Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold701
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: 37315
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Found at i:749 original size:27 final size:27
Alignment explanation
Indices: 713--1096 Score: 475
Period size: 27 Copynumber: 14.3 Consensus size: 27
703 TAAAACACAA
713 TCATTTTACCTCATAAGGGCAAAACAG
1 TCATTTTACCTCATAAGGGCAAAACAG
* *
740 TCATTTTACCACATAATGGCAAAA-AG
1 TCATTTTACCTCATAAGGGCAAAACAG
766 TCATTTTACCTCATAAGGGCAAAACAG
1 TCATTTTACCTCATAAGGGCAAAACAG
* * * *
793 TCATTATACCTCATAAAGGTAAAATAG
1 TCATTTTACCTCATAAGGGCAAAACAG
* * * *
820 TCATTATACCTCACAAGGGTAAAATAG
1 TCATTTTACCTCATAAGGGCAAAACAG
**
847 TCATTTTACCAAATAAGGGCAAAACAG
1 TCATTTTACCTCATAAGGGCAAAACAG
* ** *
874 TTATTTTACCAAATAAGAGCAAAACAG
1 TCATTTTACCTCATAAGGGCAAAACAG
* * * *
901 TCATTTTACCTCACAAAGGCAAAATAA
1 TCATTTTACCTCATAAGGGCAAAACAG
* *
928 TCATTTTACCTCATAAGGGAAAAATAG
1 TCATTTTACCTCATAAGGGCAAAACAG
* *
955 TCA-TTTACCACATAAGGGCAAAATAG
1 TCATTTTACCTCATAAGGGCAAAACAG
* *
981 TTATTTTACCTCACAAGGGCAAAACAG
1 TCATTTTACCTCATAAGGGCAAAACAG
* *
1008 TTATTTTACCTCATAAGGGCAAAACAA
1 TCATTTTACCTCATAAGGGCAAAACAG
* *
1035 TCATTTTACCACAAAAGGGCAAAACAG
1 TCATTTTACCTCATAAGGGCAAAACAG
*
1062 TCATTTTACCTCATAAGGGCAAAACAA
1 TCATTTTACCTCATAAGGGCAAAACAG
1089 TCATTTTA
1 TCATTTTA
1097 TTAATTTGGG
Statistics
Matches: 310, Mismatches: 45, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
26 47 0.15
27 263 0.85
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (27 bp):
TCATTTTACCTCATAAGGGCAAAACAG
Found at i:978 original size:134 final size:132
Alignment explanation
Indices: 713--1094 Score: 505
Period size: 134 Copynumber: 2.8 Consensus size: 132
703 TAAAACACAA
*
713 TCATTTTACCTCATAAGGGCAAAACAGTCATTTTACCACATAATGGCAAAA-AGTCATTTTACCT
1 TCATTTTACCTCATAAGGGCAAAACAGTTATTTTACCACATAA-GGCAAAACAGTCATTTTACCT
* * * * * *
777 CATAAGGGCAAAACAGTCATTATACCTCATAAAGGTAAAATAGTCATTATACCTCACAAGGGTAA
65 CA-AAAGGCAAAACAGTCATTTTACCTCATAAGGGAAAAATAGTCATT-TACCACACAAGGGCAA
842 AATAG
128 AATAG
** *
847 TCATTTTACCAAATAAGGGCAAAACAGTTATTTTACCAAATAAGAGCAAAACAGTCATTTTACCT
1 TCATTTTACCTCATAAGGGCAAAACAGTTATTTTACCACATAAG-GCAAAACAGTCATTTTACCT
* * *
912 CACAAAGGCAAAATAATCATTTTACCTCATAAGGGAAAAATAGTCATTTACCACATAAGGGCAAA
65 CA-AAAGGCAAAACAGTCATTTTACCTCATAAGGGAAAAATAGTCATTTACCACACAAGGGCAAA
977 ATAG
129 ATAG
* * * * *
981 TTATTTTACCTCACAAGGGCAAAACAGTTATTTTACCTCATAAGGGCAAAACAATCATTTTACCA
1 TCATTTTACCTCATAAGGGCAAAACAGTTATTTTACCACATAA-GGCAAAACAGTCATTTTACCT
* * *
1046 CAAAAGGGCAAAACAGTCATTTTACCTCATAAGGGCAAAACAATCATTT
65 CAAAA-GGCAAAACAGTCATTTTACCTCATAAGGGAAAAATAGTCATTT
1095 TATTAATTTG
Statistics
Matches: 217, Mismatches: 27, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
133 4 0.02
134 158 0.73
135 55 0.25
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.26
Consensus pattern (132 bp):
TCATTTTACCTCATAAGGGCAAAACAGTTATTTTACCACATAAGGCAAAACAGTCATTTTACCTC
AAAAGGCAAAACAGTCATTTTACCTCATAAGGGAAAAATAGTCATTTACCACACAAGGGCAAAAT
AG
Found at i:980 original size:161 final size:161
