: 12066736--12066773 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
12066726 GTTACATTTA
12066736 TTTTTACTTTTT
1 TTTTTACTTTTT
* *
12066748 GTTTTAGTTTTT
1 TTTTTACTTTTT
12066760 TTTTTA-TTTTT
1 TTTTTACTTTTT
12066771 TTT
1 TTT
12066774 ATTTGATCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 8 0.35
12 15 0.65
ACGTcount: A:0.08, C:0.03, G:0.05, T:0.84
Consensus pattern (12 bp):
TTTTTACTTTTT
Found at i:12069742 original size:17 final size:16
Alignment explanation
Indices: 12069693--12069748 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 16
12069683 TCTCTATCAC
12069693 AAAAAAA-TGTT-GAA
1 AAAAAAACTGTTCGAA
*
12069707 AAAAAATAGCAGTTCGAA
1 AAAAAA-A-CTGTTCGAA
12069725 AAAAAAACTGTTCGGAA
1 AAAAAAACTGTTC-GAA
12069742 AAAAAAA
1 AAAAAAA
12069749 GACATGAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
14 6 0.17
15 1 0.03
16 5 0.14
17 14 0.40
18 9 0.26
ACGTcount: A:0.62, C:0.07, G:0.14, T:0.16
Consensus pattern (16 bp):
AAAAAAACTGTTCGAA
Done.