Alignment explanation
Indices: 709--1096 Score: 537
Period size: 161 Copynumber: 2.4 Consensus size: 161
699 AGAATAAAAC
** * * *
709 ACAATCATTTTACCTCATAAGGGCAAAACAGTCATTTTACCACATAATGGCAAAAAGTCATTTTA
1 ACAATCATTTTACCAAATAAGGGCAAAACAGTCATTTTACCTCATAAAGGCAAAAAATCATTTTA
* * *
774 CCTCATAAGGGCAAAACAGTCATTATACCTCATAAAGGTAAAATAGTCATTATACCTCACAAGGG
66 CCTCATAAGGGAAAAACAGTCATTATACCACATAAAGGCAAAATAGTCATTATACCTCACAAGGG
* *
839 TAAAATAGTCATTTTACCAAATAAGGGCAAA
131 CAAAACAGTCATTTTACCAAATAAGGGCAAA
* * * *
870 ACAGTTATTTTACCAAATAAGAGCAAAACAGTCATTTTACCTCACAAAGGCAAAATAATCATTTT
1 ACAATCATTTTACCAAATAAGGGCAAAACAGTCATTTTACCTCATAAAGGCAAAA-AATCATTTT
* * * *
935 ACCTCATAAGGGAAAAATAGTCATT-TACCACATAAGGGCAAAATAGTTATTTTACCTCACAAGG
65 ACCTCATAAGGGAAAAACAGTCATTATACCACATAAAGGCAAAATAGTCATTATACCTCACAAGG
* **
999 GCAAAACAGTTATTTTACCTCATAAGGGCAAA
130 GCAAAACAGTCATTTTACCAAATAAGGGCAAA
*
1031 ACAATCATTTTACCACAA-AAGGGCAAAACAGTCATTTTACCTCATAAGGGCAAAACAATCATTT
1 ACAATCATTTTACCA-AATAAGGGCAAAACAGTCATTTTACCTCATAAAGGCAAAA-AATCATTT
1095 TA
64 TA
1097 TTAATTTGGG
Statistics
Matches: 198, Mismatches: 27, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
161 165 0.83
162 33 0.17
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (161 bp):
ACAATCATTTTACCAAATAAGGGCAAAACAGTCATTTTACCTCATAAAGGCAAAAAATCATTTTA
CCTCATAAGGGAAAAACAGTCATTATACCACATAAAGGCAAAATAGTCATTATACCTCACAAGGG
CAAAACAGTCATTTTACCAAATAAGGGCAAA
Found at i:18414 original size:24 final size:24
Alignment explanation
Indices: 18370--18415 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
18360 TTACATGGGA
*
18370 ATATACTCATTAAGCTTTAATTTC
1 ATATACTCATTAAGCTCTAATTTC
*
18394 ATAT-CTCATTCAGCCTCTAATT
1 ATATACTCATTAAG-CTCTAATT
18416 AAATTCCTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.30, C:0.22, G:0.04, T:0.43
Consensus pattern (24 bp):
ATATACTCATTAAGCTCTAATTTC
Found at i:21068 original size:37 final size:37
Alignment explanation
Indices: 21009--21188 Score: 297
Period size: 37 Copynumber: 4.9 Consensus size: 37
20999 AGCTCAGACG
* * *
21009 AAATCTCCACATGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
21046 AAATCTTCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
21083 AAATCTCCACACGTAGTCATCGGGTCTTACCCGAACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
21120 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
21157 TAATCTCCACACGTAGTCATCGGGTCTTACCC
1 AAATCTCCACACGTAGTCATCGGGTCTTACCC
21189 AGAATTTATT
Statistics
Matches: 135, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 135 1.00
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:21462 original size:47 final size:47
Alignment explanation
Indices: 21400--21788 Score: 499
Period size: 47 Copynumber: 8.1 Consensus size: 47
21390 ACACGTTTCG
* * **
21400 CATTAGCCATTCGGCCTTACCACATATATTCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATACGCATGTTCACATTCATCA
* *
21447 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATACGCATGTTCACATTCATCA
*
21494 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATACGCATGTTCACATTCATCA
* *
21541 CATTGGTCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATACGCATGTTCACATTCATCA
* ** *
21588 CATTGGCCATTCGGCCTTCTCACGCATATATATATACAGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCA--C----ATATACGCATGTTCACATTCATCA
*
21641 CATTGGCCATTCGGCCTTATCACGTATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATACGCATGTTCACATTCATCA
** **
21688 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTAT--CAC--ATATACGCATGTTCACATTCATCA
* * *
21739 CATTGTCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACATATACGCATGTTCACATTCATCA
21786 CAT
1 CAT
21789 AAAATCCTAA
Statistics
Matches: 301, Mismatches: 31, Indels: 20
0.86 0.09 0.06
Matches are distributed among these distances:
47 214 0.71
49 7 0.02
51 39 0.13
53 41 0.14
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.32
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACATATACGCATGTTCACATTCATCA
Found at i:21663 original size:100 final size:98
Alignment explanation
Indices: 21400--21788 Score: 560
Period size: 94 Copynumber: 4.0 Consensus size: 98
21390 ACACGTTTCG
* *
21400 CATTAGCCATTCGGCCTTA-C-CACATATAT-T-CATGTTCACATTCATCACATTGGCCATTCGG
1 CATTGGCCATTCGGCCTTATCACACATATATATACAGGTTCACATTCATCACATTGGCCATTCGG
* * *
21461 CCTTATCTCATATATGCATGTTCACATTCATCA
66 CCTTATCACACATACGCATGTTCACATTCATCA
** * *
21494 CATTGGCCATTCGGCCTTATCACAC----ATACGCATGTTCACATTCATCACATTGGTCATTCGG
1 CATTGGCCATTCGGCCTTATCACACATATATATACAGGTTCACATTCATCACATTGGCCATTCGG
21555 CCTTATCACACATACGCATGTTCACATTCATCA
66 CCTTATCACACATACGCATGTTCACATTCATCA
* *
21588 CATTGGCCATTCGGCCTTCTCACGCATATATATATACAGGTTCACATTCATCACATTGGCCATTC
1 CATTGGCCATTCGGCCTTATCA--CACATATATATACAGGTTCACATTCATCACATTGGCCATTC
**
21653 GGCCTTATCACGTATACGCATGTTCACATTCATCA
64 GGCCTTATCACACATACGCATGTTCACATTCATCA
* *
21688 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCACATTGTCCATTCGG
1 CATTGGCCATTCGGCCTTATCACACATATATATACAGGTTCACATTCATCACATTGGCCATTCGG
*
21753 CCTTATCACACATACGCATGTTCACATCCATCA
66 CCTTATCACACATACGCATGTTCACATTCATCA
21786 CAT
1 CAT
21789 AAAATCCTAA
Statistics
Matches: 264, Mismatches: 21, Indels: 16
0.88 0.07 0.05
Matches are distributed among these distances:
92 2 0.01
94 99 0.38
95 1 0.00
96 5 0.02
98 73 0.28
100 84 0.32
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.32
Consensus pattern (98 bp):
CATTGGCCATTCGGCCTTATCACACATATATATACAGGTTCACATTCATCACATTGGCCATTCGG
CCTTATCACACATACGCATGTTCACATTCATCA
Found at i:21670 original size:147 final size:146
Alignment explanation
Indices: 21400--21767 Score: 503
Period size: 147 Copynumber: 2.5 Consensus size: 146
21390 ACACGTTTCG
* * * *
21400 CATTAGCCATTCGGCCTTACCACATATATTCATGTTCACATTCATCACATTGGCCATTCGGCC-T
1 CATTGGCCATTCGGCCTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGCCTT
* * *
21464 T-A-TC-T-CATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGC
66 TCACACATACATATATACAGGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGC
21525 ATGTTCACATTCATCA
131 ATGTTCACATTCATCA
* **
21541 CATTGGTCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGCCTT
* * **
21606 CTCACGCATATATATATACAGGTTCACATTCATCACATTGGCCATTCGGCCTTATCACGTATACG
66 -TCACACATACATATATACAGGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACG
21671 CATGTTCACATTCATCA
130 CATGTTCACATTCATCA
* *
21688 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCACATTGTCCATTCGG
1 CATTGGCCATTCGGCCTTATCACACATATACAT----GTTCACATTCATCACATTGGCCATTCGG
21753 CCTTATCACACATAC
62 CCTT-TCACACATAC
21768 GCATGTTCAC
Statistics
Matches: 197, Mismatches: 20, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
141 57 0.29
142 1 0.01
143 1 0.01
144 1 0.01
145 1 0.01
146 1 0.01
147 96 0.49
151 39 0.20
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.32
Consensus pattern (146 bp):
CATTGGCCATTCGGCCTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGCCTT
TCACACATACATATATACAGGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGC
ATGTTCACATTCATCA
Found at i:21828 original size:194 final size:191
Alignment explanation
Indices: 21434--21812 Score: 507
Period size: 194 Copynumber: 2.0 Consensus size: 191
21424 TATATTCATG
* *
21434 TTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCACATTG
1 TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACGCATGTTCACATTCATCACATTG
*
21499 GCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGTCATTCGGCCTTATCAC
66 GCCATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGTCATTCGGCCTTATCAC
* ** * ** * * *
21564 ACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTTCTCACGCATATATATATACAGG
131 ACATACGCATGTTCACATCCATCACATT-GAAAAT--GCCTAATCACGAATATAAATATACAGA
*
21628 TTCACATTCATCACATTGGCCATTCGGCCTTATCACGTATACGCATGTTCACATTCATCACATTG
1 TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACGCATGTTCACATTCATCACATTG
* *
21693 GCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCACATT-GTCCATTCGGCCTT
66 GCCATTCGGCCTTATCACACATACACAT----GTTCACATTCATCACATTGGT-CATTCGGCCTT
21757 ATCACACATACGCATGTTCACATCCATCACA-T-AAAAT-CCTAAATCA-GAATATAAAT
126 ATCACACATACGCATGTTCACATCCATCACATTGAAAATGCCT-AATCACGAATATAAAT
21813 TTTCATGTAT
Statistics
Matches: 165, Mismatches: 14, Indels: 14
0.85 0.07 0.07
Matches are distributed among these distances:
192 11 0.07
193 3 0.02
194 87 0.53
195 2 0.01
197 3 0.02
198 59 0.36
ACGTcount: A:0.28, C:0.29, G:0.12, T:0.32
Consensus pattern (191 bp):
TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACGCATGTTCACATTCATCACATTG
GCCATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGTCATTCGGCCTTATCAC
ACATACGCATGTTCACATCCATCACATTGAAAATGCCTAATCACGAATATAAATATACAGA
Found at i:22545 original size:29 final size:29
Alignment explanation
Indices: 22499--22554 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
22489 AATGGAATAA
*
22499 TGATGGTCGTCACAATCCCTTTTCATAGT
1 TGATGGTCATCACAATCCCTTTTCATAGT
*
22528 TGATGGTCATCACCATCCCTTTTCATA
1 TGATGGTCATCACAATCCCTTTTCATA
22555 ATCAACAGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.21, C:0.27, G:0.14, T:0.38
Consensus pattern (29 bp):
TGATGGTCATCACAATCCCTTTTCATAGT
Found at i:22574 original size:29 final size:29
Alignment explanation
Indices: 22542--22641 Score: 94
Period size: 29 Copynumber: 3.4 Consensus size: 29
22532 GGTCATCACC
*
22542 ATCCCTTTTCATAATCAACAGCCGAAGCT
1 ATCCCTTTTCATAATCAATAGCCGAAGCT
* * * * * * *
22571 ATCCCTTTTCGTATTTAATGGTCGTCA-CC
1 ATCCCTTTTCATAATCAATAGCCG-AAGCT
*
22600 ATCCCTTTTTCATAATCGATAGCCGAAGCT
1 ATCCC-TTTTCATAATCAATAGCCGAAGCT
22630 ATCCCTTTTCAT
1 ATCCCTTTTCAT
22642 TGGTCGATGA
Statistics
Matches: 52, Mismatches: 16, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
29 32 0.62
30 20 0.38
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.36
Consensus pattern (29 bp):
ATCCCTTTTCATAATCAATAGCCGAAGCT
Found at i:22592 original size:58 final size:59
Alignment explanation
Indices: 22513--22641 Score: 197
Period size: 59 Copynumber: 2.2 Consensus size: 59
22503 GGTCGTCACA
*
22513 ATCCCTTTTCATAGTTGATGGTCATCACCATCCC-TTTTCATAATCAACAGCCGAAGCT
1 ATCCCTTTTCATAGTTAATGGTCATCACCATCCCTTTTTCATAATCAACAGCCGAAGCT
* * * * *
22571 ATCCCTTTTCGTATTTAATGGTCGTCACCATCCCTTTTTCATAATCGATAGCCGAAGCT
1 ATCCCTTTTCATAGTTAATGGTCATCACCATCCCTTTTTCATAATCAACAGCCGAAGCT
22630 ATCCCTTTTCAT
1 ATCCCTTTTCAT
22642 TGGTCGATGA
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
58 30 0.48
59 33 0.52
ACGTcount: A:0.23, C:0.29, G:0.12, T:0.36
Consensus pattern (59 bp):
ATCCCTTTTCATAGTTAATGGTCATCACCATCCCTTTTTCATAATCAACAGCCGAAGCT
Found at i:25255 original size:21 final size:21
Alignment explanation
Indices: 25229--25268 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
25219 GGTGAAAATT
*
25229 GTAACCCCATGTCGCAACACC
1 GTAACCCCATATCGCAACACC
*
25250 GTAACCCCATATCGTAACA
1 GTAACCCCATATCGCAACA
25269 TCAAGGGAAG
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:0.33, C:0.38, G:0.12, T:0.17
Consensus pattern (21 bp):
GTAACCCCATATCGCAACACC
Found at i:27965 original size:27 final size:27
Alignment explanation
Indices: 27929--28003 Score: 71
Period size: 27 Copynumber: 2.8 Consensus size: 27
27919 CAGTGACGGT
* *
27929 AATATCATCGGCACACAGCCATGC-GTA
1 AATATGATCGGCACACAGCCAT-CAATA
* * *
27956 AATATGATCGACACAGAGTCATCAATA
1 AATATGATCGGCACACAGCCATCAATA
* *
27983 AATATGATAGGCACATAGCCA
1 AATATGATCGGCACACAGCCA
28004 CAGGTAAATA
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
26 1 0.03
27 37 0.97
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (27 bp):
AATATGATCGGCACACAGCCATCAATA
Found at i:29860 original size:40 final size:40
Alignment explanation
Indices: 29759--29974 Score: 282
Period size: 40 Copynumber: 5.5 Consensus size: 40
29749 TGGATGATAA
* * *
29759 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
**
29799 TTGGGC-AAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
29838 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTTACTATAT
*
29878 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
29918 CCGGGCTAAGTCCCGAAGGCATTTGAGC-AG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
**
29957 CC-GGCTAAACCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
29975 TACTTGGTTG
Statistics
Matches: 159, Mismatches: 12, Indels: 12
0.87 0.07 0.07
Matches are distributed among these distances:
38 17 0.11
39 43 0.27
40 97 0.61
41 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:35317 original size:39 final size:39
Alignment explanation
Indices: 35205--35418 Score: 251
Period size: 40 Copynumber: 5.5 Consensus size: 39
35195 AACCAAGTAC
* * *
35205 CCTTCGGG-TTTAGCCGGATATAGCT-ACT-GCTCAAATG
1 CCTTCGGGACTTAGCCCGATATAG-TAACTCGCACAAATG
*
35242 CCTTCGGGACTTAGCCCGGTTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCC-G-ATATAGTAACTCGCACAAATG
35283 CCTTCGGGACTTAGCCCGATATAGT-ACTTCGCACAAATG
1 CCTTCGGGACTTAGCCCGATATAGTAAC-TCGCACAAATG
35322 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCC-GATATAGTAACTCGCACAAATG
* * * *
35362 CCTTCGGGACTT-GCCC-AAACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGATA-TAGTAACTCGCACAAATG
35400 CCTTCGGGACTTTAGCCCG
1 CCTTCGGGAC-TTAGCCCG
35419 GTTATCATCA
Statistics
Matches: 156, Mismatches: 9, Indels: 20
0.84 0.05 0.11
Matches are distributed among these distances:
37 10 0.06
38 33 0.21
39 42 0.27
40 44 0.28
41 27 0.17
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCCGATATAGTAACTCGCACAAATG
Found at i:35353 original size:79 final size:78
Alignment explanation
Indices: 35205--35420 Score: 287
Period size: 79 Copynumber: 2.7 Consensus size: 78
35195 AACCAAGTAC
* * * *
35205 CCTTCGGG-TTTAGCCGGATATAGCTACTGCTCAAATGCCTTCGGGACTTAGCCCGGTTTATAGT
1 CCTTCGGGACTTAGCCCGATATAG-TACTGCACAAATGCCTTCGGGACTTAGCCCGGTATATAGT
35269 AACTCGCACAAATG
65 AACTCGCACAAATG
35283 CCTTCGGGACTTAGCCCGATATAGTACTTCGCACAAATGCCTTCGGGACTTAGCCCGG-ATATAG
1 CCTTCGGGACTTAGCCCGATATAGTAC-T-GCACAAATGCCTTCGGGACTTAGCCCGGTATATAG
35347 TAACTCGCACAAATG
64 TAACTCGCACAAATG
* *
35362 CCTTCGGGACTT-GCCC-AAACTAGTCACTAGCGCAAATGCCTTCGGGACTTTAGCCCGGT
1 CCTTCGGGACTTAGCCCGATA-TAGT-ACT-GCACAAATGCCTTCGGGAC-TTAGCCCGGT
35421 TATCATCAAA
Statistics
Matches: 124, Mismatches: 7, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
77 2 0.02
78 38 0.31
79 57 0.46
80 27 0.22
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (78 bp):
CCTTCGGGACTTAGCCCGATATAGTACTGCACAAATGCCTTCGGGACTTAGCCCGGTATATAGTA
ACTCGCACAAATG
Found at i:35355 original size:40 final size:39
Alignment explanation
Indices: 35205--35419 Score: 255
Period size: 39 Copynumber: 5.5 Consensus size: 39
35195 AACCAAGTAC
* *
35205 CCTTCGGG-TTTAG-CCGGATATAGCTACT-GCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TACTCGCACAAATG
*
35242 CCTTCGGGACTTAGCCCGGTTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGG-ATATAGT-ACTCGCACAAATG
35283 CCTTCGGGACTTAGCCC-GATATAGTACTTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAC-TCGCACAAATG
35322 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGT-ACTCGCACAAATG
* * *
35362 CCTTCGGGACTT-GCCC--AAACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGT-ACTCGCACAAATG
35400 CCTTCGGGACTTTAGCCCGG
1 CCTTCGGGAC-TTAGCCCGG
35420 TTATCATCAA
Statistics
Matches: 157, Mismatches: 8, Indels: 21
0.84 0.04 0.11
Matches are distributed among these distances:
37 10 0.06
38 31 0.20
39 45 0.29
40 44 0.28
41 27 0.17
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCCGGATATAGTACTCGCACAAATG
Done.